From 71471acf1be92050bda6d22ff0252b8fb214b08f Mon Sep 17 00:00:00 2001 From: StevenCannon-USDA Date: Tue, 10 Sep 2024 16:44:51 -0500 Subject: [PATCH 01/18] Added Glycine max studies that had been in glyma.traits.yml but not in separate per-study yml files. --- Glycine/max/studies/glyma.Dietz_Chan_2023.yml | 98 ++++++++++++ Glycine/max/studies/glyma.Fan_Hu_2014.yml | 108 ++++++++++++++ Glycine/max/studies/glyma.Fang_Li_2014.yml | 2 +- Glycine/max/studies/glyma.Guo_Xu_2015.yml | 52 +++++++ Glycine/max/studies/glyma.Kong_Liu_2010.yml | 67 +++++++++ Glycine/max/studies/glyma.Liu_Jiang_2008.yml | 27 ++++ Glycine/max/studies/glyma.Liu_Liao_2020.yml | 4 +- Glycine/max/studies/glyma.Lu_Dong_2020.yml | 54 +++++++ Glycine/max/studies/glyma.Lu_Zhao_2017.yml | 141 ++++++++++++++++++ .../max/studies/glyma.Noh_Bizzell_2004.yml | 44 ++++++ .../studies/glyma.Tsubokura_Watanabe_2013.yml | 35 +++++ Glycine/max/studies/glyma.Wang_Guo_2021.yml | 35 +++++ Glycine/max/studies/glyma.Wang_Wang_2015.yml | 8 +- Glycine/max/studies/glyma.Wang_Zhou_2015.yml | 26 ++++ .../studies/glyma.Watanabe_Hideshima_2009.yml | 27 ++++ .../max/studies/glyma.Watanabe_Xia_2011.yml | 26 ++++ Glycine/max/studies/glyma.Wu_Kang_2019.yml | 22 +++ Glycine/max/studies/glyma.Wu_Price_2014.yml | 4 +- Glycine/max/studies/glyma.Xia_Zhai_2012.yml | 33 ++++ .../max/studies/glyma.Xu_Yamagishi_2015.yml | 26 ++++ Glycine/max/studies/glyma.Yu_Chang_2019.yml | 2 +- Glycine/max/studies/glyma.Zhai_Lu_2014.yml | 30 ++++ Glycine/max/studies/glyma.Zhao_Bi_2019.yml | 8 +- 23 files changed, 865 insertions(+), 14 deletions(-) create mode 100644 Glycine/max/studies/glyma.Dietz_Chan_2023.yml create mode 100644 Glycine/max/studies/glyma.Fan_Hu_2014.yml create mode 100644 Glycine/max/studies/glyma.Guo_Xu_2015.yml create mode 100644 Glycine/max/studies/glyma.Kong_Liu_2010.yml create mode 100644 Glycine/max/studies/glyma.Liu_Jiang_2008.yml create mode 100644 Glycine/max/studies/glyma.Lu_Dong_2020.yml create mode 100644 Glycine/max/studies/glyma.Lu_Zhao_2017.yml create mode 100644 Glycine/max/studies/glyma.Noh_Bizzell_2004.yml create mode 100644 Glycine/max/studies/glyma.Tsubokura_Watanabe_2013.yml create mode 100644 Glycine/max/studies/glyma.Wang_Zhou_2015.yml create mode 100644 Glycine/max/studies/glyma.Watanabe_Hideshima_2009.yml create mode 100644 Glycine/max/studies/glyma.Watanabe_Xia_2011.yml create mode 100644 Glycine/max/studies/glyma.Wu_Kang_2019.yml create mode 100644 Glycine/max/studies/glyma.Xia_Zhai_2012.yml create mode 100644 Glycine/max/studies/glyma.Xu_Yamagishi_2015.yml create mode 100644 Glycine/max/studies/glyma.Zhai_Lu_2014.yml diff --git a/Glycine/max/studies/glyma.Dietz_Chan_2023.yml b/Glycine/max/studies/glyma.Dietz_Chan_2023.yml new file mode 100644 index 0000000..b2ccd50 --- /dev/null +++ b/Glycine/max/studies/glyma.Dietz_Chan_2023.yml @@ -0,0 +1,98 @@ +--- +gene_symbols: + - GmPHYE1 +gene_symbol_long: Phytochrome E1 +gene_model_pub_name: Glyma.09G088500 +gene_model_full_id: glyma.Wm82.gnm2.ann1.Glyma.09G088500 +confidence: 3 +curators: + - Steven Cannon +phenotype_synopsis: Photoperiodic flowering time regulation +traits: + - entity_name: flowering time + entity: TO:0002616 + - entity_name: days to maturity + entity: TO:0000469 +references: + - citation: Dietz, Chan et al., 2023 + doi: 10.3389/fpls.2022.889066 + pmid: 35574141 +--- +gene_symbols: + - GmTOC1 +gene_symbol_long: Timing of CAB Expression 1 +gene_model_pub_name: Glyma.06G196200 +gene_model_full_id: glyma.Wm82.gnm2.ann1.Glyma.06G196200 +confidence: 2 +curators: + - Steven Cannon +phenotype_synopsis: Photoperiodic flowering time regulation +traits: + - entity_name: flowering time + entity: TO:0002616 + - entity_name: days to maturity + entity: TO:0000469 +references: + - citation: Dietz, Chan et al., 2023 + doi: 10.3389/fpls.2022.889066 + pmid: 35574141 +--- +gene_symbols: + - GmGA2OX5 +gene_symbol_long: Gibberellin 2 Oxidase 5 +gene_model_pub_name: Glyma.13G218200 +gene_model_full_id: glyma.Wm82.gnm2.ann1.Glyma.13G218200 +confidence: 2 +curators: + - Steven Cannon +phenotype_synopsis: Photoperiodic flowering time regulation +traits: + - entity_name: flowering time + entity: TO:0002616 + - entity_name: days to maturity + entity: TO:0000469 +references: + - citation: Dietz, Chan et al., 2023 + doi: 10.3389/fpls.2022.889066 + pmid: 35574141 +--- +gene_symbols: + - GmGA2OX6 +gene_symbol_long: Gibberellin 2 Oxidase 6 +gene_model_pub_name: Glyma.13G259400 +gene_model_full_id: glyma.Wm82.gnm2.ann1.Glyma.13G259400 +confidence: 2 +curators: + - Steven Cannon +phenotype_synopsis: Photoperiodic flowering time regulation +traits: + - entity_name: flowering time + entity: TO:0002616 + - entity_name: days to maturity + entity: TO:0000469 +references: + - citation: Dietz, Chan et al., 2023 + doi: 10.3389/fpls.2022.889066 + pmid: 35574141 +--- +gene_symbols: + - GmMSI1 +gene_symbol_long: Multicopy Suppressor of IRA 1 +gene_model_pub_name: Glyma.05G131200 +gene_model_full_id: glyma.Wm82.gnm2.ann1.Glyma.05G131200 +confidence: 5 +curators: + - Steven Cannon +phenotype_synopsis: Photoperiodic flowering time regulation +traits: + - entity_name: flowering time + entity: TO:0002616 + - entity_name: days to maturity + entity: TO:0000469 +references: + - citation: Wu, Kang et al., 2019 + doi: 10.3389/fpls.2019.01221 + pmid: 31787988 + - citation: Dietz, Chan et al., 2023 + doi: 10.3389/fpls.2022.889066 + pmid: 35574141 diff --git a/Glycine/max/studies/glyma.Fan_Hu_2014.yml b/Glycine/max/studies/glyma.Fan_Hu_2014.yml new file mode 100644 index 0000000..1aeea96 --- /dev/null +++ b/Glycine/max/studies/glyma.Fan_Hu_2014.yml @@ -0,0 +1,108 @@ +--- +gene_symbols: + - GmFT2b +gene_symbol_long: Flowering Time 2b +gene_model_pub_name: Glyma.16G151000 +gene_model_full_id: glyma.Wm82.gnm2.ann1.Glyma.16G151000 +confidence: 5 +curators: + - Steven Cannon + - Greg Murrell +phenotype_synopsis: Photoperiodic flowering time regulation +traits: + - entity_name: flowering time + entity: TO:0002616 + relation_name: positively regulates + relation: RO:0002213 + - entity_name: days to maturity + entity: TO:0000469 + relation_name: positively regulates + relation: RO:0002213 +references: + - citation: Fan, Hu et al., 2014 + doi: 10.1186/1471-2229-14-9 + pmid: 24397545 + - citation: Lin, Liu et al., 2021 + doi: 10.1111/jipb.13021 + pmid: 33090664 + - citation: Chen, Cai et al., 2020 + doi: 10.1111/pce.13695 + pmid: 31981430 +--- +gene_symbols: + - GmFT3a +gene_symbol_long: Flowering Time 3a +gene_model_pub_name: Glyma.16G044200 +gene_model_full_id: glyma.Wm82.gnm2.ann1.Glyma.16G044200 +confidence: 5 +curators: + - Steven Cannon +phenotype_synopsis: Photoperiodic flowering time regulation +traits: + - entity_name: flowering time + entity: TO:0002616 + relation_name: positively regulates + relation: RO:0002213 + - entity_name: days to maturity + entity: TO:0000469 + relation_name: positively regulates + relation: RO:0002213 +references: + - citation: Fan, Hu et al., 2014 + doi: 10.1186/1471-2229-14-9 + pmid: 24397545 + - citation: Lin, Liu et al., 2021 + doi: 10.1111/jipb.13021 + pmid: 33090664 +--- +gene_symbols: + - GmFT3b +gene_symbol_long: Flowering Time 3b +gene_model_pub_name: Glyma.19G108100 +gene_model_full_id: glyma.Wm82.gnm2.ann1.Glyma.19G108100 +confidence: 5 +curators: + - Steven Cannon +phenotype_synopsis: Photoperiodic flowering time regulation +traits: + - entity_name: flowering time + entity: TO:0002616 + relation_name: positively regulates + relation: RO:0002213 + - entity_name: days to maturity + entity: TO:0000469 + relation_name: positively regulates + relation: RO:0002213 +references: + - citation: Fan, Hu et al., 2014 + doi: 10.1186/1471-2229-14-9 + pmid: 24397545 + - citation: Lin, Liu et al., 2021 + doi: 10.1111/jipb.13021 + pmid: 33090664 +--- +gene_symbols: + - GmFT5b +gene_symbol_long: Flowering Time 5b +gene_model_pub_name: Glyma.19G108200 +gene_model_full_id: glyma.Wm82.gnm2.ann1.Glyma.19G108200 +confidence: 5 +curators: + - Steven Cannon +phenotype_synopsis: Photoperiodic flowering time regulation +traits: + - entity_name: flowering time + entity: TO:0002616 + relation_name: positively regulates + relation: RO:0002213 + - entity_name: days to maturity + entity: TO:0000469 + relation_name: positively regulates + relation: RO:0002213 +references: + - citation: Fan, Hu et al., 2014 + doi: 10.1186/1471-2229-14-9 + pmid: 24397545 + - citation: Lin, Liu et al., 2021 + doi: 10.1111/jipb.13021 + pmid: 33090664 diff --git a/Glycine/max/studies/glyma.Fang_Li_2014.yml b/Glycine/max/studies/glyma.Fang_Li_2014.yml index e81392d..8a8b829 100644 --- a/Glycine/max/studies/glyma.Fang_Li_2014.yml +++ b/Glycine/max/studies/glyma.Fang_Li_2014.yml @@ -30,7 +30,7 @@ classical_locus: D2 gene_symbols: - GmD2 gene_model_pub_name: Glyma11g02980 -gene_model_full_id: glyma.Wm82.gnm1.ann1.Glyma11g02980.1 +gene_model_full_id: glyma.Wm82.gnm1.ann1.Glyma11g02980 confidence: 4 curators: - William Hardison diff --git a/Glycine/max/studies/glyma.Guo_Xu_2015.yml b/Glycine/max/studies/glyma.Guo_Xu_2015.yml new file mode 100644 index 0000000..bf41d81 --- /dev/null +++ b/Glycine/max/studies/glyma.Guo_Xu_2015.yml @@ -0,0 +1,52 @@ +--- +gene_symbols: + - GmFT1a +gene_symbol_long: Flowering Timne 1a +gene_model_pub_name: Glyma.18G298900 +gene_model_full_id: glyma.Wm82.gnm2.ann1.Glyma.18G298900 +confidence: 5 +curators: + - Steven Cannon +phenotype_synopsis: Photoperiodic flowering time regulation +traits: + - entity_name: flowering time + entity: TO:0002616 + relation_name: negatively regulates + relation: RO:0002212 + - entity_name: days to maturity + entity: TO:0000469 + relation_name: negatively regulates + relation: RO:0002212 +references: + - citation: Guo, Xu et al., 2015 + doi: 10.1371/journal.pone.0136601 + pmid: 26371882 + - citation: Lin, Liu et al., 2021 + doi: 10.1111/jipb.13021 + pmid: 33090664 +--- +gene_symbols: + - GmFT1b +gene_symbol_long: Flowering Time 1b +gene_model_pub_name: Glyma.18G299000 +gene_model_full_id: glyma.Wm82.gnm2.ann1.Glyma.18G299000 +confidence: 5 +curators: + - Steven Cannon +phenotype_synopsis: Photoperiodic flowering time regulation +traits: + - entity_name: flowering time + entity: TO:0002616 + relation_name: negatively regulates + relation: RO:0002212 + - entity_name: days to maturity + entity: TO:0000469 + relation_name: negatively regulates + relation: RO:0002212 +references: + - citation: Guo, Xu et al., 2015 + doi: 10.1371/journal.pone.0136601 + pmid: 26371882 + - citation: Lin, Liu et al., 2021 + doi: 10.1111/jipb.13021 + pmid: 33090664 diff --git a/Glycine/max/studies/glyma.Kong_Liu_2010.yml b/Glycine/max/studies/glyma.Kong_Liu_2010.yml new file mode 100644 index 0000000..bc307df --- /dev/null +++ b/Glycine/max/studies/glyma.Kong_Liu_2010.yml @@ -0,0 +1,67 @@ +--- +classical_locus: E9 +gene_symbols: + - GmFT2a +gene_symbol_long: Flowering Time 2a +gene_model_pub_name: Glyma.16g150700 +gene_model_full_id: glyma.Wm82.gnm4.ann1.Glyma.16G150700 +confidence: 5 +curators: + - Steven Cannon +phenotype_synopsis: Photoperiodic flowering time regulation +traits: + - entity_name: flowering time + entity: TO:0002616 + relation_name: positively regulates + relation: RO:0002213 + - entity_name: days to maturity + entity: TO:0000469 + relation_name: positively regulates + relation: RO:0002213 +references: + - citation: Kong, Liu et al., 2010 + doi: 10.1104/pp.110.160796 + pmid: 20864544 + - citation: Kong, Nan et al., 2014 + doi: 10.2135/cropsci2014.03.0228 + - citation: Takeshima, Hayashi et al., 2016 + doi: 10.1093/jxb/erw283 + pmid: 27422993 + - citation: Zhao, Takeshima et al., 2016 + doi: 10.1186/s12870-016-0704-9 + pmid: 26786479 + - citation: Dietz, Chan et al., 2023 + doi: 10.3389/fpls.2022.889066 + pmid: 35574141 + - citation: Lin, Liu et al., 2021 + doi: 10.1111/jipb.13021 + pmid: 33090664 +--- +gene_symbols: + - GmFT5a +gene_symbol_long: Flowering Time 5a +gene_model_pub_name: Gyma.16G044100 +gene_model_full_id: glyma.Wm82.gnm2.ann1.Gyma.16G044100 +confidence: 5 +curators: + - Steven Cannon +phenotype_synopsis: Photoperiodic flowering time regulation +traits: + - entity_name: flowering time + entity: TO:0002616 + relation_name: positively regulates + relation: RO:0002213 + - entity_name: days to maturity + entity: TO:0000469 + relation_name: positively regulates + relation: RO:0002213 +references: + - citation: Kong, Liu et al., 2010 + doi: 10.1104/pp.110.160796 + pmid: 20864544 + - citation: Fan, Hu et al., 2014 + doi: 10.1186/1471-2229-14-9 + pmid: 24397545 + - citation: Lin, Liu et al., 2021 + doi: 10.1111/jipb.13021 + pmid: 33090664 diff --git a/Glycine/max/studies/glyma.Liu_Jiang_2008.yml b/Glycine/max/studies/glyma.Liu_Jiang_2008.yml new file mode 100644 index 0000000..3408055 --- /dev/null +++ b/Glycine/max/studies/glyma.Liu_Jiang_2008.yml @@ -0,0 +1,27 @@ +--- +classical_locus: E4 +gene_symbols: + - GmphyA2 +gene_symbol_long: Earliness 4 +gene_model_pub_name: Glyma.20G090000 +gene_model_full_id: glyma.Wm82.gnm2.ann1.Glyma.20G090000 +confidence: 5 +curators: + - Steven Cannon +phenotype_synopsis: Photoperiodic flowering time regulation +traits: + - entity_name: flowering time + entity: TO:0002616 + relation_name: negatively regulates + relation: RO:0002212 + - entity_name: days to maturity + entity: TO:0000469 + relation_name: negatively regulates + relation: RO:0002212 +references: + - citation: Liu, Jiang et al., 2008 + doi: 10.1111/nph.14884 + pmid: 29120038 + - citation: Lin, Liu et al., 2021 + doi: 10.1111/jipb.13021 + pmid: 33090664 \ No newline at end of file diff --git a/Glycine/max/studies/glyma.Liu_Liao_2020.yml b/Glycine/max/studies/glyma.Liu_Liao_2020.yml index 61a9180..e0d4b36 100644 --- a/Glycine/max/studies/glyma.Liu_Liao_2020.yml +++ b/Glycine/max/studies/glyma.Liu_Liao_2020.yml @@ -4,7 +4,7 @@ gene_symbols: - GmVTL1a gene_symbol_long: Vacuolar Iron Transporter Like 1A gene_model_pub_name: Glyma.05G121600 -gene_model_full_id: glyma.Wm82.gnm4.ann1.Glyma.05G121600.1 +gene_model_full_id: glyma.Wm82.gnm4.ann1.Glyma.05G121600 confidence: 3 curators: - William Hardison @@ -25,7 +25,7 @@ gene_symbols: - GmVTL1b gene_symbol_long: Vacuolar Iron Transporter Like 1B gene_model_pub_name: Glyma.08G076300 -gene_model_full_id: glyma.Wm82.gnm2.ann1.Glyma.08G076300.1 +gene_model_full_id: glyma.Wm82.gnm2.ann1.Glyma.08G076300 confidence: 3 curators: - William Hardison diff --git a/Glycine/max/studies/glyma.Lu_Dong_2020.yml b/Glycine/max/studies/glyma.Lu_Dong_2020.yml new file mode 100644 index 0000000..f955fe9 --- /dev/null +++ b/Glycine/max/studies/glyma.Lu_Dong_2020.yml @@ -0,0 +1,54 @@ +--- +gene_symbols: + - Tof11 + - PRR3a +gene_symbol_long: Time of Flowering 11 +gene_model_pub_name: SoyZH13_11G141200 +gene_model_full_id: glyma.Zh13.gnm1.ann1.SoyZH13_11G141200 +confidence: 5 +curators: + - Steven Cannon +phenotype_synopsis: Photoperiodic flowering time regulation +traits: + - entity_name: flowering time + entity: TO:0002616 + relation_name: negatively regulates + relation: RO:0002212 + - entity_name: days to maturity + entity: TO:0000469 + relation_name: negatively regulates + relation: RO:0002212 +references: + - citation: Lu, Dong et al., 2020 + doi: 10.1038/s41588-020-0604-7 + pmid: 32231277 + - citation: Lin, Liu et al., 2021 + doi: 10.1111/jipb.13021 + pmid: 33090664 +--- +gene_symbols: + - Tof12 + - PRR3b +gene_symbol_long: Time of Flowering 12 +gene_model_pub_name: SoyZH13_12G067700 +gene_model_full_id: glyma.Zh13.gnm1.ann1.SoyZH13_12G067700 +confidence: 5 +curators: + - Steven Cannon +phenotype_synopsis: Photoperiodic flowering time regulation +traits: + - entity_name: flowering time + entity: TO:0002616 + relation_name: negatively regulates + relation: RO:0002212 + - entity_name: days to maturity + entity: TO:0000469 + relation_name: negatively regulates + relation: RO:0002212 +references: + - citation: Lu, Dong et al., 2020 + doi: 10.1038/s41588-020-0604-7 + pmid: 32231277 + - citation: Lin, Liu et al., 2021 + doi: 10.1111/jipb.13021 + pmid: 33090664 diff --git a/Glycine/max/studies/glyma.Lu_Zhao_2017.yml b/Glycine/max/studies/glyma.Lu_Zhao_2017.yml new file mode 100644 index 0000000..1716ffc --- /dev/null +++ b/Glycine/max/studies/glyma.Lu_Zhao_2017.yml @@ -0,0 +1,141 @@ +--- +classical_locus: J +gene_symbols: + - GmELF3 +gene_symbol_long: Early Flowering 3 +gene_model_pub_name: Glyma.04G050200 +gene_model_full_id: glyma.Wm82.gnm2.ann1.Glyma.04G050200 +confidence: 5 +curators: + - Steven Cannon +phenotype_synopsis: Photoperiodic flowering time regulation +traits: + - entity_name: flowering time + entity: TO:0002616 + relation_name: positively regulates + relation: RO:0002213 + - entity_name: days to maturity + entity: TO:0000469 + relation_name: positively regulates + relation: RO:0002213 +references: + - citation: Lu, Zhao et al., 2017 + doi: 10.1038/ng.3819 + pmid: 28319089 + - citation: Yue, Liu et al., 2017 + doi: 10.1016/j.molp.2016.12.004 + pmid: 27979775 + - citation: Lin, Liu et al., 2021 + doi: 10.1111/jipb.13021 + pmid: 33090664 +--- +gene_symbols: + - LHY1a +gene_symbol_long: Leafy 1a +gene_model_pub_name: Glyma.16G017400 +gene_model_full_id: glyma.Wm82.gnm2.ann1.Glyma.16G017400 +confidence: 5 +curators: + - Steven Cannon +phenotype_synopsis: Photoperiodic flowering time regulation +traits: + - entity_name: flowering time + entity: TO:0002616 + relation_name: positively regulates + relation: RO:0002213 + - entity_name: days to maturity + entity: TO:0000469 + relation_name: positively regulates + relation: RO:0002213 +references: + - citation: Lu, Zhao et al., 2017 + doi: 10.1038/ng.3819 + pmid: 28319089 + - citation: Lin, Liu et al., 2021 + doi: 10.1111/jipb.13021 + pmid: 33090664 +--- +gene_symbols: + - LHY1b +gene_symbol_long: Leafy 1b +gene_model_pub_name: Glyma.07G048500 +gene_model_full_id: glyma.Wm82.gnm2.ann1.Glyma.07G048500 +confidence: 5 +curators: + - Steven Cannon +phenotype_synopsis: Photoperiodic flowering time regulation +traits: + - entity_name: flowering time + entity: TO:0002616 + relation_name: positively regulates + relation: RO:0002213 + - entity_name: days to maturity + entity: TO:0000469 + relation_name: positively regulates + relation: RO:0002213 +references: + - citation: Lu, Zhao et al., 2017 + doi: 10.1038/ng.3819 + pmid: 28319089 + - citation: Lin, Liu et al., 2021 + doi: 10.1111/jipb.13021 + pmid: 33090664 +--- +gene_symbols: + - LHY2a + - GmLHY2a + - LCL3 + - MYB156 +gene_symbol_long: Leafy 2a +gene_model_pub_name: Glyma.19G260900 +gene_model_full_id: glyma.Wm82.gnm2.ann1.Glyma.19G260900 +confidence: 5 +curators: + - Steven Cannon +phenotype_synopsis: Photoperiodic flowering time regulation +comments: Encodes a MYB transciption factor that affects plant height through mediating the GA pathway in soybean +traits: + - entity_name: flowering time + entity: TO:0002616 + relation_name: positively regulates + relation: RO:0002213 + - entity_name: days to maturity + entity: TO:0000469 + relation_name: positively regulates + relation: RO:0002213 +references: + - citation: Lu, Zhao et al., 2017 + doi: 10.1038/ng.3819 + pmid: 28319089 + - citation: Lin, Liu et al., 2021 + doi: 10.1111/jipb.13021 + pmid: 33090664 + - citation: Chen, Cai et al., 2020 + doi: 10.1111/pce.13695 + pmid: 31981430 +--- +gene_symbols: + - LHY2b +gene_symbol_long: Leafy 2b +gene_model_pub_name: Glyma.03G261800 +gene_model_full_id: glyma.Wm82.gnm2.ann1.Glyma.03G261800 +confidence: 5 +curators: + - Steven Cannon +phenotype_synopsis: Photoperiodic flowering time regulation +traits: + - entity_name: flowering time + entity: TO:0002616 + relation_name: positively regulates + relation: RO:0002213 + - entity_name: days to maturity + entity: TO:0000469 + relation_name: positively regulates + relation: RO:0002213 +references: + - citation: Lu, Zhao et al., 2017 + doi: 10.1038/ng.3819 + pmid: 28319089 + - citation: Lin, Liu et al., 2021 + doi: 10.1111/jipb.13021 + pmid: 33090664 diff --git a/Glycine/max/studies/glyma.Noh_Bizzell_2004.yml b/Glycine/max/studies/glyma.Noh_Bizzell_2004.yml new file mode 100644 index 0000000..2458acf --- /dev/null +++ b/Glycine/max/studies/glyma.Noh_Bizzell_2004.yml @@ -0,0 +1,44 @@ +--- +gene_symbols: + - GmELF5 +gene_symbol_long: Early Flowering 5 +gene_model_pub_name: Glyma.05G031100 +gene_model_full_id: glyma.Wm82.gnm2.ann1.Glyma.05G031100 +confidence: 5 +curators: + - Steven Cannon +phenotype_synopsis: Photoperiodic flowering time regulation +traits: + - entity_name: flowering time + entity: TO:0002616 + - entity_name: days to maturity + entity: TO:0000469 +references: + - citation: Noh, Bizzell et al., 2004 + doi: 10.1111/j.1365-313x.2004.02072.x + pmid: 15125772 + - citation: Dietz, Chan et al., 2023 + doi: 10.3389/fpls.2022.889066 + pmid: 35574141 +--- +gene_symbols: + - GmTEM1a +gene_symbol_long: Tempranillo 1a +gene_model_pub_name: Glyma.20G186200 +gene_model_full_id: glyma.Wm82.gnm2.ann1.Glyma.20G186200 +confidence: 3 +curators: + - Steven Cannon +phenotype_synopsis: Photoperiodic flowering time regulation +traits: + - entity_name: flowering time + entity: TO:0002616 + - entity_name: days to maturity + entity: TO:0000469 +references: + - citation: Noh, Bizzell et al., 2004 + doi: 10.1111/j.1365-313x.2004.02072.x + pmid: 15125772 + - citation: Dietz, Chan et al., 2023 + doi: 10.3389/fpls.2022.889066 + pmid: 35574141 diff --git a/Glycine/max/studies/glyma.Tsubokura_Watanabe_2013.yml b/Glycine/max/studies/glyma.Tsubokura_Watanabe_2013.yml new file mode 100644 index 0000000..bc66c61 --- /dev/null +++ b/Glycine/max/studies/glyma.Tsubokura_Watanabe_2013.yml @@ -0,0 +1,35 @@ +classical_locus: E2 +gene_symbols: + - GmGI +gene_symbol_long: Earliness 2 +gene_model_pub_name: Glyma.10G221500 +gene_model_full_id: glyma.Wm82.gnm2.ann1.Glyma.10G221500 +confidence: 5 +curators: + - Steven Cannon +phenotype_synopsis: Photoperiodic flowering time regulation +traits: + - entity_name: flowering time + entity: TO:0002616 + relation_name: negatively regulates + relation: RO:0002212 + - entity_name: days to maturity + entity: TO:0000469 + relation_name: negatively regulates + relation: RO:0002212 +references: + - citation: Tsubokura, Watanabe et al., 2013 + doi: 10.1093/aob/mct269 + pmid: 24284817 + - citation: Dietz, Chan et al., 2023 + doi: 10.3389/fpls.2022.889066 + pmid: 35574141 + - citation: Lin, Liu et al., 2021 + doi: 10.1111/jipb.13021 + pmid: 33090664 + - citation: Watanabe, Xia et al., 2011 + doi: 10.1534/genetics.110.125062 + pmid: 21406680 + - citation: Xu, Yamagishi et al., 2015 + doi: 10.1104/pp.15.00763 + pmid: 26134161 \ No newline at end of file diff --git a/Glycine/max/studies/glyma.Wang_Guo_2021.yml b/Glycine/max/studies/glyma.Wang_Guo_2021.yml index eeade53..e64fa3a 100644 --- a/Glycine/max/studies/glyma.Wang_Guo_2021.yml +++ b/Glycine/max/studies/glyma.Wang_Guo_2021.yml @@ -33,8 +33,26 @@ references: - citation: Yang, Lan et. al., 2022 doi: 10.1111/jipb.13207 pmid: 34962095 + - citation: Kong, Liu et al., 2010 + doi: 10.1104/pp.110.160796 + pmid: 20864544 + - citation: Kong, Nan et al., 2014 + doi: 10.2135/cropsci2014.03.0228 + - citation: Takeshima, Hayashi et al., 2016 + doi: 10.1093/jxb/erw283 + pmid: 27422993 + - citation: Zhao, Takeshima et al., 2016 + doi: 10.1186/s12870-016-0704-9 + pmid: 26786479 + - citation: Dietz, Chan et al., 2023 + doi: 10.3389/fpls.2022.889066 + pmid: 35574141 + - citation: Lin, Liu et al., 2021 + doi: 10.1111/jipb.13021 + pmid: 33090664 --- scientific_name: Glycine max +classical_locus: E9 gene_symbols: - GmFT2a gene_symbol_long: Flowering locus T2a @@ -68,3 +86,20 @@ references: - citation: Yang, Lan et. al., 2022 doi: 10.1111/jipb.13207 pmid: 34962095 + - citation: Kong, Liu et al., 2010 + doi: 10.1104/pp.110.160796 + pmid: 20864544 + - citation: Kong, Nan et al., 2014 + doi: 10.2135/cropsci2014.03.0228 + - citation: Takeshima, Hayashi et al., 2016 + doi: 10.1093/jxb/erw283 + pmid: 27422993 + - citation: Zhao, Takeshima et al., 2016 + doi: 10.1186/s12870-016-0704-9 + pmid: 26786479 + - citation: Dietz, Chan et al., 2023 + doi: 10.3389/fpls.2022.889066 + pmid: 35574141 + - citation: Lin, Liu et al., 2021 + doi: 10.1111/jipb.13021 + pmid: 33090664 diff --git a/Glycine/max/studies/glyma.Wang_Wang_2015.yml b/Glycine/max/studies/glyma.Wang_Wang_2015.yml index a481ac9..6d9b255 100644 --- a/Glycine/max/studies/glyma.Wang_Wang_2015.yml +++ b/Glycine/max/studies/glyma.Wang_Wang_2015.yml @@ -2,8 +2,8 @@ scientific_name: Glycine max gene_symbols: - GmVSPβ -gene_model_pub_name: Glyma08g21410.1 -gene_model_full_id: glyma.Wm82.gnm1.ann1.Glyma08g21410.1 +gene_model_pub_name: Glyma08g21410 +gene_model_full_id: glyma.Wm82.gnm1.ann1.Glyma08g21410 confidence: 3 curators: - William Hardison @@ -22,8 +22,8 @@ references: scientific_name: Glycine max gene_symbols: - GmN:IFR -gene_model_pub_name: Glyma01g37810.1 -gene_model_full_id: glyma.Wm82.gnm1.ann1.Glyma01g37810.1 +gene_model_pub_name: Glyma01g37810 +gene_model_full_id: glyma.Wm82.gnm1.ann1.Glyma01g37810 confidence: 3 curators: - William Hardison diff --git a/Glycine/max/studies/glyma.Wang_Zhou_2015.yml b/Glycine/max/studies/glyma.Wang_Zhou_2015.yml new file mode 100644 index 0000000..8cc07ae --- /dev/null +++ b/Glycine/max/studies/glyma.Wang_Zhou_2015.yml @@ -0,0 +1,26 @@ +--- +gene_symbols: + - GmFT6 +gene_symbol_long: Flowering Time 6 +gene_model_pub_name: Glyma.08G363200 +gene_model_full_id: glyma.Wm82.gnm2.ann1.Glyma.08G363200 +confidence: 5 +curators: + - Steven Cannon +phenotype_synopsis: Photoperiodic flowering time regulation +traits: + - entity_name: flowering time + entity: TO:0002616 + relation_name: negatively regulates + relation: RO:0002212 + - entity_name: days to maturity + entity: TO:0000469 + relation_name: negatively regulates + relation: RO:0002212 +references: + - citation: Wang, Zhou et al., 2015 + doi: 10.1105/tpc.114.135103 + pmid: 25663621 + - citation: Lin, Liu et al., 2021 + doi: 10.1111/jipb.13021 + pmid: 33090664 diff --git a/Glycine/max/studies/glyma.Watanabe_Hideshima_2009.yml b/Glycine/max/studies/glyma.Watanabe_Hideshima_2009.yml new file mode 100644 index 0000000..5e3108e --- /dev/null +++ b/Glycine/max/studies/glyma.Watanabe_Hideshima_2009.yml @@ -0,0 +1,27 @@ +--- +classical_locus: E3 +gene_symbols: + - GmphyA3 +gene_symbol_long: Earliness 3 +gene_model_pub_name: Glyma.19G224200 +gene_model_full_id: glyma.Wm82.gnm2.ann1.Glyma.19G224200 +confidence: 5 +curators: + - Steven Cannon +phenotype_synopsis: Photoperiodic flowering time regulation +traits: + - entity_name: flowering time + entity: TO:0002616 + relation_name: negatively regulates + relation: RO:0002212 + - entity_name: days to maturity + entity: TO:0000469 + relation_name: negatively regulates + relation: RO:0002212 +references: + - citation: Watanabe, Hideshima et al., 2009 + doi: 10.1534/genetics.108.098772 + pmid: 19474204 + - citation: Lin, Liu et al., 2021 + doi: 10.1111/jipb.13021 + pmid: 33090664 diff --git a/Glycine/max/studies/glyma.Watanabe_Xia_2011.yml b/Glycine/max/studies/glyma.Watanabe_Xia_2011.yml new file mode 100644 index 0000000..adb12b8 --- /dev/null +++ b/Glycine/max/studies/glyma.Watanabe_Xia_2011.yml @@ -0,0 +1,26 @@ +--- +gene_symbols: + - E1Lb +gene_symbol_long: E1-like-b +gene_model_pub_name: Glyma.04G143300 +gene_model_full_id: glyma.Wm82.gnm2.ann1.Glyma.04G143300 +confidence: 5 +curators: + - Steven Cannon +phenotype_synopsis: Photoperiodic flowering time regulation +traits: + - entity_name: flowering time + entity: TO:0002616 + relation_name: negatively regulates + relation: RO:0002212 + - entity_name: days to maturity + entity: TO:0000469 + relation_name: negatively regulates + relation: RO:0002212 +references: + - citation: Watanabe, Xia et al., 2011 + doi: 10.1534/genetics.110.125062 + pmid: 21406680 + - citation: Lin, Liu et al., 2021 + doi: 10.1111/jipb.13021 + pmid: 33090664 diff --git a/Glycine/max/studies/glyma.Wu_Kang_2019.yml b/Glycine/max/studies/glyma.Wu_Kang_2019.yml new file mode 100644 index 0000000..2cdbd76 --- /dev/null +++ b/Glycine/max/studies/glyma.Wu_Kang_2019.yml @@ -0,0 +1,22 @@ +--- +gene_symbols: + - GmSWN +gene_symbol_long: Swinger +gene_model_pub_name: Glyma.03G224300 +gene_model_full_id: glyma.Wm82.gnm2.ann1.Glyma.03G224300 +confidence: 5 +curators: + - Steven Cannon +phenotype_synopsis: Photoperiodic flowering time regulation +traits: + - entity_name: flowering time + entity: TO:0002616 + - entity_name: days to maturity + entity: TO:0000469 +references: + - citation: Wu, Kang et al., 2019 + doi: 10.3389/fpls.2019.01221 + pmid: 31787988 + - citation: Dietz, Chan et al., 2023 + doi: 10.3389/fpls.2022.889066 + pmid: 35574141 diff --git a/Glycine/max/studies/glyma.Wu_Price_2014.yml b/Glycine/max/studies/glyma.Wu_Price_2014.yml index d963431..75cc5bc 100644 --- a/Glycine/max/studies/glyma.Wu_Price_2014.yml +++ b/Glycine/max/studies/glyma.Wu_Price_2014.yml @@ -4,7 +4,7 @@ gene_symbols: - GmCOL1a gene_symbol_long: CONSTANS-Like 1a gene_model_pub_name: Glyma08g28370 -gene_model_full_id: glyma.Wm82.gnm1.ann1.Glyma08g28370.1 +gene_model_full_id: glyma.Wm82.gnm1.ann1.Glyma08g28370 confidence: 5 curators: - William Hardison @@ -30,7 +30,7 @@ gene_symbols: - GmCOL1b gene_symbol_long: CONSTANS-Like 1b gene_model_pub_name: Glyma18g51320 -gene_model_full_id: glyma.Wm82.gnm1.ann1.Glyma18g51320.1 +gene_model_full_id: glyma.Wm82.gnm1.ann1.Glyma18g51320 confidence: 3 curators: - William Hardison diff --git a/Glycine/max/studies/glyma.Xia_Zhai_2012.yml b/Glycine/max/studies/glyma.Xia_Zhai_2012.yml new file mode 100644 index 0000000..07f7e4f --- /dev/null +++ b/Glycine/max/studies/glyma.Xia_Zhai_2012.yml @@ -0,0 +1,33 @@ +--- +classical_locus: E1 +gene_symbols: + - E1 +gene_symbol_long: Earliness 1 +gene_model_pub_name: Glyma.06G207800 +gene_model_full_id: glyma.Wm82.gnm4.ann1.Glyma.06G207800 +confidence: 5 +curators: + - Steven Cannon +phenotype_synopsis: Photoperiodic flowering time regulation +traits: + - entity_name: flowering time + entity: TO:0002616 + relation_name: negatively regulates + relation: RO:0002212 + - entity_name: days to maturity + entity: TO:0000469 + relation_name: negatively regulates + relation: RO:0002212 +references: + - citation: Xia, Zhai et al., 2012 + doi: 10.3389/fpls.2021.632754 + pmid: 33995435 + - citation: Watanabe, Xia et al., 2011 + doi: 10.1534/genetics.110.125062 + pmid: 21406680 + - citation: Dietz, Chan et al., 2023 + doi: 10.3389/fpls.2022.889066 + pmid: 35574141 + - citation: Lin, Liu et al., 2021 + doi: 10.1111/jipb.13021 + pmid: 33090664 diff --git a/Glycine/max/studies/glyma.Xu_Yamagishi_2015.yml b/Glycine/max/studies/glyma.Xu_Yamagishi_2015.yml new file mode 100644 index 0000000..b5d5246 --- /dev/null +++ b/Glycine/max/studies/glyma.Xu_Yamagishi_2015.yml @@ -0,0 +1,26 @@ +--- +gene_symbols: + - E1La +gene_symbol_long: E1-like-a +gene_model_pub_name: Glyma.04G156400 +gene_model_full_id: glyma.Wm82.gnm2.ann1.Glyma.04G156400 +confidence: 5 +curators: + - Steven Cannon +phenotype_synopsis: Photoperiodic flowering time regulation +traits: + - entity_name: flowering time + entity: TO:0002616 + relation_name: negatively regulates + relation: RO:0002212 + - entity_name: days to maturity + entity: TO:0000469 + relation_name: negatively regulates + relation: RO:0002212 +references: + - citation: Xu, Yamagishi et al., 2015 + doi: 10.1104/pp.15.00763 + pmid: 26134161 + - citation: Lin, Liu et al., 2021 + doi: 10.1111/jipb.13021 + pmid: 33090664 diff --git a/Glycine/max/studies/glyma.Yu_Chang_2019.yml b/Glycine/max/studies/glyma.Yu_Chang_2019.yml index 06f613f..b24ff25 100644 --- a/Glycine/max/studies/glyma.Yu_Chang_2019.yml +++ b/Glycine/max/studies/glyma.Yu_Chang_2019.yml @@ -4,7 +4,7 @@ gene_symbols: - GmSFT gene_symbol_long: Seed-Flooding Tolerance gene_model_pub_name: Glyma.13g248000 -gene_model_full_id: glyma.Wm82.gnm4.ann1.Glyma.13G248000.1 +gene_model_full_id: glyma.Wm82.gnm4.ann1.Glyma.13G248000 confidence: 3 curators: - William Hardison diff --git a/Glycine/max/studies/glyma.Zhai_Lu_2014.yml b/Glycine/max/studies/glyma.Zhai_Lu_2014.yml new file mode 100644 index 0000000..e556943 --- /dev/null +++ b/Glycine/max/studies/glyma.Zhai_Lu_2014.yml @@ -0,0 +1,30 @@ +--- +classical_locus: E10 +gene_symbols: + - GmFT4 +gene_symbol_long: Earliness 10 +gene_model_pub_name: Glyma.08G363100 +gene_model_full_id: glyma.Wm82.gnm2.ann1.Glyma.08G363100 +confidence: 5 +curators: + - Steven Cannon +phenotype_synopsis: Photoperiodic flowering time regulation +traits: + - entity_name: flowering time + entity: TO:0002616 + relation_name: negatively regulates + relation: RO:0002212 + - entity_name: days to maturity + entity: TO:0000469 + relation_name: negatively regulates + relation: RO:0002212 +references: + - citation: Zhai, Lu et al., 2014 + doi: 10.1371/journal.pone.0089030 + pmid: 24586488 + - citation: Samanfar, Molnar et al., 2017 + doi: 10.1007/s00122-016-2819-7 + pmid: 27832313 + - citation: Lin, Liu et al., 2021 + doi: 10.1111/jipb.13021 + pmid: 33090664 diff --git a/Glycine/max/studies/glyma.Zhao_Bi_2019.yml b/Glycine/max/studies/glyma.Zhao_Bi_2019.yml index 8ddf638..fdc28f9 100644 --- a/Glycine/max/studies/glyma.Zhao_Bi_2019.yml +++ b/Glycine/max/studies/glyma.Zhao_Bi_2019.yml @@ -4,7 +4,7 @@ gene_symbols: - GmDGAT1A gene_symbol_long: Acyl-CoA:Diacylglycerol Acyltransferase 1A gene_model_pub_name: Glyma13g16560 -gene_model_full_id: glyma.Wm82.gnm1.ann1.Glyma13g16560.2 +gene_model_full_id: glyma.Wm82.gnm1.ann1.Glyma13g16560 confidence: 3 curators: - William Hardison @@ -24,7 +24,7 @@ gene_symbols: - GmDGAT1B gene_symbol_long: Acyl-CoA:Diacylglycerol Acyltransferase 1B gene_model_pub_name: Glyma17g06120 -gene_model_full_id: glyma.Wm82.gnm1.ann1.Glyma17g06120.1 +gene_model_full_id: glyma.Wm82.gnm1.ann1.Glyma17g06120 confidence: 3 curators: - William Hardison @@ -47,7 +47,7 @@ gene_symbols: - GmDGAT1C gene_symbol_long: Acyl-CoA:Diacylglycerol Acyltransferase 1C gene_model_pub_name: Glyma09g07520 -gene_model_full_id: glyma.Wm82.gnm1.ann1.Glyma09g07520.2 +gene_model_full_id: glyma.Wm82.gnm1.ann1.Glyma09g07520 confidence: 2 curators: - William Hardison @@ -68,7 +68,7 @@ gene_symbols: - GmDGAT2D gene_symbol_long: Acyl-CoA:Diacylglycerol Acyltransferase 2D gene_model_pub_name: Glyma01g36010 -gene_model_full_id: glyma.Wm82.gnm4.ann1.Glyma01g36010.1 +gene_model_full_id: glyma.Wm82.gnm4.ann1.Glyma01g36010 confidence: 3 curators: - William Hardison From 43ee942dfeb09b849b9ace804248d7f79fc566a0 Mon Sep 17 00:00:00 2001 From: StevenCannon-USDA Date: Tue, 10 Sep 2024 16:51:05 -0500 Subject: [PATCH 02/18] Correct yaml format for two files --- Glycine/max/studies/glyma.Liu_Jiang_2008.yml | 3 ++- Glycine/max/studies/glyma.Tsubokura_Watanabe_2013.yml | 3 ++- 2 files changed, 4 insertions(+), 2 deletions(-) diff --git a/Glycine/max/studies/glyma.Liu_Jiang_2008.yml b/Glycine/max/studies/glyma.Liu_Jiang_2008.yml index 3408055..cf1275c 100644 --- a/Glycine/max/studies/glyma.Liu_Jiang_2008.yml +++ b/Glycine/max/studies/glyma.Liu_Jiang_2008.yml @@ -24,4 +24,5 @@ references: pmid: 29120038 - citation: Lin, Liu et al., 2021 doi: 10.1111/jipb.13021 - pmid: 33090664 \ No newline at end of file + pmid: 33090664 + diff --git a/Glycine/max/studies/glyma.Tsubokura_Watanabe_2013.yml b/Glycine/max/studies/glyma.Tsubokura_Watanabe_2013.yml index bc66c61..77721e3 100644 --- a/Glycine/max/studies/glyma.Tsubokura_Watanabe_2013.yml +++ b/Glycine/max/studies/glyma.Tsubokura_Watanabe_2013.yml @@ -1,3 +1,4 @@ +--- classical_locus: E2 gene_symbols: - GmGI @@ -32,4 +33,4 @@ references: pmid: 21406680 - citation: Xu, Yamagishi et al., 2015 doi: 10.1104/pp.15.00763 - pmid: 26134161 \ No newline at end of file + pmid: 26134161 From a010274964912dc142eaf316a1dce75b6517dd9f Mon Sep 17 00:00:00 2001 From: StevenCannon-USDA Date: Wed, 11 Sep 2024 08:55:36 -0500 Subject: [PATCH 03/18] Add Medicago truncatula studies that had been in glyma.traits.yml but not in separate per-study yml files. Add citation for glyma.Tsubokura_Watanabe_2013.yml and curator for vicfa.Jayakodi_Golicz_2023.yml. --- .../studies/glyma.Tsubokura_Watanabe_2013.yml | 1 + .../medtr.Campalans_Kondorosi_2017.yml | 21 + .../studies/medtr.Carelli_Biazzi_2014.yml | 23 + .../studies/medtr.Chen_Liu_2015.yml | 22 + .../studies/medtr.Cheng_Li_2021.yml | 29 + .../studies/medtr.Cheng_Peng_2012.yml | 60 + .../studies/medtr.Floss_Schliemann_2008.yml | 23 + .../medtr.Gargantini_Gonzalez-Rizzo_2006.yml | 25 + .../studies/medtr.Godiard_Lepage_2011.yml | 29 + .../studies/medtr.Herrbach_Chirinos_2017.yml | 49 + .../studies/medtr.Isayenkov_Mrosk_2005.yml | 23 + .../studies/medtr.Ivashuta_Liu_2005.yml | 31 + .../studies/medtr.Jiao_Wang_2020.yml | 29 + .../truncatula/studies/medtr.Jun_Liu_2015.yml | 25 + .../studies/medtr.Kevei_Lougnon_2007.yml | 25 + .../studies/medtr.Kuppusamy_Ivashuta_2009.yml | 31 + .../truncatula/studies/medtr.Lace_Su_2023.yml | 21 + .../studies/medtr.Laffont_Huault_2019.yml | 29 + .../studies/medtr.Laurie_Diwadkar_2011.yml | 41 + .../studies/medtr.Liu_Breakspear_2019.yml | 22 + .../truncatula/studies/medtr.Liu_Lin_2022.yml | 25 + .../studies/medtr.Mitra_Gleason_2004.yml | 25 + .../studies/medtr.Miyahara_Richens_2010.yml | 31 + .../studies/medtr.Oellrich_Walls_2015.yml | 1142 ----------------- .../studies/medtr.Pecrix_Staton_2018.yml | 27 + .../truncatula/studies/medtr.Peng_Yu_2011.yml | 29 + .../studies/medtr.Pumplin_Mondo_2009.yml | 25 + .../studies/medtr.Qiao_Pingault_2016.yml | 83 ++ .../studies/medtr.Rey_Nars_2013.yml | 21 + .../studies/medtr.Ribeiro_Lacchini_2020.yml | 32 + .../studies/medtr.Salzer_Bonanomi_2000.yml | 21 + .../studies/medtr.Vernie_Kim_2015.yml | 168 +++ .../studies/medtr.Weller_Foo_2015.yml | 44 + .../studies/vicfa.Jayakodi_Golicz_2023.yml | 4 + 34 files changed, 1094 insertions(+), 1142 deletions(-) create mode 100644 Medicago/truncatula/studies/medtr.Campalans_Kondorosi_2017.yml create mode 100644 Medicago/truncatula/studies/medtr.Carelli_Biazzi_2014.yml create mode 100644 Medicago/truncatula/studies/medtr.Chen_Liu_2015.yml create mode 100644 Medicago/truncatula/studies/medtr.Cheng_Li_2021.yml create mode 100644 Medicago/truncatula/studies/medtr.Cheng_Peng_2012.yml create mode 100644 Medicago/truncatula/studies/medtr.Floss_Schliemann_2008.yml create mode 100644 Medicago/truncatula/studies/medtr.Gargantini_Gonzalez-Rizzo_2006.yml create mode 100644 Medicago/truncatula/studies/medtr.Godiard_Lepage_2011.yml create mode 100644 Medicago/truncatula/studies/medtr.Herrbach_Chirinos_2017.yml create mode 100644 Medicago/truncatula/studies/medtr.Isayenkov_Mrosk_2005.yml create mode 100644 Medicago/truncatula/studies/medtr.Ivashuta_Liu_2005.yml create mode 100644 Medicago/truncatula/studies/medtr.Jiao_Wang_2020.yml create mode 100644 Medicago/truncatula/studies/medtr.Jun_Liu_2015.yml create mode 100644 Medicago/truncatula/studies/medtr.Kevei_Lougnon_2007.yml create mode 100644 Medicago/truncatula/studies/medtr.Kuppusamy_Ivashuta_2009.yml create mode 100644 Medicago/truncatula/studies/medtr.Lace_Su_2023.yml create mode 100644 Medicago/truncatula/studies/medtr.Laffont_Huault_2019.yml create mode 100644 Medicago/truncatula/studies/medtr.Laurie_Diwadkar_2011.yml create mode 100644 Medicago/truncatula/studies/medtr.Liu_Breakspear_2019.yml create mode 100644 Medicago/truncatula/studies/medtr.Liu_Lin_2022.yml create mode 100644 Medicago/truncatula/studies/medtr.Mitra_Gleason_2004.yml create mode 100644 Medicago/truncatula/studies/medtr.Miyahara_Richens_2010.yml delete mode 100644 Medicago/truncatula/studies/medtr.Oellrich_Walls_2015.yml create mode 100644 Medicago/truncatula/studies/medtr.Pecrix_Staton_2018.yml create mode 100644 Medicago/truncatula/studies/medtr.Peng_Yu_2011.yml create mode 100644 Medicago/truncatula/studies/medtr.Pumplin_Mondo_2009.yml create mode 100644 Medicago/truncatula/studies/medtr.Qiao_Pingault_2016.yml create mode 100644 Medicago/truncatula/studies/medtr.Rey_Nars_2013.yml create mode 100644 Medicago/truncatula/studies/medtr.Ribeiro_Lacchini_2020.yml create mode 100644 Medicago/truncatula/studies/medtr.Salzer_Bonanomi_2000.yml create mode 100644 Medicago/truncatula/studies/medtr.Vernie_Kim_2015.yml create mode 100644 Medicago/truncatula/studies/medtr.Weller_Foo_2015.yml diff --git a/Glycine/max/studies/glyma.Tsubokura_Watanabe_2013.yml b/Glycine/max/studies/glyma.Tsubokura_Watanabe_2013.yml index 77721e3..ca03a18 100644 --- a/Glycine/max/studies/glyma.Tsubokura_Watanabe_2013.yml +++ b/Glycine/max/studies/glyma.Tsubokura_Watanabe_2013.yml @@ -34,3 +34,4 @@ references: - citation: Xu, Yamagishi et al., 2015 doi: 10.1104/pp.15.00763 pmid: 26134161 + diff --git a/Medicago/truncatula/studies/medtr.Campalans_Kondorosi_2017.yml b/Medicago/truncatula/studies/medtr.Campalans_Kondorosi_2017.yml new file mode 100644 index 0000000..a75d417 --- /dev/null +++ b/Medicago/truncatula/studies/medtr.Campalans_Kondorosi_2017.yml @@ -0,0 +1,21 @@ +--- +gene_symbols: + - ENOD40 +gene_symbol_long: Abnormal tissue development +gene_model_pub_name: CAD48198.1 +gene_model_full_id: medtr.A17_HM341.gnm4.ann2.Medtr6g034835 +confidence: 5 +curators: + - Steven Cannon +phenotype_synopsis: Use of antisense constructs of Mtenod40 arrested callus growth of Medicago explants, while overexpressing Mtenod40 embryos developed into teratomas. Enod40 genes might have a role in plant development, acting as 'riboregulators'. +traits: + - entity_name: plant tissue development trait + entity: TO:0006015 +references: + - citation: Campalans, Kondorosi et al., 2017 + doi: 10.1105/tpc.019406 + pmid: 15037734 + - citation: Oellrich, Walls et al., 2015 + doi: 10.1186/s13007-015-0053-y + pmid: 25774204 + diff --git a/Medicago/truncatula/studies/medtr.Carelli_Biazzi_2014.yml b/Medicago/truncatula/studies/medtr.Carelli_Biazzi_2014.yml new file mode 100644 index 0000000..5de661b --- /dev/null +++ b/Medicago/truncatula/studies/medtr.Carelli_Biazzi_2014.yml @@ -0,0 +1,23 @@ +--- +gene_symbols: + - cyp716A12 +gene_symbol_long: cytochrome P450 monoxygenase +gene_model_pub_name: Medtr3g021350 +gene_model_full_id: medtr.A17_HM341.gnm4.ann2.Medtr3g021350 +confidence: 5 +curators: + - Steven Cannon +phenotype_synopsis: A cytochrome P450 gene (CYP716A12) is involved in an early step in saponin biosynthesis and is found in most tissues. CYP716A12 loss-of-function mutants do not produce hemolytic saponins and only synthetize soyasaponins, and were thus named lacking hemolytic activity (lha). CYP716A12 catalyzes the oxidation of _-amyrin and erythrodiol at the C-28 position, yielding oleanolic acid. Transcriptome changes in the lha mutant showed a modulation in the main steps of the triterpenic saponin biosynthetic pathway, which includes squalene cyclization, _-amyrin oxidation, and glycosylation. Growth of homozygous lha/lha plants was stunted. +traits: + - entity_name: plant structure growth and development trait + entity: TO:0000928 + - entity_name: whole plant + entity: PO:0000003 +references: + - citation: Carelli, Biazzi et al., 2014 + doi: 10.1111/nph.13162 + pmid: 25406544 + - citation: Oellrich, Walls et al., 2015 + doi: 10.1186/s13007-015-0053-y + pmid: 25774204 + diff --git a/Medicago/truncatula/studies/medtr.Chen_Liu_2015.yml b/Medicago/truncatula/studies/medtr.Chen_Liu_2015.yml new file mode 100644 index 0000000..d3ecdeb --- /dev/null +++ b/Medicago/truncatula/studies/medtr.Chen_Liu_2015.yml @@ -0,0 +1,22 @@ +--- +gene_symbols: + - HAP2.1 +gene_model_pub_name: Medtr1g056530 +gene_model_full_id: medtr.A17_HM341.gnm4.ann2.Medtr1g056530 +confidence: 5 +curators: + - Steven Cannon +phenotype_synopsis: Small and nonfunctional nodules arrested in growth when both normally spliced and alternatively spliced variants repressed. When only the alternative spliced form repressed the nodules are small but still fix nitrogen successfully. +traits: + - entity_name: root nodule morphology trait + entity: TO:0000898 + - entity_name: root nodule + entity: PO:0003023 +references: + - citation: Chen, Liu et al., 2015 + doi: 10.3389/fpls.2015.00575 + pmid: 26284091 + - citation: Oellrich, Walls et al., 2015 + doi: 10.1186/s13007-015-0053-y + pmid: 25774204 + diff --git a/Medicago/truncatula/studies/medtr.Cheng_Li_2021.yml b/Medicago/truncatula/studies/medtr.Cheng_Li_2021.yml new file mode 100644 index 0000000..b132857 --- /dev/null +++ b/Medicago/truncatula/studies/medtr.Cheng_Li_2021.yml @@ -0,0 +1,29 @@ +--- +gene_symbols: + - SGL1 +gene_symbol_long: single leaflet1 +gene_model_pub_name: Medtr3g098560 +gene_model_full_id: medtr.A17_HM341.gnm4.ann2.Medtr3g098560 +confidence: 5 +curators: + - Steven Cannon +phenotype_synopsis: Mutant displays simple, unifoliate (not compound) leaves. Petiole length is decreased. Defective, fused flowers +traits: + - entity_name: petiole length + entity: TO:0000766 + - entity_name: flower morphology trait + entity: TO:0000499 + - entity_name: leaf shape + entity: TO:0000492 + - entity_name: petiole + entity: PO:0020038 + - entity_name: flower + entity: PO:0009046 +references: + - citation: Cheng, Li et al., 2021 + doi: 10.1093/plphys/kiaa005 + pmid: 33631796 + - citation: Oellrich, Walls et al., 2015 + doi: 10.1186/s13007-015-0053-y + pmid: 25774204 + diff --git a/Medicago/truncatula/studies/medtr.Cheng_Peng_2012.yml b/Medicago/truncatula/studies/medtr.Cheng_Peng_2012.yml new file mode 100644 index 0000000..eb51067 --- /dev/null +++ b/Medicago/truncatula/studies/medtr.Cheng_Peng_2012.yml @@ -0,0 +1,60 @@ +--- +gene_symbols: + - NAM + - NAM-2 +gene_symbol_long: No Apical Meristem (weak allele) +gene_model_pub_name: AFI56799.1 +gene_model_full_id: medtr.A17_HM341.gnm4.ann2.Medtr2g078700 +confidence: 5 +curators: + - Steven Cannon +phenotype_synopsis: null +traits: + - entity_name: shoot apical meristem development + entity: TO:0006020 + - entity_name: carpel morphology trait + entity: TO:0006012 + - entity_name: trichome morphology trait + entity: TO:0000911 + - entity_name: cotyledon morphology trait + entity: TO:0000749 + - entity_name: male sterility + entity: TO:0000437 + - entity_name: vascular leaf morphology trait + entity: TO:0000419 + - entity_name: female sterility + entity: TO:0000358 + - entity_name: stamen morphology trait + entity: TO:0000215 + - entity_name: embryo shape + entity: TO:0000193 + - entity_name: carpel trichome + entity: PO:0025208 + - entity_name: reproductive shoot system + entity: PO:0025082 + - entity_name: leaflet + entity: PO:0020049 + - entity_name: cotyledon + entity: PO:0020030 + - entity_name: plant ovule + entity: PO:0020003 + - entity_name: flower + entity: PO:0009046 + - entity_name: carpel + entity: PO:0009030 + - entity_name: stamen + entity: PO:0009029 + - entity_name: plant embryo + entity: PO:0009009 + - entity_name: fruit + entity: PO:0009001 + - entity_name: juvenile vascular leaf + entity: PO:0006339 +references: + - citation: Cheng, Peng et al., 2012 + doi: 10.1111/j.1469-8137.2012.04147.x + pmid: 22530598 + - citation: Oellrich, Walls et al., 2015 + doi: 10.1186/s13007-015-0053-y + pmid: 25774204 + diff --git a/Medicago/truncatula/studies/medtr.Floss_Schliemann_2008.yml b/Medicago/truncatula/studies/medtr.Floss_Schliemann_2008.yml new file mode 100644 index 0000000..0817a50 --- /dev/null +++ b/Medicago/truncatula/studies/medtr.Floss_Schliemann_2008.yml @@ -0,0 +1,23 @@ +--- +gene_symbols: + - MtCCD1 +gene_symbol_long: carotenoid cleavage dioxygenase 1 +gene_model_pub_name: CAR57918.1 +gene_model_full_id: medtr.A17_HM341.gnm4.ann2.Medtr6g034835 +confidence: 5 +curators: + - Steven Cannon +phenotype_synopsis: RNA interference (RNAi) was used to repress a M. truncatula CCD1 gene in hairy roots colonized by the arbuscular mycorrhizal (AM) fungus Glomus intraradices. The normal AM-mediated accumulation of apocarotenoids (C13 cyclohexenone and C14 mycorradicin derivatives) was reduced in repressed plants; mycorradicin derivatives were reduced to 3% to 6% of the controls and the cyclohexenone derivatives were reduced to 30% to 47%. The RNAi roots turned a yellow-orange color because of C27 apocarotenoid accumulation (the probable substrate of the CCD1 enzyme). More degenerating arbuscules was observed in RNAi roots. +traits: + - entity_name: carotene content + entity: TO:0000289 + - entity_name: root + entity: PO:0009005 +references: + - citation: Floss, Schliemann et al., 2008 + doi: 10.1104/pp.108.125062 + pmid: 18790999 + - citation: Oellrich, Walls et al., 2015 + doi: 10.1186/s13007-015-0053-y + pmid: 25774204 + diff --git a/Medicago/truncatula/studies/medtr.Gargantini_Gonzalez-Rizzo_2006.yml b/Medicago/truncatula/studies/medtr.Gargantini_Gonzalez-Rizzo_2006.yml new file mode 100644 index 0000000..84f4905 --- /dev/null +++ b/Medicago/truncatula/studies/medtr.Gargantini_Gonzalez-Rizzo_2006.yml @@ -0,0 +1,25 @@ +--- +gene_symbols: + - CPK3 +gene_symbol_long: calcium dependent protein kinase 3 +gene_model_pub_name: ABE72958.1 +gene_model_full_id: medtr.A17_HM341.gnm4.ann2.Medtr3g051770 +confidence: 5 +curators: + - Steven Cannon +phenotype_synopsis: Expression of MtCPK3 in Medicago truncatula is regulated during nodulation. RNAi silenced CPK3 in transformed roots but no major phenotype was detected. When infected with rhizobia the nodule number was twice as high as the controls. +traits: + - entity_name: root nodule number + entity: TO:0000900 + - entity_name: root system + entity: PO:0025025 + - entity_name: root nodule + entity: PO:0003023 +references: + - citation: Gargantini, Gonzalez-Rizzo et al., 2006 + doi: 10.1111/j.1365-313x.2006.02910.x + pmid: 17132148 + - citation: Oellrich, Walls et al., 2015 + doi: 10.1186/s13007-015-0053-y + pmid: 25774204 + diff --git a/Medicago/truncatula/studies/medtr.Godiard_Lepage_2011.yml b/Medicago/truncatula/studies/medtr.Godiard_Lepage_2011.yml new file mode 100644 index 0000000..e67c748 --- /dev/null +++ b/Medicago/truncatula/studies/medtr.Godiard_Lepage_2011.yml @@ -0,0 +1,29 @@ +--- +gene_symbols: + - bHLH1 +gene_symbol_long: basic helix loop helix 1 +gene_model_pub_name: Medtr3g099620 +gene_model_full_id: medtr.A17_HM341.gnm4.ann2.Medtr3g099620 +confidence: 5 +curators: + - Steven Cannon +phenotype_synopsis: Repressing MtbHLH1 (using Chimeric REpressor Silencing Technology) caused an assymetrical pattern of nodule vascular bundle development with variable angles of growth in inoculated roots. The growth and vigor of aerial parts of the plant was impaired; the nodules were still able to fix atmospheric Nitrogen but the aboveground tissues could not benefit for whatever reason. Nodules on repressed plants appeared later than in control plants and were smaller in size. +traits: + - entity_name: vascular bundle development trait + entity: TO:0020109 + - entity_name: plant organ growth and development trait + entity: TO:0000927 + - entity_name: shoot system + entity: PO:0009006 + - entity_name: vascular bundle + entity: PO:0005020 + - entity_name: root nodule + entity: PO:0003023 +references: + - citation: Godiard, Lepage et al., 2011 + doi: 10.1111/j.1469-8137.2011.03718.x + pmid: 21679315 + - citation: Oellrich, Walls et al., 2015 + doi: 10.1186/s13007-015-0053-y + pmid: 25774204 + diff --git a/Medicago/truncatula/studies/medtr.Herrbach_Chirinos_2017.yml b/Medicago/truncatula/studies/medtr.Herrbach_Chirinos_2017.yml new file mode 100644 index 0000000..b87a7ff --- /dev/null +++ b/Medicago/truncatula/studies/medtr.Herrbach_Chirinos_2017.yml @@ -0,0 +1,49 @@ +--- +gene_symbols: + - LYK3 +gene_symbol_long: LYSIN MOTIF RECEPTOR-LIKE KINASE 3 +gene_model_pub_name: Medtr5g086130 +gene_model_full_id: medtr.A17_HM341.gnm4.ann2.Medtr5g086130 +confidence: 5 +curators: + - Steven Cannon +phenotype_synopsis: Doesn't make nodules; infection thread aborts +traits: + - entity_name: root nodule number + entity: TO:0000900 + - entity_name: root system + entity: PO:0025025 + - entity_name: root nodule + entity: PO:0003023 +references: + - citation: Herrbach, Chirinos et al., 2017 + doi: 10.1093/jxb/erw474 + pmid: 28073951 + - citation: Oellrich, Walls et al., 2015 + doi: 10.1186/s13007-015-0053-y + pmid: 25774204 +--- +gene_symbols: + - LYK4 +gene_symbol_long: LYSIN MOTIF RECEPTOR-LIKE KINASE 4 +gene_model_pub_name: Medtr5g086120 +gene_model_full_id: medtr.A17_HM341.gnm4.ann2.Medtr5g086120 +confidence: 5 +curators: + - Steven Cannon +phenotype_synopsis: Doesn't make nodules; infection thread aborts +traits: + - entity_name: root nodule number + entity: TO:0000900 + - entity_name: root system + entity: PO:0025025 + - entity_name: root nodule + entity: PO:0003023 +references: + - citation: Herrbach, Chirinos et al., 2017 + doi: 10.1093/jxb/erw474 + pmid: 28073951 + - citation: Oellrich, Walls et al., 2015 + doi: 10.1186/s13007-015-0053-y + pmid: 25774204 + diff --git a/Medicago/truncatula/studies/medtr.Isayenkov_Mrosk_2005.yml b/Medicago/truncatula/studies/medtr.Isayenkov_Mrosk_2005.yml new file mode 100644 index 0000000..d829c83 --- /dev/null +++ b/Medicago/truncatula/studies/medtr.Isayenkov_Mrosk_2005.yml @@ -0,0 +1,23 @@ +--- +gene_symbols: + - MtAOC +gene_symbol_long: Allene-oxide cyclase +gene_model_pub_name: CAI29046.1 +gene_model_full_id: medtr.A17_HM341.gnm4.ann2.Medtr7g417750 +confidence: 5 +curators: + - Steven Cannon +phenotype_synopsis: MtAOC (allene oxide cyclase) gene expression was partially suppressed in roots following transformation with cDNA in the antisense direction. These roots exhibited lower jasmonic acid levels and delayed colonization by Glomus intraradices. The number of arbuscles decreased and their development was delayed, yet their physical structure was unaltered. +traits: + - entity_name: root system + entity: PO:0025025 + - entity_name: root + entity: PO:0009005 +references: + - citation: Isayenkov, Mrosk et al., 2005 + doi: 10.1104/pp.105.069054 + pmid: 16244141 + - citation: Oellrich, Walls et al., 2015 + doi: 10.1186/s13007-015-0053-y + pmid: 25774204 + diff --git a/Medicago/truncatula/studies/medtr.Ivashuta_Liu_2005.yml b/Medicago/truncatula/studies/medtr.Ivashuta_Liu_2005.yml new file mode 100644 index 0000000..11f33bb --- /dev/null +++ b/Medicago/truncatula/studies/medtr.Ivashuta_Liu_2005.yml @@ -0,0 +1,31 @@ +--- +gene_symbols: + - CDPK1 +gene_symbol_long: calcium-dependent protein kinase 1 +gene_model_pub_name: Medtr5g022030 +gene_model_full_id: medtr.A17_HM341.gnm4.ann2.Medtr5g022030 +confidence: 5 +curators: + - Steven Cannon +phenotype_synopsis: Reduced root hair and root cell lengths; diminution of rhizobial and mycorrhizal symbiotic colonization +traits: + - entity_name: root cortical cell length + entity: TO:0020108 + - entity_name: root hair length + entity: TO:0002665 + - entity_name: root nodule morphology trait + entity: TO:0000898 + - entity_name: root system + entity: PO:0025025 + - entity_name: root nodule + entity: PO:0003023 + - entity_name: root hair cell + entity: PO:0000256 +references: + - citation: Ivashuta, Liu et al., 2005 + doi: 10.1105/tpc.105.035394 + pmid: 16199614 + - citation: Oellrich, Walls et al., 2015 + doi: 10.1186/s13007-015-0053-y + pmid: 25774204 + diff --git a/Medicago/truncatula/studies/medtr.Jiao_Wang_2020.yml b/Medicago/truncatula/studies/medtr.Jiao_Wang_2020.yml new file mode 100644 index 0000000..773e8d8 --- /dev/null +++ b/Medicago/truncatula/studies/medtr.Jiao_Wang_2020.yml @@ -0,0 +1,29 @@ +--- +gene_symbols: + - PALM1 +gene_symbol_long: PALMATE-LIKE PENTAFOLIATA1 +gene_model_pub_name: Medtr5g014400 +gene_model_full_id: medtr.A17_HM341.gnm4.ann2.Medtr5g014400 +confidence: 5 +curators: + - Steven Cannon +phenotype_synopsis: Forms dissected leaves with five leaflets clustered at the tip (palmate-like pentafoliate in contrast to the trifoliate WT leaves). The distal lateral leaflets developed in a manner morphologically/anatomically similar to terminal leaflets. The length of the petiole increased and that of the rachis decreased. +traits: + - entity_name: petiole length + entity: TO:0000766 + - entity_name: TO:0000748 + entity: TO:0000748 + - entity_name: leaf + entity: PO:0025034 + - entity_name: leaf rachis + entity: PO:0020055 + - entity_name: petiole + entity: PO:0020038 +references: + - citation: Jiao, Wang et al., 2020 + doi: 10.1186/s12870-020-02619-6 + pmid: 32867687 + - citation: Oellrich, Walls et al., 2015 + doi: 10.1186/s13007-015-0053-y + pmid: 25774204 + diff --git a/Medicago/truncatula/studies/medtr.Jun_Liu_2015.yml b/Medicago/truncatula/studies/medtr.Jun_Liu_2015.yml new file mode 100644 index 0000000..292886b --- /dev/null +++ b/Medicago/truncatula/studies/medtr.Jun_Liu_2015.yml @@ -0,0 +1,25 @@ +--- +gene_symbols: + - ANS +gene_symbol_long: Anthocyanidin synthase +gene_model_pub_name: Medtr5g011250 +gene_model_full_id: medtr.A17_HM341.gnm4.ann2.Medtr5g011250 +confidence: 5 +curators: + - Steven Cannon +phenotype_synopsis: MtANS (anthocyanidin synthase) gene expression was down-regulated in M. truncatula genotype R108 using an antisense construct. Anthocyanin levels were strongly reduced in leaf tissues of antisense lines. The presence of a red anthocyanin-rich circle at the base of the axial side of the leaflet and small red dots on the adaxial side results from anthocyanin deposition. Six independent transgenic antisense MtANS lines lacked the red circle and spots and another 10 such lines had reduced levels of pigmentation. There was a strong reduction in the levels of both soluble and insoluble PAs (Oligomeric proanthocyanidins) in seeds, consistent with involvement of ANS in PA biosynthesis. +traits: + - entity_name: anthocyanin content + entity: TO:0000071 + - entity_name: leaf + entity: PO:0025034 + - entity_name: seed + entity: PO:0009010 +references: + - citation: Jun, Liu et al., 2015 + doi: 10.1105/tpc.15.00476 + pmid: 26410301 + - citation: Oellrich, Walls et al., 2015 + doi: 10.1186/s13007-015-0053-y + pmid: 25774204 + diff --git a/Medicago/truncatula/studies/medtr.Kevei_Lougnon_2007.yml b/Medicago/truncatula/studies/medtr.Kevei_Lougnon_2007.yml new file mode 100644 index 0000000..3b4314a --- /dev/null +++ b/Medicago/truncatula/studies/medtr.Kevei_Lougnon_2007.yml @@ -0,0 +1,25 @@ +--- +gene_symbols: + - nork +gene_symbol_long: nodulation receptor kinase +gene_model_pub_name: Medtr5g030920 +gene_model_full_id: medtr.A17_HM341.gnm4.ann2.Medtr5g030920 +confidence: 5 +curators: + - Steven Cannon +phenotype_synopsis: Lacks symbiotic root responses in the presence of compatible Sinorhizobium meliloti or Nod factor, and resists mycorrhizal colonization +traits: + - entity_name: root nodule number + entity: TO:0000900 + - entity_name: root system + entity: PO:0025025 + - entity_name: root nodule + entity: PO:0003023 +references: + - citation: Kevei, Lougnon et al., 2007 + doi: 10.1105/tpc.107.053975 + pmid: 18156218 + - citation: Oellrich, Walls et al., 2015 + doi: 10.1186/s13007-015-0053-y + pmid: 25774204 + diff --git a/Medicago/truncatula/studies/medtr.Kuppusamy_Ivashuta_2009.yml b/Medicago/truncatula/studies/medtr.Kuppusamy_Ivashuta_2009.yml new file mode 100644 index 0000000..5cc498c --- /dev/null +++ b/Medicago/truncatula/studies/medtr.Kuppusamy_Ivashuta_2009.yml @@ -0,0 +1,31 @@ +--- +gene_symbols: + - CDC16 +gene_symbol_long: cell division cycle 16 +gene_model_pub_name: Medtr8g058380 +gene_model_full_id: medtr.A17_HM341.gnm4.ann2.Medtr8g058380 +confidence: 5 +curators: + - Steven Cannon +phenotype_synopsis: Partial suppression of the CDC16 gene homolog in Medicago truncatula leads to a decreased number of lateral roots, an increased number of nodules, and reduced auxin sensitivity. +traits: + - entity_name: root nodule morphology trait + entity: TO:0000898 + - entity_name: auxin sensitivity + entity: TO:0000163 + - entity_name: root system + entity: PO:0025025 + - entity_name: lateral root + entity: PO:0020121 + - entity_name: root + entity: PO:0009005 + - entity_name: root nodule + entity: PO:0003023 +references: + - citation: Kuppusamy, Ivashuta et al., 2009 + doi: 10.1104/pp.109.143024 + pmid: 19789288 + - citation: Oellrich, Walls et al., 2015 + doi: 10.1186/s13007-015-0053-y + pmid: 25774204 + diff --git a/Medicago/truncatula/studies/medtr.Lace_Su_2023.yml b/Medicago/truncatula/studies/medtr.Lace_Su_2023.yml new file mode 100644 index 0000000..02a6b4f --- /dev/null +++ b/Medicago/truncatula/studies/medtr.Lace_Su_2023.yml @@ -0,0 +1,21 @@ +--- +gene_symbols: + - LIN +gene_symbol_long: Lumpy infections +gene_model_pub_name: Medtr1g090320 +gene_model_full_id: medtr.A17_HM341.gnm4.ann2.Medtr1g090320 +confidence: 5 +curators: + - Steven Cannon +phenotype_synopsis: Rhizobial infection was reduced in quantity and infections were not persistent, i.e. infection threads were arrested after very limited progression within root hair cells. Nodule differentiation was arrested at an early primordial stage as an indirect result of the aborted infection. +traits: + - entity_name: root nodule + entity: PO:0003023 +references: + - citation: Lace, Su et al., 2023 + doi: 10.7554/elife.80741 + pmid: 36856086 + - citation: Oellrich, Walls et al., 2015 + doi: 10.1186/s13007-015-0053-y + pmid: 25774204 + diff --git a/Medicago/truncatula/studies/medtr.Laffont_Huault_2019.yml b/Medicago/truncatula/studies/medtr.Laffont_Huault_2019.yml new file mode 100644 index 0000000..a283475 --- /dev/null +++ b/Medicago/truncatula/studies/medtr.Laffont_Huault_2019.yml @@ -0,0 +1,29 @@ +--- +gene_symbols: + - SUNN +gene_symbol_long: super numeric nodules +gene_model_pub_name: Medtr4g070970 +gene_model_full_id: medtr.A17_HM341.gnm4.ann2.Medtr4g070970 +confidence: 5 +curators: + - Steven Cannon +phenotype_synopsis: Shortened roots even in the absence of rhizobia. A dramatic increase in the number of root nodules. Nodulation occurred even under a high nitrogen regime. Unlike wild type, both infection by rhizobia and nodulation occur randomly throughout the circumference of the developing root. Nodulation is normally sensitive to ethylene, similar to wild type. +traits: + - entity_name: root nodule number + entity: TO:0000900 + - entity_name: root length + entity: TO:0000227 + - entity_name: root system + entity: PO:0025025 + - entity_name: root + entity: PO:0009005 + - entity_name: root nodule + entity: PO:0003023 +references: + - citation: Laffont, Huault et al., 2019 + doi: 10.1104/pp.18.01588 + pmid: 30782966 + - citation: Oellrich, Walls et al., 2015 + doi: 10.1186/s13007-015-0053-y + pmid: 25774204 + diff --git a/Medicago/truncatula/studies/medtr.Laurie_Diwadkar_2011.yml b/Medicago/truncatula/studies/medtr.Laurie_Diwadkar_2011.yml new file mode 100644 index 0000000..3c16a3e --- /dev/null +++ b/Medicago/truncatula/studies/medtr.Laurie_Diwadkar_2011.yml @@ -0,0 +1,41 @@ +--- +gene_symbols: + - FTa1 +gene_symbol_long: Delayed flowering +gene_model_pub_name: Medtr7g084970 +gene_model_full_id: medtr.A17_HM341.gnm4.ann2.Medtr7g084970 +confidence: 5 +curators: + - Steven Cannon +phenotype_synopsis: Delayed flowering +traits: + - entity_name: flowering time trait + entity: TO:0002616 +references: + - citation: Laurie, Diwadkar et al., 2011 + doi: 10.1104/pp.111.180182 + pmid: 21685176 + - citation: Oellrich, Walls et al., 2015 + doi: 10.1186/s13007-015-0053-y + pmid: 25774204 +--- +gene_symbols: + - FTc +gene_symbol_long: Flower development normal under long days +gene_model_pub_name: Medtr7g085040 +gene_model_full_id: medtr.A17_HM341.gnm4.ann2.Medtr7g085040 +confidence: 5 +curators: + - Steven Cannon +phenotype_synopsis: null +traits: + - entity_name: flower development trait + entity: TO:0000622 +references: + - citation: Laurie, Diwadkar et al., 2011 + doi: 10.1104/pp.111.180182 + pmid: 21685176 + - citation: Oellrich, Walls et al., 2015 + doi: 10.1186/s13007-015-0053-y + pmid: 25774204 + diff --git a/Medicago/truncatula/studies/medtr.Liu_Breakspear_2019.yml b/Medicago/truncatula/studies/medtr.Liu_Breakspear_2019.yml new file mode 100644 index 0000000..795733f --- /dev/null +++ b/Medicago/truncatula/studies/medtr.Liu_Breakspear_2019.yml @@ -0,0 +1,22 @@ +--- +gene_symbols: + - CYCLOPS +gene_model_pub_name: Medtr5g026850 +gene_model_full_id: medtr.A17_HM341.gnm4.ann2.Medtr5g026850 +confidence: 5 +curators: + - Steven Cannon +phenotype_synopsis: Symbiotic infection of roots by rhizobia bacteria and arbuscular mycorrhiza fungi was inhibited or blocked, i.e. infection threads were not observed despite colonization of root hairs by rhizobia and AM fungal hyphae formed abnormal hyphal swellings with no arbuscles observed. Nodule organogenesis was initiated but arrested prematurely at the level of primordia as an indirect consequence of the aborted infection. +traits: + - entity_name: root nodule morphology trait + entity: TO:0000898 + - entity_name: root system + entity: PO:0025025 +references: + - citation: Liu, Breakspear et al., 2019 + doi: 10.1104/pp.18.01572 + pmid: null + - citation: Oellrich, Walls et al., 2015 + doi: 10.1186/s13007-015-0053-y + pmid: 25774204 + diff --git a/Medicago/truncatula/studies/medtr.Liu_Lin_2022.yml b/Medicago/truncatula/studies/medtr.Liu_Lin_2022.yml new file mode 100644 index 0000000..1e1237c --- /dev/null +++ b/Medicago/truncatula/studies/medtr.Liu_Lin_2022.yml @@ -0,0 +1,25 @@ +--- +gene_symbols: + - DMI1 +gene_symbol_long: doesn't make infections 1 +gene_model_pub_name: Medtr2g005870 +gene_model_full_id: medtr.A17_HM341.gnm4.ann2.Medtr2g005870 +confidence: 5 +curators: + - Steven Cannon +phenotype_synopsis: Doesn't make nodules; infection thread aborts +traits: + - entity_name: root nodule number + entity: TO:0000900 + - entity_name: root system + entity: PO:0025025 + - entity_name: root nodule + entity: PO:0003023 +references: + - citation: Liu, Lin et al., 2022 + doi: 10.1073/pnas.2205920119 + pmid: 35972963 + - citation: Oellrich, Walls et al., 2015 + doi: 10.1186/s13007-015-0053-y + pmid: 25774204 + diff --git a/Medicago/truncatula/studies/medtr.Mitra_Gleason_2004.yml b/Medicago/truncatula/studies/medtr.Mitra_Gleason_2004.yml new file mode 100644 index 0000000..298a810 --- /dev/null +++ b/Medicago/truncatula/studies/medtr.Mitra_Gleason_2004.yml @@ -0,0 +1,25 @@ +--- +gene_symbols: + - DMI3 +gene_symbol_long: doesn't make infections 3 +gene_model_pub_name: Medtr8g043970 +gene_model_full_id: medtr.A17_HM341.gnm4.ann2.Medtr8g043970 +confidence: 5 +curators: + - Steven Cannon +phenotype_synopsis: Doesn't make nodules or mycorrhizae +traits: + - entity_name: root nodule number + entity: TO:0000900 + - entity_name: root system + entity: PO:0025025 + - entity_name: root nodule + entity: PO:0003023 +references: + - citation: Mitra, Gleason et al., 2004 + doi: 10.1073/pnas.0400595101 + pmid: 15070781 + - citation: Oellrich, Walls et al., 2015 + doi: 10.1186/s13007-015-0053-y + pmid: 25774204 + diff --git a/Medicago/truncatula/studies/medtr.Miyahara_Richens_2010.yml b/Medicago/truncatula/studies/medtr.Miyahara_Richens_2010.yml new file mode 100644 index 0000000..7a7f539 --- /dev/null +++ b/Medicago/truncatula/studies/medtr.Miyahara_Richens_2010.yml @@ -0,0 +1,31 @@ +--- +gene_symbols: + - MtNAP1 +gene_symbol_long: Nick-associated protein 1 +gene_model_pub_name: Medtr4g084140 +gene_model_full_id: medtr.A17_HM341.gnm4.ann2.Medtr4g084140 +confidence: 5 +curators: + - Steven Cannon +phenotype_synopsis: Reduced levels of nodulation, reduced acetylene reduction, and limited nodule development. Aborted and deformed infection threads restricted to epidermal root hair cells. The few nodules that did form had very low rhizobial colonization and nitrogenase activity. +traits: + - entity_name: root nodule number + entity: TO:0000900 + - entity_name: root nodule morphology trait + entity: TO:0000898 + - entity_name: enzyme activity trait + entity: TO:0000599 + - entity_name: root system + entity: PO:0025025 + - entity_name: root nodule + entity: PO:0003023 + - entity_name: root hair cell + entity: PO:0000256 +references: + - citation: Miyahara, Richens et al., 2010 + doi: 10.1094/mpmi-06-10-0144 + pmid: 20731530 + - citation: Oellrich, Walls et al., 2015 + doi: 10.1186/s13007-015-0053-y + pmid: 25774204 + diff --git a/Medicago/truncatula/studies/medtr.Oellrich_Walls_2015.yml b/Medicago/truncatula/studies/medtr.Oellrich_Walls_2015.yml deleted file mode 100644 index 08c1d08..0000000 --- a/Medicago/truncatula/studies/medtr.Oellrich_Walls_2015.yml +++ /dev/null @@ -1,1142 +0,0 @@ ---- -scientific_name: Medicago truncatula -gene_symbols: - - MtANS -gene_symbol_long: Anthocyanidin synthase -gene_model_pub_name: Medtr5g011250 -gene_model_full_id: medtr.A17_HM341.gnm4.ann2.Medtr5g011250 -confidence: 5 -curators: - - Steven Cannon -phenotype_synopsis: MtANS (anthocyanidin synthase) gene expression was down-regulated in M. truncatula genotype R108 using an antisense construct. Anthocyanin levels were strongly reduced in leaf tissues of antisense lines. The presence of a red anthocyanin-rich circle at the base of the axial side of the leaflet and small red dots on the adaxial side results from anthocyanin deposition. Six independent transgenic antisense MtANS lines lacked the red circle and spots and another 10 such lines had reduced levels of pigmentation. There was a strong reduction in the levels of both soluble and insoluble PAs (Oligomeric proanthocyanidins) in seeds, consistent with involvement of ANS in PA biosynthesis. -traits: - - entity_name: anthocyanin content - entity: TO:0000071 - - entity_name: leaf - entity: PO:0025034 - - entity_name: seed - entity: PO:0009010 -references: - - citation: Jun, Liu et al., 2015 - doi: 10.1105/tpc.15.00476 - pmid: 26410301 - - citation: Oellrich, Walls et al., 2015 - doi: 10.1186/s13007-015-0053-y - pmid: 25774204 - ---- -scientific_name: Medicago truncatula -gene_symbols: - - MtbHLH1 -gene_symbol_long: basic helix loop helix 1 -gene_model_pub_name: Medtr3g099620 -gene_model_full_id: medtr.A17_HM341.gnm4.ann2.Medtr3g099620 -confidence: 5 -curators: - - Steven Cannon -phenotype_synopsis: Repressing MtbHLH1 (using Chimeric REpressor Silencing Technology) caused an assymetrical pattern of nodule vascular bundle development with variable angles of growth in inoculated roots. The growth and vigor of aerial parts of the plant was impaired; the nodules were still able to fix atmospheric Nitrogen but the aboveground tissues could not benefit for whatever reason. Nodules on repressed plants appeared later than in control plants and were smaller in size. -traits: - - entity_name: vascular bundle development trait - entity: TO:0020109 - - entity_name: plant organ growth and development trait - entity: TO:0000927 - - entity_name: shoot system - entity: PO:0009006 - - entity_name: vascular bundle - entity: PO:0005020 - - entity_name: root nodule - entity: PO:0003023 -references: - - citation: Godiard, Lepage et al., 2011 - doi: 10.1111/j.1469-8137.2011.03718.x - pmid: 21679315 - - citation: Oellrich, Walls et al., 2015 - doi: 10.1186/s13007-015-0053-y - pmid: 25774204 - ---- -scientific_name: Medicago truncatula -gene_symbols: - - MtCBF4 -gene_symbol_long: C-repeat binding factor 4 -gene_model_pub_name: Medtr1g101600 -gene_model_full_id: medtr.A17_HM341.gnm4.ann2.Medtr1g101600 -confidence: 5 -curators: - - Steven Cannon -phenotype_synopsis: Expression of MtCBF4 (transcription factor) in M. truncatula was induced by most of the abiotic stresses, including salt, drought, cold, and abscisic acid, suggesting crosstalk between these abiotic stresses. Upon exposure to a salt medium the primary root growth in the MtCBF4-overexpressing lines was greater than that of the control plants. MtCAS31 belongs to the CBF regulon and is associated with salt tolerance; under salt treatment, expression of MtCAS31 increased more in d35S:MtCBF4 transgenic plants than in controls. To summarize, over-expression of MtCBF4 enhanced tolerance to salt stress. -traits: - - entity_name: salt tolerance - entity: TO:0006001 - - entity_name: root length - entity: TO:0000227 - - entity_name: primary root - entity: PO:0020127 - - entity_name: whole plant - entity: PO:0000003 -references: - - citation: Pecrix, Staton et al., 2018 - doi: 10.1038/s41477-018-0286-7 - pmid: 30397259 - - citation: Oellrich, Walls et al., 2015 - doi: 10.1186/s13007-015-0053-y - pmid: 25774204 - ---- -scientific_name: Medicago truncatula -gene_symbols: - - MtCDC16 -gene_symbol_long: cell division cycle 16 -gene_model_pub_name: Medtr8g058380 -gene_model_full_id: medtr.A17_HM341.gnm4.ann2.Medtr8g058380 -confidence: 5 -curators: - - Steven Cannon -phenotype_synopsis: Partial suppression of the CDC16 gene homolog in Medicago truncatula leads to a decreased number of lateral roots, an increased number of nodules, and reduced auxin sensitivity. -traits: - - entity_name: root nodule morphology trait - entity: TO:0000898 - - entity_name: auxin sensitivity - entity: TO:0000163 - - entity_name: root system - entity: PO:0025025 - - entity_name: lateral root - entity: PO:0020121 - - entity_name: root - entity: PO:0009005 - - entity_name: root nodule - entity: PO:0003023 -references: - - citation: Kuppusamy, Ivashuta et al., 2009 - doi: 10.1104/pp.109.143024 - pmid: 19789288 - - citation: Oellrich, Walls et al., 2015 - doi: 10.1186/s13007-015-0053-y - pmid: 25774204 - ---- -scientific_name: Medicago truncatula -gene_symbols: - - MtCDPK1 -gene_symbol_long: calcium-dependent protein kinase 1 -gene_model_pub_name: Medtr5g022030 -gene_model_full_id: medtr.A17_HM341.gnm4.ann2.Medtr5g022030 -confidence: 5 -curators: - - Steven Cannon -phenotype_synopsis: Reduced root hair and root cell lengths; diminution of rhizobial and mycorrhizal symbiotic colonization -traits: - - entity_name: root cortical cell length - entity: TO:0020108 - - entity_name: root hair length - entity: TO:0002665 - - entity_name: root nodule morphology trait - entity: TO:0000898 - - entity_name: root system - entity: PO:0025025 - - entity_name: root nodule - entity: PO:0003023 - - entity_name: root hair cell - entity: PO:0000256 -references: - - citation: Ivashuta, Liu et al., 2005 - doi: 10.1105/tpc.105.035394 - pmid: 16199614 - - citation: Oellrich, Walls et al., 2015 - doi: 10.1186/s13007-015-0053-y - pmid: 25774204 - ---- -scientific_name: Medicago truncatula -gene_symbols: - - MtchitIII-3 -gene_symbol_long: class III chitinase -gene_model_pub_name: Medtr8g055940 -gene_model_full_id: medtr.A17_HM341.gnm4.ann2.Medtr8g055940 -confidence: 5 -curators: - - Steven Cannon -phenotype_synopsis: Mtchit 3-3 expression (class III chitinase gene) is specifically induced by arbuscular mycorrhizal (AM) fungi in roots of the model legume Medicago truncatula. Mtchit 3-3 expression was artificially induced with a CaMV 35S promoter in root cells; this stimulated spore germination of Glomus intraradices and Glomus constrictum, and in the case of G. intraradices resulted in a higher probability of root colonization and spore formation. There was no measurable effect on the abundance of arbuscules within colonized roots. -traits: - - entity_name: root system - entity: PO:0025025 -references: - - citation: Salzer, Bonanomi et al., 2000 - doi: 10.1094/mpmi.2000.13.7.763 - pmid: 10875337 - - citation: Oellrich, Walls et al., 2015 - doi: 10.1186/s13007-015-0053-y - pmid: 25774204 - ---- -scientific_name: Medicago truncatula -gene_symbols: - - MtCPK3 -gene_symbol_long: calcium dependent protein kinase 3 -gene_model_pub_name: ABE72958.1 -gene_model_full_id: medtr.A17_HM341.gnm4.ann2.Medtr3g051770 -confidence: 5 -curators: - - Steven Cannon -phenotype_synopsis: Expression of MtCPK3 in Medicago truncatula is regulated during nodulation. RNAi silenced CPK3 in transformed roots but no major phenotype was detected. When infected with rhizobia the nodule number was twice as high as the controls. -traits: - - entity_name: root nodule number - entity: TO:0000900 - - entity_name: root system - entity: PO:0025025 - - entity_name: root nodule - entity: PO:0003023 -references: - - citation: Gargantini, Gonzalez-Rizzo et al., 2006 - doi: 10.1111/j.1365-313x.2006.02910.x - pmid: 17132148 - - citation: Oellrich, Walls et al., 2015 - doi: 10.1186/s13007-015-0053-y - pmid: 25774204 - ---- -scientific_name: Medicago truncatula -gene_symbols: - - MtCYCLOPS -gene_model_pub_name: Medtr5g026850 -gene_model_full_id: medtr.A17_HM341.gnm4.ann2.Medtr5g026850 -confidence: 5 -curators: - - Steven Cannon -phenotype_synopsis: Symbiotic infection of roots by rhizobia bacteria and arbuscular mycorrhiza fungi was inhibited or blocked, i.e. infection threads were not observed despite colonization of root hairs by rhizobia and AM fungal hyphae formed abnormal hyphal swellings with no arbuscles observed. Nodule organogenesis was initiated but arrested prematurely at the level of primordia as an indirect consequence of the aborted infection. -traits: - - entity_name: root nodule morphology trait - entity: TO:0000898 - - entity_name: root system - entity: PO:0025025 -references: - - citation: Liu, Breakspear et al., 2019 - doi: 10.1104/pp.18.01572 - pmid: null - - citation: Oellrich, Walls et al., 2015 - doi: 10.1186/s13007-015-0053-y - pmid: 25774204 - ---- -scientific_name: Medicago truncatula -gene_symbols: - - Mtcyp716A12 -gene_symbol_long: cytochrome P450 monoxygenase -gene_model_pub_name: Medtr3g021350 -gene_model_full_id: medtr.A17_HM341.gnm4.ann2.Medtr3g021350 -confidence: 5 -curators: - - Steven Cannon -phenotype_synopsis: A cytochrome P450 gene (CYP716A12) is involved in an early step in saponin biosynthesis and is found in most tissues. CYP716A12 loss-of-function mutants do not produce hemolytic saponins and only synthetize soyasaponins, and were thus named lacking hemolytic activity (lha). CYP716A12 catalyzes the oxidation of _-amyrin and erythrodiol at the C-28 position, yielding oleanolic acid. Transcriptome changes in the lha mutant showed a modulation in the main steps of the triterpenic saponin biosynthetic pathway, which includes squalene cyclization, _-amyrin oxidation, and glycosylation. Growth of homozygous lha/lha plants was stunted. -traits: - - entity_name: plant structure growth and development trait - entity: TO:0000928 - - entity_name: whole plant - entity: PO:0000003 -references: - - citation: Carelli, Biazzi et al., 2014 - doi: 10.1111/nph.13162 - pmid: 25406544 - - citation: Oellrich, Walls et al., 2015 - doi: 10.1186/s13007-015-0053-y - pmid: 25774204 - ---- -scientific_name: Medicago truncatula -gene_symbols: - - MtDMI1 -gene_symbol_long: doesn't make infections 1 -gene_model_pub_name: Medtr2g005870 -gene_model_full_id: medtr.A17_HM341.gnm4.ann2.Medtr2g005870 -confidence: 5 -curators: - - Steven Cannon -phenotype_synopsis: Doesn't make nodules; infection thread aborts -traits: - - entity_name: root nodule number - entity: TO:0000900 - - entity_name: root system - entity: PO:0025025 - - entity_name: root nodule - entity: PO:0003023 -references: - - citation: Liu, Lin et al., 2022 - doi: 10.1073/pnas.2205920119 - pmid: 35972963 - - citation: Oellrich, Walls et al., 2015 - doi: 10.1186/s13007-015-0053-y - pmid: 25774204 - ---- -scientific_name: Medicago truncatula -gene_symbols: - - MtDMI3 -gene_symbol_long: doesn't make infections 3 -gene_model_pub_name: Medtr8g043970 -gene_model_full_id: medtr.A17_HM341.gnm4.ann2.Medtr8g043970 -confidence: 5 -curators: - - Steven Cannon -phenotype_synopsis: Doesn't make nodules or mycorrhizae -traits: - - entity_name: root nodule number - entity: TO:0000900 - - entity_name: root system - entity: PO:0025025 - - entity_name: root nodule - entity: PO:0003023 -references: - - citation: Mitra, Gleason et al., 2004 - doi: 10.1073/pnas.0400595101 - pmid: 15070781 - - citation: Oellrich, Walls et al., 2015 - doi: 10.1186/s13007-015-0053-y - pmid: 25774204 - ---- -scientific_name: Medicago truncatula -gene_symbols: - - MtENOD40 -gene_symbol_long: Abnormal tissue development -gene_model_pub_name: CAD48198.1 -gene_model_full_id: medtr.A17_HM341.gnm4.ann2.Medtr6g034835 -confidence: 5 -curators: - - Steven Cannon -phenotype_synopsis: Use of antisense constructs of Mtenod40 arrested callus growth of Medicago explants, while overexpressing Mtenod40 embryos developed into teratomas. Enod40 genes might have a role in plant development, acting as 'riboregulators'. -traits: - - entity_name: plant tissue development trait - entity: TO:0006015 -references: - - citation: Campalans, Kondorosi et al., 2017 - doi: 10.1105/tpc.019406 - pmid: 15037734 - - citation: Oellrich, Walls et al., 2015 - doi: 10.1186/s13007-015-0053-y - pmid: 25774204 - ---- -scientific_name: Medicago truncatula -gene_symbols: - - MtFCL1 -gene_symbol_long: fused compound leaf 1 -gene_model_pub_name: Medtr6g071190 -gene_model_full_id: medtr.A17_HM341.gnm4.ann2.Medtr6g071190 -confidence: 5 -curators: - - Steven Cannon -phenotype_synopsis: Leaflets fused or partially fused, rachis between leaflets is absent, petiole is foreshortened. -traits: - - entity_name: petiole length - entity: TO:0000766 - - entity_name: vascular leaf morphology trait - entity: TO:0000419 - - entity_name: leaf rachis - entity: PO:0020055 - - entity_name: leaflet - entity: PO:0020049 - - entity_name: petiole - entity: PO:0020038 -references: - - citation: Peng, Yu et al., 2011 - doi: 10.1105/tpc.111.089128 - pmid: 22080596 - - citation: Oellrich, Walls et al., 2015 - doi: 10.1186/s13007-015-0053-y - pmid: 25774204 - ---- -scientific_name: Medicago truncatula -gene_symbols: - - MtFLOT2 -gene_symbol_long: Flotillin-like protein 2 -gene_model_pub_name: Medtr3g106420 -gene_model_full_id: medtr.A17_HM341.gnm4.ann2.Medtr3g106420 -confidence: 5 -curators: - - Steven Cannon -phenotype_synopsis: Fewer nodules per plant, an increase in no-nodule plants, and a decrease in plants that form pink nodules. A decrease in primary root length and long primary lateral roots, reduced reduction of acetylene, and reduced number of infection events. -traits: - - entity_name: lateral root length - entity: TO:0001012 - - entity_name: root nodule number - entity: TO:0000900 - - entity_name: seminal root length - entity: TO:0000586 - - entity_name: root system - entity: PO:0025025 - - entity_name: primary root - entity: PO:0020127 - - entity_name: lateral root - entity: PO:0020121 - - entity_name: root nodule - entity: PO:0003023 -references: - - citation: Qiao, Pingault et al., 2016 - doi: 10.3389/fpls.2016.00034 - pmid: 26858743 - - citation: Oellrich, Walls et al., 2015 - doi: 10.1186/s13007-015-0053-y - pmid: 25774204 - ---- -scientific_name: Medicago truncatula -gene_symbols: - - MtFLOT3 -gene_symbol_long: Flotillin-like protein 3 -gene_model_pub_name: Medtr3g106480 -gene_model_full_id: medtr.A17_HM341.gnm4.ann2.Medtr3g106480 -confidence: 5 -curators: - - Steven Cannon -phenotype_synopsis: Shorter roots and reduced root weight. -traits: - - entity_name: root weight - entity: TO:0000279 - - entity_name: root length - entity: TO:0000227 - - entity_name: root - entity: PO:0009005 -references: - - citation: Qiao, Pingault et al., 2016 - doi: 10.3389/fpls.2016.00034 - pmid: 26858743 - - citation: Oellrich, Walls et al., 2015 - doi: 10.1186/s13007-015-0053-y - pmid: 25774204 - ---- -scientific_name: Medicago truncatula -gene_symbols: - - MtFLOT4 -gene_symbol_long: Flotillin-like protein 4 -gene_model_pub_name: Medtr3g106430 -gene_model_full_id: medtr.A17_HM341.gnm4.ann2.Medtr3g106430 -confidence: 5 -curators: - - Steven Cannon -phenotype_synopsis: Decrease in plants that form pink nodules and an increase in numbers of secondary lateral roots, reduced reduction of acetylene. Weak association with reduction in nodule numbers. Both decreased number of infection events and defective infection thread elongation. -traits: - - entity_name: root nodule number - entity: TO:0000900 - - entity_name: root number - entity: TO:0000084 - - entity_name: root system - entity: PO:0025025 - - entity_name: root nodule - entity: PO:0003023 -references: - - citation: Qiao, Pingault et al., 2016 - doi: 10.3389/fpls.2016.00034 - pmid: 26858743 - - citation: Oellrich, Walls et al., 2015 - doi: 10.1186/s13007-015-0053-y - pmid: 25774204 - ---- -scientific_name: Medicago truncatula -gene_symbols: - - FTa1 -gene_symbol_long: Delayed flowering -gene_model_pub_name: Medtr7g084970 -gene_model_full_id: medtr.A17_HM341.gnm4.ann2.Medtr7g084970 -confidence: 5 -curators: - - Steven Cannon -phenotype_synopsis: Delayed flowering -traits: - - entity_name: flowering time trait - entity: TO:0002616 -references: - - citation: Laurie, Diwadkar et al., 2011 - doi: 10.1104/pp.111.180182 - pmid: 21685176 - - citation: Oellrich, Walls et al., 2015 - doi: 10.1186/s13007-015-0053-y - pmid: 25774204 - ---- -scientific_name: Medicago truncatula -gene_symbols: - - FTc -gene_symbol_long: Flower development normal under long days -gene_model_pub_name: Medtr7g085040 -gene_model_full_id: medtr.A17_HM341.gnm4.ann2.Medtr7g085040 -confidence: 5 -curators: - - Steven Cannon -phenotype_synopsis: null -traits: - - entity_name: flower development trait - entity: TO:0000622 -references: - - citation: Laurie, Diwadkar et al., 2011 - doi: 10.1104/pp.111.180182 - pmid: 21685176 - - citation: Oellrich, Walls et al., 2015 - doi: 10.1186/s13007-015-0053-y - pmid: 25774204 - ---- -scientific_name: Medicago truncatula -gene_symbols: - - GT3 - - UGT73F3 -gene_symbol_long: Glycosyltransferase 3 -gene_model_pub_name: Medtr2g035020 -gene_model_full_id: medtr.A17_HM341.gnm4.ann2.Medtr2g035020 -confidence: 5 -curators: - - Steven Cannon -phenotype_synopsis: The uridine diphosphate glycosyltransferase (GT3, UGT73F3) showed specificity for multiple sapogenins and functions in saponin biosynthesis. Homozygous plants were retarded in growth relative to normal plants, whereas heterozygous plants did not show dwarfism. Homozygous plants could flower and produce a few pods. The seeds did not show visible morphological changes but took an unusually long time to germinate (at least 3 weeks). Roots in homozygous lines were very short and less branched compared with the wild type. Leaf saponin levels did not differ between controls and mutants. Levels of 5 different saponins were lower in mutant lines (approx. 3-fold) compared with controls, while only one saponin was higher in the mutants. The large (10-fold) increase of 3-Glc-28-Ara-Rha-Xyl-medicagenic acid in UGT73F3 knockout lines suggests that the UDP-glucose pool is being diverted toward increased formation of non-C-28-glucosylated sapogenins. Levels of the isoflavone formononetin and its conjugates were also increased in UGT73F3 knockouts. -traits: - - entity_name: plant structure growth and development trait - entity: TO:0000928 - - entity_name: germination rate - entity: TO:0000430 - - entity_name: root branching - entity: TO:0000257 - - entity_name: root length - entity: TO:0000227 - - entity_name: root - entity: PO:0009005 - - entity_name: whole plant - entity: PO:0000003 -references: - - citation: Ribeiro, Lacchini et al., 2020 - doi: 10.1105/tpc.19.00609 - pmid: 32303662 - - citation: Oellrich, Walls et al., 2015 - doi: 10.1186/s13007-015-0053-y - pmid: 25774204 - ---- -scientific_name: Medicago truncatula -gene_symbols: - - MtHAP2.1 -gene_model_pub_name: Medtr1g056530 -gene_model_full_id: medtr.A17_HM341.gnm4.ann2.Medtr1g056530 -confidence: 5 -curators: - - Steven Cannon -phenotype_synopsis: Small and nonfunctional nodules arrested in growth when both normally spliced and alternatively spliced variants repressed. When only the alternative spliced form repressed the nodules are small but still fix nitrogen successfully. -traits: - - entity_name: root nodule morphology trait - entity: TO:0000898 - - entity_name: root nodule - entity: PO:0003023 -references: - - citation: Chen, Liu et al., 2015 - doi: 10.3389/fpls.2015.00575 - pmid: 26284091 - - citation: Oellrich, Walls et al., 2015 - doi: 10.1186/s13007-015-0053-y - pmid: 25774204 - ---- -scientific_name: Medicago truncatula -gene_symbols: - - MtLIN -gene_symbol_long: Lumpy infections -gene_model_pub_name: Medtr1g090320 -gene_model_full_id: medtr.A17_HM341.gnm4.ann2.Medtr1g090320 -confidence: 5 -curators: - - Steven Cannon -phenotype_synopsis: Rhizobial infection was reduced in quantity and infections were not persistent, i.e. infection threads were arrested after very limited progression within root hair cells. Nodule differentiation was arrested at an early primordial stage as an indirect result of the aborted infection. -traits: - - entity_name: root nodule - entity: PO:0003023 -references: - - citation: Lace, Su et al., 2023 - doi: 10.7554/elife.80741 - pmid: 36856086 - - citation: Oellrich, Walls et al., 2015 - doi: 10.1186/s13007-015-0053-y - pmid: 25774204 - ---- -scientific_name: Medicago truncatula -gene_symbols: - - MtLYK3 -gene_symbol_long: LYSIN MOTIF RECEPTOR-LIKE KINASE 3 -gene_model_pub_name: Medtr5g086130 -gene_model_full_id: medtr.A17_HM341.gnm4.ann2.Medtr5g086130 -confidence: 5 -curators: - - Steven Cannon -phenotype_synopsis: Doesn't make nodules; infection thread aborts -traits: - - entity_name: root nodule number - entity: TO:0000900 - - entity_name: root system - entity: PO:0025025 - - entity_name: root nodule - entity: PO:0003023 -references: - - citation: Herrbach, Chirinos et al., 2017 - doi: 10.1093/jxb/erw474 - pmid: 28073951 - - citation: Oellrich, Walls et al., 2015 - doi: 10.1186/s13007-015-0053-y - pmid: 25774204 - ---- -scientific_name: Medicago truncatula -gene_symbols: - - MtLYK4 -gene_symbol_long: LYSIN MOTIF RECEPTOR-LIKE KINASE 4 -gene_model_pub_name: Medtr5g086120 -gene_model_full_id: medtr.A17_HM341.gnm4.ann2.Medtr5g086120 -confidence: 5 -curators: - - Steven Cannon -phenotype_synopsis: Doesn't make nodules; infection thread aborts -traits: - - entity_name: root nodule number - entity: TO:0000900 - - entity_name: root system - entity: PO:0025025 - - entity_name: root nodule - entity: PO:0003023 -references: - - citation: Herrbach, Chirinos et al., 2017 - doi: 10.1093/jxb/erw474 - pmid: 28073951 - - citation: Oellrich, Walls et al., 2015 - doi: 10.1186/s13007-015-0053-y - pmid: 25774204 - ---- -scientific_name: Medicago truncatula -gene_symbols: - - MtAOC -gene_symbol_long: Allene-oxide cyclase -gene_model_pub_name: CAI29046.1 -gene_model_full_id: medtr.A17_HM341.gnm4.ann2.Medtr7g417750 -confidence: 5 -curators: - - Steven Cannon -phenotype_synopsis: MtAOC (allene oxide cyclase) gene expression was partially suppressed in roots following transformation with cDNA in the antisense direction. These roots exhibited lower jasmonic acid levels and delayed colonization by Glomus intraradices. The number of arbuscles decreased and their development was delayed, yet their physical structure was unaltered. -traits: - - entity_name: root system - entity: PO:0025025 - - entity_name: root - entity: PO:0009005 -references: - - citation: Isayenkov, Mrosk et al., 2005 - doi: 10.1104/pp.105.069054 - pmid: 16244141 - - citation: Oellrich, Walls et al., 2015 - doi: 10.1186/s13007-015-0053-y - pmid: 25774204 - ---- -scientific_name: Medicago truncatula -gene_symbols: - - MtCCD1 -gene_symbol_long: carotenoid cleavage dioxygenase 1 -gene_model_pub_name: CAR57918.1 -gene_model_full_id: medtr.A17_HM341.gnm4.ann2.Medtr6g034835 -confidence: 5 -curators: - - Steven Cannon -phenotype_synopsis: RNA interference (RNAi) was used to repress a M. truncatula CCD1 gene in hairy roots colonized by the arbuscular mycorrhizal (AM) fungus Glomus intraradices. The normal AM-mediated accumulation of apocarotenoids (C13 cyclohexenone and C14 mycorradicin derivatives) was reduced in repressed plants; mycorradicin derivatives were reduced to 3% to 6% of the controls and the cyclohexenone derivatives were reduced to 30% to 47%. The RNAi roots turned a yellow-orange color because of C27 apocarotenoid accumulation (the probable substrate of the CCD1 enzyme). More degenerating arbuscules was observed in RNAi roots. -traits: - - entity_name: carotene content - entity: TO:0000289 - - entity_name: root - entity: PO:0009005 -references: - - citation: Floss, Schliemann et al., 2008 - doi: 10.1104/pp.108.125062 - pmid: 18790999 - - citation: Oellrich, Walls et al., 2015 - doi: 10.1186/s13007-015-0053-y - pmid: 25774204 - ---- -scientific_name: Medicago truncatula -gene_symbols: - - MtCre1 -gene_symbol_long: Cytokinin Response1 -gene_model_pub_name: Medtr8g106150 -gene_model_full_id: medtr.A17_HM341.gnm4.ann2.Medtr8g106150 -confidence: 5 -curators: - - Steven Cannon -phenotype_synopsis: Roots growth was not inhibited by exogenous cytokinin application. Expression of the primary cytokinin response gene, Mt RR4, was not induced by cytokinins. Plants had an increased number of lateral roots (higher lateral root density) and a strong reduction in numbers of root nodules. The development of infection threads was inhibited and early nodule primordia development was also impaired. Expression of early nodulation genes was reduced in plants in which expression of MtCre1 was interfered with by RNAi. -traits: - - entity_name: root nodule number - entity: TO:0000900 - - entity_name: cytokinin sensitivity - entity: TO:0000167 - - entity_name: root number - entity: TO:0000084 - - entity_name: root system - entity: PO:0025025 - - entity_name: lateral root - entity: PO:0020121 - - entity_name: root nodule - entity: PO:0003023 -references: - - citation: Vernie, Kim et al., 2015 - doi: 10.1105/tpc.15.00461 - pmid: 26672071 - - citation: Oellrich, Walls et al., 2015 - doi: 10.1186/s13007-015-0053-y - pmid: 25774204 - ---- -scientific_name: Medicago truncatula -gene_symbols: - - MtNAP1 -gene_symbol_long: Nick-associated protein 1 -gene_model_pub_name: Medtr4g084140 -gene_model_full_id: medtr.A17_HM341.gnm4.ann2.Medtr4g084140 -confidence: 5 -curators: - - Steven Cannon -phenotype_synopsis: Reduced levels of nodulation, reduced acetylene reduction, and limited nodule development. Aborted and deformed infection threads restricted to epidermal root hair cells. The few nodules that did form had very low rhizobial colonization and nitrogenase activity. -traits: - - entity_name: root nodule number - entity: TO:0000900 - - entity_name: root nodule morphology trait - entity: TO:0000898 - - entity_name: enzyme activity trait - entity: TO:0000599 - - entity_name: root system - entity: PO:0025025 - - entity_name: root nodule - entity: PO:0003023 - - entity_name: root hair cell - entity: PO:0000256 -references: - - citation: Miyahara, Richens et al., 2010 - doi: 10.1094/mpmi-06-10-0144 - pmid: 20731530 - - citation: Oellrich, Walls et al., 2015 - doi: 10.1186/s13007-015-0053-y - pmid: 25774204 - ---- -scientific_name: Medicago truncatula -gene_symbols: - - MtNAM - - NAM-2 -gene_symbol_long: No Apical Meristem (weak allele) -gene_model_pub_name: AFI56799.1 -gene_model_full_id: medtr.A17_HM341.gnm4.ann2.Medtr2g078700 -confidence: 5 -curators: - - Steven Cannon -phenotype_synopsis: null -traits: - - entity_name: shoot apical meristem development - entity: TO:0006020 - - entity_name: carpel morphology trait - entity: TO:0006012 - - entity_name: trichome morphology trait - entity: TO:0000911 - - entity_name: cotyledon morphology trait - entity: TO:0000749 - - entity_name: male sterility - entity: TO:0000437 - - entity_name: vascular leaf morphology trait - entity: TO:0000419 - - entity_name: female sterility - entity: TO:0000358 - - entity_name: stamen morphology trait - entity: TO:0000215 - - entity_name: embryo shape - entity: TO:0000193 - - entity_name: carpel trichome - entity: PO:0025208 - - entity_name: reproductive shoot system - entity: PO:0025082 - - entity_name: leaflet - entity: PO:0020049 - - entity_name: cotyledon - entity: PO:0020030 - - entity_name: plant ovule - entity: PO:0020003 - - entity_name: flower - entity: PO:0009046 - - entity_name: carpel - entity: PO:0009030 - - entity_name: stamen - entity: PO:0009029 - - entity_name: plant embryo - entity: PO:0009009 - - entity_name: fruit - entity: PO:0009001 - - entity_name: juvenile vascular leaf - entity: PO:0006339 -references: - - citation: Cheng, Peng et al., 2012 - doi: 10.1111/j.1469-8137.2012.04147.x - pmid: 22530598 - - citation: Oellrich, Walls et al., 2015 - doi: 10.1186/s13007-015-0053-y - pmid: 25774204 - ---- -scientific_name: Medicago truncatula -gene_symbols: - - MtNFP -gene_symbol_long: Nod Factor Perception -gene_model_pub_name: Medtr5g019040 -gene_model_full_id: medtr.A17_HM341.gnm4.ann2.Medtr5g019040 -confidence: 5 -curators: - - Steven Cannon -phenotype_synopsis: Root nodules did not form and infection threads aborted during development. -traits: - - entity_name: root nodule - entity: PO:0003023 -references: - - citation: Rey, Nars et al., 2013 - doi: 10.1111/nph.12198 - pmid: 23432463 - - citation: Oellrich, Walls et al., 2015 - doi: 10.1186/s13007-015-0053-y - pmid: 25774204 - ---- -scientific_name: Medicago truncatula -gene_symbols: - - MtNORK -gene_symbol_long: nodulation receptor kinase -gene_model_pub_name: Medtr5g030920 -gene_model_full_id: medtr.A17_HM341.gnm4.ann2.Medtr5g030920 -confidence: 5 -curators: - - Steven Cannon -phenotype_synopsis: Lacks symbiotic root responses in the presence of compatible Sinorhizobium meliloti or Nod factor, and resists mycorrhizal colonization -traits: - - entity_name: root nodule number - entity: TO:0000900 - - entity_name: root system - entity: PO:0025025 - - entity_name: root nodule - entity: PO:0003023 -references: - - citation: Kevei, Lougnon et al., 2007 - doi: 10.1105/tpc.107.053975 - pmid: 18156218 - - citation: Oellrich, Walls et al., 2015 - doi: 10.1186/s13007-015-0053-y - pmid: 25774204 - ---- -scientific_name: Medicago truncatula -gene_symbols: - - MtPALM1 -gene_symbol_long: PALMATE-LIKE PENTAFOLIATA1 -gene_model_pub_name: Medtr5g014400 -gene_model_full_id: medtr.A17_HM341.gnm4.ann2.Medtr5g014400 -confidence: 5 -curators: - - Steven Cannon -phenotype_synopsis: Forms dissected leaves with five leaflets clustered at the tip (palmate-like pentafoliate in contrast to the trifoliate WT leaves). The distal lateral leaflets developed in a manner morphologically/anatomically similar to terminal leaflets. The length of the petiole increased and that of the rachis decreased. -traits: - - entity_name: petiole length - entity: TO:0000766 - - entity_name: TO:0000748 - entity: TO:0000748 - - entity_name: leaf - entity: PO:0025034 - - entity_name: leaf rachis - entity: PO:0020055 - - entity_name: petiole - entity: PO:0020038 -references: - - citation: Jiao, Wang et al., 2020 - doi: 10.1186/s12870-020-02619-6 - pmid: 32867687 - - citation: Oellrich, Walls et al., 2015 - doi: 10.1186/s13007-015-0053-y - pmid: 25774204 - ---- -scientific_name: Medicago truncatula -gene_symbols: - - MtSGL1 -gene_symbol_long: single leaflet1 -gene_model_pub_name: Medtr3g098560 -gene_model_full_id: medtr.A17_HM341.gnm4.ann2.Medtr3g098560 -confidence: 5 -curators: - - Steven Cannon -phenotype_synopsis: Mutant displays simple, unifoliate (not compound) leaves. Petiole length is decreased. Defective, fused flowers -traits: - - entity_name: petiole length - entity: TO:0000766 - - entity_name: flower morphology trait - entity: TO:0000499 - - entity_name: leaf shape - entity: TO:0000492 - - entity_name: petiole - entity: PO:0020038 - - entity_name: flower - entity: PO:0009046 -references: - - citation: Cheng, Li et al., 2021 - doi: 10.1093/plphys/kiaa005 - pmid: 33631796 - - citation: Oellrich, Walls et al., 2015 - doi: 10.1186/s13007-015-0053-y - pmid: 25774204 - ---- -scientific_name: Medicago truncatula -gene_symbols: - - MtEIN2 - - Skl1 -gene_symbol_long: Ethylene Insensitive2 -gene_model_pub_name: Medtr7g101410 -gene_model_full_id: medtr.A17.gnm5.ann1_6.MtrunA17Chr7g0264231 -confidence: 5 -curators: - - Steven Cannon -phenotype_synopsis: Absence of discrete nodules, increased persistant rhizobila infection, radial swelling of primary infection zone, larger cotyledons, reduced apical hook angle, reduced develoment of ectopic root hairs, no loss of geotropism,and a lack of inhibition of both hypocotyl and root growth. Reduced inhibition of root growth in response to application of exogenous cytokinin benzyl adenine. Increased primary mycorrhizal infections by Glomus versiforme and Glomus intraradices. Increased susceptability to damage caused by infection with R. solani necrotrophic fungus and P. medicaginis necrotrophic oomycete as well as larger numbers of P. medicaginis reproductive structures. Reduced biphasic ethylene production after inoculation with P. medicaginis, reduced gene expression for one isoform of ACC oxidase transcripts, and reduced responsiveness of ethylene levels to exogenous ACC (all indicators of impaired autocatalytic ethylene production). -traits: - - entity_name: gravity response trait - entity: TO:0002693 - - entity_name: root hair length - entity: TO:0002665 - - entity_name: root nodule number - entity: TO:0000900 - - entity_name: TO:0000757 - entity: TO:0000757 - - entity_name: seedling cotyledon size - entity: TO:0000752 - - entity_name: root development trait - entity: TO:0000656 - - entity_name: root system - entity: PO:0025025 - - entity_name: hypocotyl - entity: PO:0020100 - - entity_name: cotyledon - entity: PO:0020030 - - entity_name: root - entity: PO:0009005 - - entity_name: non-hair root epidermal cell - entity: PO:0000263 - - entity_name: apical hook - entity: PO:0000012 -references: - - citation: Weller, Foo et al., 2015 - doi: 10.1104/pp.15.00164 - pmid: 25792252 - - citation: Oellrich, Walls et al., 2015 - doi: 10.1186/s13007-015-0053-y - pmid: 25774204 - ---- -scientific_name: Medicago truncatula -gene_symbols: - - MtSUNN -gene_symbol_long: super numeric nodules -gene_model_pub_name: Medtr4g070970 -gene_model_full_id: medtr.A17_HM341.gnm4.ann2.Medtr4g070970 -confidence: 5 -curators: - - Steven Cannon -phenotype_synopsis: Shortened roots even in the absence of rhizobia. A dramatic increase in the number of root nodules. Nodulation occurred even under a high nitrogen regime. Unlike wild type, both infection by rhizobia and nodulation occur randomly throughout the circumference of the developing root. Nodulation is normally sensitive to ethylene, similar to wild type. -traits: - - entity_name: root nodule number - entity: TO:0000900 - - entity_name: root length - entity: TO:0000227 - - entity_name: root system - entity: PO:0025025 - - entity_name: root - entity: PO:0009005 - - entity_name: root nodule - entity: PO:0003023 -references: - - citation: Laffont, Huault et al., 2019 - doi: 10.1104/pp.18.01588 - pmid: 30782966 - - citation: Oellrich, Walls et al., 2015 - doi: 10.1186/s13007-015-0053-y - pmid: 25774204 - ---- -scientific_name: Medicago truncatula -gene_symbols: - - MtVPY -gene_symbol_long: Vapyrin -gene_model_pub_name: ADC33495.1 -gene_model_full_id: medtr.A17_HM341.gnm4.ann2.Medtr6g027840 -confidence: 5 -curators: - - Steven Cannon -phenotype_synopsis: In Medicago truncatula, the Vapyrin (VPY) gene is essential for the establishment of the arbuscular mycorrhizal symbiosis. Analyses of mutants shows that the same VPYgene is also required for rhizobial colonization and nodulation. Plants mutated in this gene have abnormal rhizobial infection threads and fewer nodules, and in the case of interactions with AM fungi, epidermal penetration defects and aborted arbuscule formation. -traits: - - entity_name: root nodule number - entity: TO:0000900 - - entity_name: root system - entity: PO:0025025 - - entity_name: root nodule - entity: PO:0003023 -references: - - citation: Pumplin, Mondo et al., 2009 - doi: 10.1111/j.1365-313x.2009.04072.x - pmid: 19912567 - - citation: Oellrich, Walls et al., 2015 - doi: 10.1186/s13007-015-0053-y - pmid: 25774204 - ---- -scientific_name: Medicago truncatula -gene_symbols: - - MtERN1 -gene_symbol_long: Ethylene Response Factor Required for Nodulation1 -gene_model_pub_name: EU038802 -gene_model_full_id: medtr.A17_HM341.gnm4.ann2.Medtr7g085810 -confidence: 5 -curators: - - Steven Cannon -phenotype_synopsis: Control of symbiotic nitrogen fixation -traits: - - entity_name: root nodule - entity: PO:0003023 -references: - - citation: Vernie, Kim et al., 2015 - doi: 10.1105/tpc.15.00461 - pmid: 26672071 - - citation: Oellrich, Walls et al., 2015 - doi: 10.1186/s13007-015-0053-y - pmid: 25774204 - ---- -scientific_name: Medicago truncatula -gene_symbols: - - MtERN2 -gene_symbol_long: Ethylene Response Factor Required for Nodulation2 -gene_model_pub_name: EU038803 -gene_model_full_id: medtr.A17_HM341.gnm4.ann2.Medtr6g029180 -confidence: 5 -curators: - - Steven Cannon -phenotype_synopsis: Control of symbiotic nitrogen fixation -traits: - - entity_name: root nodule - entity: PO:0003023 -references: - - citation: Vernie, Kim et al., 2015 - doi: 10.1105/tpc.15.00461 - pmid: 26672071 - - citation: Oellrich, Walls et al., 2015 - doi: 10.1186/s13007-015-0053-y - pmid: 25774204 - ---- -scientific_name: Medicago truncatula -gene_symbols: - - MtEXPA -gene_symbol_long: EXPANSIN A7 -gene_model_pub_name: DQ899790 -gene_model_full_id: medtr.A17_HM341.gnm4.ann2.Medtr4g102450 -confidence: 5 -curators: - - Steven Cannon -phenotype_synopsis: Control of symbiotic nitrogen fixation -traits: - - entity_name: root nodule - entity: PO:0003023 -references: - - citation: Vernie, Kim et al., 2015 - doi: 10.1105/tpc.15.00461 - pmid: 26672071 - - citation: Oellrich, Walls et al., 2015 - doi: 10.1186/s13007-015-0053-y - pmid: 25774204 - ---- -scientific_name: Medicago truncatula -gene_symbols: - - MtNIN -gene_symbol_long: Nodule Inception -gene_model_pub_name: Medtr5g099060 -gene_model_full_id: medtr.A17_HM341.gnm4.ann2.Medtr5g099060 -confidence: 5 -curators: - - Steven Cannon -phenotype_synopsis: Control of symbiotic nitrogen fixation -traits: - - entity_name: root nodule - entity: PO:0003023 -references: - - citation: Vernie, Kim et al., 2015 - doi: 10.1105/tpc.15.00461 - pmid: 26672071 - - citation: Oellrich, Walls et al., 2015 - doi: 10.1186/s13007-015-0053-y - pmid: 25774204 - ---- -scientific_name: Medicago truncatula -gene_symbols: - - MtNRT1.3 -gene_symbol_long: Nitrate Transporter 1.3 -gene_model_pub_name: GU966590 -gene_model_full_id: medtr.A17_HM341.gnm4.ann2.Medtr5g085850 -confidence: 5 -curators: - - Steven Cannon -phenotype_synopsis: Control of symbiotic nitrogen fixation -traits: - - entity_name: root nodule - entity: PO:0003023 -references: - - citation: Vernie, Kim et al., 2015 - doi: 10.1105/tpc.15.00461 - pmid: 26672071 - - citation: Oellrich, Walls et al., 2015 - doi: 10.1186/s13007-015-0053-y - pmid: 25774204 - ---- -scientific_name: Medicago truncatula -gene_symbols: - - MtNSP1 -gene_symbol_long: Nodulation signaling pathway 1 -gene_model_pub_name: AJ972478 -gene_model_full_id: medtr.A17_HM341.gnm4.ann2.Medtr8g020840 -confidence: 5 -curators: - - Steven Cannon -phenotype_synopsis: Control of symbiotic nitrogen fixation -traits: - - entity_name: root nodule - entity: PO:0003023 -references: - - citation: Vernie, Kim et al., 2015 - doi: 10.1105/tpc.15.00461 - pmid: 26672071 - - citation: Oellrich, Walls et al., 2015 - doi: 10.1186/s13007-015-0053-y - pmid: 25774204 - ---- -scientific_name: Medicago truncatula -gene_symbols: - - MtRR4 -gene_symbol_long: Response Regulator 4 -gene_model_pub_name: Medtr5g036480 -gene_model_full_id: medtr.A17_HM341.gnm4.ann2.Medtr5g036480 -confidence: 5 -curators: - - Steven Cannon -phenotype_synopsis: Control of symbiotic nitrogen fixation -traits: - - entity_name: root nodule - entity: PO:0003023 -references: - - citation: Vernie, Kim et al., 2015 - doi: 10.1105/tpc.15.00461 - pmid: 26672071 - diff --git a/Medicago/truncatula/studies/medtr.Pecrix_Staton_2018.yml b/Medicago/truncatula/studies/medtr.Pecrix_Staton_2018.yml new file mode 100644 index 0000000..513b7b5 --- /dev/null +++ b/Medicago/truncatula/studies/medtr.Pecrix_Staton_2018.yml @@ -0,0 +1,27 @@ +--- +gene_symbols: + - CBF4 +gene_symbol_long: C-repeat binding factor 4 +gene_model_pub_name: Medtr1g101600 +gene_model_full_id: medtr.A17_HM341.gnm4.ann2.Medtr1g101600 +confidence: 5 +curators: + - Steven Cannon +phenotype_synopsis: Expression of MtCBF4 (transcription factor) in M. truncatula was induced by most of the abiotic stresses, including salt, drought, cold, and abscisic acid, suggesting crosstalk between these abiotic stresses. Upon exposure to a salt medium the primary root growth in the MtCBF4-overexpressing lines was greater than that of the control plants. MtCAS31 belongs to the CBF regulon and is associated with salt tolerance; under salt treatment, expression of MtCAS31 increased more in d35S:MtCBF4 transgenic plants than in controls. To summarize, over-expression of MtCBF4 enhanced tolerance to salt stress. +traits: + - entity_name: salt tolerance + entity: TO:0006001 + - entity_name: root length + entity: TO:0000227 + - entity_name: primary root + entity: PO:0020127 + - entity_name: whole plant + entity: PO:0000003 +references: + - citation: Pecrix, Staton et al., 2018 + doi: 10.1038/s41477-018-0286-7 + pmid: 30397259 + - citation: Oellrich, Walls et al., 2015 + doi: 10.1186/s13007-015-0053-y + pmid: 25774204 + diff --git a/Medicago/truncatula/studies/medtr.Peng_Yu_2011.yml b/Medicago/truncatula/studies/medtr.Peng_Yu_2011.yml new file mode 100644 index 0000000..5913956 --- /dev/null +++ b/Medicago/truncatula/studies/medtr.Peng_Yu_2011.yml @@ -0,0 +1,29 @@ +--- +gene_symbols: + - FCL1 +gene_symbol_long: fused compound leaf 1 +gene_model_pub_name: Medtr6g071190 +gene_model_full_id: medtr.A17_HM341.gnm4.ann2.Medtr6g071190 +confidence: 5 +curators: + - Steven Cannon +phenotype_synopsis: Leaflets fused or partially fused, rachis between leaflets is absent, petiole is foreshortened. +traits: + - entity_name: petiole length + entity: TO:0000766 + - entity_name: vascular leaf morphology trait + entity: TO:0000419 + - entity_name: leaf rachis + entity: PO:0020055 + - entity_name: leaflet + entity: PO:0020049 + - entity_name: petiole + entity: PO:0020038 +references: + - citation: Peng, Yu et al., 2011 + doi: 10.1105/tpc.111.089128 + pmid: 22080596 + - citation: Oellrich, Walls et al., 2015 + doi: 10.1186/s13007-015-0053-y + pmid: 25774204 + diff --git a/Medicago/truncatula/studies/medtr.Pumplin_Mondo_2009.yml b/Medicago/truncatula/studies/medtr.Pumplin_Mondo_2009.yml new file mode 100644 index 0000000..e5588e4 --- /dev/null +++ b/Medicago/truncatula/studies/medtr.Pumplin_Mondo_2009.yml @@ -0,0 +1,25 @@ +--- +gene_symbols: + - VPY +gene_symbol_long: Vapyrin +gene_model_pub_name: ADC33495.1 +gene_model_full_id: medtr.A17_HM341.gnm4.ann2.Medtr6g027840 +confidence: 5 +curators: + - Steven Cannon +phenotype_synopsis: In Medicago truncatula, the Vapyrin (VPY) gene is essential for the establishment of the arbuscular mycorrhizal symbiosis. Analyses of mutants shows that the same VPYgene is also required for rhizobial colonization and nodulation. Plants mutated in this gene have abnormal rhizobial infection threads and fewer nodules, and in the case of interactions with AM fungi, epidermal penetration defects and aborted arbuscule formation. +traits: + - entity_name: root nodule number + entity: TO:0000900 + - entity_name: root system + entity: PO:0025025 + - entity_name: root nodule + entity: PO:0003023 +references: + - citation: Pumplin, Mondo et al., 2009 + doi: 10.1111/j.1365-313x.2009.04072.x + pmid: 19912567 + - citation: Oellrich, Walls et al., 2015 + doi: 10.1186/s13007-015-0053-y + pmid: 25774204 + diff --git a/Medicago/truncatula/studies/medtr.Qiao_Pingault_2016.yml b/Medicago/truncatula/studies/medtr.Qiao_Pingault_2016.yml new file mode 100644 index 0000000..e38e0ac --- /dev/null +++ b/Medicago/truncatula/studies/medtr.Qiao_Pingault_2016.yml @@ -0,0 +1,83 @@ +--- +gene_symbols: + - FLOT2 +gene_symbol_long: Flotillin-like protein 2 +gene_model_pub_name: Medtr3g106420 +gene_model_full_id: medtr.A17_HM341.gnm4.ann2.Medtr3g106420 +confidence: 5 +curators: + - Steven Cannon +phenotype_synopsis: Fewer nodules per plant, an increase in no-nodule plants, and a decrease in plants that form pink nodules. A decrease in primary root length and long primary lateral roots, reduced reduction of acetylene, and reduced number of infection events. +traits: + - entity_name: lateral root length + entity: TO:0001012 + - entity_name: root nodule number + entity: TO:0000900 + - entity_name: seminal root length + entity: TO:0000586 + - entity_name: root system + entity: PO:0025025 + - entity_name: primary root + entity: PO:0020127 + - entity_name: lateral root + entity: PO:0020121 + - entity_name: root nodule + entity: PO:0003023 +references: + - citation: Qiao, Pingault et al., 2016 + doi: 10.3389/fpls.2016.00034 + pmid: 26858743 + - citation: Oellrich, Walls et al., 2015 + doi: 10.1186/s13007-015-0053-y + pmid: 25774204 +--- +gene_symbols: + - FLOT3 +gene_symbol_long: Flotillin-like protein 3 +gene_model_pub_name: Medtr3g106480 +gene_model_full_id: medtr.A17_HM341.gnm4.ann2.Medtr3g106480 +confidence: 5 +curators: + - Steven Cannon +phenotype_synopsis: Shorter roots and reduced root weight. +traits: + - entity_name: root weight + entity: TO:0000279 + - entity_name: root length + entity: TO:0000227 + - entity_name: root + entity: PO:0009005 +references: + - citation: Qiao, Pingault et al., 2016 + doi: 10.3389/fpls.2016.00034 + pmid: 26858743 + - citation: Oellrich, Walls et al., 2015 + doi: 10.1186/s13007-015-0053-y + pmid: 25774204 +--- +gene_symbols: + - FLOT4 +gene_symbol_long: Flotillin-like protein 4 +gene_model_pub_name: Medtr3g106430 +gene_model_full_id: medtr.A17_HM341.gnm4.ann2.Medtr3g106430 +confidence: 5 +curators: + - Steven Cannon +phenotype_synopsis: Decrease in plants that form pink nodules and an increase in numbers of secondary lateral roots, reduced reduction of acetylene. Weak association with reduction in nodule numbers. Both decreased number of infection events and defective infection thread elongation. +traits: + - entity_name: root nodule number + entity: TO:0000900 + - entity_name: root number + entity: TO:0000084 + - entity_name: root system + entity: PO:0025025 + - entity_name: root nodule + entity: PO:0003023 +references: + - citation: Qiao, Pingault et al., 2016 + doi: 10.3389/fpls.2016.00034 + pmid: 26858743 + - citation: Oellrich, Walls et al., 2015 + doi: 10.1186/s13007-015-0053-y + pmid: 25774204 + diff --git a/Medicago/truncatula/studies/medtr.Rey_Nars_2013.yml b/Medicago/truncatula/studies/medtr.Rey_Nars_2013.yml new file mode 100644 index 0000000..1532c01 --- /dev/null +++ b/Medicago/truncatula/studies/medtr.Rey_Nars_2013.yml @@ -0,0 +1,21 @@ +--- +gene_symbols: + - NFP +gene_symbol_long: Nod Factor Perception +gene_model_pub_name: Medtr5g019040 +gene_model_full_id: medtr.A17_HM341.gnm4.ann2.Medtr5g019040 +confidence: 5 +curators: + - Steven Cannon +phenotype_synopsis: Root nodules did not form and infection threads aborted during development. +traits: + - entity_name: root nodule + entity: PO:0003023 +references: + - citation: Rey, Nars et al., 2013 + doi: 10.1111/nph.12198 + pmid: 23432463 + - citation: Oellrich, Walls et al., 2015 + doi: 10.1186/s13007-015-0053-y + pmid: 25774204 + diff --git a/Medicago/truncatula/studies/medtr.Ribeiro_Lacchini_2020.yml b/Medicago/truncatula/studies/medtr.Ribeiro_Lacchini_2020.yml new file mode 100644 index 0000000..52d5cb2 --- /dev/null +++ b/Medicago/truncatula/studies/medtr.Ribeiro_Lacchini_2020.yml @@ -0,0 +1,32 @@ +--- +gene_symbols: + - GT3 + - UGT73F3 +gene_symbol_long: Glycosyltransferase 3 +gene_model_pub_name: Medtr2g035020 +gene_model_full_id: medtr.A17_HM341.gnm4.ann2.Medtr2g035020 +confidence: 5 +curators: + - Steven Cannon +phenotype_synopsis: The uridine diphosphate glycosyltransferase (GT3, UGT73F3) showed specificity for multiple sapogenins and functions in saponin biosynthesis. Homozygous plants were retarded in growth relative to normal plants, whereas heterozygous plants did not show dwarfism. Homozygous plants could flower and produce a few pods. The seeds did not show visible morphological changes but took an unusually long time to germinate (at least 3 weeks). Roots in homozygous lines were very short and less branched compared with the wild type. Leaf saponin levels did not differ between controls and mutants. Levels of 5 different saponins were lower in mutant lines (approx. 3-fold) compared with controls, while only one saponin was higher in the mutants. The large (10-fold) increase of 3-Glc-28-Ara-Rha-Xyl-medicagenic acid in UGT73F3 knockout lines suggests that the UDP-glucose pool is being diverted toward increased formation of non-C-28-glucosylated sapogenins. Levels of the isoflavone formononetin and its conjugates were also increased in UGT73F3 knockouts. +traits: + - entity_name: plant structure growth and development trait + entity: TO:0000928 + - entity_name: germination rate + entity: TO:0000430 + - entity_name: root branching + entity: TO:0000257 + - entity_name: root length + entity: TO:0000227 + - entity_name: root + entity: PO:0009005 + - entity_name: whole plant + entity: PO:0000003 +references: + - citation: Ribeiro, Lacchini et al., 2020 + doi: 10.1105/tpc.19.00609 + pmid: 32303662 + - citation: Oellrich, Walls et al., 2015 + doi: 10.1186/s13007-015-0053-y + pmid: 25774204 + diff --git a/Medicago/truncatula/studies/medtr.Salzer_Bonanomi_2000.yml b/Medicago/truncatula/studies/medtr.Salzer_Bonanomi_2000.yml new file mode 100644 index 0000000..86c3daa --- /dev/null +++ b/Medicago/truncatula/studies/medtr.Salzer_Bonanomi_2000.yml @@ -0,0 +1,21 @@ +--- +gene_symbols: + - chitIII-3 +gene_symbol_long: class III chitinase +gene_model_pub_name: Medtr8g055940 +gene_model_full_id: medtr.A17_HM341.gnm4.ann2.Medtr8g055940 +confidence: 5 +curators: + - Steven Cannon +phenotype_synopsis: Mtchit 3-3 expression (class III chitinase gene) is specifically induced by arbuscular mycorrhizal (AM) fungi in roots of the model legume Medicago truncatula. Mtchit 3-3 expression was artificially induced with a CaMV 35S promoter in root cells; this stimulated spore germination of Glomus intraradices and Glomus constrictum, and in the case of G. intraradices resulted in a higher probability of root colonization and spore formation. There was no measurable effect on the abundance of arbuscules within colonized roots. +traits: + - entity_name: root system + entity: PO:0025025 +references: + - citation: Salzer, Bonanomi et al., 2000 + doi: 10.1094/mpmi.2000.13.7.763 + pmid: 10875337 + - citation: Oellrich, Walls et al., 2015 + doi: 10.1186/s13007-015-0053-y + pmid: 25774204 + diff --git a/Medicago/truncatula/studies/medtr.Vernie_Kim_2015.yml b/Medicago/truncatula/studies/medtr.Vernie_Kim_2015.yml new file mode 100644 index 0000000..5689a40 --- /dev/null +++ b/Medicago/truncatula/studies/medtr.Vernie_Kim_2015.yml @@ -0,0 +1,168 @@ +--- +gene_symbols: + - MtCre1 +gene_symbol_long: Cytokinin Response1 +gene_model_pub_name: Medtr8g106150 +gene_model_full_id: medtr.A17_HM341.gnm4.ann2.Medtr8g106150 +confidence: 5 +curators: + - Steven Cannon +phenotype_synopsis: Roots growth was not inhibited by exogenous cytokinin application. Expression of the primary cytokinin response gene, Mt RR4, was not induced by cytokinins. Plants had an increased number of lateral roots (higher lateral root density) and a strong reduction in numbers of root nodules. The development of infection threads was inhibited and early nodule primordia development was also impaired. Expression of early nodulation genes was reduced in plants in which expression of MtCre1 was interfered with by RNAi. +traits: + - entity_name: root nodule number + entity: TO:0000900 + - entity_name: cytokinin sensitivity + entity: TO:0000167 + - entity_name: root number + entity: TO:0000084 + - entity_name: root system + entity: PO:0025025 + - entity_name: lateral root + entity: PO:0020121 + - entity_name: root nodule + entity: PO:0003023 +references: + - citation: Vernie, Kim et al., 2015 + doi: 10.1105/tpc.15.00461 + pmid: 26672071 + - citation: Oellrich, Walls et al., 2015 + doi: 10.1186/s13007-015-0053-y + pmid: 25774204 +--- +gene_symbols: + - ERN1 +gene_symbol_long: Ethylene Response Factor Required for Nodulation1 +gene_model_pub_name: EU038802 +gene_model_full_id: medtr.A17_HM341.gnm4.ann2.Medtr7g085810 +confidence: 5 +curators: + - Steven Cannon +phenotype_synopsis: Control of symbiotic nitrogen fixation +traits: + - entity_name: root nodule + entity: PO:0003023 +references: + - citation: Vernie, Kim et al., 2015 + doi: 10.1105/tpc.15.00461 + pmid: 26672071 + - citation: Oellrich, Walls et al., 2015 + doi: 10.1186/s13007-015-0053-y + pmid: 25774204 +--- +gene_symbols: + - ERN2 +gene_symbol_long: Ethylene Response Factor Required for Nodulation2 +gene_model_pub_name: EU038803 +gene_model_full_id: medtr.A17_HM341.gnm4.ann2.Medtr6g029180 +confidence: 5 +curators: + - Steven Cannon +phenotype_synopsis: Control of symbiotic nitrogen fixation +traits: + - entity_name: root nodule + entity: PO:0003023 +references: + - citation: Vernie, Kim et al., 2015 + doi: 10.1105/tpc.15.00461 + pmid: 26672071 + - citation: Oellrich, Walls et al., 2015 + doi: 10.1186/s13007-015-0053-y + pmid: 25774204 +--- +gene_symbols: + - EXPA +gene_symbol_long: EXPANSIN A7 +gene_model_pub_name: DQ899790 +gene_model_full_id: medtr.A17_HM341.gnm4.ann2.Medtr4g102450 +confidence: 5 +curators: + - Steven Cannon +phenotype_synopsis: Control of symbiotic nitrogen fixation +traits: + - entity_name: root nodule + entity: PO:0003023 +references: + - citation: Vernie, Kim et al., 2015 + doi: 10.1105/tpc.15.00461 + pmid: 26672071 + - citation: Oellrich, Walls et al., 2015 + doi: 10.1186/s13007-015-0053-y + pmid: 25774204 +--- +gene_symbols: + - NIN +gene_symbol_long: Nodule Inception +gene_model_pub_name: Medtr5g099060 +gene_model_full_id: medtr.A17_HM341.gnm4.ann2.Medtr5g099060 +confidence: 5 +curators: + - Steven Cannon +phenotype_synopsis: Control of symbiotic nitrogen fixation +traits: + - entity_name: root nodule + entity: PO:0003023 +references: + - citation: Vernie, Kim et al., 2015 + doi: 10.1105/tpc.15.00461 + pmid: 26672071 + - citation: Oellrich, Walls et al., 2015 + doi: 10.1186/s13007-015-0053-y + pmid: 25774204 +--- +gene_symbols: + - NRT1.3 +gene_symbol_long: Nitrate Transporter 1.3 +gene_model_pub_name: GU966590 +gene_model_full_id: medtr.A17_HM341.gnm4.ann2.Medtr5g085850 +confidence: 5 +curators: + - Steven Cannon +phenotype_synopsis: Control of symbiotic nitrogen fixation +traits: + - entity_name: root nodule + entity: PO:0003023 +references: + - citation: Vernie, Kim et al., 2015 + doi: 10.1105/tpc.15.00461 + pmid: 26672071 + - citation: Oellrich, Walls et al., 2015 + doi: 10.1186/s13007-015-0053-y + pmid: 25774204 +--- +gene_symbols: + - NSP1 +gene_symbol_long: Nodulation signaling pathway 1 +gene_model_pub_name: AJ972478 +gene_model_full_id: medtr.A17_HM341.gnm4.ann2.Medtr8g020840 +confidence: 5 +curators: + - Steven Cannon +phenotype_synopsis: Control of symbiotic nitrogen fixation +traits: + - entity_name: root nodule + entity: PO:0003023 +references: + - citation: Vernie, Kim et al., 2015 + doi: 10.1105/tpc.15.00461 + pmid: 26672071 + - citation: Oellrich, Walls et al., 2015 + doi: 10.1186/s13007-015-0053-y + pmid: 25774204 +--- +gene_symbols: + - RR4 +gene_symbol_long: Response Regulator 4 +gene_model_pub_name: Medtr5g036480 +gene_model_full_id: medtr.A17_HM341.gnm4.ann2.Medtr5g036480 +confidence: 5 +curators: + - Steven Cannon +phenotype_synopsis: Control of symbiotic nitrogen fixation +traits: + - entity_name: root nodule + entity: PO:0003023 +references: + - citation: Vernie, Kim et al., 2015 + doi: 10.1105/tpc.15.00461 + pmid: 26672071 + diff --git a/Medicago/truncatula/studies/medtr.Weller_Foo_2015.yml b/Medicago/truncatula/studies/medtr.Weller_Foo_2015.yml new file mode 100644 index 0000000..425547b --- /dev/null +++ b/Medicago/truncatula/studies/medtr.Weller_Foo_2015.yml @@ -0,0 +1,44 @@ +--- +gene_symbols: + - EIN2 + - Skl1 +gene_symbol_long: Ethylene Insensitive2 +gene_model_pub_name: Medtr7g101410 +gene_model_full_id: medtr.A17.gnm5.ann1_6.MtrunA17Chr7g0264231 +confidence: 5 +curators: + - Steven Cannon +phenotype_synopsis: Absence of discrete nodules, increased persistant rhizobila infection, radial swelling of primary infection zone, larger cotyledons, reduced apical hook angle, reduced develoment of ectopic root hairs, no loss of geotropism,and a lack of inhibition of both hypocotyl and root growth. Reduced inhibition of root growth in response to application of exogenous cytokinin benzyl adenine. Increased primary mycorrhizal infections by Glomus versiforme and Glomus intraradices. Increased susceptability to damage caused by infection with R. solani necrotrophic fungus and P. medicaginis necrotrophic oomycete as well as larger numbers of P. medicaginis reproductive structures. Reduced biphasic ethylene production after inoculation with P. medicaginis, reduced gene expression for one isoform of ACC oxidase transcripts, and reduced responsiveness of ethylene levels to exogenous ACC (all indicators of impaired autocatalytic ethylene production). +traits: + - entity_name: gravity response trait + entity: TO:0002693 + - entity_name: root hair length + entity: TO:0002665 + - entity_name: root nodule number + entity: TO:0000900 + - entity_name: TO:0000757 + entity: TO:0000757 + - entity_name: seedling cotyledon size + entity: TO:0000752 + - entity_name: root development trait + entity: TO:0000656 + - entity_name: root system + entity: PO:0025025 + - entity_name: hypocotyl + entity: PO:0020100 + - entity_name: cotyledon + entity: PO:0020030 + - entity_name: root + entity: PO:0009005 + - entity_name: non-hair root epidermal cell + entity: PO:0000263 + - entity_name: apical hook + entity: PO:0000012 +references: + - citation: Weller, Foo et al., 2015 + doi: 10.1104/pp.15.00164 + pmid: 25792252 + - citation: Oellrich, Walls et al., 2015 + doi: 10.1186/s13007-015-0053-y + pmid: 25774204 + diff --git a/Vicia/faba/studies/vicfa.Jayakodi_Golicz_2023.yml b/Vicia/faba/studies/vicfa.Jayakodi_Golicz_2023.yml index 3e14d3f..3230db2 100644 --- a/Vicia/faba/studies/vicfa.Jayakodi_Golicz_2023.yml +++ b/Vicia/faba/studies/vicfa.Jayakodi_Golicz_2023.yml @@ -4,6 +4,8 @@ gene_symbols: VfCYP78A gene_model_pub_name: Vfaba.Hedin2.R1.4g051440.1 gene_model_full_id: vicfa.Hedin2.gnm1.ann1.4g051440.1 confidence: 4 +curators: + - Steven Cannon comments: - Evidence based on GWAS, allele analysis, and homology to an Arabidopsis gene (CYP78A) involved in seed size regulation phenotype_synopsis: Seed size regulation @@ -22,6 +24,8 @@ gene_symbol_long: polyphenol oxidase 2 gene_model_pub_name: Vfaba.Tiffany.R1.1g391400.1 gene_model_full_id: vicfa.Tiffany.gnm1.ann1.1g391400.1 confidence: 4 +curators: + - Steven Cannon comments: - Evidence based on association and allelic variant analysis, and homology to an orthologous locus in pea (gene Psat1g2063360) that controls hilum color. - \[Evidence suggests that the] regulation of expression of VfPPO-2 controls hilum colour variation in faba bean.\ From 88717fc3c52da387bdb4e0ce8b4eed8c46cf5662 Mon Sep 17 00:00:00 2001 From: ScottKalberer <78100602+ScottKalberer@users.noreply.github.com> Date: Wed, 11 Sep 2024 14:25:27 -0500 Subject: [PATCH 04/18] Update glyma.Guo_Xu_2015.yml Corrected spelling of Time in gene_symbol_long Flowering Time 1a. --- Glycine/max/studies/glyma.Guo_Xu_2015.yml | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/Glycine/max/studies/glyma.Guo_Xu_2015.yml b/Glycine/max/studies/glyma.Guo_Xu_2015.yml index bf41d81..30bdf92 100644 --- a/Glycine/max/studies/glyma.Guo_Xu_2015.yml +++ b/Glycine/max/studies/glyma.Guo_Xu_2015.yml @@ -1,7 +1,7 @@ --- gene_symbols: - GmFT1a -gene_symbol_long: Flowering Timne 1a +gene_symbol_long: Flowering Time 1a gene_model_pub_name: Glyma.18G298900 gene_model_full_id: glyma.Wm82.gnm2.ann1.Glyma.18G298900 confidence: 5 From c57416c4757b80314817d5cd8a072c8d3dfa8e03 Mon Sep 17 00:00:00 2001 From: ScottKalberer <78100602+ScottKalberer@users.noreply.github.com> Date: Wed, 11 Sep 2024 14:33:58 -0500 Subject: [PATCH 05/18] Update glyma.Kong_Liu_2010.yml Corrected spelling to "Glyma" from "Gyma" for GmFT5a gene_model_pub_name and gene_model_full_id. --- Glycine/max/studies/glyma.Kong_Liu_2010.yml | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/Glycine/max/studies/glyma.Kong_Liu_2010.yml b/Glycine/max/studies/glyma.Kong_Liu_2010.yml index bc307df..db63374 100644 --- a/Glycine/max/studies/glyma.Kong_Liu_2010.yml +++ b/Glycine/max/studies/glyma.Kong_Liu_2010.yml @@ -40,8 +40,8 @@ references: gene_symbols: - GmFT5a gene_symbol_long: Flowering Time 5a -gene_model_pub_name: Gyma.16G044100 -gene_model_full_id: glyma.Wm82.gnm2.ann1.Gyma.16G044100 +gene_model_pub_name: Glyma.16G044100 +gene_model_full_id: glyma.Wm82.gnm2.ann1.Glyma.16G044100 confidence: 5 curators: - Steven Cannon From c6f6039d8d2ea9b6cb7334b6f852116151457b5c Mon Sep 17 00:00:00 2001 From: ScottKalberer <78100602+ScottKalberer@users.noreply.github.com> Date: Wed, 11 Sep 2024 15:14:18 -0500 Subject: [PATCH 06/18] Update glyma.Wang_Guo_2021.yml Various alterations to gene_model_pub_names, traits, and references. --- Glycine/max/studies/glyma.Wang_Guo_2021.yml | 23 +++++++++++---------- 1 file changed, 12 insertions(+), 11 deletions(-) diff --git a/Glycine/max/studies/glyma.Wang_Guo_2021.yml b/Glycine/max/studies/glyma.Wang_Guo_2021.yml index e64fa3a..6dc722c 100644 --- a/Glycine/max/studies/glyma.Wang_Guo_2021.yml +++ b/Glycine/max/studies/glyma.Wang_Guo_2021.yml @@ -2,12 +2,13 @@ scientific_name: Glycine max gene_symbols: - GmSTF3 -gene_symbol_long: Soybean TGACG-motif binding Factor 3 -gene_model_pub_name: Glyma14G088300 +gene_symbol_long: Soybean TGACG-motif Binding Factor 3 +gene_model_pub_name: Glyma.14G088300 gene_model_full_id: glyma.Wm82.gnm2.ann1.Glyma.14G088300 confidence: 5 curators: - Marlene Dorneich-Hayes + - Scott Kalberer comments: - Overexpression of STF3 increased nodulation, RNAi knockdown decreased nodulation. - STF3 is induced by the blue light activated transcription factor CRY1 and expressed mainly in leaves. @@ -25,12 +26,12 @@ traits: - entity_name: positive regulation of lateral root development entity: GO:1901333 references: - - citation: Wang, Guo et. al., 2021 + - citation: Wang, Guo et al., 2021 doi: 10.1126/science.abh2890 pmid: 34591638 - - citation: Hasan, Corpas et. al., 2022 + - citation: Hasan, Corpas et al., 2022 doi: 10.1016/j.tplants.2022.07.002 - - citation: Yang, Lan et. al., 2022 + - citation: Yang, Lan et al., 2022 doi: 10.1111/jipb.13207 pmid: 34962095 - citation: Kong, Liu et al., 2010 @@ -55,12 +56,13 @@ scientific_name: Glycine max classical_locus: E9 gene_symbols: - GmFT2a -gene_symbol_long: Flowering locus T2a -gene_model_pub_name: Glyma16G150700 +gene_symbol_long: Flowering Locus T2a +gene_model_pub_name: Glyma.16G150700 gene_model_full_id: glyma.Wm82.gnm2.ann1.Glyma.16G150700 confidence: 5 curators: - Marlene Dorneich-Hayes + - Scott Kalberer comments: - Overexpression of FT2a increased nodulation while RNAi knockdown decreased nodulation. - FT2a is induced by the transcription factors GmCRY1 and CONSTANS. @@ -76,14 +78,13 @@ traits: relation: RO:0002213 - entity_name: positive regulation of lateral root development entity: GO:1901333 - - entity_name: flowering references: - - citation: Wang, Guo et. al., 2021 + - citation: Wang, Guo et al., 2021 doi: 10.1126/science.abh2890 pmid: 34591638 - - citation: Hasan, Corpas et. al., 2022 + - citation: Hasan, Corpas et al., 2022 doi: 10.1016/j.tplants.2022.07.002 - - citation: Yang, Lan et. al., 2022 + - citation: Yang, Lan et al., 2022 doi: 10.1111/jipb.13207 pmid: 34962095 - citation: Kong, Liu et al., 2010 From 8d91672e9685a82b1dd9579b2718b5bb2606193b Mon Sep 17 00:00:00 2001 From: ScottKalberer <78100602+ScottKalberer@users.noreply.github.com> Date: Wed, 11 Sep 2024 15:57:38 -0500 Subject: [PATCH 07/18] Update medtr.Jiao_Wang_2020.yml Added entity_name to ontology term "leaf morphology trait". --- Medicago/truncatula/studies/medtr.Jiao_Wang_2020.yml | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/Medicago/truncatula/studies/medtr.Jiao_Wang_2020.yml b/Medicago/truncatula/studies/medtr.Jiao_Wang_2020.yml index 773e8d8..1eda944 100644 --- a/Medicago/truncatula/studies/medtr.Jiao_Wang_2020.yml +++ b/Medicago/truncatula/studies/medtr.Jiao_Wang_2020.yml @@ -11,7 +11,7 @@ phenotype_synopsis: Forms dissected leaves with five leaflets clustered at the t traits: - entity_name: petiole length entity: TO:0000766 - - entity_name: TO:0000748 + - entity_name: leaf morphology trait entity: TO:0000748 - entity_name: leaf entity: PO:0025034 From 3cd88b9f8beb766206300e085b3fa5743d0ed297 Mon Sep 17 00:00:00 2001 From: ScottKalberer <78100602+ScottKalberer@users.noreply.github.com> Date: Wed, 11 Sep 2024 16:10:26 -0500 Subject: [PATCH 08/18] Update medtr.Laurie_Diwadkar_2011.yml Added phenotype synopsis. --- Medicago/truncatula/studies/medtr.Laurie_Diwadkar_2011.yml | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/Medicago/truncatula/studies/medtr.Laurie_Diwadkar_2011.yml b/Medicago/truncatula/studies/medtr.Laurie_Diwadkar_2011.yml index 3c16a3e..5fb919e 100644 --- a/Medicago/truncatula/studies/medtr.Laurie_Diwadkar_2011.yml +++ b/Medicago/truncatula/studies/medtr.Laurie_Diwadkar_2011.yml @@ -27,7 +27,7 @@ gene_model_full_id: medtr.A17_HM341.gnm4.ann2.Medtr7g085040 confidence: 5 curators: - Steven Cannon -phenotype_synopsis: null +phenotype_synopsis: Normal flower development traits: - entity_name: flower development trait entity: TO:0000622 From fb53bf08d7b2e9ee6057596efa6118985f7095d1 Mon Sep 17 00:00:00 2001 From: ScottKalberer <78100602+ScottKalberer@users.noreply.github.com> Date: Wed, 11 Sep 2024 16:27:52 -0500 Subject: [PATCH 09/18] Update medtr.Liu_Breakspear_2019.yml Added PubMed ID for Liu, Breakspear et al., 2019. --- Medicago/truncatula/studies/medtr.Liu_Breakspear_2019.yml | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/Medicago/truncatula/studies/medtr.Liu_Breakspear_2019.yml b/Medicago/truncatula/studies/medtr.Liu_Breakspear_2019.yml index 795733f..b462c57 100644 --- a/Medicago/truncatula/studies/medtr.Liu_Breakspear_2019.yml +++ b/Medicago/truncatula/studies/medtr.Liu_Breakspear_2019.yml @@ -15,7 +15,7 @@ traits: references: - citation: Liu, Breakspear et al., 2019 doi: 10.1104/pp.18.01572 - pmid: null + pmid: 30710053 - citation: Oellrich, Walls et al., 2015 doi: 10.1186/s13007-015-0053-y pmid: 25774204 From 1c98e299e9ce29e002cd5172cee8a23e4648d7b2 Mon Sep 17 00:00:00 2001 From: ScottKalberer <78100602+ScottKalberer@users.noreply.github.com> Date: Wed, 11 Sep 2024 16:46:16 -0500 Subject: [PATCH 10/18] Update medtr.Vernie_Kim_2015.yml --- Medicago/truncatula/studies/medtr.Vernie_Kim_2015.yml | 8 ++++---- 1 file changed, 4 insertions(+), 4 deletions(-) diff --git a/Medicago/truncatula/studies/medtr.Vernie_Kim_2015.yml b/Medicago/truncatula/studies/medtr.Vernie_Kim_2015.yml index 5689a40..47c73f2 100644 --- a/Medicago/truncatula/studies/medtr.Vernie_Kim_2015.yml +++ b/Medicago/truncatula/studies/medtr.Vernie_Kim_2015.yml @@ -1,13 +1,13 @@ --- gene_symbols: - MtCre1 -gene_symbol_long: Cytokinin Response1 +gene_symbol_long: Cytokinin Response 1 gene_model_pub_name: Medtr8g106150 gene_model_full_id: medtr.A17_HM341.gnm4.ann2.Medtr8g106150 confidence: 5 curators: - Steven Cannon -phenotype_synopsis: Roots growth was not inhibited by exogenous cytokinin application. Expression of the primary cytokinin response gene, Mt RR4, was not induced by cytokinins. Plants had an increased number of lateral roots (higher lateral root density) and a strong reduction in numbers of root nodules. The development of infection threads was inhibited and early nodule primordia development was also impaired. Expression of early nodulation genes was reduced in plants in which expression of MtCre1 was interfered with by RNAi. +phenotype_synopsis: Roots growth was not inhibited by exogenous cytokinin application. Expression of the primary cytokinin response gene, MtRR4, was not induced by cytokinins. Plants had an increased number of lateral roots (higher lateral root density) and a strong reduction in numbers of root nodules. The development of infection threads was inhibited and early nodule primordia development was also impaired. Expression of early nodulation genes was reduced in plants in which expression of MtCre1 was interfered with by RNAi. traits: - entity_name: root nodule number entity: TO:0000900 @@ -31,7 +31,7 @@ references: --- gene_symbols: - ERN1 -gene_symbol_long: Ethylene Response Factor Required for Nodulation1 +gene_symbol_long: Ethylene Response Factor Required for Nodulation 1 gene_model_pub_name: EU038802 gene_model_full_id: medtr.A17_HM341.gnm4.ann2.Medtr7g085810 confidence: 5 @@ -51,7 +51,7 @@ references: --- gene_symbols: - ERN2 -gene_symbol_long: Ethylene Response Factor Required for Nodulation2 +gene_symbol_long: Ethylene Response Factor Required for Nodulation 2 gene_model_pub_name: EU038803 gene_model_full_id: medtr.A17_HM341.gnm4.ann2.Medtr6g029180 confidence: 5 From 06143072bc9270f6a9448e89df4684e901823c83 Mon Sep 17 00:00:00 2001 From: ScottKalberer <78100602+ScottKalberer@users.noreply.github.com> Date: Wed, 11 Sep 2024 16:49:34 -0500 Subject: [PATCH 11/18] Update medtr.Weller_Foo_2015.yml Added entity_name for hypocotyl morphology trait. --- Medicago/truncatula/studies/medtr.Weller_Foo_2015.yml | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/Medicago/truncatula/studies/medtr.Weller_Foo_2015.yml b/Medicago/truncatula/studies/medtr.Weller_Foo_2015.yml index 425547b..7db38ed 100644 --- a/Medicago/truncatula/studies/medtr.Weller_Foo_2015.yml +++ b/Medicago/truncatula/studies/medtr.Weller_Foo_2015.yml @@ -2,7 +2,7 @@ gene_symbols: - EIN2 - Skl1 -gene_symbol_long: Ethylene Insensitive2 +gene_symbol_long: Ethylene Insensitive 2 gene_model_pub_name: Medtr7g101410 gene_model_full_id: medtr.A17.gnm5.ann1_6.MtrunA17Chr7g0264231 confidence: 5 @@ -16,7 +16,7 @@ traits: entity: TO:0002665 - entity_name: root nodule number entity: TO:0000900 - - entity_name: TO:0000757 + - entity_name: hypocotyl morphology trait entity: TO:0000757 - entity_name: seedling cotyledon size entity: TO:0000752 From 04c0991db6a9e9c3b44dd54c5ba7da8f4db18fe1 Mon Sep 17 00:00:00 2001 From: Steven Cannon Date: Thu, 12 Sep 2024 13:58:16 -0500 Subject: [PATCH 12/18] Move comment into array form --- Glycine/max/studies/glyma.Lu_Zhao_2017.yml | 3 ++- 1 file changed, 2 insertions(+), 1 deletion(-) diff --git a/Glycine/max/studies/glyma.Lu_Zhao_2017.yml b/Glycine/max/studies/glyma.Lu_Zhao_2017.yml index 1716ffc..ef68823 100644 --- a/Glycine/max/studies/glyma.Lu_Zhao_2017.yml +++ b/Glycine/max/studies/glyma.Lu_Zhao_2017.yml @@ -93,7 +93,8 @@ confidence: 5 curators: - Steven Cannon phenotype_synopsis: Photoperiodic flowering time regulation -comments: Encodes a MYB transciption factor that affects plant height through mediating the GA pathway in soybean +comments: + - Encodes a MYB transciption factor that affects plant height through mediating the GA pathway in soybean traits: - entity_name: flowering time entity: TO:0002616 From ed3ce774a57862a26a856d34b7481572e26ff862 Mon Sep 17 00:00:00 2001 From: Steven Cannon Date: Thu, 12 Sep 2024 13:58:47 -0500 Subject: [PATCH 13/18] Move gene symbol into array form --- Vicia/faba/studies/vicfa.Jayakodi_Golicz_2023.yml | 5 +++-- 1 file changed, 3 insertions(+), 2 deletions(-) diff --git a/Vicia/faba/studies/vicfa.Jayakodi_Golicz_2023.yml b/Vicia/faba/studies/vicfa.Jayakodi_Golicz_2023.yml index 3230db2..1adf853 100644 --- a/Vicia/faba/studies/vicfa.Jayakodi_Golicz_2023.yml +++ b/Vicia/faba/studies/vicfa.Jayakodi_Golicz_2023.yml @@ -1,6 +1,7 @@ --- scientific_name: Vicia faba -gene_symbols: VfCYP78A +gene_symbols: + - VfCYP78A gene_model_pub_name: Vfaba.Hedin2.R1.4g051440.1 gene_model_full_id: vicfa.Hedin2.gnm1.ann1.4g051440.1 confidence: 4 @@ -28,7 +29,7 @@ curators: - Steven Cannon comments: - Evidence based on association and allelic variant analysis, and homology to an orthologous locus in pea (gene Psat1g2063360) that controls hilum color. - - \[Evidence suggests that the] regulation of expression of VfPPO-2 controls hilum colour variation in faba bean.\ + - Evidence suggests that the regulation of expression of VfPPO-2 controls hilum colour variation in faba bean. phenotype_synopsis: Control of hilum color traits: - entity_name: hilum color From 427c60529f4b118dbf94c7b20d2ed974615f6685 Mon Sep 17 00:00:00 2001 From: Steven Cannon Date: Thu, 12 Sep 2024 14:00:30 -0500 Subject: [PATCH 14/18] Update citations.txt and traits.yml files to correspond to studies/*yml files as of 2024-09-12 --- .../max/gene_functions/glyma.citations.txt | 155 +- .../max/gene_functions/glyma.references.txt | 5821 ----------------- Glycine/max/gene_functions/glyma.traits.yml | 4538 ++++++++++--- .../soja/gene_functions/glyso.citations.txt | 2 + Glycine/soja/gene_functions/glyso.traits.yml | 60 + .../gene_functions/lotja.citations.txt | 4 + .../japonicus/gene_functions/lotja.traits.yml | 41 + .../gene_functions/medtr.citations.txt | 63 +- .../gene_functions/medtr.references.txt | 3519 ---------- .../gene_functions/medtr.traits.yml | 1174 ++-- .../gene_functions/phavu.citations.txt | 3 + .../vulgaris/gene_functions/phavu.traits.yml | 71 + .../gene_functions/pissa.citations.txt | 4 + Pisum/sativum/gene_functions/pissa.traits.yml | 40 + .../faba/gene_functions/vicfa.references.txt | 342 - Vicia/faba/gene_functions/vicfa.traits.yml | 9 +- .../gene_functions/vigra.citations.txt | 1 + Vigna/radiata/gene_functions/vigra.traits.yml | 28 + 18 files changed, 4499 insertions(+), 11376 deletions(-) delete mode 100644 Glycine/max/gene_functions/glyma.references.txt create mode 100644 Glycine/soja/gene_functions/glyso.citations.txt create mode 100644 Glycine/soja/gene_functions/glyso.traits.yml create mode 100644 Lotus/japonicus/gene_functions/lotja.citations.txt create mode 100644 Lotus/japonicus/gene_functions/lotja.traits.yml delete mode 100644 Medicago/truncatula/gene_functions/medtr.references.txt create mode 100644 Phaseolus/vulgaris/gene_functions/phavu.citations.txt create mode 100644 Phaseolus/vulgaris/gene_functions/phavu.traits.yml create mode 100644 Pisum/sativum/gene_functions/pissa.citations.txt create mode 100644 Pisum/sativum/gene_functions/pissa.traits.yml delete mode 100644 Vicia/faba/gene_functions/vicfa.references.txt create mode 100644 Vigna/radiata/gene_functions/vigra.citations.txt create mode 100644 Vigna/radiata/gene_functions/vigra.traits.yml diff --git a/Glycine/max/gene_functions/glyma.citations.txt b/Glycine/max/gene_functions/glyma.citations.txt index 20b8a12..68df91b 100644 --- a/Glycine/max/gene_functions/glyma.citations.txt +++ b/Glycine/max/gene_functions/glyma.citations.txt @@ -1,47 +1,120 @@ -10.1007/s00122-016-2819-7 27832313 null Samanfar et al., 2017 "Samanfar B, Molnar SJ, Charette M, Schoenrock A, Dehne F, Golshani A, Belzile F, Cober ER. Mapping and identification of a potential candidate gene for a novel maturity locus, E10, in soybean. Theor Appl Genet. 2017 Feb;130(2):377-390. doi: 10.1007/s00122-016-2819-7. Epub 2016 Nov 10. PMID: 27832313." -10.1016/j.molp.2016.12.004 27979775 null Yue et al., 2017 "Yue Y, Liu N, Jiang B, Li M, Wang H, Jiang Z, Pan H, Xia Q, Ma Q, Han T, Nian H. A Single Nucleotide Deletion in J Encoding GmELF3 Confers Long Juvenility and Is Associated with Adaption of Tropic Soybean. Mol Plant. 2017 Apr 3;10(4):656-658. doi: 10.1016/j.molp.2016.12.004. Epub 2016 Dec 12. PMID: 27979775." -10.1038/ng.3819 28319089 null Lu, Zhao et al., 2017 "Lu S, Zhao X, Hu Y, Liu S, Nan H, Li X, Fang C, Cao D, Shi X, Kong L, Su T, Zhang F, Li S, Wang Z, Yuan X, Cober ER, Weller JL, Liu B, Hou X, Tian Z, Kong F. Natural variation at the soybean J locus improves adaptation to the tropics and enhances yield. Nat Genet. 2017 May;49(5):773-779. doi: 10.1038/ng.3819. Epub 2017 Mar 20. PMID: 28319089." -10.1038/s41588-020-0604-7 32231277 null Lu, Dong et al., 2020 "Lu S, Dong L, Fang C, Liu S, Kong L, Cheng Q, Chen L, Su T, Nan H, Zhang D, Zhang L, Wang Z, Yang Y, Yu D, Liu X, Yang Q, Lin X, Tang Y, Zhao X, Yang X, Tian C, Xie Q, Li X, Yuan X, Tian Z, Liu B, Weller JL, Kong F. Stepwise selection on homeologous PRR genes controlling flowering and maturity during soybean domestication. Nat Genet. 2020 Apr;52(4):428-436. doi: 10.1038/s41588-020-0604-7. Epub 2020 Mar 30. PMID: 32231277." -10.1093/aob/mct269 24284817 PMC3906962 Tsubokura, Watanabe et al., 2013 "Tsubokura Y, Watanabe S, Xia Z, Kanamori H, Yamagata H, Kaga A, Katayose Y, Abe J, Ishimoto M, Harada K. Natural variation in the genes responsible for maturity loci E1, E2, E3 and E4 in soybean. Ann Bot. 2014 Feb;113(3):429-41. doi: 10.1093/aob/mct269. Epub 2013 Nov 26. PMID: 24284817; PMCID: PMC3906962." -10.1093/jxb/erw283 27422993 PMC5014162 Takeshima, Hayashi et al., 2016 "Takeshima R, Hayashi T, Zhu J, Zhao C, Xu M, Yamaguchi N, Sayama T, Ishimoto M, Kong L, Shi X, Liu B, Tian Z, Yamada T, Kong F, Abe J. A soybean quantitative trait locus that promotes flowering under long days is identified as FT5a, a FLOWERING LOCUS T ortholog. J Exp Bot. 2016 Sep;67(17):5247-58. doi: 10.1093/jxb/erw283. Epub 2016 Jul 15. PMID: 27422993; PMCID: PMC5014162." -10.1104/pp.15.00763 26134161 PMC4528769 Xu, Yamagishi et al., 2015 "Xu M, Yamagishi N, Zhao C, Takeshima R, Kasai M, Watanabe S, Kanazawa A, Yoshikawa N, Liu B, Yamada T, Abe J. The Soybean-Specific Maturity Gene E1 Family of Floral Repressors Controls Night-Break Responses through Down-Regulation of FLOWERING LOCUS T Orthologs. Plant Physiol. 2015 Aug;168(4):1735-46. doi: 10.1104/pp.15.00763. Epub 2015 Jul 1. PMID: 26134161; PMCID: PMC4528769." -10.1104/pp.110.160796 20864544 PMC2971601 Kong, Liu et al., 2010 "Kong F, Liu B, Xia Z, Sato S, Kim BM, Watanabe S, Yamada T, Tabata S, Kanazawa A, Harada K, Abe J. Two coordinately regulated homologs of FLOWERING LOCUS T are involved in the control of photoperiodic flowering in soybean. Plant Physiol. 2010 Nov;154(3):1220-31. doi: 10.1104/pp.110.160796. Epub 2010 Sep 23. PMID: 20864544; PMCID: PMC2971601." -10.1105/tpc.114.135103 25663621 PMC4456927 Wang, Zhou et al., 2015 "Wang Z, Zhou Z, Liu Y, Liu T, Li Q, Ji Y, Li C, Fang C, Wang M, Wu M, Shen Y, Tang T, Ma J, Tian Z. Functional evolution of phosphatidylethanolamine binding proteins in soybean and Arabidopsis. Plant Cell. 2015 Feb;27(2):323-36. doi: 10.1105/tpc.114.135103. Epub 2015 Feb 6. PMID: 25663621; PMCID: PMC4456927." -10.1111/j.1365-313x.2004.02072.x 15125772 null Noh, Bizzell et al., 2004 "Noh YS, Bizzell CM, Noh B, Schomburg FM, Amasino RM. EARLY FLOWERING 5 acts as a floral repressor in Arabidopsis. Plant J. 2004 May;38(4):664-72. doi: 10.1111/j.1365-313X.2004.02072.x. PMID: 15125772." -10.1111/jipb.13021 33090664 null Lin, Liu et al., 2021 "Lin X, Liu B, Weller JL, Abe J, Kong F. Molecular mechanisms for the photoperiodic regulation of flowering in soybean. J Integr Plant Biol. 2021 Jun;63(6):981-994. doi: 10.1111/jipb.13021. Epub 2021 Apr 26. PMID: 33090664." -10.1111/nph.14884 29120038 PMC5900889 Liu, Jiang et al., 2008a "Liu W, Jiang B, Ma L, Zhang S, Zhai H, Xu X, Hou W, Xia Z, Wu C, Sun S, Wu T, Chen L, Han T. Functional diversification of Flowering Locus T homologs in soybean: GmFT1a and GmFT2a/5a have opposite roles in controlling flowering and maturation. New Phytol. 2018 Feb;217(3):1335-1345. doi: 10.1111/nph.14884. Epub 2017 Nov 9. PMID: 29120038; PMCID: PMC5900889." -10.1186/1471-2229-14-9 24397545 PMC3890618 Fan, Hu et al., 2014 "Fan C, Hu R, Zhang X, Wang X, Zhang W, Zhang Q, Ma J, Fu YF. Conserved CO-FT regulons contribute to the photoperiod flowering control in soybean. BMC Plant Biol. 2014 Jan 7;14:9. doi: 10.1186/1471-2229-14-9. PMID: 24397545; PMCID: PMC3890618." -10.1186/s12870-016-0704-9 26786479 PMC4719747 Zhao, Takeshima et al., 2016 "Zhao C, Takeshima R, Zhu J, Xu M, Sato M, Watanabe S, Kanazawa A, Liu B, Kong F, Yamada T, Abe J. A recessive allele for delayed flowering at the soybean maturity locus E9 is a leaky allele of FT2a, a FLOWERING LOCUS T ortholog. BMC Plant Biol. 2016 Jan 19;16:20. doi: 10.1186/s12870-016-0704-9. PMID: 26786479; PMCID: PMC4719747." -10.1371/journal.pone.0089030 24586488 PMC3929636 Zhai et al., 2014 "Zhai H, Lü S, Liang S, Wu H, Zhang X, Liu B, Kong F, Yuan X, Li J, Xia Z. GmFT4, a homolog of FLOWERING LOCUS T, is positively regulated by E1 and functions as a flowering repressor in soybean. PLoS One. 2014 Feb 19;9(2):e89030. doi: 10.1371/journal.pone.0089030. PMID: 24586488; PMCID: PMC3929636." -10.1371/journal.pone.0097669 24845624 PMC4028237 Nan, Cao et al., 2014 "Nan H, Cao D, Zhang D, Li Y, Lu S, Tang L, Yuan X, Liu B, Kong F. GmFT2a and GmFT5a redundantly and differentially regulate flowering through interaction with and upregulation of the bZIP transcription factor GmFDL19 in soybean. PLoS One. 2014 May 20;9(5):e97669. doi: 10.1371/journal.pone.0097669. PMID: 24845624; PMCID: PMC4028237." -10.1371/journal.pone.0136601 26371882 PMC4570765 Guo, Xu et al., 2015 "Guo G, Xu K, Zhang X, Zhu J, Lu M, Chen F, Liu L, Xi ZY, Bachmair A, Chen Q, Fu YF. Extensive Analysis of GmFTL and GmCOL Expression in Northern Soybean Cultivars in Field Conditions. PLoS One. 2015 Sep 15;10(9):e0136601. doi: 10.1371/journal.pone.0136601. PMID: 26371882; PMCID: PMC4570765." -10.1534/genetics.108.098772 19474204 PMC2728863 Watanabe, Hideshima et al., 2009 "Watanabe S, Hideshima R, Xia Z, Tsubokura Y, Sato S, Nakamoto Y, Yamanaka N, Takahashi R, Ishimoto M, Anai T, Tabata S, Harada K. Map-based cloning of the gene associated with the soybean maturity locus E3. Genetics. 2009 Aug;182(4):1251-62. doi: 10.1534/genetics.108.098772. Epub 2009 May 27. PMID: 19474204; PMCID: PMC2728863." -10.1534/genetics.110.125062 21406680 PMC3122305 Watanabe, Xia et al., 2011 "Watanabe S, Xia Z, Hideshima R, Tsubokura Y, Sato S, Yamanaka N, Takahashi R, Anai T, Tabata S, Kitamura K, Harada K. A map-based cloning strategy employing a residual heterozygous line reveals that the GIGANTEA gene is involved in soybean maturity and flowering. Genetics. 2011 Jun;188(2):395-407. doi: 10.1534/genetics.110.125062. Epub 2011 Mar 15. PMID: 21406680; PMCID: PMC3122305." -10.3389/fpls.2019.01221 31787988 PMC6856076 Wu, Kang et al., 2019 "Wu F, Kang X, Wang M, Haider W, Price WB, Hajek B, Hanzawa Y. Transcriptome-Enabled Network Inference Revealed the GmCOL1 Feed-Forward Loop and Its Roles in Photoperiodic Flowering of Soybean. Front Plant Sci. 2019 Nov 8;10:1221. doi: 10.3389/fpls.2019.01221. PMID: 31787988; PMCID: PMC6856076." -10.3389/fpls.2021.632754 33995435 PMC8113421 Xia, Zhai et al., 2012 "Xia Z, Zhai H, Wu H, Xu K, Watanabe S, Harada K. The Synchronized Efforts to Decipher the Molecular Basis for Soybean Maturity Loci E1, E2, and E3 That Regulate Flowering and Maturity. Front Plant Sci. 2021 Apr 28;12:632754. doi: 10.3389/fpls.2021.632754. PMID: 33995435; PMCID: PMC8113421." -10.3389/fpls.2022.889066 35574141 PMC9100572 Dietz, Chan et al., 2023 "Dietz N, Chan YO, Scaboo A, Graef G, Hyten D, Happ M, Diers B, Lorenz A, Wang D, Joshi T, Bilyeu K. Candidate Genes Modulating Reproductive Timing in Elite US Soybean Lines Identified in Soybean Alleles of Arabidopsis Flowering Orthologs With Divergent Latitude Distribution. Front Plant Sci. 2022 Apr 29;13:889066. doi: 10.3389/fpls.2022.889066. PMID: 35574141; PMCID: PMC9100572." +10.1016/j.pbi.2005.05.010 15939664 null Weirmer, Feys et al., 2005 "Wiermer M, Feys BJ, Parker JE. Plant immunity: the EDS1 regulatory node. Curr Opin Plant Biol. 2005 Aug;8(4):383-9. doi: 10.1016/j.pbi.2005.05.010. PMID: 15939664." +10.1111/j.1365-313x.2010.04214.x 20345602 null Yi, Jinxin et al., 2010 "Yi J, Derynck MR, Li X, Telmer P, Marsolais F, Dhaubhadel S. A single-repeat MYB transcription factor, GmMYB176, regulates CHS8 gene expression and affects isoflavonoid biosynthesis in soybean. Plant J. 2010 Jun 1;62(6):1019-34. doi: 10.1111/j.1365-313X.2010.04214.x. Epub 2010 Mar 25. PMID: 20345602." +10.1111/pce.13695 31981430 PMC7154755 Chen, Cai et al., 2020 "Chen L, Cai Y, Qu M, Wang L, Sun H, Jiang B, Wu T, Liu L, Sun S, Wu C, Yao W, Yuan S, Han T, Hou W. Soybean adaption to high-latitude regions is associated with natural variations of GmFT2b, an ortholog of FLOWERING LOCUS T. Plant Cell Environ. 2020 Apr;43(4):934-944. doi: 10.1111/pce.13695. Epub 2020 Jan 25. PMID: 31981430; PMCID: PMC7154755." +10.3389/fpls.2022.842597 35599880 PMC9114929 Khatri, Pant et al., 2022 "" +10.1111/mpp.12741 30113770 PMC6430474 Zhang, Gao et al., 2018 "" +10.1186/s12870-019-2201-4 31856712 PMC6921446 Yu, Jin et al., 2019 "" +10.1038/s42003-021-01907-7 33742112 PMC7979691 Zhang, Cheng et al., 2021 "" +10.1038/s41598-018-25910-x 29769571 PMC5955893 Yan, Wang et. al., 2018 "Yan Q, Wang L, Li X. GmBEHL1, a BES1/BZR1 family protein, negatively regulates soybean nodulation. Sci Rep. 2018 May 16;8(1):7614. doi: 10.1038/s41598-018-25910-x. PMID: 29769571; PMCID: PMC5955893." 10.1038/s41598-019-42332-5 30979945 PMC6461667 Chen, Fang et al., 2019 "Chen LM, Fang YS, Zhang CJ, Hao QN, Cao D, Yuan SL, Chen HF, Yang ZL, Chen SL, Shan ZH, Liu BH, Jing-Wang, Zhan Y, Zhang XJ, Qiu DZ, Li WB, Zhou XA. GmSYP24, a putative syntaxin gene, confers osmotic/drought, salt stress tolerances and ABA signal pathway. Sci Rep. 2019 Apr 12;9(1):5990. doi: 10.1038/s41598-019-42332-5. PMID: 30979945; PMCID: PMC6461667." -10.1007/s11248-019-00180-z 31673914 null Zhang, Luo, et al., 2020 "Zhang L, Luo Y, Liu B, Zhang L, Zhang W, Chen R, Wang L. Overexpression of the maize γ-tocopherol methyltransferase gene (ZmTMT) increases α-tocopherol content in transgenic Arabidopsis and maize seeds. Transgenic Res. 2020 Feb;29(1):95-104. doi: 10.1007/s11248-019-00180-z. Epub 2019 Oct 31. PMID: 31673914." -10.1371/journal.pone.0222469 31518373 PMC6743760 Sugawara, Umehara et al., 2019 "Sugawara M, Umehara Y, Kaga A, Hayashi M, Ishimoto M, Sato S, Mitsui H, Minamisawa K. Symbiotic incompatibility between soybean and Bradyrhizobium arises from one amino acid determinant in soybean Rj2 protein. PLoS One. 2019 Sep 13;14(9):e0222469. doi: 10.1371/journal.pone.0222469. PMID: 31518373; PMCID: PMC6743760." -10.1038/ncomms5340 25004933 PMC4104456 Qi, Li et al., 2014 "Qi X, Li MW, Xie M, Liu X, Ni M, Shao G, Song C, Kay-Yuen Yim A, Tao Y, Wong FL, Isobe S, Wong CF, Wong KS, Xu C, Li C, Wang Y, Guan R, Sun F, Fan G, Xiao Z, Zhou F, Phang TH, Liu X, Tong SW, Chan TF, Yiu SM, Tabata S, Wang J, Xu X, Lam HM. Identification of a novel salt tolerance gene in wild soybean by whole-genome sequencing. Nat Commun. 2014 Jul 9;5:4340. doi: 10.1038/ncomms5340. PMID: 25004933; PMCID: PMC4104456." +10.1105/tpc.114.126938 25005919 PMC4145117 Ping, Liu, et al., 2014 "Ping J, Liu Y, Sun L, Zhao M, Li Y, She M, Sui Y, Lin F, Liu X, Tang Z, Nguyen H, Tian Z, Qiu L, Nelson RL, Clemente TE, Specht JE, Ma J. Dt2 is a gain-of-function MADS-domain factor gene that specifies semideterminacy in soybean. Plant Cell. 2014 Jul;26(7):2831-42. doi: 10.1105/tpc.114.126938. Epub 2014 Jul 8. PMID: 25005919; PMCID: PMC4145117." +10.1186/1471-2229-14-143 24886084 PMC4058718 Gillman, Stacey et. al., 2014 "" +10.1104/pp.114.242495 24872380 PMC4081336 Wang, Shine et al., 2014 "" +10.1111/pce.13678 31724182 null Wang, Yuan, et. al., 2019 "" +10.1371/journal.pone.0085754 24465684 PMC3897488 Wu, Price et al., 2014 "" +10.1534/g3.114.015255 25452420 PMC4291463 Campbell, Mani et al., 2014 "Campbell BW, Mani D, Curtin SJ, Slattery RA, Michno JM, Ort DR, Schaus PJ, Palmer RG, Orf JH, Stupar RM. Identical substitutions in magnesium chelatase paralogs result in chlorophyll-deficient soybean mutants. G3 (Bethesda). 2014 Dec 1;5(1):123-31. doi: 10.1534/g3.114.015255. PMID: 25452420; PMCID: PMC4291463." 10.1534/g3.116.038596 28235823 PMC5386870 Dobbels, Michno et al., 2017 "Dobbels AA, Michno JM, Campbell BW, Virdi KS, Stec AO, Muehlbauer GJ, Naeve SL, Stupar RM. An Induced Chromosomal Translocation in Soybean Disrupts a KASI Ortholog and Is Associated with a High-Sucrose and Low-Oil Seed Phenotype. G3 (Bethesda). 2017 Apr 3;7(4):1215-1223. doi: 10.1534/g3.116.038596. PMID: 28235823; PMCID: PMC5386870." +10.1094/mpmi-01-20-0017-r 32186464 null Shi, Zhang et al., 2020 "Shi Y, Zhang Z, Wen Y, Yu G, Zou J, Huang S, Wang J, Zhu J, Wang J, Chen L, Ma C, Liu X, Zhu R, Li Q, Li J, Guo M, Liu H, Zhu Y, Sun Z, Han L, Jiang H, Wu X, Wang N, Zhang W, Yin Z, Li C, Hu Z, Qi Z, Liu C, Chen Q, Xin D. RNA Sequencing-Associated Study Identifies GmDRR1 as Positively Regulating the Establishment of Symbiosis in Soybean. Mol Plant Microbe Interact. 2020 Jun;33(6):798-807. doi: 10.1094/MPMI-01-20-0017-R. Epub 2020 May 7. PMID: 32186464." +10.1371/journal.pone.0094150 24727730 PMC3984090 Langewisch, Zhang, 2014 "" +10.1038/s41588-020-0604-7 32231277 null Lu, Dong et al., 2020 "" +10.1007/s11103-013-0062-z 23636865 null Zhao, Wang et al., 2013 "" +10.1093/jxb/ert238 23963672 PMC3808315 Song, Li et al., 2013 "Song QX, Li QT, Liu YF, Zhang FX, Ma B, Zhang WK, Man WQ, Du WG, Wang GD, Chen SY, Zhang JS. Soybean GmbZIP123 gene enhances lipid content in the seeds of transgenic Arabidopsis plants. J Exp Bot. 2013 Nov;64(14):4329-41. doi: 10.1093/jxb/ert238. Epub 2013 Aug 20. PMID: 23963672; PMCID: PMC3808315." +10.1073/pnas.1611763113 27791139 PMC5098654 Ge, Yu et al., 2016 "" +10.1111/tpj.14789 32344464 null Isidra-Arellano, Pozas-Rodrguez et al., 2020 "Isidra-Arellano MC, Pozas-Rodríguez EA, Del Rocío Reyero-Saavedra M, Arroyo-Canales J, Ferrer-Orgaz S, Del Socorro Sánchez-Correa M, Cardenas L, Covarrubias AA, Valdés-López O. Inhibition of legume nodulation by Pi deficiency is dependent on the autoregulation of nodulation (AON) pathway. Plant J. 2020 Aug;103(3):1125-1139. doi: 10.1111/tpj.14789. Epub 2020 May 28. PMID: 32344464." 10.3389/fpls.2017.01604 28979275 PMC5611487 Manan, Ahmad et al., 2017 "Manan S, Ahmad MZ, Zhang G, Chen B, Haq BU, Yang J, Zhao J. Soybean LEC2 Regulates Subsets of Genes Involved in Controlling the Biosynthesis and Catabolism of Seed Storage Substances and Seed Development. Front Plant Sci. 2017 Sep 20;8:1604. doi: 10.3389/fpls.2017.01604. PMID: 28979275; PMCID: PMC5611487." +10.1186/1471-2229-10-195 20828382 PMC2956544 Pham, Lee et al., 2010 "" +10.1534/genetics.108.098772 19474204 PMC2728863 Watanabe, Hideshima et al., 2009 "" +10.1104/pp.19.01209 32680974 PMC7479890 Lu, Cheng et al., 2020 "Lu M, Cheng Z, Zhang XM, Huang P, Fan C, Yu G, Chen F, Xu K, Chen Q, Miao Y, Han Y, Feng X, Liu L, Fu YF. Spatial Divergence of PHR-PHT1 Modules Maintains Phosphorus Homeostasis in Soybean Nodules. Plant Physiol. 2020 Sep;184(1):236-250. doi: 10.1104/pp.19.01209. Epub 2020 Jul 17. PMID: 32680974; PMCID: PMC7479890." +10.1186/s12870-019-2145-8 31852439 PMC6921449 Cheng, Dong et al., 2019 "" +10.1016/j.plantsci.2019.110298 31779909 null Bai, Jing et al., 2020 "Bai Y, Jing G, Zhou J, Li S, Bi R, Zhao J, Jia Q, Zhang Q, Zhang W. Overexpression of soybean GmPLDγ enhances seed oil content and modulates fatty acid composition in transgenic Arabidopsis. Plant Sci. 2020 Jan;290:110298. doi: 10.1016/j.plantsci.2019.110298. Epub 2019 Oct 6. Erratum in: Plant Sci. 2021 Jun;307:110881. doi: 10.1016/j.plantsci.2021.110881. PMID: 31779909." +10.1104/pp.107.1.253 12228359 PMC161196 Chao et al., 1995 "Chao WS, Liu V, Thomson WW, Platt K, Walling LL. The Impact of Chlorophyll-Retention Mutations, d1d2 and cyt-G1, during Embryogeny in Soybean. Plant Physiol. 1995 Jan;107(1):253-262. doi: 10.1104/pp.107.1.253. PMID: 12228359; PMCID: PMC161196." +10.3389/fpls.2021.632754 33995435 PMC8113421 Xia, Zhai et al., 2012 "" +10.1073/pnas.1312801111 24707045 PMC3977234 Chiasson, Loughlin et al., 2014 "" +10.1186/s12870-016-0704-9 26786479 PMC4719747 Zhao, Takeshima et al., 2016 "" +10.1111/j.1365-313x.2010.04398.x 21175888 null Indrasumunar, Searle et al., 2011 "Indrasumunar A, Searle I, Lin MH, Kereszt A, Men A, Carroll BJ, Gresshoff PM. Nodulation factor receptor kinase 1α controls nodule organ number in soybean (Glycine max L. Merr). Plant J. 2011 Jan;65(1):39-50. doi: 10.1111/j.1365-313X.2010.04398.x. Epub 2010 Nov 10. PMID: 21175888." +10.1093/aob/mcu147 25074550 PMC4204674 Yao, Tian et. al., 2014 "" +10.1111/tpj.14025 30004144 null Zhao, Li et al., 2018 "Zhao L, Li M, Xu C, Yang X, Li D, Zhao X, Wang K, Li Y, Zhang X, Liu L, Ding F, Du H, Wang C, Sun J, Li W. Natural variation in GmGBP1 promoter affects photoperiod control of flowering time and maturity in soybean. Plant J. 2018 Oct;96(1):147-162. doi: 10.1111/tpj.14025. Epub 2018 Aug 16. PMID: 30004144." +10.1186/s12864-019-5577-5 30894121 PMC6425728 Jiang, Zhang, et al., 2019 "Jiang B, Zhang S, Song W, Khan MAA, Sun S, Zhang C, Wu T, Wu C, Han T. Natural variations of FT family genes in soybean varieties covering a wide range of maturity groups. BMC Genomics. 2019 Mar 20;20(1):230. doi: 10.1186/s12864-019-5577-5. PMID: 30894121; PMCID: PMC6425728." +10.1093/jxb/erw283 27422993 PMC5014162 Takeshima, Hayashi et al., 2016 "" +10.1105/tpc.114.135103 25663621 PMC4456927 Wang, Zhou et al., 2015 "" +10.1104/pp.109.150607 20219831 PMC2862436 Liu, Watanabe, et al., 2010 "" +10.1007/s10142-012-0306-z 23322364 null Li, Hatanaka et al., 2013 "Li R, Hatanaka T, Yu K, Wu Y, Fukushige H, Hildebrand D. Soybean oil biosynthesis: role of diacylglycerol acyltransferases. Funct Integr Genomics. 2013 Mar;13(1):99-113. doi: 10.1007/s10142-012-0306-z. Epub 2013 Jan 16. PMID: 23322364." +10.1007/s11248-013-9713-8 23645501 null Zhang, Luo et al., 2013 "" +10.1371/journal.pone.0097891 24846334 PMC4028252 Carrero-Colon, Abshire et. al., 2014 "Carrero-Colón M, Abshire N, Sweeney D, Gaskin E, Hudson K. Mutations in SACPD-C result in a range of elevated stearic acid concentration in soybean seed. PLoS One. 2014 May 20;9(5):e97891. doi: 10.1371/journal.pone.0097891. PMID: 24846334; PMCID: PMC4028252." 10.1007/s11103-013-0133-1 24072327 null RojasRodas, Rodriguez et al., 2013 "Rojas Rodas F, Rodriguez TO, Murai Y, Iwashina T, Sugawara S, Suzuki M, Nakabayashi R, Yonekura-Sakakibara K, Saito K, Kitajima J, Toda K, Takahashi R. Linkage mapping, molecular cloning and functional analysis of soybean gene Fg2 encoding flavonol 3-O-glucoside (1 → 6) rhamnosyltransferase. Plant Mol Biol. 2014 Feb;84(3):287-300. doi: 10.1007/s11103-013-0133-1. Epub 2013 Sep 27. PMID: 24072327." -10.1016/j.plantsci.2019.110298 31779909 null Bai, Jing et al., 2021 "Bai Y, Jing G, Zhou J, Li S, Bi R, Zhao J, Jia Q, Zhang Q, Zhang W. Overexpression of soybean GmPLDγ enhances seed oil content and modulates fatty acid composition in transgenic Arabidopsis. Plant Sci. 2020 Jan;290:110298. doi: 10.1016/j.plantsci.2019.110298. Epub 2019 Oct 6. Erratum in: Plant Sci. 2021 Jun;307:110881. PMID: 31779909." -10.1007/s11248-013-9713-8 23645501 null Zhang, Luo et al., 2013 "Zhang L, Luo Y, Zhu Y, Zhang L, Zhang W, Chen R, Xu M, Fan Y, Wang L. GmTMT2a from soybean elevates the α-tocopherol content in corn and Arabidopsis. Transgenic Res. 2013 Oct;22(5):1021-8. doi: 10.1007/s11248-013-9713-8. Epub 2013 May 4. PMID: 23645501." -10.1016/j.yrtph.2017.01.004 28132846 null Fang, Feng, et al., 2017 "Fang J, Feng Y, Zhi Y, Zhang L, Yu Z, Jia X. A 90-day toxicity study of GmTMT transgenic maize in Sprague-Dawley rats. Regul Toxicol Pharmacol. 2017 Apr;85:48-54. doi: 10.1016/j.yrtph.2017.01.004. Epub 2017 Jan 27. PMID: 28132846." -10.1038/s41467-022-34153-4 36307423 PMC9616897 Liang, Chen, et al., 2022 "Liang Q, Chen L, Yang X, Yang H, Liu S, Kou K, Fan L, Zhang Z, Duan Z, Yuan Y, Liang S, Liu Y, Lu X, Zhou G, Zhang M, Kong F, Tian Z. Natural variation of Dt2 determines branching in soybean. Nat Commun. 2022 Oct 28;13(1):6429. doi: 10.1038/s41467-022-34153-4. PMID: 36307423; PMCID: PMC9616897." -10.1105/tpc.114.126938 25005919 PMC4145117 Ping, Liu, et al., 2014 "Ping J, Liu Y, Sun L, Zhao M, Li Y, She M, Sui Y, Lin F, Liu X, Tang Z, Nguyen H, Tian Z, Qiu L, Nelson RL, Clemente TE, Specht JE, Ma J. Dt2 is a gain-of-function MADS-domain factor gene that specifies semideterminacy in soybean. Plant Cell. 2014 Jul;26(7):2831-42. doi: 10.1105/tpc.114.126938. Epub 2014 Jul 8. PMID: 25005919; PMCID: PMC4145117." -10.1016/j.plantsci.2019.110386 32005391 null Tian, Liu et al., 2019 "Tian SN, Liu DD, Zhong CL, Xu HY, Yang S, Fang Y, Ran J, Liu JZ. Silencing GmFLS2 enhances the susceptibility of soybean to bacterial pathogen through attenuating the activation of GmMAPK signaling pathway. Plant Sci. 2020 Mar;292:110386. doi: 10.1016/j.plantsci.2019.110386. Epub 2019 Dec 24. PMID: 32005391." -10.1104/pp.114.242495 24872380 PMC4081336 Wang, Shine et al., 2014 "Wang J, Shine MB, Gao QM, Navarre D, Jiang W, Liu C, Chen Q, Hu G, Kachroo A. Enhanced Disease Susceptibility1 Mediates Pathogen Resistance and Virulence Function of a Bacterial Effector in Soybean. Plant Physiol. 2014 Jul;165(3):1269-1284. doi: 10.1104/pp.114.242495. Epub 2014 May 28. PMID: 24872380; PMCID: PMC4081336." -10.1016/j.pbi.2005.05.010 15939664 null Weirmer, Feys et al., 2005 "Wiermer M, Feys BJ, Parker JE. Plant immunity: the EDS1 regulatory node. Curr Opin Plant Biol. 2005 Aug;8(4):383-9. doi: 10.1016/j.pbi.2005.05.010. PMID: 15939664." +10.1111/nph.16506 32119117 null Liu, Liao et al., 2020 "" +10.1371/journal.pone.0089030 24586488 PMC3929636 Zhai, Lu et al., 2014 "" +10.3390/ijms22083877 33918544 PMC8069101 Ma, Sun et. al., 2021 "" +10.3389/fpls.2020.00450 32499790 PMC7243344 Wang, Yang et al., 2020 "Wang Y, Yang Z, Kong Y, Li X, Li W, Du H, Zhang C. GmPAP12 Is Required for Nodule Development and Nitrogen Fixation Under Phosphorus Starvation in Soybean. Front Plant Sci. 2020 May 14;11:450. doi: 10.3389/fpls.2020.00450. PMID: 32499790; PMCID: PMC7243344." +10.1093/pcp/pcy215 30418611 null Li, Liu et al., 2019 "" +10.1104/pp.125.4.1941 11299373 PMC88849 Hegeman, Good et al., 2001 "Hegeman CE, Good LL, Grabau EA. Expression of D-myo-inositol-3-phosphate synthase in soybean. Implications for phytic acid biosynthesis. Plant Physiol. 2001 Apr;125(4):1941-8. doi: 10.1104/pp.125.4.1941. PMID: 11299373; PMCID: PMC88849." +10.1093/aob/mct269 24284817 PMC3906962 Tsubokura, Watanabe et al., 2013 "Tsubokura Y, Watanabe S, Xia Z, Kanamori H, Yamagata H, Kaga A, Katayose Y, Abe J, Ishimoto M, Harada K. Natural variation in the genes responsible for maturity loci E1, E2, E3 and E4 in soybean. Ann Bot. 2014 Feb;113(3):429-41. doi: 10.1093/aob/mct269. Epub 2013 Nov 26. PMID: 24284817; PMCID: PMC3906962." +10.1105/tpc.114.131607 25549672 PMC4311200 Wang, Wang et al., 2014 "" +10.1073/pnas.1000088107 20421496 PMC2889302 Tian, Wang, et al., 2010 "" +10.1111/tpj.15520 34587329 null Zhuang, Xue et. al., 2021 "" +10.1111/tpj.13181 27062090 null Lu, Li et al., 2016 "Lu X, Li QT, Xiong Q, Li W, Bi YD, Lai YC, Liu XL, Man WQ, Zhang WK, Ma B, Chen SY, Zhang JS. The transcriptomic signature of developing soybean seeds reveals the genetic basis of seed trait adaptation during domestication. Plant J. 2016 Jun;86(6):530-44. doi: 10.1111/tpj.13181. Epub 2016 Jun 20. PMID: 27062090." +10.1186/s12870-018-1551-7 30509166 PMC6276260 Du, Zhao, et al., 2018 "" 10.3389/fpls.2021.629069 33841461 PMC8029582 Yang, Zhang et al., 2021 "Yang X, Zhang Y, Shan J, Sun J, Li D, Zhang X, Li W, Zhao L. GmIDD Is Induced by Short Days in Soybean and May Accelerate Flowering When Overexpressed in Arabidopsis via Inhibiting AGAMOUS-LIKE 18. Front Plant Sci. 2021 Feb 26;12:629069. doi: 10.3389/fpls.2021.629069. PMID: 33841461; PMCID: PMC8029582." -10.1534/g3.114.015255 25452420 PMC4291463 Campbell, Mani et al., 2014 "Campbell BW, Mani D, Curtin SJ, Slattery RA, Michno JM, Ort DR, Schaus PJ, Palmer RG, Orf JH, Stupar RM. Identical substitutions in magnesium chelatase paralogs result in chlorophyll-deficient soybean mutants. G3 (Bethesda). 2014 Dec 1;5(1):123-31. doi: 10.1534/g3.114.015255. PMID: 25452420; PMCID: PMC4291463." -10.1186/1471-2229-14-154 24893844 PMC4074861 Zhou, He et al., 2014 "Zhou L, He H, Liu R, Han Q, Shou H, Liu B. Overexpression of GmAKT2 potassium channel enhances resistance to soybean mosaic virus. BMC Plant Biol. 2014 Jun 3;14:154. doi: 10.1186/1471-2229-14-154. PMID: 24893844; PMCID: PMC4074861." -10.1007/s11103-013-0062-z 23636865 null Zhao, Wang et al., 2013 "Zhao L, Wang Z, Lu Q, Wang P, Li Y, Lv Q, Song X, Li D, Gu Y, Liu L, Li W. Overexpression of a GmGBP1 ortholog of soybean enhances the responses to flowering, stem elongation and heat tolerance in transgenic tobaccos. Plant Mol Biol. 2013 Jun;82(3):279-99. doi: 10.1007/s11103-013-0062-z. Epub 2013 May 1. PMID: 23636865." -10.1093/pcp/pcy215 30418611 null Li, Liu et al., 2019 "Li MW, Liu W, Lam HM, Gendron JM. Characterization of Two Growth Period QTLs Reveals Modification of PRR3 Genes During Soybean Domestication. Plant Cell Physiol. 2019 Feb 1;60(2):407-420. doi: 10.1093/pcp/pcy215. PMID: 30418611." -10.1111/tpj.15414 34245624 null Wang, Li et al., 2021 "Wang X, Li MW, Wong FL, Luk CY, Chung CY, Yung WS, Wang Z, Xie M, Song S, Chung G, Chan TF, Lam HM. Increased copy number of gibberellin 2-oxidase 8 genes reduced trailing growth and shoot length during soybean domestication. Plant J. 2021 Sep;107(6):1739-1755. doi: 10.1111/tpj.15414. Epub 2021 Jul 29. PMID: 34245624." +10.3389/fpls.2022.820348 35498680 PMC9048599 Song, Montes-Luz et al., 2022 "Song JH, Montes-Luz B, Tadra-Sfeir MZ, Cui Y, Su L, Xu D, Stacey G. High-Resolution Translatome Analysis Reveals Cortical Cell Programs During Early Soybean Nodulation. Front Plant Sci. 2022 Apr 14;13:820348. doi: 10.3389/fpls.2022.820348. PMID: 35498680; PMCID: PMC9048599." +10.3390/ijms20194849 31569565 PMC6801534 Noman, Jameel et al., 2019 "" +10.1111/pbi.13536 33368860 PMC8196659 Jin, Sun et al., 2021 "" +10.1371/journal.pone.0097669 24845624 PMC4028237 Nan, Cao, et al., 2014 "" 10.1186/1471-2229-13-21 23388059 PMC3571917 Zhang, Zhao et al., 2013 "Zhang Y, Zhao L, Li H, Gao Y, Li Y, Wu X, Teng W, Han Y, Zhao X, Li W. GmGBP1, a homolog of human ski interacting protein in soybean, regulates flowering and stress tolerance in Arabidopsis. BMC Plant Biol. 2013 Feb 6;13:21. doi: 10.1186/1471-2229-13-21. PMID: 23388059; PMCID: PMC3571917." -10.1111/tpj.14025 30004144 null Zhao, Li et al., 2018 "Zhao L, Li M, Xu C, Yang X, Li D, Zhao X, Wang K, Li Y, Zhang X, Liu L, Ding F, Du H, Wang C, Sun J, Li W. Natural variation in GmGBP1 promoter affects photoperiod control of flowering time and maturity in soybean. Plant J. 2018 Oct;96(1):147-162. doi: 10.1111/tpj.14025. Epub 2018 Aug 16. PMID: 30004144." -10.1111/j.1365-313x.2010.04214.x 20345602 null Yi, Jinxin et al., 2010 "Yi J, Derynck MR, Li X, Telmer P, Marsolais F, Dhaubhadel S. A single-repeat MYB transcription factor, GmMYB176, regulates CHS8 gene expression and affects isoflavonoid biosynthesis in soybean. Plant J. 2010 Jun 1;62(6):1019-34. doi: 10.1111/j.1365-313X.2010.04214.x. Epub 2010 Mar 25. PMID: 20345602." -10.1038/s42003-021-01889-6 33742087 null Vadivel, Anguraj AK, et al., 2021 "Anguraj Vadivel AK, McDowell T, Renaud JB, Dhaubhadel S. A combinatorial action of GmMYB176 and GmbZIP5 controls isoflavonoid biosynthesis in soybean (Glycine max). Commun Biol. 2021 Mar 19;4(1):356. doi: 10.1038/s42003-021-01889-6. PMID: 33742087; PMCID: PMC7979867." +10.1111/nph.14884 29120038 PMC5900889 Liu, Jiang et al., 2008 "" +10.1371/journal.pone.0136601 26371882 PMC4570765 Guo, Xu et al., 2015 "Guo G, Xu K, Zhang X, Zhu J, Lu M, Chen F, Liu L, Xi ZY, Bachmair A, Chen Q, Fu YF. Extensive Analysis of GmFTL and GmCOL Expression in Northern Soybean Cultivars in Field Conditions. PLoS One. 2015 Sep 15;10(9):e0136601. doi: 10.1371/journal.pone.0136601. PMID: 26371882; PMCID: PMC4570765." +10.1093/jxb/erz199 31035293 PMC6685666 Takeshima, Nan, et al., 2019 "Takeshima R, Nan H, Harigai K, Dong L, Zhu J, Lu S, Xu M, Yamagishi N, Yoshikawa N, Liu B, Yamada T, Kong F, Abe J. Functional divergence between soybean FLOWERING LOCUS T orthologues FT2a and FT5a in post-flowering stem growth. J Exp Bot. 2019 Aug 7;70(15):3941-3953. doi: 10.1093/jxb/erz199. PMID: 31035293; PMCID: PMC6685666." +10.1126/science.281.5380.1202 9712587 null Kaiser, Finnegan et al., 1998 "" +10.1093/jxb/erw425 28204559 PMC5441900 Tang, Su et. al., 2017 "" +10.1007/s00122-016-2819-7 27832313 null Samanfar, Molnar et al., 2017 "Samanfar B, Molnar SJ, Charette M, Schoenrock A, Dehne F, Golshani A, Belzile F, Cober ER. Mapping and identification of a potential candidate gene for a novel maturity locus, E10, in soybean. Theor Appl Genet. 2017 Feb;130(2):377-390. doi: 10.1007/s00122-016-2819-7. Epub 2016 Nov 10. PMID: 27832313." +10.1111/tpj.12419 24372721 null Fang, Li et al., 2014 "" +10.1038/ncomms5340 25004933 PMC4104456 Qi, Li et al., 2014 "Qi X, Li MW, Xie M, Liu X, Ni M, Shao G, Song C, Kay-Yuen Yim A, Tao Y, Wong FL, Isobe S, Wong CF, Wong KS, Xu C, Li C, Wang Y, Guan R, Sun F, Fan G, Xiao Z, Zhou F, Phang TH, Liu X, Tong SW, Chan TF, Yiu SM, Tabata S, Wang J, Xu X, Lam HM. Identification of a novel salt tolerance gene in wild soybean by whole-genome sequencing. Nat Commun. 2014 Jul 9;5:4340. doi: 10.1038/ncomms5340. PMID: 25004933; PMCID: PMC4104456." +10.3389/fpls.2022.817544 35371153 PMC8969907 Awal Khan, Mohammad, et al., 2022 "Awal Khan MA, Zhang S, Emon RM, Chen F, Song W, Wu T, Yuan S, Wu C, Hou W, Sun S, Fu Y, Jiang B, Han T. CONSTANS Polymorphism Modulates Flowering Time and Maturity in Soybean. Front Plant Sci. 2022 Mar 17;13:817544. doi: 10.3389/fpls.2022.817544. PMID: 35371153; PMCID: PMC8969907." +10.1016/j.heliyon.2019.e01868 31206092 PMC6558309 Li, Guo et. al., 2019 "" +10.1111/jipb.13207 34962095 null Yang, Lan et al., 2022 "Yang J, Lan L, Jin Y, Yu N, Wang D, Wang E. Mechanisms underlying legume-rhizobium symbioses. J Integr Plant Biol. 2022 Feb;64(2):244-267. doi: 10.1111/jipb.13207. PMID: 34962095." +10.1038/s41477-017-0084-7 29292374 null Zhang, Sun et. al., 2017 "Zhang D, Sun L, Li S, Wang W, Ding Y, Swarm SA, Li L, Wang X, Tang X, Zhang Z, Tian Z, Brown PJ, Cai C, Nelson RL, Ma J. Elevation of soybean seed oil content through selection for seed coat shininess. Nat Plants. 2018 Jan;4(1):30-35. doi: 10.1038/s41477-017-0084-7. Epub 2018 Jan 1. PMID: 29292374." +10.3389/fpls.2019.01221 31787988 PMC6856076 Wu, Kang et al., 2019 "Wu F, Kang X, Wang M, Haider W, Price WB, Hajek B, Hanzawa Y. Transcriptome-Enabled Network Inference Revealed the GmCOL1 Feed-Forward Loop and Its Roles in Photoperiodic Flowering of Soybean. Front Plant Sci. 2019 Nov 8;10:1221. doi: 10.3389/fpls.2019.01221. PMID: 31787988; PMCID: PMC6856076." +10.1371/journal.pone.0222469 31518373 PMC6743760 Sugawara, Umehara et al., 2019 "" +10.1111/pbi.13199 31240772 PMC6920152 Cai, Wang, et al., 2020 "" +10.1111/jipb.13021 33090664 null Lin, Liu et al., 2021 "" +10.1038/s41467-018-05663-x 30087346 PMC6081438 Sugawara, Takahashi et. al., 2018 "" +10.1016/j.plantsci.2019.110386 32005391 null Tian, Liu et al., 2019 "Tian SN, Liu DD, Zhong CL, Xu HY, Yang S, Fang Y, Ran J, Liu JZ. Silencing GmFLS2 enhances the susceptibility of soybean to bacterial pathogen through attenuating the activation of GmMAPK signaling pathway. Plant Sci. 2020 Mar;292:110386. doi: 10.1016/j.plantsci.2019.110386. Epub 2019 Dec 24. PMID: 32005391." +10.1007/s00122-021-03917-9 34319424 null Zhou, Lakhssassi et. al., 2021 "Zhou Z, Lakhssassi N, Knizia D, Cullen MA, El Baz A, Embaby MG, Liu S, Badad O, Vuong TD, AbuGhazaleh A, Nguyen HT, Meksem K. Genome-wide identification and analysis of soybean acyl-ACP thioesterase gene family reveals the role of GmFAT to improve fatty acid composition in soybean seed. Theor Appl Genet. 2021 Nov;134(11):3611-3623. doi: 10.1007/s00122-021-03917-9. Epub 2021 Jul 28. PMID: 34319424." +10.1111/pbi.13668 34265872 PMC8541785 Lu, Wei et al., 2021 "Lu L, Wei W, Tao JJ, Lu X, Bian XH, Hu Y, Cheng T, Yin CC, Zhang WK, Chen SY, Zhang JS. Nuclear factor Y subunit GmNFYA competes with GmHDA13 for interaction with GmFVE to positively regulate salt tolerance in soybean. Plant Biotechnol J. 2021 Nov;19(11):2362-2379. doi: 10.1111/pbi.13668. Epub 2021 Aug 2. PMID: 34265872; PMCID: PMC8541785." +10.1126/science.1077937 12411574 null Searle, Men et al., 2003 "" +10.1007/s00425-005-0201-0 16395584 null Nunes, Vianna et al., 2006 "" +10.3390/genes10120957 31766569 PMC6947551 Yu, Chang et al., 2019 "" +10.1073/pnas.2100136118 33846264 PMC8072331 Pan, Yu et al., 2021 "Pan L, Yu Q, Wang J, Han H, Mao L, Nyporko A, Maguza A, Fan L, Bai L, Powles S. An ABCC-type transporter endowing glyphosate resistance in plants. Proc Natl Acad Sci U S A. 2021 Apr 20;118(16):e2100136118. doi: 10.1073/pnas.2100136118. PMID: 33846264; PMCID: PMC8072331." +10.1111/nph.14632 28598036 null Cai, Wang et al., 2017 "Cai Z, Wang Y, Zhu L, Tian Y, Chen L, Sun Z, Ullah I, Li X. GmTIR1/GmAFB3-based auxin perception regulated by miR393 modulates soybean nodulation. New Phytol. 2017 Jul;215(2):672-686. doi: 10.1111/nph.14632. Epub 2017 Jun 9. PMID: 28598036." +10.1111/tpj.15414 34245624 null Wang, Li et al., 2021 "" +10.1111/jipb.13070 33458938 null Yue, Li et al., 2021 "Yue L, Li X, Fang C, Chen L, Yang H, Yang J, Chen Z, Nan H, Chen L, Zhang Y, Li H, Hou X, Dong Z, Weller JL, Abe J, Liu B, Kong F. FT5a interferes with the Dt1-AP1 feedback loop to control flowering time and shoot determinacy in soybean. J Integr Plant Biol. 2021 Jun;63(6):1004-1020. doi: 10.1111/jipb.13070. Epub 2021 Mar 26. PMID: 33458938." +10.1038/nature08670 20075913 null Schmutz et al., 2010 "" +10.1016/j.molp.2016.12.004 27979775 null Yue, Liu et al., 2017 "Yue Y, Liu N, Jiang B, Li M, Wang H, Jiang Z, Pan H, Xia Q, Ma Q, Han T, Nian H. A Single Nucleotide Deletion in J Encoding GmELF3 Confers Long Juvenility and Is Associated with Adaption of Tropic Soybean. Mol Plant. 2017 Apr 3;10(4):656-658. doi: 10.1016/j.molp.2016.12.004. Epub 2016 Dec 12. PMID: 27979775." +10.1038/s41467-022-34153-4 36307423 PMC9616897 Liang, Chen, et al., 2022 "Liang Q, Chen L, Yang X, Yang H, Liu S, Kou K, Fan L, Zhang Z, Duan Z, Yuan Y, Liang S, Liu Y, Lu X, Zhou G, Zhang M, Kong F, Tian Z. Natural variation of Dt2 determines branching in soybean. Nat Commun. 2022 Oct 28;13(1):6429. doi: 10.1038/s41467-022-34153-4. PMID: 36307423; PMCID: PMC9616897." +10.1007/s00122-004-1887-2 15731930 null Kim, Van et al., 2005 "" +10.1111/j.1467-7652.2012.00729.x 22863334 null Hayashi, Reid et al., 2012 "Hayashi S, Reid DE, Lorenc MT, Stiller J, Edwards D, Gresshoff PM, Ferguson BJ. Transient Nod factor-dependent gene expression in the nodulation-competent zone of soybean (Glycine max [L.] Merr.) roots. Plant Biotechnol J. 2012 Oct;10(8):995-1010. doi: 10.1111/j.1467-7652.2012.00729.x. Epub 2012 Aug 2. PMID: 22863334." +10.1371/journal.pone.0235120 32584851 PMC7316244 Redekar, Glover et al., 2020 "" +10.3390/ijms19082395 30110937 PMC6121457 Su, Han et. al., 2018 "" +10.1534/genetics.110.125062 21406680 PMC3122305 Watanabe, Xia et al., 2011 "Watanabe S, Xia Z, Hideshima R, Tsubokura Y, Sato S, Yamanaka N, Takahashi R, Anai T, Tabata S, Kitamura K, Harada K. A map-based cloning strategy employing a residual heterozygous line reveals that the GIGANTEA gene is involved in soybean maturity and flowering. Genetics. 2011 Jun;188(2):395-407. doi: 10.1534/genetics.110.125062. Epub 2011 Mar 15. PMID: 21406680; PMCID: PMC3122305." +10.1093/jxb/erw394 28338712 null Cao, Takeshima, et al., 2017 "" +10.1038/ng.3819 28319089 null Lu, Zhao et al., 2017 "Lu S, Zhao X, Hu Y, Liu S, Nan H, Li X, Fang C, Cao D, Shi X, Kong L, Su T, Zhang F, Li S, Wang Z, Yuan X, Cober ER, Weller JL, Liu B, Hou X, Tian Z, Kong F. Natural variation at the soybean J locus improves adaptation to the tropics and enhances yield. Nat Genet. 2017 May;49(5):773-779. doi: 10.1038/ng.3819. Epub 2017 Mar 20. PMID: 28319089." +10.1111/nph.16250 31596499 PMC7496907 Miao, Yang et. al., 2020 "" +10.3389/fpls.2022.889066 35574141 PMC9100572 Dietz, Chan et al., 2023 "Dietz N, Chan YO, Scaboo A, Graef G, Hyten D, Happ M, Diers B, Lorenz A, Wang D, Joshi T, Bilyeu K. Candidate Genes Modulating Reproductive Timing in Elite US Soybean Lines Identified in Soybean Alleles of Arabidopsis Flowering Orthologs With Divergent Latitude Distribution. Front Plant Sci. 2022 Apr 29;13:889066. doi: 10.3389/fpls.2022.889066. PMID: 35574141; PMCID: PMC9100572." +10.1186/1471-2229-14-154 24893844 PMC4074861 Zhou, He et al., 2014 "" +10.1111/jipb.12201 24673766 null Hayashi, Gresshoff et al., 2014 "" +10.1038/s41477-020-00832-7 33452487 null Zhang, Wang et. al, 2021 "Zhang B, Wang M, Sun Y, Zhao P, Liu C, Qing K, Hu X, Zhong Z, Cheng J, Wang H, Peng Y, Shi J, Zhuang L, Du S, He M, Wu H, Liu M, Chen S, Wang H, Chen X, Fan W, Tian K, Wang Y, Chen Q, Wang S, Dong F, Yang C, Zhang M, Song Q, Li Y, Wang X. Glycine max NNL1 restricts symbiotic compatibility with widely distributed bradyrhizobia via root hair infection. Nat Plants. 2021 Jan;7(1):73-86. doi: 10.1038/s41477-020-00832-7. Epub 2021 Jan 15. Erratum in: Nat Plants. 2021 Feb;7(2):239. doi: 10.1038/s41477-021-00872-7. PMID: 33452487." +10.1104/pp.15.00763 26134161 PMC4528769 Xu, Yamagishi et al., 2015 "Xu M, Yamagishi N, Zhao C, Takeshima R, Kasai M, Watanabe S, Kanazawa A, Yoshikawa N, Liu B, Yamada T, Abe J. The Soybean-Specific Maturity Gene E1 Family of Floral Repressors Controls Night-Break Responses through Down-Regulation of FLOWERING LOCUS T Orthologs. Plant Physiol. 2015 Aug;168(4):1735-46. doi: 10.1104/pp.15.00763. Epub 2015 Jul 1. PMID: 26134161; PMCID: PMC4528769." +10.1038/s41598-019-44255-7 31123331 PMC6533290 Kumar, Kumar et al., 2019 "" +10.1016/j.csbj.2022.06.014 35782726 PMC9213226 Zuo, Ikram et al., 2022 "Zuo JF, Ikram M, Liu JY, Han CY, Niu Y, Dunwell JM, Zhang YM. Domestication and improvement genes reveal the differences of seed size- and oil-related traits in soybean domestication and improvement. Comput Struct Biotechnol J. 2022 Jun 13;20:2951-2964. doi: 10.1016/j.csbj.2022.06.014. PMID: 35782726; PMCID: PMC9213226." +10.1094/mpmi-09-10-0207 21198362 null Reid, Ferguson et al., 2011 "" +10.1371/journal.pgen.1009114 33175845 PMC7721174 Zhang, Goettel et. al., 2020 "" +10.1126/science.abh2890 34591638 null Wang, Guo et al., 2021 "Wang T, Guo J, Peng Y, Lyu X, Liu B, Sun S, Wang X. Light-induced mobile factors from shoots regulate rhizobium-triggered soybean root nodulation. Science. 2021 Oct;374(6563):65-71. doi: 10.1126/science.abh2890. Epub 2021 Sep 30. Erratum in: Science. 2023 Jul 28;381(6656):eadj7468. doi: 10.1126/science.adj7468. PMID: 34591638." +10.1038/srep28541 27345221 PMC4921965 Chen, Wang et al., 2016 "" +10.1186/1471-2229-14-9 24397545 PMC3890618 Fan, Hu et al., 2014 "Fan C, Hu R, Zhang X, Wang X, Zhang W, Zhang Q, Ma J, Fu YF. Conserved CO-FT regulons contribute to the photoperiod flowering control in soybean. BMC Plant Biol. 2014 Jan 7;14:9. doi: 10.1186/1471-2229-14-9. PMID: 24397545; PMCID: PMC3890618." +10.1007/s11248-019-00180-z 31673914 null Zhang, Luo, et al., 2020 "Zhang L, Luo Y, Liu B, Zhang L, Zhang W, Chen R, Wang L. Overexpression of the maize γ-tocopherol methyltransferase gene (ZmTMT) increases α-tocopherol content in transgenic Arabidopsis and maize seeds. Transgenic Res. 2020 Feb;29(1):95-104. doi: 10.1007/s11248-019-00180-z. Epub 2019 Oct 31. PMID: 31673914." +10.1186/s12870-014-0263-x 25287450 PMC4190295 Hu, Jin et al., 2014 "" +10.1104/pp.110.160796 20864544 PMC2971601 Kong, Liu et al., 2010 "" +10.1111/j.1365-313x.2004.02072.x 15125772 null Noh, Bizzell et al., 2004 "Noh YS, Bizzell CM, Noh B, Schomburg FM, Amasino RM. EARLY FLOWERING 5 acts as a floral repressor in Arabidopsis. Plant J. 2004 May;38(4):664-72. doi: 10.1111/j.1365-313X.2004.02072.x. PMID: 15125772." +10.1038/s42003-021-01889-6 33742087 PMC7979867 Vadivel, Anguraj AK, et al., 2021 "" +10.1016/j.tplants.2022.07.002 35840482 null Hasan, Corpas et al., 2022 "Hasan MM, Corpas FJ, Fang XW. Light: a crucial factor for rhizobium-induced root nodulation. Trends Plant Sci. 2022 Oct;27(10):955-957. doi: 10.1016/j.tplants.2022.07.002. Epub 2022 Jul 12. PMID: 35840482." +10.1016/j.jplph.2019.153019 31437808 null Zhau, Bi et al., 2019 "Zhao J, Bi R, Li S, Zhou D, Bai Y, Jing G, Zhang K, Zhang W. Genome-wide analysis and functional characterization of Acyl-CoA:diacylglycerol acyltransferase from soybean identify GmDGAT1A and 1B roles in oil synthesis in Arabidopsis seeds. J Plant Physiol. 2019 Nov;242:153019. doi: 10.1016/j.jplph.2019.153019. Epub 2019 Aug 11. PMID: 31437808." +10.1016/j.yrtph.2017.01.004 28132846 null Fang, Feng, et al., 2017 "" diff --git a/Glycine/max/gene_functions/glyma.references.txt b/Glycine/max/gene_functions/glyma.references.txt deleted file mode 100644 index 12c46c0..0000000 --- a/Glycine/max/gene_functions/glyma.references.txt +++ /dev/null @@ -1,5821 +0,0 @@ -##### PUB RECORD ##### -## 10.1007/s00122-016-2819-7 27832313 null Samanfar et al., 2017 "Samanfar B, Molnar SJ, Charette M, Schoenrock A, Dehne F, Golshani A, Belzile F, Cober ER. Mapping and identification of a potential candidate gene for a novel maturity locus, E10, in soybean. Theor Appl Genet. 2017 Feb;130(2):377-390. doi: 10.1007/s00122-016-2819-7. Epub 2016 Nov 10. PMID: 27832313." ## - -PMID- 27832313 -OWN - NLM -STAT- MEDLINE -DCOM- 20170209 -LR - 20220310 -IS - 1432-2242 (Electronic) -IS - 0040-5752 (Linking) -VI - 130 -IP - 2 -DP - 2017 Feb -TI - Mapping and identification of a potential candidate gene for a novel maturity - locus, E10, in soybean. -PG - 377-390 -LID - 10.1007/s00122-016-2819-7 [doi] -AB - E10 is a new maturity locus in soybean and FT4 is the predicted/potential - functional gene underlying the locus. Flowering and maturity time traits play - crucial roles in economic soybean production. Early maturity is critical for - north and west expansion of soybean in Canada. To date, 11 genes/loci have been - identified which control time to flowering and maturity; however, the molecular - bases of almost half of them are not yet clear. We have identified a new maturity - locus called "E10" located at the end of chromosome Gm08. The gene symbol E10e10 - has been approved by the Soybean Genetics Committee. The e10e10 genotype results - in 5-10 days earlier maturity than E10E10. A set of presumed E10E10 and e10e10 - genotypes was used to identify contrasting SSR and SNP haplotypes. These - haplotypes, and their association with maturity, were maintained through five - backcross generations. A functional genomics approach using a predicted - protein-protein interaction (PPI) approach (Protein-protein Interaction - Prediction Engine, PIPE) was used to investigate approximately 75 genes located - in the genomic region that SSR and SNP analyses identified as the location of the - E10 locus. The PPI analysis identified FT4 as the most likely candidate gene - underlying the E10 locus. Sequence analysis of the two FT4 alleles identified - three SNPs, in the 5'UTR, 3'UTR and fourth exon in the coding region, which - result in differential mRNA structures. Allele-specific markers were developed - for this locus and are available for soybean breeders to efficiently develop - earlier maturing cultivars using molecular marker assisted breeding. -FAU - Samanfar, Bahram -AU - Samanfar B -AD - Agriculture and Agri-Food Canada, Ottawa Research and Development Centre, Ottawa, - ON, K1A 0C6, Canada. -FAU - Molnar, Stephen J -AU - Molnar SJ -AD - Agriculture and Agri-Food Canada, Ottawa Research and Development Centre, Ottawa, - ON, K1A 0C6, Canada. -FAU - Charette, Martin -AU - Charette M -AD - Agriculture and Agri-Food Canada, Ottawa Research and Development Centre, Ottawa, - ON, K1A 0C6, Canada. -FAU - Schoenrock, Andrew -AU - Schoenrock A -AD - School of Computer Science, Carleton University, Ottawa, ON, K1S 5B6, Canada. -FAU - Dehne, Frank -AU - Dehne F -AD - School of Computer Science, Carleton University, Ottawa, ON, K1S 5B6, Canada. -FAU - Golshani, Ashkan -AU - Golshani A -AD - Department of Biology and Ottawa Institute of Systems Biology, Carleton - University, Ottawa, ON, K1S 5B6, Canada. -FAU - Belzile, Francois -AU - Belzile F -AD - Departement de Phytologie and Institut de Biologie Integrative et des Systemes, - Universite Laval, Quebec City, QC, G1V 0A6, Canada. -FAU - Cober, Elroy R -AU - Cober ER -AUID- ORCID: 0000-0002-4673-1808 -AD - Agriculture and Agri-Food Canada, Ottawa Research and Development Centre, Ottawa, - ON, K1A 0C6, Canada. elroy.cober@agr.gc.ca. -LA - eng -PT - Journal Article -DEP - 20161110 -PL - Germany -TA - Theor Appl Genet -JT - TAG. Theoretical and applied genetics. Theoretische und angewandte Genetik -JID - 0145600 -RN - 0 (DNA, Plant) -RN - 0 (Genetic Markers) -RN - 0 (RNA, Messenger) -SB - IM -MH - *Chromosome Mapping -MH - Computational Biology -MH - DNA, Plant/genetics -MH - *Genetic Loci -MH - Genetic Markers -MH - Genotype -MH - Haplotypes -MH - Microsatellite Repeats -MH - Nucleic Acid Conformation -MH - Plant Breeding -MH - Polymorphism, Single Nucleotide -MH - RNA, Messenger/chemistry -MH - Soybeans/*genetics/physiology -EDAT- 2016/11/11 06:00 -MHDA- 2017/02/10 06:00 -CRDT- 2016/11/11 06:00 -PHST- 2016/07/18 00:00 [received] -PHST- 2016/10/27 00:00 [accepted] -PHST- 2016/11/11 06:00 [pubmed] -PHST- 2017/02/10 06:00 [medline] -PHST- 2016/11/11 06:00 [entrez] -AID - 10.1007/s00122-016-2819-7 [pii] -AID - 10.1007/s00122-016-2819-7 [doi] -PST - ppublish -SO - Theor Appl Genet. 2017 Feb;130(2):377-390. doi: 10.1007/s00122-016-2819-7. Epub - 2016 Nov 10. - - -##### PUB RECORD ##### -## 10.1016/j.molp.2016.12.004 27979775 null Yue et al., 2017 "Yue Y, Liu N, Jiang B, Li M, Wang H, Jiang Z, Pan H, Xia Q, Ma Q, Han T, Nian H. A Single Nucleotide Deletion in J Encoding GmELF3 Confers Long Juvenility and Is Associated with Adaption of Tropic Soybean. Mol Plant. 2017 Apr 3;10(4):656-658. doi: 10.1016/j.molp.2016.12.004. Epub 2016 Dec 12. PMID: 27979775." ## - -PMID- 27979775 -OWN - NLM -STAT- MEDLINE -DCOM- 20181113 -LR - 20181113 -IS - 1752-9867 (Electronic) -IS - 1674-2052 (Linking) -VI - 10 -IP - 4 -DP - 2017 Apr 3 -TI - A Single Nucleotide Deletion in J Encoding GmELF3 Confers Long Juvenility and Is - Associated with Adaption of Tropic Soybean. -PG - 656-658 -LID - S1674-2052(16)30303-3 [pii] -LID - 10.1016/j.molp.2016.12.004 [doi] -FAU - Yue, Yanlei -AU - Yue Y -AD - State Key Laboratory for Conservation and Utilization of Subtropical - Agro-Bioresources, South China Agricultural University, Guangzhou 510642, China; - MOA Key Lab of Soybean Biology (Beijing), Institute of Crop Science, The Chinese - Academy of Agricultural Sciences, Beijing 100081, China; Guangdong Provincial Key - Laboratory of Plant Molecular Breeding, South China Agricultural University, - Guangzhou 510642, China. -FAU - Liu, Nianxi -AU - Liu N -AD - State Key Laboratory for Conservation and Utilization of Subtropical - Agro-Bioresources, South China Agricultural University, Guangzhou 510642, China; - Guangdong Provincial Key Laboratory of Plant Molecular Breeding, South China - Agricultural University, Guangzhou 510642, China. -FAU - Jiang, Bingjun -AU - Jiang B -AD - MOA Key Lab of Soybean Biology (Beijing), Institute of Crop Science, The Chinese - Academy of Agricultural Sciences, Beijing 100081, China. -FAU - Li, Mu -AU - Li M -AD - State Key Laboratory for Conservation and Utilization of Subtropical - Agro-Bioresources, South China Agricultural University, Guangzhou 510642, China; - Guangdong Provincial Key Laboratory of Plant Molecular Breeding, South China - Agricultural University, Guangzhou 510642, China. -FAU - Wang, Haijie -AU - Wang H -AD - State Key Laboratory for Conservation and Utilization of Subtropical - Agro-Bioresources, South China Agricultural University, Guangzhou 510642, China; - Institute of Crop Sciences, Hainan Academy of Agricultural Sciences, Haikou - 571100, China. -FAU - Jiang, Ze -AU - Jiang Z -AD - State Key Laboratory for Conservation and Utilization of Subtropical - Agro-Bioresources, South China Agricultural University, Guangzhou 510642, China; - Guangdong Provincial Key Laboratory of Plant Molecular Breeding, South China - Agricultural University, Guangzhou 510642, China. -FAU - Pan, Huanting -AU - Pan H -AD - State Key Laboratory for Conservation and Utilization of Subtropical - Agro-Bioresources, South China Agricultural University, Guangzhou 510642, China; - Guangdong Provincial Key Laboratory of Plant Molecular Breeding, South China - Agricultural University, Guangzhou 510642, China. -FAU - Xia, Qiuju -AU - Xia Q -AD - BGI-Shenzhen, Shenzhen 518083, China. -FAU - Ma, Qibin -AU - Ma Q -AD - State Key Laboratory for Conservation and Utilization of Subtropical - Agro-Bioresources, South China Agricultural University, Guangzhou 510642, China; - Guangdong Provincial Key Laboratory of Plant Molecular Breeding, South China - Agricultural University, Guangzhou 510642, China. -FAU - Han, Tianfu -AU - Han T -AD - MOA Key Lab of Soybean Biology (Beijing), Institute of Crop Science, The Chinese - Academy of Agricultural Sciences, Beijing 100081, China. Electronic address: - hantianfu@caas.cn. -FAU - Nian, Hai -AU - Nian H -AD - State Key Laboratory for Conservation and Utilization of Subtropical - Agro-Bioresources, South China Agricultural University, Guangzhou 510642, China; - Guangdong Provincial Key Laboratory of Plant Molecular Breeding, South China - Agricultural University, Guangzhou 510642, China. Electronic address: - hnian@scau.edu.cn. -LA - eng -PT - Letter -PT - Research Support, Non-U.S. Gov't -DEP - 20161212 -PL - England -TA - Mol Plant -JT - Molecular plant -JID - 101465514 -RN - 0 (Nucleotides) -RN - 0 (Plant Proteins) -SB - IM -MH - Adaptation, Physiological/*genetics -MH - Alleles -MH - Nucleotides/*genetics -MH - Plant Proteins/*genetics -MH - Polymorphism, Single Nucleotide/*genetics -MH - *Quantitative Trait, Heritable -MH - Sequence Deletion/*genetics -MH - Soybeans/*genetics/*physiology -EDAT- 2016/12/17 06:00 -MHDA- 2018/11/14 06:00 -CRDT- 2016/12/17 06:00 -PHST- 2016/09/02 00:00 [received] -PHST- 2016/11/10 00:00 [revised] -PHST- 2016/12/06 00:00 [accepted] -PHST- 2016/12/17 06:00 [pubmed] -PHST- 2018/11/14 06:00 [medline] -PHST- 2016/12/17 06:00 [entrez] -AID - S1674-2052(16)30303-3 [pii] -AID - 10.1016/j.molp.2016.12.004 [doi] -PST - ppublish -SO - Mol Plant. 2017 Apr 3;10(4):656-658. doi: 10.1016/j.molp.2016.12.004. Epub 2016 - Dec 12. - - -##### PUB RECORD ##### -## 10.1038/ng.3819 28319089 null Lu, Zhao et al., 2017 "Lu S, Zhao X, Hu Y, Liu S, Nan H, Li X, Fang C, Cao D, Shi X, Kong L, Su T, Zhang F, Li S, Wang Z, Yuan X, Cober ER, Weller JL, Liu B, Hou X, Tian Z, Kong F. Natural variation at the soybean J locus improves adaptation to the tropics and enhances yield. Nat Genet. 2017 May;49(5):773-779. doi: 10.1038/ng.3819. Epub 2017 Mar 20. PMID: 28319089." ## - -PMID- 28319089 -OWN - NLM -STAT- MEDLINE -DCOM- 20170918 -LR - 20220330 -IS - 1546-1718 (Electronic) -IS - 1061-4036 (Linking) -VI - 49 -IP - 5 -DP - 2017 May -TI - Natural variation at the soybean J locus improves adaptation to the tropics and - enhances yield. -PG - 773-779 -LID - 10.1038/ng.3819 [doi] -AB - Soybean is a major legume crop originating in temperate regions, and photoperiod - responsiveness is a key factor in its latitudinal adaptation. Varieties from - temperate regions introduced to lower latitudes mature early and have extremely - low grain yields. Introduction of the long-juvenile (LJ) trait extends the - vegetative phase and improves yield under short-day conditions, thereby enabling - expansion of cultivation in tropical regions. Here we report the cloning and - characterization of J, the major classical locus conferring the LJ trait, and - identify J as the ortholog of Arabidopsis thaliana EARLY FLOWERING 3 (ELF3). J - depends genetically on the legume-specific flowering repressor E1, and J protein - physically associates with the E1 promoter to downregulate its transcription, - relieving repression of two important FLOWERING LOCUS T (FT) genes and promoting - flowering under short days. Our findings identify an important new component in - flowering-time control in soybean and provide new insight into soybean adaptation - to tropical regions. -FAU - Lu, Sijia -AU - Lu S -AD - Key Laboratory of Soybean Molecular Design Breeding, Northeast Institute of - Geography and Agroecology, Chinese Academy of Sciences, Harbin, China. -AD - School of Life Sciences, Guangzhou University, Guangzhou, China. -FAU - Zhao, Xiaohui -AU - Zhao X -AD - Key Laboratory of Soybean Molecular Design Breeding, Northeast Institute of - Geography and Agroecology, Chinese Academy of Sciences, Harbin, China. -AD - School of Life Sciences, Guangzhou University, Guangzhou, China. -FAU - Hu, Yilong -AU - Hu Y -AD - Key Laboratory of South China Agricultural Plant Molecular Analysis and Genetic - Improvement, and Guangdong Provincial Key Laboratory of Applied Botany, South - China Botanical Garden, Chinese Academy of Sciences, Guangzhou, China. -AD - University of the Chinese Academy of Sciences, Beijing, China. -FAU - Liu, Shulin -AU - Liu S -AD - University of the Chinese Academy of Sciences, Beijing, China. -AD - State Key Laboratory of Plant Cell and Chromosome Engineering, Institute of - Genetics and Developmental Biology, Chinese Academy of Sciences, Beijing, China. -FAU - Nan, Haiyang -AU - Nan H -AD - Key Laboratory of Soybean Molecular Design Breeding, Northeast Institute of - Geography and Agroecology, Chinese Academy of Sciences, Harbin, China. -FAU - Li, Xiaoming -AU - Li X -AD - Key Laboratory of Soybean Molecular Design Breeding, Northeast Institute of - Geography and Agroecology, Chinese Academy of Sciences, Harbin, China. -AD - University of the Chinese Academy of Sciences, Beijing, China. -FAU - Fang, Chao -AU - Fang C -AD - Key Laboratory of Soybean Molecular Design Breeding, Northeast Institute of - Geography and Agroecology, Chinese Academy of Sciences, Harbin, China. -AD - University of the Chinese Academy of Sciences, Beijing, China. -FAU - Cao, Dong -AU - Cao D -AD - Key Laboratory of Soybean Molecular Design Breeding, Northeast Institute of - Geography and Agroecology, Chinese Academy of Sciences, Harbin, China. -AD - School of Life Sciences, Guangzhou University, Guangzhou, China. -FAU - Shi, Xinyi -AU - Shi X -AD - Key Laboratory of Soybean Molecular Design Breeding, Northeast Institute of - Geography and Agroecology, Chinese Academy of Sciences, Harbin, China. -FAU - Kong, Lingping -AU - Kong L -AD - Key Laboratory of Soybean Molecular Design Breeding, Northeast Institute of - Geography and Agroecology, Chinese Academy of Sciences, Harbin, China. -AD - University of the Chinese Academy of Sciences, Beijing, China. -FAU - Su, Tong -AU - Su T -AD - Key Laboratory of Soybean Molecular Design Breeding, Northeast Institute of - Geography and Agroecology, Chinese Academy of Sciences, Harbin, China. -AD - University of the Chinese Academy of Sciences, Beijing, China. -FAU - Zhang, Fengge -AU - Zhang F -AD - Key Laboratory of Soybean Molecular Design Breeding, Northeast Institute of - Geography and Agroecology, Chinese Academy of Sciences, Harbin, China. -AD - University of the Chinese Academy of Sciences, Beijing, China. -FAU - Li, Shichen -AU - Li S -AD - Key Laboratory of Soybean Molecular Design Breeding, Northeast Institute of - Geography and Agroecology, Chinese Academy of Sciences, Harbin, China. -AD - University of the Chinese Academy of Sciences, Beijing, China. -FAU - Wang, Zheng -AU - Wang Z -AD - State Key Laboratory of Plant Cell and Chromosome Engineering, Institute of - Genetics and Developmental Biology, Chinese Academy of Sciences, Beijing, China. -FAU - Yuan, Xiaohui -AU - Yuan X -AD - Key Laboratory of Soybean Molecular Design Breeding, Northeast Institute of - Geography and Agroecology, Chinese Academy of Sciences, Harbin, China. -FAU - Cober, Elroy R -AU - Cober ER -AUID- ORCID: 0000-0002-4673-1808 -AD - Eastern Cereal and Oilseed Research Centre, Agriculture and Agri-Food Canada, - Central Experimental Farm, Ottawa, Ontario, Canada. -FAU - Weller, James L -AU - Weller JL -AD - School of Plant Science, University of Tasmania, Hobart, Tasmania, Australia. -FAU - Liu, Baohui -AU - Liu B -AD - Key Laboratory of Soybean Molecular Design Breeding, Northeast Institute of - Geography and Agroecology, Chinese Academy of Sciences, Harbin, China. -AD - School of Life Sciences, Guangzhou University, Guangzhou, China. -FAU - Hou, Xingliang -AU - Hou X -AD - Key Laboratory of South China Agricultural Plant Molecular Analysis and Genetic - Improvement, and Guangdong Provincial Key Laboratory of Applied Botany, South - China Botanical Garden, Chinese Academy of Sciences, Guangzhou, China. -FAU - Tian, Zhixi -AU - Tian Z -AUID- ORCID: 0000-0001-6051-9670 -AD - State Key Laboratory of Plant Cell and Chromosome Engineering, Institute of - Genetics and Developmental Biology, Chinese Academy of Sciences, Beijing, China. -FAU - Kong, Fanjiang -AU - Kong F -AD - Key Laboratory of Soybean Molecular Design Breeding, Northeast Institute of - Geography and Agroecology, Chinese Academy of Sciences, Harbin, China. -AD - School of Life Sciences, Guangzhou University, Guangzhou, China. -LA - eng -PT - Journal Article -DEP - 20170320 -PL - United States -TA - Nat Genet -JT - Nature genetics -JID - 9216904 -RN - 0 (Plant Proteins) -SB - IM -MH - Adaptation, Physiological/*genetics -MH - Amino Acid Sequence -MH - Base Sequence -MH - *Biomass -MH - China -MH - Flowers/genetics/growth & development -MH - Gene Expression Regulation, Developmental -MH - Gene Expression Regulation, Plant -MH - Gene Regulatory Networks -MH - Genetic Loci/*genetics -MH - *Genetic Variation -MH - Geography -MH - Mutation -MH - Plant Proteins/genetics/metabolism -MH - Promoter Regions, Genetic/genetics -MH - Sequence Homology, Amino Acid -MH - Sequence Homology, Nucleic Acid -MH - Soybeans/classification/*genetics/growth & development -MH - Species Specificity -MH - *Tropical Climate -EDAT- 2017/03/21 06:00 -MHDA- 2017/09/19 06:00 -CRDT- 2017/03/21 06:00 -PHST- 2016/10/10 00:00 [received] -PHST- 2017/02/24 00:00 [accepted] -PHST- 2017/03/21 06:00 [pubmed] -PHST- 2017/09/19 06:00 [medline] -PHST- 2017/03/21 06:00 [entrez] -AID - ng.3819 [pii] -AID - 10.1038/ng.3819 [doi] -PST - ppublish -SO - Nat Genet. 2017 May;49(5):773-779. doi: 10.1038/ng.3819. Epub 2017 Mar 20. - - -##### PUB RECORD ##### -## 10.1038/s41588-020-0604-7 32231277 null Lu, Dong et al., 2020 "Lu S, Dong L, Fang C, Liu S, Kong L, Cheng Q, Chen L, Su T, Nan H, Zhang D, Zhang L, Wang Z, Yang Y, Yu D, Liu X, Yang Q, Lin X, Tang Y, Zhao X, Yang X, Tian C, Xie Q, Li X, Yuan X, Tian Z, Liu B, Weller JL, Kong F. Stepwise selection on homeologous PRR genes controlling flowering and maturity during soybean domestication. Nat Genet. 2020 Apr;52(4):428-436. doi: 10.1038/s41588-020-0604-7. Epub 2020 Mar 30. PMID: 32231277." ## - -PMID- 32231277 -OWN - NLM -STAT- MEDLINE -DCOM- 20200626 -LR - 20220607 -IS - 1546-1718 (Electronic) -IS - 1061-4036 (Linking) -VI - 52 -IP - 4 -DP - 2020 Apr -TI - Stepwise selection on homeologous PRR genes controlling flowering and maturity - during soybean domestication. -PG - 428-436 -LID - 10.1038/s41588-020-0604-7 [doi] -AB - Adaptive changes in plant phenology are often considered to be a feature of the - so-called 'domestication syndrome' that distinguishes modern crops from their - wild progenitors, but little detailed evidence supports this idea. In soybean, a - major legume crop, flowering time variation is well characterized within - domesticated germplasm and is critical for modern production, but its importance - during domestication is unclear. Here, we identify sequential contributions of - two homeologous pseudo-response-regulator genes, Tof12 and Tof11, to ancient - flowering time adaptation, and demonstrate that they act via LHY homologs to - promote expression of the legume-specific E1 gene and delay flowering under long - photoperiods. We show that Tof12-dependent acceleration of maturity accompanied a - reduction in dormancy and seed dispersal during soybean domestication, possibly - predisposing the incipient crop to latitudinal expansion. Better understanding of - this early phase of crop evolution will help to identify functional variation - lost during domestication and exploit its potential for future crop improvement. -FAU - Lu, Sijia -AU - Lu S -AUID- ORCID: 0000-0002-3110-0915 -AD - Innovative Center of Molecular Genetics and Evolution, School of Life Sciences, - Guangzhou University, Guangzhou, China. -AD - The Innovative Academy of Seed Design, Key Laboratory of Soybean Molecular Design - Breeding, Northeast Institute of Geography and Agroecology, Chinese Academy of - Sciences, Harbin, China. -FAU - Dong, Lidong -AU - Dong L -AUID- ORCID: 0000-0002-8085-1678 -AD - Innovative Center of Molecular Genetics and Evolution, School of Life Sciences, - Guangzhou University, Guangzhou, China. -FAU - Fang, Chao -AU - Fang C -AUID- ORCID: 0000-0003-0564-7586 -AD - Innovative Center of Molecular Genetics and Evolution, School of Life Sciences, - Guangzhou University, Guangzhou, China. -FAU - Liu, Shulin -AU - Liu S -AUID- ORCID: 0000-0002-0154-2966 -AD - State Key Laboratory of Plant Cell and Chromosome Engineering, Institute of - Genetics and Developmental Biology, Innovative Academy of Seed Design, Chinese - Academy of Sciences, Beijing, China. -AD - University of Chinese Academy of Sciences, Beijing, China. -FAU - Kong, Lingping -AU - Kong L -AUID- ORCID: 0000-0002-2671-7443 -AD - Innovative Center of Molecular Genetics and Evolution, School of Life Sciences, - Guangzhou University, Guangzhou, China. -FAU - Cheng, Qun -AU - Cheng Q -AUID- ORCID: 0000-0001-5595-2058 -AD - Innovative Center of Molecular Genetics and Evolution, School of Life Sciences, - Guangzhou University, Guangzhou, China. -FAU - Chen, Liyu -AU - Chen L -AD - Innovative Center of Molecular Genetics and Evolution, School of Life Sciences, - Guangzhou University, Guangzhou, China. -FAU - Su, Tong -AU - Su T -AD - The Innovative Academy of Seed Design, Key Laboratory of Soybean Molecular Design - Breeding, Northeast Institute of Geography and Agroecology, Chinese Academy of - Sciences, Harbin, China. -AD - University of Chinese Academy of Sciences, Beijing, China. -FAU - Nan, Haiyang -AU - Nan H -AD - Innovative Center of Molecular Genetics and Evolution, School of Life Sciences, - Guangzhou University, Guangzhou, China. -FAU - Zhang, Dan -AU - Zhang D -AD - Collaborative Innovation Center of Henan Grain Crops, Henan Agricultural - University, Zhengzhou, China. -FAU - Zhang, Lei -AU - Zhang L -AD - Anhui Academy of Agricultural Sciences, Hefei, China. -FAU - Wang, Zhijuan -AU - Wang Z -AD - State Key Laboratory of Agricultural Microbiology, College of Plant Science and - Technology, Huazhong Agricultural University, Wuhan, China. -FAU - Yang, Yongqing -AU - Yang Y -AD - Root Biology Center, College of Resources and Environment, Fujian Agriculture and - Forestry University, Fuzhou, China. -FAU - Yu, Deyue -AU - Yu D -AD - National Center for Soybean Improvement, National Key Laboratory of Crop Genetics - and Germplasm Enhancement, Nanjing Agricultural University, Nanjing, China. -FAU - Liu, Xiaolei -AU - Liu X -AD - Key Laboratory of Agricultural Animal Genetics, Breeding and Reproduction, - Ministry of Education & College of Animal Science and Technology, Huazhong - Agricultural University, Wuhan, China. -FAU - Yang, Qingyong -AU - Yang Q -AUID- ORCID: 0000-0002-3510-8906 -AD - Hubei Key Laboratory of Agricultural Bioinformatics, College of Informatics, - Huazhong Agricultural University, Wuhan, China. -FAU - Lin, Xiaoya -AU - Lin X -AD - Innovative Center of Molecular Genetics and Evolution, School of Life Sciences, - Guangzhou University, Guangzhou, China. -FAU - Tang, Yang -AU - Tang Y -AD - Innovative Center of Molecular Genetics and Evolution, School of Life Sciences, - Guangzhou University, Guangzhou, China. -FAU - Zhao, Xiaohui -AU - Zhao X -AD - Innovative Center of Molecular Genetics and Evolution, School of Life Sciences, - Guangzhou University, Guangzhou, China. -FAU - Yang, Xinquan -AU - Yang X -AD - Innovative Center of Molecular Genetics and Evolution, School of Life Sciences, - Guangzhou University, Guangzhou, China. -FAU - Tian, Changen -AU - Tian C -AUID- ORCID: 0000-0002-8410-6624 -AD - Innovative Center of Molecular Genetics and Evolution, School of Life Sciences, - Guangzhou University, Guangzhou, China. -FAU - Xie, Qiguang -AU - Xie Q -AD - Key Laboratory of Plant Stress Biology, School of Life Sciences, Henan - University, Kaifeng, China. -FAU - Li, Xia -AU - Li X -AD - State Key Laboratory of Agricultural Microbiology, College of Plant Science and - Technology, Huazhong Agricultural University, Wuhan, China. -FAU - Yuan, Xiaohui -AU - Yuan X -AUID- ORCID: 0000-0003-0661-5332 -AD - School of Computer Science and Technology, Wuhan University of Technology, Wuhan, - China. yuanxiaohui@whut.edu.cn. -FAU - Tian, Zhixi -AU - Tian Z -AUID- ORCID: 0000-0001-6051-9670 -AD - State Key Laboratory of Plant Cell and Chromosome Engineering, Institute of - Genetics and Developmental Biology, Innovative Academy of Seed Design, Chinese - Academy of Sciences, Beijing, China. zxtian@genetics.ac.cn. -AD - University of Chinese Academy of Sciences, Beijing, China. zxtian@genetics.ac.cn. -FAU - Liu, Baohui -AU - Liu B -AUID- ORCID: 0000-0003-3491-8293 -AD - Innovative Center of Molecular Genetics and Evolution, School of Life Sciences, - Guangzhou University, Guangzhou, China. liubh@iga.ac.cn. -AD - The Innovative Academy of Seed Design, Key Laboratory of Soybean Molecular Design - Breeding, Northeast Institute of Geography and Agroecology, Chinese Academy of - Sciences, Harbin, China. liubh@iga.ac.cn. -FAU - Weller, James L -AU - Weller JL -AUID- ORCID: 0000-0003-2423-8286 -AD - School of Natural Sciences, University of Tasmania, Hobart, Tasmania, Australia. - jim.weller@utas.edu.au. -FAU - Kong, Fanjiang -AU - Kong F -AUID- ORCID: 0000-0001-7138-1478 -AD - Innovative Center of Molecular Genetics and Evolution, School of Life Sciences, - Guangzhou University, Guangzhou, China. kongfj@gzhu.edu.cn. -AD - The Innovative Academy of Seed Design, Key Laboratory of Soybean Molecular Design - Breeding, Northeast Institute of Geography and Agroecology, Chinese Academy of - Sciences, Harbin, China. kongfj@gzhu.edu.cn. -AD - University of Chinese Academy of Sciences, Beijing, China. kongfj@gzhu.edu.cn. -LA - eng -PT - Journal Article -PT - Research Support, Non-U.S. Gov't -DEP - 20200330 -PL - United States -TA - Nat Genet -JT - Nature genetics -JID - 9216904 -SB - IM -MH - Crops, Agricultural/*genetics -MH - Domestication -MH - Fabaceae/genetics -MH - Flowers/*genetics -MH - Genes, Plant/*genetics -MH - Photoperiod -MH - Seeds/genetics -MH - Soybeans/*genetics -EDAT- 2020/04/02 06:00 -MHDA- 2020/06/27 06:00 -CRDT- 2020/04/02 06:00 -PHST- 2019/10/09 00:00 [received] -PHST- 2020/02/27 00:00 [accepted] -PHST- 2020/04/02 06:00 [pubmed] -PHST- 2020/06/27 06:00 [medline] -PHST- 2020/04/02 06:00 [entrez] -AID - 10.1038/s41588-020-0604-7 [pii] -AID - 10.1038/s41588-020-0604-7 [doi] -PST - ppublish -SO - Nat Genet. 2020 Apr;52(4):428-436. doi: 10.1038/s41588-020-0604-7. Epub 2020 Mar - 30. - - -##### PUB RECORD ##### -## 10.1093/aob/mct269 24284817 PMC3906962 Tsubokura, Watanabe et al., 2013 "Tsubokura Y, Watanabe S, Xia Z, Kanamori H, Yamagata H, Kaga A, Katayose Y, Abe J, Ishimoto M, Harada K. Natural variation in the genes responsible for maturity loci E1, E2, E3 and E4 in soybean. Ann Bot. 2014 Feb;113(3):429-41. doi: 10.1093/aob/mct269. Epub 2013 Nov 26. PMID: 24284817; PMCID: PMC3906962." ## - -PMID- 24284817 -OWN - NLM -STAT- MEDLINE -DCOM- 20140929 -LR - 20220309 -IS - 1095-8290 (Electronic) -IS - 0305-7364 (Print) -IS - 0305-7364 (Linking) -VI - 113 -IP - 3 -DP - 2014 Feb -TI - Natural variation in the genes responsible for maturity loci E1, E2, E3 and E4 in - soybean. -PG - 429-41 -LID - 10.1093/aob/mct269 [doi] -AB - BACKGROUND AND AIMS: The timing of flowering has a direct impact on successful - seed production in plants. Flowering of soybean (Glycine max) is controlled by - several E loci, and previous studies identified the genes responsible for the - flowering loci E1, E2, E3 and E4. However, natural variation in these genes has - not been fully elucidated. The aims of this study were the identification of new - alleles, establishment of allele diagnoses, examination of allelic combinations - for adaptability, and analysis of the integrated effect of these loci on - flowering. METHODS: The sequences of these genes and their flanking regions were - determined for 39 accessions by primer walking. Systematic discrimination among - alleles was performed using DNA markers. Genotypes at the E1-E4 loci were - determined for 63 accessions covering several ecological types using DNA markers - and sequencing, and flowering times of these accessions at three sowing times - were recorded. KEY RESULTS: A new allele with an insertion of a long interspersed - nuclear element (LINE) at the promoter of the E1 locus (e1-re) was identified. - Insertion and deletion of 36 bases in the eighth intron (E2-in and E2-dl) were - observed at the E2 locus. Systematic discrimination among the alleles at the - E1-E3 loci was achieved using PCR-based markers. Allelic combinations at the - E1-E4 loci were found to be associated with ecological types, and about 62-66 % - of variation of flowering time could be attributed to these loci. CONCLUSIONS: - The study advances understanding of the combined roles of the E1-E4 loci in - flowering and geographic adaptation, and suggests the existence of unidentified - genes for flowering in soybean. -FAU - Tsubokura, Yasutaka -AU - Tsubokura Y -AD - National Institute of Agrobiological Sciences, Tsukuba, Ibaraki 306-8602, Japan. -FAU - Watanabe, Satoshi -AU - Watanabe S -FAU - Xia, Zhengjun -AU - Xia Z -FAU - Kanamori, Hiroyuki -AU - Kanamori H -FAU - Yamagata, Harumi -AU - Yamagata H -FAU - Kaga, Akito -AU - Kaga A -FAU - Katayose, Yuichi -AU - Katayose Y -FAU - Abe, Jun -AU - Abe J -FAU - Ishimoto, Masao -AU - Ishimoto M -FAU - Harada, Kyuya -AU - Harada K -LA - eng -SI - GENBANK/AB795360 -SI - GENBANK/AB795361 -SI - GENBANK/AB795362 -SI - GENBANK/AB795363 -SI - GENBANK/AB795364 -SI - GENBANK/AB795365 -SI - GENBANK/AB795366 -SI - GENBANK/AB795367 -SI - GENBANK/AB795368 -SI - GENBANK/AB795369 -SI - GENBANK/AB795370 -SI - GENBANK/AB795371 -SI - GENBANK/AB795372 -SI - GENBANK/AB795373 -SI - GENBANK/AB795374 -SI - GENBANK/AB795375 -SI - GENBANK/AB795376 -SI - GENBANK/AB795377 -SI - GENBANK/AB795378 -SI - GENBANK/AB795379 -SI - GENBANK/AB795380 -SI - GENBANK/AB795381 -SI - GENBANK/AB795382 -SI - GENBANK/AB795383 -SI - GENBANK/AB795384 -SI - GENBANK/AB795385 -SI - GENBANK/AB795386 -SI - GENBANK/AB795387 -SI - GENBANK/AB795388 -SI - GENBANK/AB795389 -SI - GENBANK/AB795390 -SI - GENBANK/AB795391 -SI - GENBANK/AB795392 -SI - GENBANK/AB797147 -SI - GENBANK/AB797148 -SI - GENBANK/AB797149 -SI - GENBANK/AB797150 -SI - GENBANK/AB797151 -SI - GENBANK/AB797152 -SI - GENBANK/AB797153 -SI - GENBANK/AB797154 -SI - GENBANK/AB797155 -SI - GENBANK/AB797156 -SI - GENBANK/AB797157 -SI - GENBANK/AB797158 -SI - GENBANK/AB797159 -SI - GENBANK/AB797160 -SI - GENBANK/AB797161 -SI - GENBANK/AB797162 -SI - GENBANK/AB797163 -SI - GENBANK/AB797164 -SI - GENBANK/AB797165 -SI - GENBANK/AB797166 -SI - GENBANK/AB797167 -SI - GENBANK/AB797168 -SI - GENBANK/AB797169 -SI - GENBANK/AB797170 -SI - GENBANK/AB797171 -SI - GENBANK/AB797172 -SI - GENBANK/AB797173 -SI - GENBANK/AB797174 -SI - GENBANK/AB797175 -SI - GENBANK/AB797176 -SI - GENBANK/AB797177 -SI - GENBANK/AB797178 -SI - GENBANK/AB797179 -SI - GENBANK/AB797180 -SI - GENBANK/AB797181 -SI - GENBANK/AB797182 -SI - GENBANK/AB797183 -SI - GENBANK/AB797184 -SI - GENBANK/AB797185 -SI - GENBANK/AB797186 -SI - GENBANK/AB797187 -SI - GENBANK/AB797188 -SI - GENBANK/AB797189 -SI - GENBANK/AB797190 -SI - GENBANK/AB797191 -SI - GENBANK/AB797192 -SI - GENBANK/AB797193 -SI - GENBANK/AB797194 -SI - GENBANK/AB797195 -SI - GENBANK/AB797196 -SI - GENBANK/AB797197 -SI - GENBANK/AB797198 -SI - GENBANK/AB797199 -SI - GENBANK/AB797200 -SI - GENBANK/AB797201 -SI - GENBANK/AB797202 -SI - GENBANK/AB797203 -SI - GENBANK/AB797204 -SI - GENBANK/AB797205 -SI - GENBANK/AB797206 -SI - GENBANK/AB797207 -SI - GENBANK/AB797208 -SI - GENBANK/AB797209 -SI - GENBANK/AB797210 -PT - Journal Article -PT - Research Support, Non-U.S. Gov't -DEP - 20131126 -PL - England -TA - Ann Bot -JT - Annals of botany -JID - 0372347 -RN - 0 (Genetic Markers) -RN - 0 (Plant Proteins) -SB - IM -MH - Adaptation, Physiological -MH - Alleles -MH - Base Sequence -MH - Chromosome Mapping -MH - Flowers/genetics/physiology -MH - *Gene Expression Regulation, Plant -MH - Genetic Loci/genetics -MH - Genetic Markers/genetics -MH - *Genetic Variation -MH - Genotype -MH - Haplotypes -MH - Molecular Sequence Data -MH - Photoperiod -MH - Plant Proteins/*genetics/metabolism -MH - Polymorphism, Single Nucleotide -MH - Quantitative Trait Loci/*genetics -MH - Seeds/genetics/physiology -MH - Sequence Alignment -MH - Sequence Analysis, DNA -MH - Soybeans/*genetics/physiology -MH - Time Factors -PMC - PMC3906962 -OTO - NOTNLM -OT - E locus -OT - Glycine max -OT - SNP -OT - ecological type -OT - flowering time -OT - haplotype -OT - marker-assisted selection -OT - single nucleotide polymorphism -OT - soybean -EDAT- 2013/11/29 06:00 -MHDA- 2014/09/30 06:00 -CRDT- 2013/11/29 06:00 -PHST- 2013/11/29 06:00 [entrez] -PHST- 2013/11/29 06:00 [pubmed] -PHST- 2014/09/30 06:00 [medline] -AID - mct269 [pii] -AID - 10.1093/aob/mct269 [doi] -PST - ppublish -SO - Ann Bot. 2014 Feb;113(3):429-41. doi: 10.1093/aob/mct269. Epub 2013 Nov 26. - - -##### PUB RECORD ##### -## 10.1093/jxb/erw283 27422993 PMC5014162 Takeshima, Hayashi et al., 2016 "Takeshima R, Hayashi T, Zhu J, Zhao C, Xu M, Yamaguchi N, Sayama T, Ishimoto M, Kong L, Shi X, Liu B, Tian Z, Yamada T, Kong F, Abe J. A soybean quantitative trait locus that promotes flowering under long days is identified as FT5a, a FLOWERING LOCUS T ortholog. J Exp Bot. 2016 Sep;67(17):5247-58. doi: 10.1093/jxb/erw283. Epub 2016 Jul 15. PMID: 27422993; PMCID: PMC5014162." ## - -PMID- 27422993 -OWN - NLM -STAT- MEDLINE -DCOM- 20171107 -LR - 20181113 -IS - 1460-2431 (Electronic) -IS - 0022-0957 (Print) -IS - 0022-0957 (Linking) -VI - 67 -IP - 17 -DP - 2016 Sep -TI - A soybean quantitative trait locus that promotes flowering under long days is - identified as FT5a, a FLOWERING LOCUS T ortholog. -PG - 5247-58 -LID - 10.1093/jxb/erw283 [doi] -AB - FLOWERING LOCUS T (FT) is an important floral integrator whose functions are - conserved across plant species. In soybean, two orthologs, FT2a and FT5a, play a - major role in initiating flowering. Their expression in response to different - photoperiods is controlled by allelic combinations at the maturity loci E1 to E4, - generating variation in flowering time among cultivars. We determined the - molecular basis of a quantitative trait locus (QTL) for flowering time in linkage - group J (Chromosome 16). Fine-mapping delimited the QTL to a genomic region of - 107kb that harbors FT5a We detected 15 DNA polymorphisms between parents with the - early-flowering (ef) and late-flowering (lf) alleles in the promoter region, an - intron, and the 3' untranslated region of FT5a, although the FT5a coding regions - were identical. Transcript abundance of FT5a was higher in near-isogenic lines - for ef than in those for lf, suggesting that different transcriptional activities - or mRNA stability caused the flowering time difference. Single-nucleotide - polymorphism (SNP) calling from re-sequencing data for 439 cultivated and wild - soybean accessions indicated that ef is a rare haplotype that is distinct from - common haplotypes including lf The ef allele at FT5a may play an adaptive role at - latitudes where early flowering is desirable. -CI - (c) The Author 2016. Published by Oxford University Press on behalf of the Society - for Experimental Biology. -FAU - Takeshima, Ryoma -AU - Takeshima R -AD - Research Faculty of Agriculture, Hokkaido University, Sapporo, Hokkaido 060-8589, - Japan. -FAU - Hayashi, Takafumi -AU - Hayashi T -AD - Research Faculty of Agriculture, Hokkaido University, Sapporo, Hokkaido 060-8589, - Japan. -FAU - Zhu, Jianghui -AU - Zhu J -AD - Research Faculty of Agriculture, Hokkaido University, Sapporo, Hokkaido 060-8589, - Japan. -FAU - Zhao, Chen -AU - Zhao C -AD - Research Faculty of Agriculture, Hokkaido University, Sapporo, Hokkaido 060-8589, - Japan. -FAU - Xu, Meilan -AU - Xu M -AD - The Key Laboratory of Soybean Molecular Design Breeding, Northeast Institute of - Geography and Agroecology, Chinese Academy of Sciences, Harbin 150081, China. -FAU - Yamaguchi, Naoya -AU - Yamaguchi N -AD - Hokkaido Research Organization Tokachi Agricultural Experiment Station, Memuro, - Hokkaido 082-0081, Japan. -FAU - Sayama, Takashi -AU - Sayama T -AD - National Institute of Agrobiological Sciences, Kannondai, Ibaraki 305-8602, - Japan. -FAU - Ishimoto, Masao -AU - Ishimoto M -AD - National Institute of Agrobiological Sciences, Kannondai, Ibaraki 305-8602, - Japan. -FAU - Kong, Lingping -AU - Kong L -AD - The Key Laboratory of Soybean Molecular Design Breeding, Northeast Institute of - Geography and Agroecology, Chinese Academy of Sciences, Harbin 150081, China. -FAU - Shi, Xinyi -AU - Shi X -AD - The Key Laboratory of Soybean Molecular Design Breeding, Northeast Institute of - Geography and Agroecology, Chinese Academy of Sciences, Harbin 150081, China. -FAU - Liu, Baohui -AU - Liu B -AD - The Key Laboratory of Soybean Molecular Design Breeding, Northeast Institute of - Geography and Agroecology, Chinese Academy of Sciences, Harbin 150081, China. -FAU - Tian, Zhixi -AU - Tian Z -AD - State Key Laboratory of Plant Cell and Chromosome Engineering, Institute of - Genetics and Developmental Biology, Chinese Academy of Sciences, Beijing 1001014, - China. -FAU - Yamada, Tetsuya -AU - Yamada T -AD - Research Faculty of Agriculture, Hokkaido University, Sapporo, Hokkaido 060-8589, - Japan. -FAU - Kong, Fanjiang -AU - Kong F -AD - The Key Laboratory of Soybean Molecular Design Breeding, Northeast Institute of - Geography and Agroecology, Chinese Academy of Sciences, Harbin 150081, China - kongfj@iga.ac.cn jabe@res.agr.hokucai.ac.jp. -FAU - Abe, Jun -AU - Abe J -AD - Research Faculty of Agriculture, Hokkaido University, Sapporo, Hokkaido 060-8589, - Japan kongfj@iga.ac.cn jabe@res.agr.hokucai.ac.jp. -LA - eng -PT - Journal Article -PT - Research Support, Non-U.S. Gov't -DEP - 20160715 -PL - England -TA - J Exp Bot -JT - Journal of experimental botany -JID - 9882906 -RN - 0 (Plant Proteins) -SB - IM -MH - Flowers/*genetics/growth & development/physiology -MH - Gene Expression Regulation, Plant -MH - Genes, Plant/genetics/physiology -MH - Photoperiod -MH - Plant Proteins/genetics/physiology -MH - Polymorphism, Single Nucleotide/genetics -MH - Quantitative Trait Loci/*genetics/physiology -MH - Sequence Analysis, DNA -MH - Soybeans/*genetics/growth & development/physiology -PMC - PMC5014162 -OTO - NOTNLM -OT - FLOWERING LOCUS T -OT - SNP calling -OT - flowering time -OT - near-isogenic line -OT - photoperiod sensitivity -OT - quantitative trait locus -OT - soybean. -EDAT- 2016/07/17 06:00 -MHDA- 2017/11/08 06:00 -CRDT- 2016/07/17 06:00 -PHST- 2016/07/17 06:00 [entrez] -PHST- 2016/07/17 06:00 [pubmed] -PHST- 2017/11/08 06:00 [medline] -AID - erw283 [pii] -AID - 10.1093/jxb/erw283 [doi] -PST - ppublish -SO - J Exp Bot. 2016 Sep;67(17):5247-58. doi: 10.1093/jxb/erw283. Epub 2016 Jul 15. - - -##### PUB RECORD ##### -## 10.1104/pp.15.00763 26134161 PMC4528769 Xu, Yamagishi et al., 2015 "Xu M, Yamagishi N, Zhao C, Takeshima R, Kasai M, Watanabe S, Kanazawa A, Yoshikawa N, Liu B, Yamada T, Abe J. The Soybean-Specific Maturity Gene E1 Family of Floral Repressors Controls Night-Break Responses through Down-Regulation of FLOWERING LOCUS T Orthologs. Plant Physiol. 2015 Aug;168(4):1735-46. doi: 10.1104/pp.15.00763. Epub 2015 Jul 1. PMID: 26134161; PMCID: PMC4528769." ## - -PMID- 26134161 -OWN - NLM -STAT- MEDLINE -DCOM- 20160511 -LR - 20220309 -IS - 1532-2548 (Electronic) -IS - 0032-0889 (Print) -IS - 0032-0889 (Linking) -VI - 168 -IP - 4 -DP - 2015 Aug -TI - The Soybean-Specific Maturity Gene E1 Family of Floral Repressors Controls - Night-Break Responses through Down-Regulation of FLOWERING LOCUS T Orthologs. -PG - 1735-46 -LID - 10.1104/pp.15.00763 [doi] -AB - Photoperiodism is a rhythmic change of sensitivity to light, which helps plants - to adjust flowering time according to seasonal changes in daylength and to adapt - to growing conditions at various latitudes. To reveal the molecular basis of - photoperiodism in soybean (Glycine max), a facultative short-day plant, we - analyzed the transcriptional profiles of the maturity gene E1 family and two - FLOWERING LOCUS T (FT) orthologs (FT2a and FT5a). E1, a repressor for FT2a and - FT5a, and its two homologs, E1-like-a (E1La) and E1Lb, exhibited two peaks of - expression in long days. Using two different approaches (experiments with - transition between light and dark phases and night-break experiments), we - revealed that the E1 family genes were expressed only during light periods and - that their induction after dawn in long days required a period of light before - dusk the previous day. In the cultivar Toyomusume, which lacks the E1 gene, - virus-induced silencing of E1La and E1Lb up-regulated the expression of FT2a and - FT5a and led to early flowering. Therefore, E1, E1La, and E1Lb function similarly - in flowering. Regulation of E1 and E1L expression by light was under the control - of E3 and E4, which encode phytochrome A proteins. Our data suggest that - phytochrome A-mediated transcriptional induction of E1 and its homologs by light - plays a critical role in photoperiodic induction of flowering in soybean. -CI - (c) 2015 American Society of Plant Biologists. All Rights Reserved. -FAU - Xu, Meilan -AU - Xu M -AD - Key Laboratory of Soybean Molecular Design Breeding, Northeast Institute of - Geography and Agroecology, Chinese Academy of Sciences, Harbin 150081, China - (M.X., B.L.);Faculty of Agriculture, Iwate University, Morioka, Iwate 020-8550, - Japan (N.Ya., N.Yo.);Research Faculty of Agriculture, Hokkaido University, - Sapporo, Hokkaido 060-8589, Japan (C.Z., R.T., M.K., A.K., T.Y., J.A.); - andandFaculty of Agriculture, Saga University, Saga 840-0027, Japan (S.W.). -FAU - Yamagishi, Noriko -AU - Yamagishi N -AD - Key Laboratory of Soybean Molecular Design Breeding, Northeast Institute of - Geography and Agroecology, Chinese Academy of Sciences, Harbin 150081, China - (M.X., B.L.);Faculty of Agriculture, Iwate University, Morioka, Iwate 020-8550, - Japan (N.Ya., N.Yo.);Research Faculty of Agriculture, Hokkaido University, - Sapporo, Hokkaido 060-8589, Japan (C.Z., R.T., M.K., A.K., T.Y., J.A.); - andandFaculty of Agriculture, Saga University, Saga 840-0027, Japan (S.W.). -FAU - Zhao, Chen -AU - Zhao C -AD - Key Laboratory of Soybean Molecular Design Breeding, Northeast Institute of - Geography and Agroecology, Chinese Academy of Sciences, Harbin 150081, China - (M.X., B.L.);Faculty of Agriculture, Iwate University, Morioka, Iwate 020-8550, - Japan (N.Ya., N.Yo.);Research Faculty of Agriculture, Hokkaido University, - Sapporo, Hokkaido 060-8589, Japan (C.Z., R.T., M.K., A.K., T.Y., J.A.); - andandFaculty of Agriculture, Saga University, Saga 840-0027, Japan (S.W.). -FAU - Takeshima, Ryoma -AU - Takeshima R -AD - Key Laboratory of Soybean Molecular Design Breeding, Northeast Institute of - Geography and Agroecology, Chinese Academy of Sciences, Harbin 150081, China - (M.X., B.L.);Faculty of Agriculture, Iwate University, Morioka, Iwate 020-8550, - Japan (N.Ya., N.Yo.);Research Faculty of Agriculture, Hokkaido University, - Sapporo, Hokkaido 060-8589, Japan (C.Z., R.T., M.K., A.K., T.Y., J.A.); - andandFaculty of Agriculture, Saga University, Saga 840-0027, Japan (S.W.). -FAU - Kasai, Megumi -AU - Kasai M -AD - Key Laboratory of Soybean Molecular Design Breeding, Northeast Institute of - Geography and Agroecology, Chinese Academy of Sciences, Harbin 150081, China - (M.X., B.L.);Faculty of Agriculture, Iwate University, Morioka, Iwate 020-8550, - Japan (N.Ya., N.Yo.);Research Faculty of Agriculture, Hokkaido University, - Sapporo, Hokkaido 060-8589, Japan (C.Z., R.T., M.K., A.K., T.Y., J.A.); - andandFaculty of Agriculture, Saga University, Saga 840-0027, Japan (S.W.). -FAU - Watanabe, Satoshi -AU - Watanabe S -AD - Key Laboratory of Soybean Molecular Design Breeding, Northeast Institute of - Geography and Agroecology, Chinese Academy of Sciences, Harbin 150081, China - (M.X., B.L.);Faculty of Agriculture, Iwate University, Morioka, Iwate 020-8550, - Japan (N.Ya., N.Yo.);Research Faculty of Agriculture, Hokkaido University, - Sapporo, Hokkaido 060-8589, Japan (C.Z., R.T., M.K., A.K., T.Y., J.A.); - andandFaculty of Agriculture, Saga University, Saga 840-0027, Japan (S.W.). -FAU - Kanazawa, Akira -AU - Kanazawa A -AD - Key Laboratory of Soybean Molecular Design Breeding, Northeast Institute of - Geography and Agroecology, Chinese Academy of Sciences, Harbin 150081, China - (M.X., B.L.);Faculty of Agriculture, Iwate University, Morioka, Iwate 020-8550, - Japan (N.Ya., N.Yo.);Research Faculty of Agriculture, Hokkaido University, - Sapporo, Hokkaido 060-8589, Japan (C.Z., R.T., M.K., A.K., T.Y., J.A.); - andandFaculty of Agriculture, Saga University, Saga 840-0027, Japan (S.W.). -FAU - Yoshikawa, Nobuyuki -AU - Yoshikawa N -AD - Key Laboratory of Soybean Molecular Design Breeding, Northeast Institute of - Geography and Agroecology, Chinese Academy of Sciences, Harbin 150081, China - (M.X., B.L.);Faculty of Agriculture, Iwate University, Morioka, Iwate 020-8550, - Japan (N.Ya., N.Yo.);Research Faculty of Agriculture, Hokkaido University, - Sapporo, Hokkaido 060-8589, Japan (C.Z., R.T., M.K., A.K., T.Y., J.A.); - andandFaculty of Agriculture, Saga University, Saga 840-0027, Japan (S.W.). -FAU - Liu, Baohui -AU - Liu B -AD - Key Laboratory of Soybean Molecular Design Breeding, Northeast Institute of - Geography and Agroecology, Chinese Academy of Sciences, Harbin 150081, China - (M.X., B.L.);Faculty of Agriculture, Iwate University, Morioka, Iwate 020-8550, - Japan (N.Ya., N.Yo.);Research Faculty of Agriculture, Hokkaido University, - Sapporo, Hokkaido 060-8589, Japan (C.Z., R.T., M.K., A.K., T.Y., J.A.); - andandFaculty of Agriculture, Saga University, Saga 840-0027, Japan (S.W.) - liubh@neigaehrb.ac.cn jabe@res.agr.hokudai.ac.jp. -FAU - Yamada, Tetsuya -AU - Yamada T -AD - Key Laboratory of Soybean Molecular Design Breeding, Northeast Institute of - Geography and Agroecology, Chinese Academy of Sciences, Harbin 150081, China - (M.X., B.L.);Faculty of Agriculture, Iwate University, Morioka, Iwate 020-8550, - Japan (N.Ya., N.Yo.);Research Faculty of Agriculture, Hokkaido University, - Sapporo, Hokkaido 060-8589, Japan (C.Z., R.T., M.K., A.K., T.Y., J.A.); - andandFaculty of Agriculture, Saga University, Saga 840-0027, Japan (S.W.). -FAU - Abe, Jun -AU - Abe J -AD - Key Laboratory of Soybean Molecular Design Breeding, Northeast Institute of - Geography and Agroecology, Chinese Academy of Sciences, Harbin 150081, China - (M.X., B.L.);Faculty of Agriculture, Iwate University, Morioka, Iwate 020-8550, - Japan (N.Ya., N.Yo.);Research Faculty of Agriculture, Hokkaido University, - Sapporo, Hokkaido 060-8589, Japan (C.Z., R.T., M.K., A.K., T.Y., J.A.); - andandFaculty of Agriculture, Saga University, Saga 840-0027, Japan (S.W.) - liubh@neigaehrb.ac.cn jabe@res.agr.hokudai.ac.jp. -LA - eng -PT - Journal Article -PT - Research Support, Non-U.S. Gov't -DEP - 20150701 -PL - United States -TA - Plant Physiol -JT - Plant physiology -JID - 0401224 -RN - 0 (Plant Proteins) -SB - IM -MH - Amino Acid Sequence -MH - *Down-Regulation -MH - Flowers/*genetics -MH - Gene Expression Regulation, Plant/radiation effects -MH - Light -MH - Molecular Sequence Data -MH - Photoperiod -MH - Plant Proteins/*genetics -MH - RNA Interference -MH - Reverse Transcriptase Polymerase Chain Reaction -MH - Sequence Homology, Amino Acid -MH - Soybeans/*genetics -PMC - PMC4528769 -EDAT- 2015/07/03 06:00 -MHDA- 2016/05/12 06:00 -CRDT- 2015/07/03 06:00 -PHST- 2015/05/21 00:00 [received] -PHST- 2015/06/29 00:00 [accepted] -PHST- 2015/07/03 06:00 [entrez] -PHST- 2015/07/03 06:00 [pubmed] -PHST- 2016/05/12 06:00 [medline] -AID - pp.15.00763 [pii] -AID - PP201500763 [pii] -AID - 10.1104/pp.15.00763 [doi] -PST - ppublish -SO - Plant Physiol. 2015 Aug;168(4):1735-46. doi: 10.1104/pp.15.00763. Epub 2015 Jul - 1. - - -##### PUB RECORD ##### -## 10.1104/pp.110.160796 20864544 PMC2971601 Kong, Liu et al., 2010 "Kong F, Liu B, Xia Z, Sato S, Kim BM, Watanabe S, Yamada T, Tabata S, Kanazawa A, Harada K, Abe J. Two coordinately regulated homologs of FLOWERING LOCUS T are involved in the control of photoperiodic flowering in soybean. Plant Physiol. 2010 Nov;154(3):1220-31. doi: 10.1104/pp.110.160796. Epub 2010 Sep 23. PMID: 20864544; PMCID: PMC2971601." ## - -PMID- 20864544 -OWN - NLM -STAT- MEDLINE -DCOM- 20110210 -LR - 20220408 -IS - 1532-2548 (Electronic) -IS - 0032-0889 (Print) -IS - 0032-0889 (Linking) -VI - 154 -IP - 3 -DP - 2010 Nov -TI - Two coordinately regulated homologs of FLOWERING LOCUS T are involved in the - control of photoperiodic flowering in soybean. -PG - 1220-31 -LID - 10.1104/pp.110.160796 [doi] -AB - FLOWERING LOCUS T (FT) is a key flowering integrator in Arabidopsis (Arabidopsis - thaliana), with homologs that encode florigens in many plant species regardless - of the type of photoperiodic response. We identified 10 FT homologs, which were - arranged as five pairs of linked genes in different homoeologous chromosomal - regions, in soybean (Glycine max), a paleopolyploid species. Two of the FT - homologs, GmFT2a and GmFT5a, were highly up-regulated under short-day (SD) - conditions (inductive for flowering in soybean) and had diurnal expression - patterns with the highest expression 4 h after dawn. Under long-day (LD) - conditions, expression of GmFT2a and GmFT5a was down-regulated and did not follow - a diurnal pattern. Flowering took much longer to initiate under LD than under SD, - and only the GmFT5a transcript accumulated late in development under LD. Ectopic - expression analysis in Arabidopsis confirmed that both GmFT2a and GmFT5a had the - same function as Arabidopsis FT, but the effect of GmFT5a was more prominent. A - double-mutant soybean line for two PHYTOCHROME A (PHYA) genes expressed high - levels of GmFT2a and GmFT5a under LD, and it flowered slightly earlier under LD - than the wild type grown under SD. The expression levels of GmFT2a and GmFT5a - were regulated by the PHYA-mediated photoperiodic regulation system, and the - GmFT5a expression was also regulated by a photoperiod-independent system in LD. - Taken together, our results suggest that GmFT2a and GmFT5a coordinately control - flowering and enable the adaptation of soybean to a wide range of photoperiodic - environments. -FAU - Kong, Fanjiang -AU - Kong F -AD - Northeast Institute of Geography and Agroecology, Chinese Academy of Sciences, - Harbin, China. -FAU - Liu, Baohui -AU - Liu B -FAU - Xia, Zhengjun -AU - Xia Z -FAU - Sato, Shusei -AU - Sato S -FAU - Kim, Bo Min -AU - Kim BM -FAU - Watanabe, Satoshi -AU - Watanabe S -FAU - Yamada, Tetsuya -AU - Yamada T -FAU - Tabata, Satoshi -AU - Tabata S -FAU - Kanazawa, Akira -AU - Kanazawa A -FAU - Harada, Kyuya -AU - Harada K -FAU - Abe, Jun -AU - Abe J -LA - eng -SI - GENBANK/AB550120 -SI - GENBANK/AB550121 -SI - GENBANK/AB550122 -SI - GENBANK/AB550124 -SI - GENBANK/AB550125 -SI - GENBANK/AB550126 -SI - GENBANK/AP011804 -SI - GENBANK/AP011805 -SI - GENBANK/AP011806 -SI - GENBANK/AP011807 -SI - GENBANK/AP011808 -PT - Journal Article -PT - Research Support, Non-U.S. Gov't -DEP - 20100923 -PL - United States -TA - Plant Physiol -JT - Plant physiology -JID - 0401224 -RN - 0 (DNA, Plant) -RN - 0 (Plant Proteins) -SB - IM -MH - Amino Acid Sequence -MH - Arabidopsis/genetics -MH - Chromosome Mapping -MH - DNA, Plant/genetics -MH - Flowers/*physiology -MH - Gene Expression Regulation, Plant -MH - Molecular Sequence Data -MH - *Photoperiod -MH - Plant Proteins/genetics/*metabolism -MH - Plants, Genetically Modified/genetics -MH - Sequence Alignment -MH - Sequence Analysis, DNA -MH - Soybeans/*genetics/metabolism/physiology -PMC - PMC2971601 -EDAT- 2010/09/25 06:00 -MHDA- 2011/02/11 06:00 -CRDT- 2010/09/25 06:00 -PHST- 2010/09/25 06:00 [entrez] -PHST- 2010/09/25 06:00 [pubmed] -PHST- 2011/02/11 06:00 [medline] -AID - pp.110.160796 [pii] -AID - 160796 [pii] -AID - 10.1104/pp.110.160796 [doi] -PST - ppublish -SO - Plant Physiol. 2010 Nov;154(3):1220-31. doi: 10.1104/pp.110.160796. Epub 2010 Sep - 23. - - -##### PUB RECORD ##### -## 10.1105/tpc.114.135103 25663621 PMC4456927 Wang, Zhou et al., 2015 "Wang Z, Zhou Z, Liu Y, Liu T, Li Q, Ji Y, Li C, Fang C, Wang M, Wu M, Shen Y, Tang T, Ma J, Tian Z. Functional evolution of phosphatidylethanolamine binding proteins in soybean and Arabidopsis. Plant Cell. 2015 Feb;27(2):323-36. doi: 10.1105/tpc.114.135103. Epub 2015 Feb 6. PMID: 25663621; PMCID: PMC4456927." ## - -PMID- 25663621 -OWN - NLM -STAT- MEDLINE -DCOM- 20151201 -LR - 20220309 -IS - 1532-298X (Electronic) -IS - 1040-4651 (Print) -IS - 1040-4651 (Linking) -VI - 27 -IP - 2 -DP - 2015 Feb -TI - Functional evolution of phosphatidylethanolamine binding proteins in soybean and - Arabidopsis. -PG - 323-36 -LID - 10.1105/tpc.114.135103 [doi] -AB - Gene duplication provides resources for novel gene functions. Identification of - the amino acids responsible for functional conservation and divergence of - duplicated genes will strengthen our understanding of their evolutionary course. - Here, we conducted a systemic functional investigation of - phosphatidylethanolamine binding proteins (PEBPs) in soybean (Glycine max) and - Arabidopsis thaliana. Our results demonstrated that after the ancestral - duplication, the lineage of the common ancestor of the FLOWERING LOCUS T (FT) and - TERMINAL FLOWER1 (TFL1) subfamilies functionally diverged from the MOTHER OF FT - AND TFL1 (MFT) subfamily to activate flowering and repress flowering, - respectively. They also underwent further specialization after subsequent - duplications. Although the functional divergence increased with duplication age, - we observed rapid functional divergence for a few pairs of young duplicates in - soybean. Association analysis between amino acids and functional variations - identified critical amino acid residues that led to functional differences in - PEBP members. Using transgenic analysis, we validated a subset of these - differences. We report clear experimental evidence for the functional evolution - of the PEBPs in the MFT, FT, and TFL1 subfamilies, which predate the origin of - angiosperms. Our results highlight the role of amino acid divergence in driving - evolutionary novelty after duplication. -CI - (c) 2015 American Society of Plant Biologists. All rights reserved. -FAU - Wang, Zheng -AU - Wang Z -AD - State Key Laboratory of Plant Cell and Chromosome Engineering, Institute of - Genetics and Developmental Biology, Chinese Academy of Sciences, Beijing 100101, - China. -FAU - Zhou, Zhengkui -AU - Zhou Z -AD - State Key Laboratory of Plant Cell and Chromosome Engineering, Institute of - Genetics and Developmental Biology, Chinese Academy of Sciences, Beijing 100101, - China. -FAU - Liu, Yunfeng -AU - Liu Y -AD - Department of Agronomy, Purdue University, West Lafayette, Indiana 47907. -FAU - Liu, Tengfei -AU - Liu T -AD - State Key Laboratory of Plant Cell and Chromosome Engineering, Institute of - Genetics and Developmental Biology, Chinese Academy of Sciences, Beijing 100101, - China University of Chinese Academy of Sciences, Beijing 100039, China. -FAU - Li, Qing -AU - Li Q -AD - State Key Laboratory of Plant Cell and Chromosome Engineering, Institute of - Genetics and Developmental Biology, Chinese Academy of Sciences, Beijing 100101, - China University of Chinese Academy of Sciences, Beijing 100039, China. -FAU - Ji, Yuanyuan -AU - Ji Y -AD - State Key Laboratory of Plant Cell and Chromosome Engineering, Institute of - Genetics and Developmental Biology, Chinese Academy of Sciences, Beijing 100101, - China University of Chinese Academy of Sciences, Beijing 100039, China. -FAU - Li, Congcong -AU - Li C -AD - State Key Laboratory of Plant Cell and Chromosome Engineering, Institute of - Genetics and Developmental Biology, Chinese Academy of Sciences, Beijing 100101, - China University of Chinese Academy of Sciences, Beijing 100039, China. -FAU - Fang, Chao -AU - Fang C -AD - State Key Laboratory of Plant Cell and Chromosome Engineering, Institute of - Genetics and Developmental Biology, Chinese Academy of Sciences, Beijing 100101, - China University of Chinese Academy of Sciences, Beijing 100039, China. -FAU - Wang, Min -AU - Wang M -AD - State Key Laboratory of Plant Cell and Chromosome Engineering, Institute of - Genetics and Developmental Biology, Chinese Academy of Sciences, Beijing 100101, - China University of Chinese Academy of Sciences, Beijing 100039, China. -FAU - Wu, Mian -AU - Wu M -AD - State Key Laboratory of Plant Cell and Chromosome Engineering, Institute of - Genetics and Developmental Biology, Chinese Academy of Sciences, Beijing 100101, - China. -FAU - Shen, Yanting -AU - Shen Y -AD - State Key Laboratory of Plant Cell and Chromosome Engineering, Institute of - Genetics and Developmental Biology, Chinese Academy of Sciences, Beijing 100101, - China University of Chinese Academy of Sciences, Beijing 100039, China. -FAU - Tang, Tian -AU - Tang T -AD - State Key Laboratory of Biocontrol and Key Laboratory of Biodiversity Dynamics - and Conservation of Guangdong Higher Education Institutes, Grant School of Life - Sciences, Sun Yat-Sen University, Guangzhou 510080, China lsstt@mail.sysu.edu.cn - maj@purdue.edu zxtian@genetics.ac.cn. -FAU - Ma, Jianxin -AU - Ma J -AD - Department of Agronomy, Purdue University, West Lafayette, Indiana 47907 - lsstt@mail.sysu.edu.cn maj@purdue.edu zxtian@genetics.ac.cn. -FAU - Tian, Zhixi -AU - Tian Z -AD - State Key Laboratory of Plant Cell and Chromosome Engineering, Institute of - Genetics and Developmental Biology, Chinese Academy of Sciences, Beijing 100101, - China lsstt@mail.sysu.edu.cn maj@purdue.edu zxtian@genetics.ac.cn. -LA - eng -PT - Journal Article -PT - Research Support, Non-U.S. Gov't -DEP - 20150206 -PL - England -TA - Plant Cell -JT - The Plant cell -JID - 9208688 -RN - 0 (Amino Acids) -RN - 0 (Phosphatidylethanolamine Binding Protein) -RN - 0 (Plant Proteins) -SB - IM -MH - Amino Acid Sequence -MH - Amino Acids/metabolism -MH - Arabidopsis/*genetics/metabolism -MH - *Evolution, Molecular -MH - Flowers/physiology -MH - Gene Expression Regulation, Plant -MH - Genes, Duplicate -MH - Genes, Plant -MH - Molecular Sequence Data -MH - Phosphatidylethanolamine Binding Protein/chemistry/*genetics/*metabolism -MH - Plant Proteins/metabolism -MH - Protein Binding -MH - Protein Transport -MH - Soybeans/*genetics/metabolism -MH - Subcellular Fractions/metabolism -PMC - PMC4456927 -EDAT- 2015/02/11 06:00 -MHDA- 2015/12/15 06:00 -CRDT- 2015/02/10 06:00 -PHST- 2015/02/10 06:00 [entrez] -PHST- 2015/02/11 06:00 [pubmed] -PHST- 2015/12/15 06:00 [medline] -AID - tpc.114.135103 [pii] -AID - 135103 [pii] -AID - 10.1105/tpc.114.135103 [doi] -PST - ppublish -SO - Plant Cell. 2015 Feb;27(2):323-36. doi: 10.1105/tpc.114.135103. Epub 2015 Feb 6. - - -##### PUB RECORD ##### -## 10.1111/j.1365-313x.2004.02072.x 15125772 null Noh, Bizzell et al., 2004 "Noh YS, Bizzell CM, Noh B, Schomburg FM, Amasino RM. EARLY FLOWERING 5 acts as a floral repressor in Arabidopsis. Plant J. 2004 May;38(4):664-72. doi: 10.1111/j.1365-313X.2004.02072.x. PMID: 15125772." ## - -PMID- 15125772 -OWN - NLM -STAT- MEDLINE -DCOM- 20040709 -LR - 20061115 -IS - 0960-7412 (Print) -IS - 0960-7412 (Linking) -VI - 38 -IP - 4 -DP - 2004 May -TI - EARLY FLOWERING 5 acts as a floral repressor in Arabidopsis. -PG - 664-72 -AB - EARLY FLOWERING 5 (ELF5) is a single-copy gene involved in flowering time - regulation in Arabidopsis. ELF5 encodes a nuclear-targeted protein that is - related to the human nuclear protein containing a WW domain (Npw)38-binding - protein (NpwBP). Lesions in ELF5 cause early flowering in both long days and - short days. elf5 mutations partially suppress the late flowering of both - autonomous-pathway mutants and FRIGIDA (FRI)-containing lines by reducing the - expression of FLOWERING LOCUS C (FLC), a floral repressor upon which many of the - flowering pathways converge. elf5 mutations also partially suppress - photoperiod-pathway mutants, and this, along with the ability of elf5 mutations - to cause early flowering in short days, indicates that ELF5 also affects - flowering independently of FLC. -FAU - Noh, Yoo-Sun -AU - Noh YS -AD - Department of Biochemistry, College of Agricultural and Life Sciences, University - of Wisconsin, Madison, WI 53706-1544, USA. -FAU - Bizzell, Colleen M -AU - Bizzell CM -FAU - Noh, Bosl -AU - Noh B -FAU - Schomburg, Fritz M -AU - Schomburg FM -FAU - Amasino, Richard M -AU - Amasino RM -LA - eng -SI - GENBANK/AY526094 -PT - Journal Article -PT - Research Support, Non-U.S. Gov't -PT - Research Support, U.S. Gov't, Non-P.H.S. -PL - England -TA - Plant J -JT - The Plant journal : for cell and molecular biology -JID - 9207397 -RN - 0 (5' Untranslated Regions) -RN - 0 (Arabidopsis Proteins) -RN - 0 (DNA Primers) -RN - 0 (ELF5 protein, Arabidopsis) -RN - 0 (Repressor Proteins) -SB - IM -MH - 5' Untranslated Regions/genetics -MH - Amino Acid Sequence -MH - Arabidopsis/*genetics -MH - Arabidopsis Proteins/*genetics -MH - Base Sequence -MH - Circadian Rhythm -MH - DNA Primers -MH - Flowers/genetics -MH - Molecular Sequence Data -MH - Polymerase Chain Reaction -MH - Protein Biosynthesis/genetics -MH - Repressor Proteins/*genetics -MH - Seasons -MH - Sequence Alignment -MH - Sequence Homology, Amino Acid -EDAT- 2004/05/06 05:00 -MHDA- 2004/07/10 05:00 -CRDT- 2004/05/06 05:00 -PHST- 2004/05/06 05:00 [pubmed] -PHST- 2004/07/10 05:00 [medline] -PHST- 2004/05/06 05:00 [entrez] -AID - TPJ2072 [pii] -AID - 10.1111/j.1365-313X.2004.02072.x [doi] -PST - ppublish -SO - Plant J. 2004 May;38(4):664-72. doi: 10.1111/j.1365-313X.2004.02072.x. - - -##### PUB RECORD ##### -## 10.1111/jipb.13021 33090664 null Lin, Liu et al., 2021 "Lin X, Liu B, Weller JL, Abe J, Kong F. Molecular mechanisms for the photoperiodic regulation of flowering in soybean. J Integr Plant Biol. 2021 Jun;63(6):981-994. doi: 10.1111/jipb.13021. Epub 2021 Apr 26. PMID: 33090664." ## - -PMID- 33090664 -OWN - NLM -STAT- MEDLINE -DCOM- 20210804 -LR - 20210804 -IS - 1744-7909 (Electronic) -IS - 1672-9072 (Linking) -VI - 63 -IP - 6 -DP - 2021 Jun -TI - Molecular mechanisms for the photoperiodic regulation of flowering in soybean. -PG - 981-994 -LID - 10.1111/jipb.13021 [doi] -AB - Photoperiodic flowering is one of the most important factors affecting regional - adaptation and yield in soybean (Glycine max). Plant adaptation to long-day - conditions at higher latitudes requires early flowering and a reduction or loss - of photoperiod sensitivity; adaptation to short-day conditions at lower latitudes - involves delayed flowering, which prolongs vegetative growth for maximum yield - potential. Due to the influence of numerous major loci and quantitative trait - loci (QTLs), soybean has broad adaptability across latitudes. Forward genetic - approaches have uncovered the molecular basis for several of these major maturity - genes and QTLs. Moreover, the molecular characterization of orthologs of - Arabidopsis thaliana flowering genes has enriched our understanding of the - photoperiodic flowering pathway in soybean. Building on early insights into the - importance of the photoreceptor phytochrome A, several circadian clock components - have been integrated into the genetic network controlling flowering in soybean: - E1, a repressor of FLOWERING LOCUS T orthologs, plays a central role in this - network. Here, we provide an overview of recent progress in elucidating - photoperiodic flowering in soybean, how it contributes to our fundamental - understanding of flowering time control, and how this information could be used - for molecular design and breeding of high-yielding soybean cultivars. -CI - (c) 2020 Institute of Botany, Chinese Academy of Sciences. -FAU - Lin, Xiaoya -AU - Lin X -AD - Innovative Center of Molecular Genetics and Evolution, School of Life Sciences, - Guangzhou University, Guangzhou, 510642, China. -FAU - Liu, Baohui -AU - Liu B -AD - Innovative Center of Molecular Genetics and Evolution, School of Life Sciences, - Guangzhou University, Guangzhou, 510642, China. -AD - Key Laboratory of Soybean Molecular Design Breeding, Northeast Institute of - Geography and Agroecology, Chinese Academy of Sciences, Harbin, 150081, China. -FAU - Weller, James L -AU - Weller JL -AD - School of Natural Sciences, University of Tasmania, Hobart, Tasmania, 7001, - Australia. -FAU - Abe, Jun -AU - Abe J -AD - Research Faculty of Agriculture, Hokkaido University, Sapporo, 060-8589, Japan. -FAU - Kong, Fanjiang -AU - Kong F -AD - Innovative Center of Molecular Genetics and Evolution, School of Life Sciences, - Guangzhou University, Guangzhou, 510642, China. -AD - Key Laboratory of Soybean Molecular Design Breeding, Northeast Institute of - Geography and Agroecology, Chinese Academy of Sciences, Harbin, 150081, China. -LA - eng -GR - National Natural Science Foundation of China/ -GR - State Key Laboratory for Conservation and Utilization of Subtropical - Agro-bioresources/ -PT - Journal Article -PT - Review -DEP - 20210426 -PL - China (Republic : 1949- ) -TA - J Integr Plant Biol -JT - Journal of integrative plant biology -JID - 101250502 -SB - IM -MH - Circadian Rhythm/genetics/physiology -MH - Flowers/genetics/*physiology -MH - Gene Expression Regulation, Plant/genetics/physiology -MH - Gene Regulatory Networks/genetics/physiology -MH - *Photoperiod -MH - Plant Breeding -MH - Quantitative Trait Loci/genetics -MH - Soybeans/genetics/*physiology -OTO - NOTNLM -OT - molecular-designed breeding -OT - photoperiodic flowering -OT - soybean -EDAT- 2020/10/23 06:00 -MHDA- 2021/08/05 06:00 -CRDT- 2020/10/22 12:22 -PHST- 2020/08/08 00:00 [received] -PHST- 2020/09/27 00:00 [accepted] -PHST- 2020/10/23 06:00 [pubmed] -PHST- 2021/08/05 06:00 [medline] -PHST- 2020/10/22 12:22 [entrez] -AID - 10.1111/jipb.13021 [doi] -PST - ppublish -SO - J Integr Plant Biol. 2021 Jun;63(6):981-994. doi: 10.1111/jipb.13021. Epub 2021 - Apr 26. - - -##### PUB RECORD ##### -## 10.1111/nph.14884 29120038 PMC5900889 Liu, Jiang et al., 2008a "Liu W, Jiang B, Ma L, Zhang S, Zhai H, Xu X, Hou W, Xia Z, Wu C, Sun S, Wu T, Chen L, Han T. Functional diversification of Flowering Locus T homologs in soybean: GmFT1a and GmFT2a/5a have opposite roles in controlling flowering and maturation. New Phytol. 2018 Feb;217(3):1335-1345. doi: 10.1111/nph.14884. Epub 2017 Nov 9. PMID: 29120038; PMCID: PMC5900889." ## - -PMID- 29120038 -OWN - NLM -STAT- MEDLINE -DCOM- 20191002 -LR - 20200930 -IS - 1469-8137 (Electronic) -IS - 0028-646X (Print) -IS - 0028-646X (Linking) -VI - 217 -IP - 3 -DP - 2018 Feb -TI - Functional diversification of Flowering Locus T homologs in soybean: GmFT1a and - GmFT2a/5a have opposite roles in controlling flowering and maturation. -PG - 1335-1345 -LID - 10.1111/nph.14884 [doi] -AB - Soybean flowering and maturation are strictly regulated by photoperiod. - Photoperiod-sensitive soybean varieties can undergo flowering reversion when - switched from short-day (SD) to long-day (LD) conditions, suggesting the presence - of a 'floral-inhibitor' under LD conditions. We combined gene expression - profiling with a study of transgenic plants and confirmed that GmFT1a, soybean - Flowering Locus T (FT) homolog, is a floral inhibitor. GmFT1a is expressed - specifically in leaves, similar to the flowering-promoting FT homologs GmFT2a/5a. - However, in Zigongdongdou (ZGDD), a model variety for studying flowering - reversion, GmFT1a expression was induced by LD but inhibited by SD conditions. - This was unexpected, as it is the complete opposite of the expression of - flowering promoters GmFT2a/5a. Moreover, the key soybean maturity gene E1 may - up-regulate GmFT1a expression. It is also notable that GmFT1a expression was - conspicuously high in late-flowering varieties. Transgenic overexpression of - GmFT1a delayed flowering and maturation in soybean, confirming that GmFT1a - functions as a flowering inhibitor. This discovery highlights the complex impacts - of the functional diversification of the FT gene family in soybean, and implies - that antagonism between flowering-inhibiting and flowering-promoting FT homologs - in this highly photoperiod-sensitive plant may specify vegetative vs reproductive - development. -CI - (c) 2017 The Authors. New Phytologist (c) 2017 New Phytologist Trust. -FAU - Liu, Wei -AU - Liu W -AD - MOA Key Laboratory of Soybean Biology (Beijing), Institute of Crop Science, The - Chinese Academy of Agricultural Sciences, 12 Zhongguancun South Street, Beijing, - 100081, China. -FAU - Jiang, Bingjun -AU - Jiang B -AD - MOA Key Laboratory of Soybean Biology (Beijing), Institute of Crop Science, The - Chinese Academy of Agricultural Sciences, 12 Zhongguancun South Street, Beijing, - 100081, China. -FAU - Ma, Liming -AU - Ma L -AD - MOA Key Laboratory of Soybean Biology (Beijing), Institute of Crop Science, The - Chinese Academy of Agricultural Sciences, 12 Zhongguancun South Street, Beijing, - 100081, China. -FAU - Zhang, Shouwei -AU - Zhang S -AD - MOA Key Laboratory of Soybean Biology (Beijing), Institute of Crop Science, The - Chinese Academy of Agricultural Sciences, 12 Zhongguancun South Street, Beijing, - 100081, China. -FAU - Zhai, Hong -AU - Zhai H -AD - Key Laboratory of Soybean Molecular Design Breeding, Northeast Institute of - Geography and Agroecology, Chinese Academy of Sciences, Harbin, 150081, China. -FAU - Xu, Xin -AU - Xu X -AD - MOA Key Laboratory of Soybean Biology (Beijing), Institute of Crop Science, The - Chinese Academy of Agricultural Sciences, 12 Zhongguancun South Street, Beijing, - 100081, China. -FAU - Hou, Wensheng -AU - Hou W -AD - MOA Key Laboratory of Soybean Biology (Beijing), Institute of Crop Science, The - Chinese Academy of Agricultural Sciences, 12 Zhongguancun South Street, Beijing, - 100081, China. -FAU - Xia, Zhengjun -AU - Xia Z -AD - Key Laboratory of Soybean Molecular Design Breeding, Northeast Institute of - Geography and Agroecology, Chinese Academy of Sciences, Harbin, 150081, China. -FAU - Wu, Cunxiang -AU - Wu C -AD - MOA Key Laboratory of Soybean Biology (Beijing), Institute of Crop Science, The - Chinese Academy of Agricultural Sciences, 12 Zhongguancun South Street, Beijing, - 100081, China. -FAU - Sun, Shi -AU - Sun S -AD - MOA Key Laboratory of Soybean Biology (Beijing), Institute of Crop Science, The - Chinese Academy of Agricultural Sciences, 12 Zhongguancun South Street, Beijing, - 100081, China. -FAU - Wu, Tingting -AU - Wu T -AD - MOA Key Laboratory of Soybean Biology (Beijing), Institute of Crop Science, The - Chinese Academy of Agricultural Sciences, 12 Zhongguancun South Street, Beijing, - 100081, China. -FAU - Chen, Li -AU - Chen L -AD - MOA Key Laboratory of Soybean Biology (Beijing), Institute of Crop Science, The - Chinese Academy of Agricultural Sciences, 12 Zhongguancun South Street, Beijing, - 100081, China. -FAU - Han, Tianfu -AU - Han T -AD - MOA Key Laboratory of Soybean Biology (Beijing), Institute of Crop Science, The - Chinese Academy of Agricultural Sciences, 12 Zhongguancun South Street, Beijing, - 100081, China. -LA - eng -SI - GENBANK/MG030499 -SI - GENBANK/MG030623 -PT - Journal Article -PT - Research Support, Non-U.S. Gov't -DEP - 20171109 -PL - England -TA - New Phytol -JT - The New phytologist -JID - 9882884 -RN - 0 (Plant Proteins) -SB - IM -MH - Flowers/genetics/*physiology -MH - Gene Expression Regulation, Plant -MH - Haplotypes/genetics -MH - Models, Biological -MH - Phenotype -MH - Plant Proteins/*genetics/metabolism -MH - Plants, Genetically Modified -MH - *Sequence Homology, Amino Acid -MH - Soybeans/*genetics -MH - Transcriptome/genetics -PMC - PMC5900889 -OTO - NOTNLM -OT - Flowering Locus T (FT) homolog -OT - GmFT1a -OT - flowering inhibitor -OT - maturation -OT - soybean -EDAT- 2017/11/10 06:00 -MHDA- 2019/10/03 06:00 -CRDT- 2017/11/10 06:00 -PHST- 2017/05/01 00:00 [received] -PHST- 2017/10/03 00:00 [accepted] -PHST- 2017/11/10 06:00 [pubmed] -PHST- 2019/10/03 06:00 [medline] -PHST- 2017/11/10 06:00 [entrez] -AID - NPH14884 [pii] -AID - 10.1111/nph.14884 [doi] -PST - ppublish -SO - New Phytol. 2018 Feb;217(3):1335-1345. doi: 10.1111/nph.14884. Epub 2017 Nov 9. - - -##### PUB RECORD ##### -## 10.1186/1471-2229-14-9 24397545 PMC3890618 Fan, Hu et al., 2014 "Fan C, Hu R, Zhang X, Wang X, Zhang W, Zhang Q, Ma J, Fu YF. Conserved CO-FT regulons contribute to the photoperiod flowering control in soybean. BMC Plant Biol. 2014 Jan 7;14:9. doi: 10.1186/1471-2229-14-9. PMID: 24397545; PMCID: PMC3890618." ## - -PMID- 24397545 -OWN - NLM -STAT- MEDLINE -DCOM- 20140910 -LR - 20211021 -IS - 1471-2229 (Electronic) -IS - 1471-2229 (Linking) -VI - 14 -DP - 2014 Jan 7 -TI - Conserved CO-FT regulons contribute to the photoperiod flowering control in - soybean. -PG - 9 -LID - 10.1186/1471-2229-14-9 [doi] -AB - BACKGROUND: CO and FT orthologs, belonging to the BBX and PEBP family, - respectively, have important and conserved roles in the photoperiod regulation of - flowering time in plants. Soybean genome experienced at least three rounds of - whole genome duplications (WGDs), which resulted in multiple copies of about 75% - of genes. Subsequent subfunctionalization is the main fate for paralogous gene - pairs during the evolutionary process. RESULTS: The phylogenic relationships - revealed that CO orthologs were widespread in the plant kingdom while FT - orthologs were present only in angiosperms. Twenty-eight CO homologous genes and - twenty-four FT homologous genes were gained in the soybean genome. Based on the - collinear relationship, the soybean ancestral CO ortholog experienced three WGD - events, but only two paralogous gene pairs (GmCOL1/2 and GmCOL5/13) survived in - the modern soybean. The paralogous gene pairs, GmCOL1/2 or GmCOL5/13, showed - similar expression patterns in pair but different between pairs, indicating that - they functionally diverged. GmFTL1 to 7 were derived from the same ancestor prior - to the whole genome triplication (WGT) event, and after the Legume WGD event the - ancestor diverged into two branches, GmFTL3/5/7 and GmFTL1/2/4/6. GmFTL7 were - truncated in the N-terminus compared to other FT-lineage genes, but ubiquitously - expressed. Expressions of GmFTL1 to 6 were higher in leaves at the flowering - stage than that at the seedling stage. GmFTL3 was expressed at the highest level - in all tissues except roots at the seedling stage, and its circadian pattern was - different from the other five ones. The transcript of GmFTL6 was highly - accumulated in seedling roots. The circadian rhythms of GmCOL5/13 and - GmFT1/2/4/5/6 were synchronized in a day, demonstrating the complicate - relationship of CO-FT regulons in soybean leaves. Over-expression of GmCOL2 did - not rescue the flowering phenotype of the Arabidopsis co mutant. However, ectopic - expression of GmCOL5 did rescue the co mutant phenotype. All GmFTL1 to 6 showed - flower-promoting activities in Arabidopsis. CONCLUSIONS: After three recent - rounds of whole genome duplications in the soybean, the paralogous genes of CO-FT - regulons showed subfunctionalization through expression divergence. Then, only - GmCOL5/13 kept flowering-promoting activities, while GmFTL1 to 6 contributed to - flowering control. Additionally, GmCOL5/13 and GmFT1/2/3/4/5/6 showed similar - circadian expression profiles. Therefore, our results suggested that GmCOL5/13 - and GmFT1/2/3/4/5/6 formed the complicate CO-FT regulons in the photoperiod - regulation of flowering time in soybean. -FAU - Fan, Chengming -AU - Fan C -FAU - Hu, Ruibo -AU - Hu R -FAU - Zhang, Xiaomei -AU - Zhang X -FAU - Wang, Xu -AU - Wang X -FAU - Zhang, Wenjing -AU - Zhang W -FAU - Zhang, Qingzhe -AU - Zhang Q -FAU - Ma, Jinhua -AU - Ma J -FAU - Fu, Yong-Fu -AU - Fu YF -AD - MOA Key Lab of Soybean Biology (Beijing), National Key Facility of Crop Gene - Resource and Genetic Improvement, Institute of Crop Sciences, Chinese Academy of - Agricultural Sciences, 12 Zhongguancun Nandajie, Haidian District, Beijing - 100081, China. fufu19cn@163.com. -LA - eng -PT - Journal Article -PT - Research Support, Non-U.S. Gov't -DEP - 20140107 -PL - England -TA - BMC Plant Biol -JT - BMC plant biology -JID - 100967807 -RN - 0 (Plant Proteins) -SB - IM -MH - Circadian Rhythm/physiology -MH - Flowers/genetics/*metabolism -MH - Gene Duplication/genetics/physiology -MH - Photoperiod -MH - Phylogeny -MH - Plant Proteins/genetics/metabolism -MH - Soybeans/genetics/*metabolism -PMC - PMC3890618 -EDAT- 2014/01/09 06:00 -MHDA- 2014/09/11 06:00 -CRDT- 2014/01/09 06:00 -PHST- 2013/07/28 00:00 [received] -PHST- 2013/11/25 00:00 [accepted] -PHST- 2014/01/09 06:00 [entrez] -PHST- 2014/01/09 06:00 [pubmed] -PHST- 2014/09/11 06:00 [medline] -AID - 1471-2229-14-9 [pii] -AID - 10.1186/1471-2229-14-9 [doi] -PST - epublish -SO - BMC Plant Biol. 2014 Jan 7;14:9. doi: 10.1186/1471-2229-14-9. - - -##### PUB RECORD ##### -## 10.1186/s12870-016-0704-9 26786479 PMC4719747 Zhao, Takeshima et al., 2016 "Zhao C, Takeshima R, Zhu J, Xu M, Sato M, Watanabe S, Kanazawa A, Liu B, Kong F, Yamada T, Abe J. A recessive allele for delayed flowering at the soybean maturity locus E9 is a leaky allele of FT2a, a FLOWERING LOCUS T ortholog. BMC Plant Biol. 2016 Jan 19;16:20. doi: 10.1186/s12870-016-0704-9. PMID: 26786479; PMCID: PMC4719747." ## - -PMID- 26786479 -OWN - NLM -STAT- MEDLINE -DCOM- 20160906 -LR - 20220330 -IS - 1471-2229 (Electronic) -IS - 1471-2229 (Linking) -VI - 16 -DP - 2016 Jan 19 -TI - A recessive allele for delayed flowering at the soybean maturity locus E9 is a - leaky allele of FT2a, a FLOWERING LOCUS T ortholog. -PG - 20 -LID - 10.1186/s12870-016-0704-9 [doi] -LID - 20 -AB - BACKGROUND: Understanding the molecular mechanisms of flowering and maturity is - important for improving the adaptability and yield of seed crops in different - environments. In soybean, a facultative short-day plant, genetic variation at - four maturity genes, E1 to E4, plays an important role in adaptation to - environments with different photoperiods. However, the molecular basis of natural - variation in time to flowering and maturity is poorly understood. Using a cross - between early-maturing soybean cultivars, we performed a genetic and molecular - study of flowering genes. The progeny of this cross segregated for two maturity - loci, E1 and E9. The latter locus was subjected to detailed molecular analysis to - identify the responsible gene. RESULTS: Fine mapping, sequencing, and expression - analysis revealed that E9 is FT2a, an ortholog of Arabidopsis FLOWERING LOCUS T. - Regardless of daylength conditions, the e9 allele was transcribed at a very low - level in comparison with the E9 allele and delayed flowering. Despite identical - coding sequences, a number of single nucleotide polymorphisms and - insertions/deletions were detected in the promoter, untranslated regions, and - introns between the two cultivars. Furthermore, the e9 allele had a - Ty1/copia-like retrotransposon, SORE-1, inserted in the first intron. Comparison - of the expression levels of different alleles among near-isogenic lines and - photoperiod-insensitive cultivars indicated that the SORE-1 insertion attenuated - FT2a expression by its allele-specific transcriptional repression. SORE-1 was - highly methylated, and did not appear to disrupt FT2a RNA processing. - CONCLUSIONS: The soybean maturity gene E9 is FT2a, and its recessive allele - delays flowering because of lower transcript abundance that is caused by - allele-specific transcriptional repression due to the insertion of SORE-1. The - FT2a transcript abundance is thus directly associated with the variation in - flowering time in soybean. The e9 allele may maintain vegetative growth in - early-flowering genetic backgrounds, and also be useful as a long-juvenile - allele, which causes late flowering under short-daylength conditions, in - low-latitude regions. -FAU - Zhao, Chen -AU - Zhao C -AD - Research Faculty of Agriculture, Hokkaido University, Sapporo, Hokkaido, - 060-8589, Japan. zhaochen_1112@126.com. -FAU - Takeshima, Ryoma -AU - Takeshima R -AD - Research Faculty of Agriculture, Hokkaido University, Sapporo, Hokkaido, - 060-8589, Japan. take-ryo@res.agr.hokudai.ac.jp. -FAU - Zhu, Jianghui -AU - Zhu J -AD - Research Faculty of Agriculture, Hokkaido University, Sapporo, Hokkaido, - 060-8589, Japan. zhu622@res.agr.hokudai.ac.jp. -FAU - Xu, Meilan -AU - Xu M -AD - The Key Laboratory of Soybean Molecular Design Breeding, Northeast Institute of - Geography and Agroecology, Chinese Academy of Sciences, Harbin, 150081, China. - xumeilan_1984@yahoo.co.jp. -FAU - Sato, Masako -AU - Sato M -AD - Research Faculty of Agriculture, Hokkaido University, Sapporo, Hokkaido, - 060-8589, Japan. satomasa@res.agr.hokudai.ac.jp. -FAU - Watanabe, Satoshi -AU - Watanabe S -AD - Faculty of Agriculture, Saga University, Saga, 840-0027, Japan. - nabemame@cc.saga-u.ac.jp. -FAU - Kanazawa, Akira -AU - Kanazawa A -AD - Research Faculty of Agriculture, Hokkaido University, Sapporo, Hokkaido, - 060-8589, Japan. kanazawa@res.agr.hokudai.ac.jp. -FAU - Liu, Baohui -AU - Liu B -AD - The Key Laboratory of Soybean Molecular Design Breeding, Northeast Institute of - Geography and Agroecology, Chinese Academy of Sciences, Harbin, 150081, China. - liubh@neigaehrb.ac.cn. -FAU - Kong, Fanjiang -AU - Kong F -AD - The Key Laboratory of Soybean Molecular Design Breeding, Northeast Institute of - Geography and Agroecology, Chinese Academy of Sciences, Harbin, 150081, China. - kongfj@iga.ac.cn. -FAU - Yamada, Tetsuya -AU - Yamada T -AD - Research Faculty of Agriculture, Hokkaido University, Sapporo, Hokkaido, - 060-8589, Japan. tetsuyay@res.agr.hokudai.ac.jp. -FAU - Abe, Jun -AU - Abe J -AD - Research Faculty of Agriculture, Hokkaido University, Sapporo, Hokkaido, - 060-8589, Japan. jabe@res.agr.hokudai.ac.jp. -LA - eng -PT - Journal Article -PT - Research Support, Non-U.S. Gov't -DEP - 20160119 -PL - England -TA - BMC Plant Biol -JT - BMC plant biology -JID - 100967807 -SB - IM -MH - Alleles -MH - Flowers/*genetics/growth & development -MH - *Genes, Plant -MH - Genes, Recessive -MH - Soybeans/*genetics/growth & development -PMC - PMC4719747 -EDAT- 2016/01/21 06:00 -MHDA- 2016/09/07 06:00 -CRDT- 2016/01/21 06:00 -PHST- 2015/10/16 00:00 [received] -PHST- 2016/01/06 00:00 [accepted] -PHST- 2016/01/21 06:00 [entrez] -PHST- 2016/01/21 06:00 [pubmed] -PHST- 2016/09/07 06:00 [medline] -AID - 10.1186/s12870-016-0704-9 [pii] -AID - 704 [pii] -AID - 10.1186/s12870-016-0704-9 [doi] -PST - epublish -SO - BMC Plant Biol. 2016 Jan 19;16:20. doi: 10.1186/s12870-016-0704-9. - - -##### PUB RECORD ##### -## 10.1371/journal.pone.0089030 24586488 PMC3929636 Zhai et al., 2014 "Zhai H, Lü S, Liang S, Wu H, Zhang X, Liu B, Kong F, Yuan X, Li J, Xia Z. GmFT4, a homolog of FLOWERING LOCUS T, is positively regulated by E1 and functions as a flowering repressor in soybean. PLoS One. 2014 Feb 19;9(2):e89030. doi: 10.1371/journal.pone.0089030. PMID: 24586488; PMCID: PMC3929636." ## - -PMID- 24586488 -OWN - NLM -STAT- MEDLINE -DCOM- 20150110 -LR - 20220409 -IS - 1932-6203 (Electronic) -IS - 1932-6203 (Linking) -VI - 9 -IP - 2 -DP - 2014 -TI - GmFT4, a homolog of FLOWERING LOCUS T, is positively regulated by E1 and - functions as a flowering repressor in soybean. -PG - e89030 -LID - 10.1371/journal.pone.0089030 [doi] -LID - e89030 -AB - The major maturity gene E1 has the most prominent effect on flowering time and - photoperiod sensitivity of soybean, but the pathway mediated by E1 is largely - unknown. Here, we found the expression of GmFT4, a homolog of Flowering Locus T, - was strongly up-regulated in transgenic soybean overexpressing E1, whereas - expression of flowering activators, GmFT2a and GmFT5a, was suppressed. GmFT4 - expression was strongly up-regulated by long days exhibiting a diurnal rhythm, - but down-regulated by short days. Notably, the basal expression level of GmFT4 - was elevated when transferred to continous light, whereas repressed when - transferred to continuous dark. GmFT4 was primarily expressed in fully expanded - leaves. Transcript abundance of GmFT4 was significantly correlated with that of - functional E1, as well as flowering time phenotype in different cultivars. - Overexpression of GmFT4 delayed the flowering time in transgenic Arabidopsis. - Taken together, we propose that GmFT4 acts downstream of E1 and functions as a - flowering repressor, and the balance of two antagonistic factors (GmFT4 vs - GmFT2a/5a) determines the flowering time of soybean. -FAU - Zhai, Hong -AU - Zhai H -AD - Key Laboratory of Soybean Molecular Design Breeding, Northeast Institute of - Geography and Agroecology, Chinese Academy of Sciences, Harbin, Heilongjiang, - China. -FAU - Lu, Shixiang -AU - Lu S -AD - Key Laboratory of Soybean Molecular Design Breeding, Northeast Institute of - Geography and Agroecology, Chinese Academy of Sciences, Harbin, Heilongjiang, - China. -FAU - Liang, Shuang -AU - Liang S -AD - College of Life Science, Northeast Agricultural University, Harbin, Heilongjiang, - China. -FAU - Wu, Hongyan -AU - Wu H -AD - Key Laboratory of Soybean Molecular Design Breeding, Northeast Institute of - Geography and Agroecology, Chinese Academy of Sciences, Harbin, Heilongjiang, - China. -FAU - Zhang, Xingzheng -AU - Zhang X -AD - Key Laboratory of Soybean Molecular Design Breeding, Northeast Institute of - Geography and Agroecology, Chinese Academy of Sciences, Harbin, Heilongjiang, - China. -FAU - Liu, Baohui -AU - Liu B -AD - Key Laboratory of Soybean Molecular Design Breeding, Northeast Institute of - Geography and Agroecology, Chinese Academy of Sciences, Harbin, Heilongjiang, - China. -FAU - Kong, Fanjiang -AU - Kong F -AD - Key Laboratory of Soybean Molecular Design Breeding, Northeast Institute of - Geography and Agroecology, Chinese Academy of Sciences, Harbin, Heilongjiang, - China. -FAU - Yuan, Xiaohui -AU - Yuan X -AD - Key Laboratory of Soybean Molecular Design Breeding, Northeast Institute of - Geography and Agroecology, Chinese Academy of Sciences, Harbin, Heilongjiang, - China. -FAU - Li, Jing -AU - Li J -AD - College of Life Science, Northeast Agricultural University, Harbin, Heilongjiang, - China. -FAU - Xia, Zhengjun -AU - Xia Z -AD - Key Laboratory of Soybean Molecular Design Breeding, Northeast Institute of - Geography and Agroecology, Chinese Academy of Sciences, Harbin, Heilongjiang, - China. -LA - eng -PT - Journal Article -PT - Research Support, Non-U.S. Gov't -DEP - 20140219 -PL - United States -TA - PLoS One -JT - PloS one -JID - 101285081 -RN - 0 (Arabidopsis Proteins) -RN - 0 (FT protein, Arabidopsis) -RN - 0 (Plant Proteins) -RN - 0 (Repressor Proteins) -RN - 0 (Transcription Factors) -SB - IM -MH - Amino Acid Sequence -MH - Arabidopsis/genetics -MH - Arabidopsis Proteins/genetics -MH - Flowers/*genetics -MH - Gene Expression Regulation, Plant -MH - Molecular Sequence Data -MH - Phylogeny -MH - Plant Proteins/*genetics -MH - Plants, Genetically Modified -MH - Repressor Proteins/*genetics -MH - Sequence Homology -MH - Soybeans/*genetics -MH - Transcription Factors/*genetics -PMC - PMC3929636 -COIS- Competing Interests: The authors have declared that no competing interests exist. -EDAT- 2014/03/04 06:00 -MHDA- 2015/01/13 06:00 -CRDT- 2014/03/04 06:00 -PHST- 2013/09/14 00:00 [received] -PHST- 2014/01/19 00:00 [accepted] -PHST- 2014/03/04 06:00 [entrez] -PHST- 2014/03/04 06:00 [pubmed] -PHST- 2015/01/13 06:00 [medline] -AID - PONE-D-13-37961 [pii] -AID - 10.1371/journal.pone.0089030 [doi] -PST - epublish -SO - PLoS One. 2014 Feb 19;9(2):e89030. doi: 10.1371/journal.pone.0089030. eCollection - 2014. - - -##### PUB RECORD ##### -## 10.1371/journal.pone.0097669 24845624 PMC4028237 Nan, Cao et al., 2014 "Nan H, Cao D, Zhang D, Li Y, Lu S, Tang L, Yuan X, Liu B, Kong F. GmFT2a and GmFT5a redundantly and differentially regulate flowering through interaction with and upregulation of the bZIP transcription factor GmFDL19 in soybean. PLoS One. 2014 May 20;9(5):e97669. doi: 10.1371/journal.pone.0097669. PMID: 24845624; PMCID: PMC4028237." ## - -PMID- 24845624 -OWN - NLM -STAT- MEDLINE -DCOM- 20150212 -LR - 20211021 -IS - 1932-6203 (Electronic) -IS - 1932-6203 (Linking) -VI - 9 -IP - 5 -DP - 2014 -TI - GmFT2a and GmFT5a redundantly and differentially regulate flowering through - interaction with and upregulation of the bZIP transcription factor GmFDL19 in - soybean. -PG - e97669 -LID - 10.1371/journal.pone.0097669 [doi] -LID - e97669 -AB - FLOWERING LOCUS T (FT) is the key flowering integrator in Arabidopsis - (Arabidopsis thaliana), and its homologs encode florigens in many plant species - regardless of their photoperiodic response. Two FT homologs, GmFT2a and GmFT5a, - are involved in photoperiod-regulated flowering and coordinately control - flowering in soybean. However, the molecular and genetic understanding of the - roles played by GmFT2a and GmFT5a in photoperiod-regulated flowering in soybean - is very limited. In this study, we demonstrated that GmFT2a and GmFT5a were able - to promote early flowering in soybean by overexpressing these two genes in the - soybean cultivar Williams 82 under noninductive long-day (LD) conditions. The - soybean homologs of several floral identity genes, such as GmAP1, GmSOC1 and - GmLFY, were significantly upregulated by GmFT2a and GmFT5a in a redundant and - differential pattern. A bZIP transcription factor, GmFDL19, was identified as - interacting with both GmFT2a and GmFT5a, and this interaction was confirmed by - yeast two-hybridization and bimolecular fluorescence complementation (BiFC). The - overexpression of GmFDL19 in soybean caused early flowering, and the - transcription levels of the flowering identity genes were also upregulated by - GmFDL19, as was consistent with the upregulation of GmFT2a and GmFT5a. The - transcription of GmFDL19 was also induced by GmFT2a. The results of the - electrophoretic mobility shift assay (EMSA) indicated that GmFDL19 was able to - bind with the cis-elements in the promoter of GmAP1a. Taken together, our results - suggest that GmFT2a and GmFT5a redundantly and differentially control - photoperiod-regulated flowering in soybean through both physical interaction with - and transcriptional upregulation of the bZIP transcription factor GmFDL19, - thereby inducing the expression of floral identity genes. -FAU - Nan, Haiyang -AU - Nan H -AD - The Key of Soybean Molecular Design Breeding, Northeast Institute of Geography - and Agroecology, Chinese Academy of Sciences, Nangang District, Harbin, China; - University of Chinese Academy of Sciences, Beijing, China. -FAU - Cao, Dong -AU - Cao D -AD - The Key of Soybean Molecular Design Breeding, Northeast Institute of Geography - and Agroecology, Chinese Academy of Sciences, Nangang District, Harbin, China. -FAU - Zhang, Dayong -AU - Zhang D -AD - Institute of Biotechnology, Jiangsu Academy of Agricultural Sciences, Nanjing, - China. -FAU - Li, Ying -AU - Li Y -AD - State Key Laboratory of Tree Genetics and Breeding, Northeast Forestry - University, Harbin, China. -FAU - Lu, Sijia -AU - Lu S -AD - The Key of Soybean Molecular Design Breeding, Northeast Institute of Geography - and Agroecology, Chinese Academy of Sciences, Nangang District, Harbin, China; - University of Chinese Academy of Sciences, Beijing, China. -FAU - Tang, Lili -AU - Tang L -AD - The Key of Soybean Molecular Design Breeding, Northeast Institute of Geography - and Agroecology, Chinese Academy of Sciences, Nangang District, Harbin, China. -FAU - Yuan, Xiaohui -AU - Yuan X -AD - The Key of Soybean Molecular Design Breeding, Northeast Institute of Geography - and Agroecology, Chinese Academy of Sciences, Nangang District, Harbin, China. -FAU - Liu, Baohui -AU - Liu B -AD - The Key of Soybean Molecular Design Breeding, Northeast Institute of Geography - and Agroecology, Chinese Academy of Sciences, Nangang District, Harbin, China. -FAU - Kong, Fanjiang -AU - Kong F -AD - The Key of Soybean Molecular Design Breeding, Northeast Institute of Geography - and Agroecology, Chinese Academy of Sciences, Nangang District, Harbin, China. -LA - eng -PT - Journal Article -PT - Research Support, Non-U.S. Gov't -DEP - 20140520 -PL - United States -TA - PLoS One -JT - PloS one -JID - 101285081 -RN - 0 (Plant Proteins) -RN - 0 (Transcription Factors) -SB - IM -MH - Flowers/genetics/*metabolism -MH - Gene Expression Regulation, Plant/*physiology -MH - Plant Proteins/genetics/*metabolism -MH - Soybeans/genetics/*metabolism -MH - Transcription Factors/genetics/*metabolism -MH - Up-Regulation/*physiology -PMC - PMC4028237 -COIS- Competing Interests: The authors have declared that no competing interests exist. -EDAT- 2014/05/23 06:00 -MHDA- 2015/02/13 06:00 -CRDT- 2014/05/22 06:00 -PHST- 2014/03/20 00:00 [received] -PHST- 2014/04/14 00:00 [accepted] -PHST- 2014/05/22 06:00 [entrez] -PHST- 2014/05/23 06:00 [pubmed] -PHST- 2015/02/13 06:00 [medline] -AID - PONE-D-14-12622 [pii] -AID - 10.1371/journal.pone.0097669 [doi] -PST - epublish -SO - PLoS One. 2014 May 20;9(5):e97669. doi: 10.1371/journal.pone.0097669. eCollection - 2014. - - -##### PUB RECORD ##### -## 10.1371/journal.pone.0136601 26371882 PMC4570765 Guo, Xu et al., 2015 "Guo G, Xu K, Zhang X, Zhu J, Lu M, Chen F, Liu L, Xi ZY, Bachmair A, Chen Q, Fu YF. Extensive Analysis of GmFTL and GmCOL Expression in Northern Soybean Cultivars in Field Conditions. PLoS One. 2015 Sep 15;10(9):e0136601. doi: 10.1371/journal.pone.0136601. PMID: 26371882; PMCID: PMC4570765." ## - -PMID- 26371882 -OWN - NLM -STAT- MEDLINE -DCOM- 20160519 -LR - 20181113 -IS - 1932-6203 (Electronic) -IS - 1932-6203 (Linking) -VI - 10 -IP - 9 -DP - 2015 -TI - Extensive Analysis of GmFTL and GmCOL Expression in Northern Soybean Cultivars in - Field Conditions. -PG - e0136601 -LID - 10.1371/journal.pone.0136601 [doi] -LID - e0136601 -AB - The FLOWERING LOCUS T (FT) gene is a highly conserved florigen gene among - flowering plants. Soybean genome encodes six homologs of FT, which display - flowering activity in Arabidopsis thaliana. However, their contributions to - flowering time in different soybean cultivars, especially in field conditions, - are unclear. We employed six soybean cultivars with different maturities to - extensively investigate expression patterns of GmFTLs (Glycine max FT-like) and - GmCOLs (Glycine max CO-like) in the field conditions. The results show that - GmFTL3 is an FT homolog with the highest transcript abundance in soybean, but - other GmFTLs may also contribute to flower induction with different extents, - because they have more or less similar expression patterns in developmental-, - leaf-, and circadian-specific modes. And four GmCOL genes (GmCOL1/2/5/13) may - confer to the expression of GmFTL genes. Artificial manipulation of GmFTL - expression by transgenic strategy (overexpression and RNAi) results in a distinct - change in soybean flowering time, indicating that GmFTLs not only impact on the - control of flowering time, but have potential applications in the manipulation of - photoperiodic adaptation in soybean. Additionally, transgenic plants show that - GmFTLs play a role in formation of the first flowers and in vegetative growth. -FAU - Guo, Guangyu -AU - Guo G -AD - College of Agriculture, Northeast Agricultural University, Harbin, China. -FAU - Xu, Kun -AU - Xu K -AD - MOA Key Lab of Soybean Biology (Beijing), National Key Facility of Crop Gene - Resource and Genetic Improvement, Institute of Crop Sciences, Chinese Academy of - Agricultural Sciences, 12 Zhongguancun Nandajie, Haidian District, Beijing, - China; Graduate School of Chinese Academy of Agricultural Sciences, Beijing, - China. -FAU - Zhang, Xiaomei -AU - Zhang X -AD - MOA Key Lab of Soybean Biology (Beijing), National Key Facility of Crop Gene - Resource and Genetic Improvement, Institute of Crop Sciences, Chinese Academy of - Agricultural Sciences, 12 Zhongguancun Nandajie, Haidian District, Beijing, - China. -FAU - Zhu, Jinlong -AU - Zhu J -AD - MOA Key Lab of Soybean Biology (Beijing), National Key Facility of Crop Gene - Resource and Genetic Improvement, Institute of Crop Sciences, Chinese Academy of - Agricultural Sciences, 12 Zhongguancun Nandajie, Haidian District, Beijing, - China. -FAU - Lu, Mingyang -AU - Lu M -AD - MOA Key Lab of Soybean Biology (Beijing), National Key Facility of Crop Gene - Resource and Genetic Improvement, Institute of Crop Sciences, Chinese Academy of - Agricultural Sciences, 12 Zhongguancun Nandajie, Haidian District, Beijing, - China; Graduate School of Chinese Academy of Agricultural Sciences, Beijing, - China. -FAU - Chen, Fulu -AU - Chen F -AD - MOA Key Lab of Soybean Biology (Beijing), National Key Facility of Crop Gene - Resource and Genetic Improvement, Institute of Crop Sciences, Chinese Academy of - Agricultural Sciences, 12 Zhongguancun Nandajie, Haidian District, Beijing, - China. -FAU - Liu, Linpo -AU - Liu L -AD - MOA Key Lab of Soybean Biology (Beijing), National Key Facility of Crop Gene - Resource and Genetic Improvement, Institute of Crop Sciences, Chinese Academy of - Agricultural Sciences, 12 Zhongguancun Nandajie, Haidian District, Beijing, - China. -FAU - Xi, Zhang-Ying -AU - Xi ZY -AD - College of Agronomy, Henan Agricultural University, Zhengzhou, China. -FAU - Bachmair, Andreas -AU - Bachmair A -AD - Dept. of Biochemistry and Cell Biology, Max F. Perutz Laboratories, University of - Vienna, Vienna Biocenter, Dr. Bohr Gasse 9, A-1030 Vienna, Austria. -FAU - Chen, Qingshan -AU - Chen Q -AD - College of Agriculture, Northeast Agricultural University, Harbin, China. -FAU - Fu, Yong-Fu -AU - Fu YF -AD - MOA Key Lab of Soybean Biology (Beijing), National Key Facility of Crop Gene - Resource and Genetic Improvement, Institute of Crop Sciences, Chinese Academy of - Agricultural Sciences, 12 Zhongguancun Nandajie, Haidian District, Beijing, - China. -LA - eng -PT - Journal Article -PT - Research Support, Non-U.S. Gov't -DEP - 20150915 -PL - United States -TA - PLoS One -JT - PloS one -JID - 101285081 -RN - 0 (Plant Proteins) -RN - 0 (Transcription Factors) -SB - IM -MH - Arabidopsis/genetics/metabolism -MH - Flowers/genetics/*metabolism -MH - Gene Expression Regulation, Plant/*physiology -MH - Plant Proteins/*biosynthesis/genetics -MH - Soybeans/genetics/*metabolism -MH - Transcription Factors/genetics/*metabolism -PMC - PMC4570765 -COIS- Competing Interests: The authors have declared that no competing interests exist. -EDAT- 2015/09/16 06:00 -MHDA- 2016/05/20 06:00 -CRDT- 2015/09/16 06:00 -PHST- 2015/04/28 00:00 [received] -PHST- 2015/08/06 00:00 [accepted] -PHST- 2015/09/16 06:00 [entrez] -PHST- 2015/09/16 06:00 [pubmed] -PHST- 2016/05/20 06:00 [medline] -AID - PONE-D-15-18351 [pii] -AID - 10.1371/journal.pone.0136601 [doi] -PST - epublish -SO - PLoS One. 2015 Sep 15;10(9):e0136601. doi: 10.1371/journal.pone.0136601. - eCollection 2015. - - -##### PUB RECORD ##### -## 10.1534/genetics.108.098772 19474204 PMC2728863 Watanabe, Hideshima et al., 2009 "Watanabe S, Hideshima R, Xia Z, Tsubokura Y, Sato S, Nakamoto Y, Yamanaka N, Takahashi R, Ishimoto M, Anai T, Tabata S, Harada K. Map-based cloning of the gene associated with the soybean maturity locus E3. Genetics. 2009 Aug;182(4):1251-62. doi: 10.1534/genetics.108.098772. Epub 2009 May 27. PMID: 19474204; PMCID: PMC2728863." ## - -PMID- 19474204 -OWN - NLM -STAT- MEDLINE -DCOM- 20100201 -LR - 20220330 -IS - 1943-2631 (Electronic) -IS - 0016-6731 (Print) -IS - 0016-6731 (Linking) -VI - 182 -IP - 4 -DP - 2009 Aug -TI - Map-based cloning of the gene associated with the soybean maturity locus E3. -PG - 1251-62 -LID - 10.1534/genetics.108.098772 [doi] -AB - Photosensitivity plays an essential role in the response of plants to their - changing environments throughout their life cycle. In soybean [Glycine max (L.) - Merrill], several associations between photosensitivity and maturity loci are - known, but only limited information at the molecular level is available. The FT3 - locus is one of the quantitative trait loci (QTL) for flowering time that - corresponds to the maturity locus E3. To identify the gene responsible for this - QTL, a map-based cloning strategy was undertaken. One phytochrome A gene - (GmPhyA3) was considered a strong candidate for the FT3 locus. Allelism tests and - gene sequence comparisons showed that alleles of Misuzudaizu (FT3/FT3; JP28856) - and Harosoy (E3/E3; PI548573) were identical. The GmPhyA3 alleles of Moshidou - Gong 503 (ft3/ft3; JP27603) and L62-667 (e3/e3; PI547716) showed weak or complete - loss of function, respectively. High red/far-red (R/FR) long-day conditions - enhanced the effects of the E3/FT3 alleles in various genetic backgrounds. - Moreover, a mutant line harboring the nonfunctional GmPhyA3 flowered earlier than - the original Bay (E3/E3; PI553043) under similar conditions. These results - suggest that the variation in phytochrome A may contribute to the complex systems - of soybean flowering response and geographic adaptation. -FAU - Watanabe, Satoshi -AU - Watanabe S -AD - National Institute of Agrobiological Sciences, Tsukuba, Ibaraki 305-8602, Japan. -FAU - Hideshima, Rumiko -AU - Hideshima R -FAU - Xia, Zhengjun -AU - Xia Z -FAU - Tsubokura, Yasutaka -AU - Tsubokura Y -FAU - Sato, Shusei -AU - Sato S -FAU - Nakamoto, Yumi -AU - Nakamoto Y -FAU - Yamanaka, Naoki -AU - Yamanaka N -FAU - Takahashi, Ryoji -AU - Takahashi R -FAU - Ishimoto, Masao -AU - Ishimoto M -FAU - Anai, Toyoaki -AU - Anai T -FAU - Tabata, Satoshi -AU - Tabata S -FAU - Harada, Kyuya -AU - Harada K -LA - eng -SI - GENBANK/AB462634 -SI - GENBANK/AB462635 -SI - GENBANK/AB462636 -SI - GENBANK/AB462637 -SI - GENBANK/AB462638 -SI - GENBANK/AB462639 -SI - GENBANK/AB462640 -SI - GENBANK/AB462641 -SI - GENBANK/AB465249 -SI - GENBANK/AB465250 -SI - GENBANK/AB465251 -SI - GENBANK/AB465252 -SI - GENBANK/AB465253 -SI - GENBANK/AB465254 -SI - GENBANK/AB465255 -SI - GENBANK/AB465256 -SI - GENBANK/AB465257 -SI - GENBANK/AB465258 -SI - GENBANK/AB468152 -SI - GENBANK/AB468153 -SI - GENBANK/AB468154 -SI - GENBANK/AB468155 -SI - GENBANK/AP010916 -SI - GENBANK/AP010917 -PT - Journal Article -PT - Research Support, Non-U.S. Gov't -DEP - 20090527 -PL - United States -TA - Genetics -JT - Genetics -JID - 0374636 -RN - 0 (Phytochrome A) -SB - IM -MH - Alleles -MH - Base Sequence -MH - Cloning, Molecular/*methods -MH - Flowers/genetics -MH - Genes, Plant/*genetics -MH - Molecular Sequence Data -MH - Phytochrome A/*genetics -MH - *Quantitative Trait Loci -MH - Soybeans/*genetics -PMC - PMC2728863 -EDAT- 2009/05/29 09:00 -MHDA- 2010/02/02 06:00 -CRDT- 2009/05/29 09:00 -PHST- 2009/05/29 09:00 [entrez] -PHST- 2009/05/29 09:00 [pubmed] -PHST- 2010/02/02 06:00 [medline] -AID - genetics.108.098772 [pii] -AID - gen18241251 [pii] -AID - 10.1534/genetics.108.098772 [doi] -PST - ppublish -SO - Genetics. 2009 Aug;182(4):1251-62. doi: 10.1534/genetics.108.098772. Epub 2009 - May 27. - - -##### PUB RECORD ##### -## 10.1534/genetics.110.125062 21406680 PMC3122305 Watanabe, Xia et al., 2011 "Watanabe S, Xia Z, Hideshima R, Tsubokura Y, Sato S, Yamanaka N, Takahashi R, Anai T, Tabata S, Kitamura K, Harada K. A map-based cloning strategy employing a residual heterozygous line reveals that the GIGANTEA gene is involved in soybean maturity and flowering. Genetics. 2011 Jun;188(2):395-407. doi: 10.1534/genetics.110.125062. Epub 2011 Mar 15. PMID: 21406680; PMCID: PMC3122305." ## - -PMID- 21406680 -OWN - NLM -STAT- MEDLINE -DCOM- 20111020 -LR - 20220420 -IS - 1943-2631 (Electronic) -IS - 0016-6731 (Print) -IS - 0016-6731 (Linking) -VI - 188 -IP - 2 -DP - 2011 Jun -TI - A map-based cloning strategy employing a residual heterozygous line reveals that - the GIGANTEA gene is involved in soybean maturity and flowering. -PG - 395-407 -LID - 10.1534/genetics.110.125062 [doi] -AB - Flowering is indicative of the transition from vegetative to reproductive phase, - a critical event in the life cycle of plants. In soybean (Glycine max), a - flowering quantitative trait locus, FT2, corresponding to the maturity locus E2, - was detected in recombinant inbred lines (RILs) derived from the varieties - "Misuzudaizu" (ft2/ft2; JP28856) and "Moshidou Gong 503" (FT2/FT2; JP27603). A - map-based cloning strategy using the progeny of a residual heterozygous line - (RHL) from the RIL was employed to isolate the gene responsible for this - quantitative trait locus. A GIGANTEA ortholog, GmGIa (Glyma10g36600), was - identified as a candidate gene. A common premature stop codon at the 10th exon - was present in the Misuzudaizu allele and in other near isogenic lines (NILs) - originating from Harosoy (e2/e2; PI548573). Furthermore, a mutant line harboring - another premature stop codon showed an earlier flowering phenotype than the - original variety, Bay (E2/E2; PI553043). The e2/e2 genotype exhibited elevated - expression of GmFT2a, one of the florigen genes that leads to early flowering. - The effects of the E2 allele on flowering time were similar among NILs and - constant under high (43 degrees N) and middle (36 degrees N) latitudinal regions in Japan. These - results indicate that GmGIa is the gene responsible for the E2 locus and that a - null mutation in GmGIa may contribute to the geographic adaptation of soybean. -FAU - Watanabe, Satoshi -AU - Watanabe S -AD - National Institute of Agrobiological Sciences, Tsukuba, Ibaraki, Japan. -FAU - Xia, Zhengjun -AU - Xia Z -FAU - Hideshima, Rumiko -AU - Hideshima R -FAU - Tsubokura, Yasutaka -AU - Tsubokura Y -FAU - Sato, Shusei -AU - Sato S -FAU - Yamanaka, Naoki -AU - Yamanaka N -FAU - Takahashi, Ryoji -AU - Takahashi R -FAU - Anai, Toyoaki -AU - Anai T -FAU - Tabata, Satoshi -AU - Tabata S -FAU - Kitamura, Keisuke -AU - Kitamura K -FAU - Harada, Kyuya -AU - Harada K -LA - eng -SI - GENBANK/AB554196 -SI - GENBANK/AB554197 -SI - GENBANK/AB554198 -SI - GENBANK/AB554199 -SI - GENBANK/AB554200 -SI - GENBANK/AB554201 -SI - GENBANK/AB554202 -SI - GENBANK/AB554203 -SI - GENBANK/AB554204 -SI - GENBANK/AB554205 -SI - GENBANK/AB554206 -SI - GENBANK/AB554207 -SI - GENBANK/AB554208 -SI - GENBANK/AB554209 -SI - GENBANK/AB554210 -SI - GENBANK/AB554211 -SI - GENBANK/AB554212 -SI - GENBANK/AB554213 -SI - GENBANK/AB554214 -SI - GENBANK/AB554215 -SI - GENBANK/AB554216 -SI - GENBANK/AB554217 -SI - GENBANK/AB554218 -SI - GENBANK/AB554219 -SI - GENBANK/AB554220 -SI - GENBANK/AB554221 -SI - GENBANK/AB554222 -SI - GENBANK/AP011810 -SI - GENBANK/AP011811 -SI - GENBANK/AP011813 -SI - GENBANK/AP011821 -SI - GENBANK/AP011822 -PT - Journal Article -PT - Research Support, Non-U.S. Gov't -DEP - 20110315 -PL - United States -TA - Genetics -JT - Genetics -JID - 0374636 -RN - 0 (DNA, Plant) -RN - 0 (Plant Proteins) -RN - 0 (Soybean Proteins) -SB - IM -MH - Acclimatization/genetics -MH - Altitude -MH - Amplified Fragment Length Polymorphism Analysis -MH - Chromosome Mapping -MH - Chromosomes, Plant/genetics -MH - Cloning, Molecular/*methods -MH - DNA, Plant/chemistry/genetics -MH - Flowers/*genetics/growth & development -MH - Gene Expression Regulation, Developmental -MH - Gene Expression Regulation, Plant -MH - Heterozygote -MH - Lod Score -MH - Molecular Sequence Data -MH - Mutation -MH - Phylogeny -MH - Plant Proteins/classification/*genetics -MH - Quantitative Trait Loci/genetics -MH - Reverse Transcriptase Polymerase Chain Reaction -MH - Sequence Analysis, DNA -MH - Soybean Proteins/genetics -MH - Soybeans/*genetics/growth & development -MH - Time Factors -PMC - PMC3122305 -EDAT- 2011/03/17 06:00 -MHDA- 2011/10/21 06:00 -CRDT- 2011/03/17 06:00 -PHST- 2011/03/17 06:00 [entrez] -PHST- 2011/03/17 06:00 [pubmed] -PHST- 2011/10/21 06:00 [medline] -AID - genetics.110.125062 [pii] -AID - 125062 [pii] -AID - 10.1534/genetics.110.125062 [doi] -PST - ppublish -SO - Genetics. 2011 Jun;188(2):395-407. doi: 10.1534/genetics.110.125062. Epub 2011 - Mar 15. - - -##### PUB RECORD ##### -## 10.3389/fpls.2019.01221 31787988 PMC6856076 Wu, Kang et al., 2019 "Wu F, Kang X, Wang M, Haider W, Price WB, Hajek B, Hanzawa Y. Transcriptome-Enabled Network Inference Revealed the GmCOL1 Feed-Forward Loop and Its Roles in Photoperiodic Flowering of Soybean. Front Plant Sci. 2019 Nov 8;10:1221. doi: 10.3389/fpls.2019.01221. PMID: 31787988; PMCID: PMC6856076." ## - -PMID- 31787988 -OWN - NLM -STAT- PubMed-not-MEDLINE -LR - 20201001 -IS - 1664-462X (Print) -IS - 1664-462X (Electronic) -IS - 1664-462X (Linking) -VI - 10 -DP - 2019 -TI - Transcriptome-Enabled Network Inference Revealed the GmCOL1 Feed-Forward Loop and - Its Roles in Photoperiodic Flowering of Soybean. -PG - 1221 -LID - 10.3389/fpls.2019.01221 [doi] -LID - 1221 -AB - Photoperiodic flowering, a plant response to seasonal photoperiod changes in the - control of reproductive transition, is an important agronomic trait that has been - a central target of crop domestication and modern breeding programs. However, our - understanding about the molecular mechanisms of photoperiodic flowering - regulation in crop species is lagging behind. To better understand the regulatory - gene networks controlling photoperiodic flowering of soybeans, we elucidated - global gene expression patterns under different photoperiod regimes using the - near isogenic lines (NILs) of maturity loci (E loci). Transcriptome signatures - identified the unique roles of the E loci in photoperiodic flowering and a set of - genes controlled by these loci. To elucidate the regulatory gene networks - underlying photoperiodic flowering regulation, we developed the network inference - algorithmic package CausNet that integrates sparse linear regression and Granger - causality heuristics, with Gaussian approximation of bootstrapping to provide - reliability scores for predicted regulatory interactions. Using the transcriptome - data, CausNet inferred regulatory interactions among soybean flowering genes. - Published reports in the literature provided empirical verification for several - of CausNet's inferred regulatory interactions. We further confirmed the inferred - regulatory roles of the flowering suppressors GmCOL1a and GmCOL1b using GmCOL1 - RNAi transgenic soybean plants. Combinations of the alleles of GmCOL1 and the - major maturity locus E1 demonstrated positive interaction between these genes, - leading to enhanced suppression of flowering transition. Our work provides novel - insights and testable hypotheses in the complex molecular mechanisms of - photoperiodic flowering control in soybean and lays a framework for de novo - prediction of biological networks controlling important agronomic traits in - crops. -CI - Copyright (c) 2019 Wu, Kang, Wang, Haider, Price, Hajek and Hanzawa. -FAU - Wu, Faqiang -AU - Wu F -AD - Department of Biology, California State University, Northridge, CA, United - States. -FAU - Kang, Xiaohan -AU - Kang X -AD - Department of Electrical Computer Engineering, University of Illinois at - Urbana-Champaign, Champaign, IL, United States. -FAU - Wang, Minglei -AU - Wang M -AD - Department of Crop Sciences, University of Illinois at Urbana-Champaign, - Champaign, IL, United States. -FAU - Haider, Waseem -AU - Haider W -AD - Department of Biosciences, COMSATS University Islamabad, Pakistan. -FAU - Price, William B -AU - Price WB -AD - Department of Electrical Computer Engineering, University of Illinois at - Urbana-Champaign, Champaign, IL, United States. -FAU - Hajek, Bruce -AU - Hajek B -AD - Department of Crop Sciences, University of Illinois at Urbana-Champaign, - Champaign, IL, United States. -FAU - Hanzawa, Yoshie -AU - Hanzawa Y -AD - Department of Biology, California State University, Northridge, CA, United - States. -LA - eng -PT - Journal Article -DEP - 20191108 -PL - Switzerland -TA - Front Plant Sci -JT - Frontiers in plant science -JID - 101568200 -PMC - PMC6856076 -OTO - NOTNLM -OT - Glycine max -OT - feedforward loop -OT - network inference -OT - photoperiodic flowering -OT - transcriptome -EDAT- 2019/12/04 06:00 -MHDA- 2019/12/04 06:01 -CRDT- 2019/12/03 06:00 -PHST- 2019/06/21 00:00 [received] -PHST- 2019/09/04 00:00 [accepted] -PHST- 2019/12/03 06:00 [entrez] -PHST- 2019/12/04 06:00 [pubmed] -PHST- 2019/12/04 06:01 [medline] -AID - 10.3389/fpls.2019.01221 [doi] -PST - epublish -SO - Front Plant Sci. 2019 Nov 8;10:1221. doi: 10.3389/fpls.2019.01221. eCollection - 2019. - - -##### PUB RECORD ##### -## 10.3389/fpls.2021.632754 33995435 PMC8113421 Xia, Zhai et al., 2012 "Xia Z, Zhai H, Wu H, Xu K, Watanabe S, Harada K. The Synchronized Efforts to Decipher the Molecular Basis for Soybean Maturity Loci E1, E2, and E3 That Regulate Flowering and Maturity. Front Plant Sci. 2021 Apr 28;12:632754. doi: 10.3389/fpls.2021.632754. PMID: 33995435; PMCID: PMC8113421." ## - -PMID- 33995435 -OWN - NLM -STAT- PubMed-not-MEDLINE -LR - 20210518 -IS - 1664-462X (Print) -IS - 1664-462X (Electronic) -IS - 1664-462X (Linking) -VI - 12 -DP - 2021 -TI - The Synchronized Efforts to Decipher the Molecular Basis for Soybean Maturity - Loci E1, E2, and E3 That Regulate Flowering and Maturity. -PG - 632754 -LID - 10.3389/fpls.2021.632754 [doi] -LID - 632754 -AB - The general concept of photoperiodism, i.e., the photoperiodic induction of - flowering, was established by Garner and Allard (1920). The genetic factor - controlling flowering time, maturity, or photoperiodic responses was observed in - soybean soon after the discovery of the photoperiodism. E1, E2, and E3 were named - in 1971 and, thereafter, genetically characterized. At the centennial celebration - of the discovery of photoperiodism in soybean, we recount our endeavors to - successfully decipher the molecular bases for the major maturity loci E1, E2, and - E3 in soybean. Through systematic efforts, we successfully cloned the E3 gene in - 2009, the E2 gene in 2011, and the E1 gene in 2012. Recently, successful - identification of several circadian-related genes such as PRR3a, LUX, and J has - enriched the known major E1-FTs pathway. Further research progresses on the - identification of new flowering and maturity-related genes as well as coordinated - regulation between flowering genes will enable us to understand profoundly - flowering gene network and determinants of latitudinal adaptation in soybean. -CI - Copyright (c) 2021 Xia, Zhai, Wu, Xu, Watanabe and Harada. -FAU - Xia, Zhengjun -AU - Xia Z -AD - Key Laboratory of Soybean Molecular Design Breeding, Northeast Institute of - Geography and Agroecology, The Innovative Academy of Seed Design, Chinese Academy - of Sciences, Harbin, China. -FAU - Zhai, Hong -AU - Zhai H -AD - Key Laboratory of Soybean Molecular Design Breeding, Northeast Institute of - Geography and Agroecology, The Innovative Academy of Seed Design, Chinese Academy - of Sciences, Harbin, China. -FAU - Wu, Hongyan -AU - Wu H -AD - Key Laboratory of Soybean Molecular Design Breeding, Northeast Institute of - Geography and Agroecology, The Innovative Academy of Seed Design, Chinese Academy - of Sciences, Harbin, China. -FAU - Xu, Kun -AU - Xu K -AD - Key Laboratory of Soybean Molecular Design Breeding, Northeast Institute of - Geography and Agroecology, The Innovative Academy of Seed Design, Chinese Academy - of Sciences, Harbin, China. -FAU - Watanabe, Satoshi -AU - Watanabe S -AD - Faculty of Agriculture, Saga University, Saga, Japan. -FAU - Harada, Kyuya -AU - Harada K -AD - Department of Biotechnology, Graduate School of Engineering, Osaka University, - Suita, Japan. -LA - eng -PT - Journal Article -PT - Review -DEP - 20210428 -PL - Switzerland -TA - Front Plant Sci -JT - Frontiers in plant science -JID - 101568200 -PMC - PMC8113421 -OTO - NOTNLM -OT - E1 -OT - flowering time -OT - maturity -OT - photoperiodic response -OT - positional cloning -OT - soybean -COIS- The authors declare that the research was conducted in the absence of any - commercial or financial relationships that could be construed as a potential - conflict of interest. -EDAT- 2021/05/18 06:00 -MHDA- 2021/05/18 06:01 -CRDT- 2021/05/17 06:04 -PHST- 2020/11/24 00:00 [received] -PHST- 2021/03/02 00:00 [accepted] -PHST- 2021/05/17 06:04 [entrez] -PHST- 2021/05/18 06:00 [pubmed] -PHST- 2021/05/18 06:01 [medline] -AID - 10.3389/fpls.2021.632754 [doi] -PST - epublish -SO - Front Plant Sci. 2021 Apr 28;12:632754. doi: 10.3389/fpls.2021.632754. - eCollection 2021. - - -##### PUB RECORD ##### -## 10.3389/fpls.2022.889066 35574141 PMC9100572 Dietz, Chan et al., 2023 "Dietz N, Chan YO, Scaboo A, Graef G, Hyten D, Happ M, Diers B, Lorenz A, Wang D, Joshi T, Bilyeu K. Candidate Genes Modulating Reproductive Timing in Elite US Soybean Lines Identified in Soybean Alleles of Arabidopsis Flowering Orthologs With Divergent Latitude Distribution. Front Plant Sci. 2022 Apr 29;13:889066. doi: 10.3389/fpls.2022.889066. PMID: 35574141; PMCID: PMC9100572." ## - -PMID- 35574141 -OWN - NLM -STAT- PubMed-not-MEDLINE -LR - 20220519 -IS - 1664-462X (Print) -IS - 1664-462X (Electronic) -IS - 1664-462X (Linking) -VI - 13 -DP - 2022 -TI - Candidate Genes Modulating Reproductive Timing in Elite US Soybean Lines - Identified in Soybean Alleles of Arabidopsis Flowering Orthologs With Divergent - Latitude Distribution. -PG - 889066 -LID - 10.3389/fpls.2022.889066 [doi] -LID - 889066 -AB - Adaptation of soybean cultivars to the photoperiod in which they are grown is - critical for optimizing plant yield. However, despite its importance, only the - major loci conferring variation in flowering time and maturity of US soybean have - been isolated. By contrast, over 200 genes contributing to floral induction in - the model organism Arabidopsis thaliana have been described. In this work, - putative alleles of a library of soybean orthologs of these Arabidopsis flowering - genes were tested for their latitudinal distribution among elite US soybean lines - developed in the United States. Furthermore, variants comprising the alleles of - genes with significant differences in latitudinal distribution were assessed for - amino acid conservation across disparate genera to infer their impact on gene - function. From these efforts, several candidate genes from various biological - pathways were identified that are likely being exploited toward adaptation of US - soybean to various maturity groups. -CI - Copyright (c) 2022 Dietz, Chan, Scaboo, Graef, Hyten, Happ, Diers, Lorenz, Wang, - Joshi and Bilyeu. -FAU - Dietz, Nicholas -AU - Dietz N -AD - Division of Plant Science and Technology, University of Missouri, Columbia, MO, - United States. -FAU - Chan, Yen On -AU - Chan YO -AD - Christopher S. Bond Life Sciences Center, University of Missouri, Columbia, MO, - United States. -AD - MU Data Science and Informatics Institute, University of Missouri, Columbia, MO, - United States. -FAU - Scaboo, Andrew -AU - Scaboo A -AD - Division of Plant Science and Technology, University of Missouri, Columbia, MO, - United States. -FAU - Graef, George -AU - Graef G -AD - Department of Agronomy and Horticulture, University of Nebraska, Lincoln, NE, - United States. -FAU - Hyten, David -AU - Hyten D -AD - Department of Agronomy and Horticulture, University of Nebraska, Lincoln, NE, - United States. -FAU - Happ, Mary -AU - Happ M -AD - Department of Agronomy and Horticulture, University of Nebraska, Lincoln, NE, - United States. -FAU - Diers, Brian -AU - Diers B -AD - Department of Crop Sciences, University of Illinois, Urbana, IL, United States. -FAU - Lorenz, Aaron -AU - Lorenz A -AD - Department of Agronomy and Plant Genetics, University of Minnesota, Saint Paul, - MN, United States. -FAU - Wang, Dechun -AU - Wang D -AD - Department of Plant, Soil and Microbial Sciences, Michigan State University, East - Lansing, MI, United States. -FAU - Joshi, Trupti -AU - Joshi T -AD - Christopher S. Bond Life Sciences Center, University of Missouri, Columbia, MO, - United States. -AD - MU Data Science and Informatics Institute, University of Missouri, Columbia, MO, - United States. -AD - Department of Electrical Engineering and Computer Science, University of - Missouri, Columbia, MO, United States. -AD - Department of Health Management and Informatics, School of Medicine, University - of Missouri, Columbia, MO, United States. -FAU - Bilyeu, Kristin -AU - Bilyeu K -AD - USDA/ARS Plant Genetics Research Unit, Columbia, MO, United States. -LA - eng -PT - Journal Article -DEP - 20220429 -PL - Switzerland -TA - Front Plant Sci -JT - Frontiers in plant science -JID - 101568200 -PMC - PMC9100572 -OTO - NOTNLM -OT - development -OT - flowering time -OT - genomics -OT - orthologs -OT - reproductive phase -OT - soybean -OT - vegetative phase -COIS- The authors declare that the research was conducted in the absence of any - commercial or financial relationships that could be construed as a potential - conflict of interest. -EDAT- 2022/05/17 06:00 -MHDA- 2022/05/17 06:01 -CRDT- 2022/05/16 04:37 -PHST- 2022/03/03 00:00 [received] -PHST- 2022/04/08 00:00 [accepted] -PHST- 2022/05/16 04:37 [entrez] -PHST- 2022/05/17 06:00 [pubmed] -PHST- 2022/05/17 06:01 [medline] -AID - 10.3389/fpls.2022.889066 [doi] -PST - epublish -SO - Front Plant Sci. 2022 Apr 29;13:889066. doi: 10.3389/fpls.2022.889066. - eCollection 2022. - - -##### PUB RECORD ##### -## 10.1038/s41598-019-42332-5 30979945 PMC6461667 Chen, Fang et al., 2019 "Chen LM, Fang YS, Zhang CJ, Hao QN, Cao D, Yuan SL, Chen HF, Yang ZL, Chen SL, Shan ZH, Liu BH, Jing-Wang, Zhan Y, Zhang XJ, Qiu DZ, Li WB, Zhou XA. GmSYP24, a putative syntaxin gene, confers osmotic/drought, salt stress tolerances and ABA signal pathway. Sci Rep. 2019 Apr 12;9(1):5990. doi: 10.1038/s41598-019-42332-5. PMID: 30979945; PMCID: PMC6461667." ## - -PMID- 30979945 -OWN - NLM -STAT- MEDLINE -DCOM- 20201007 -LR - 20210109 -IS - 2045-2322 (Electronic) -IS - 2045-2322 (Linking) -VI - 9 -IP - 1 -DP - 2019 Apr 12 -TI - GmSYP24, a putative syntaxin gene, confers osmotic/drought, salt stress - tolerances and ABA signal pathway. -PG - 5990 -LID - 10.1038/s41598-019-42332-5 [doi] -LID - 5990 -AB - As major environment factors, drought or high salinity affect crop growth, - development and yield. Transgenic approach is an effective way to improve abiotic - stress tolerance of crops. In this study, we comparatively analyzed gene - structures, genome location, and the evolution of syntaxin proteins containing - late embryogenesis abundant (LEA2) domain. GmSYP24 was identified as a - dehydration-responsive gene. Our study showed that the GmSYP24 protein was - located on the cell membrane. The overexpression of GmSYP24 (GmSYP24ox) in - soybean and heteroexpression of GmSYP24 (GmSYP24hx) in Arabidopsis exhibited - insensitivity to osmotic/drought and high salinity. However, wild type soybean, - Arabidopsis, and the mutant of GmSYP24 homologous gene of Arabidopsis were - sensitive to the stresses. Under the abiotic stresses, transgenic soybean plants - had greater water content and higher activities of POD, SOD compared with - non-transgenic controls. And the leaf stomatal density and opening were reduced - in transgenic Arabidopsis. The sensitivity to ABA was decreased during seed - germination of GmSYP24ox and GmSYP24hx. GmSYP24hx induced up-regulation of - ABA-responsive genes. GmSYP24ox alters the expression of some aquaporins under - osmotic/drought, salt, or ABA treatment. These results demonstrated that GmSYP24 - played an important role in osmotic/drought or salt tolerance in ABA signal - pathway. -FAU - Chen, Li-Miao -AU - Chen LM -AD - Key Laboratory of Oil Crop Biology, Ministry of Agriculture, Wuhan, 430062, - China. -AD - Oil Crops Research Institute of Chinese Academy of Agriculture Sciences, Wuhan, - 430062, China. -FAU - Fang, Yi-Sheng -AU - Fang YS -AD - Key Laboratory of Oil Crop Biology, Ministry of Agriculture, Wuhan, 430062, - China. -AD - Oil Crops Research Institute of Chinese Academy of Agriculture Sciences, Wuhan, - 430062, China. -FAU - Zhang, Chan-Juan -AU - Zhang CJ -AD - Key Laboratory of Oil Crop Biology, Ministry of Agriculture, Wuhan, 430062, - China. -AD - Oil Crops Research Institute of Chinese Academy of Agriculture Sciences, Wuhan, - 430062, China. -FAU - Hao, Qing-Nan -AU - Hao QN -AD - Key Laboratory of Oil Crop Biology, Ministry of Agriculture, Wuhan, 430062, - China. -AD - Oil Crops Research Institute of Chinese Academy of Agriculture Sciences, Wuhan, - 430062, China. -FAU - Cao, Dong -AU - Cao D -AD - Key Laboratory of Oil Crop Biology, Ministry of Agriculture, Wuhan, 430062, - China. -AD - Oil Crops Research Institute of Chinese Academy of Agriculture Sciences, Wuhan, - 430062, China. -FAU - Yuan, Song-Li -AU - Yuan SL -AD - Key Laboratory of Oil Crop Biology, Ministry of Agriculture, Wuhan, 430062, - China. -AD - Oil Crops Research Institute of Chinese Academy of Agriculture Sciences, Wuhan, - 430062, China. -FAU - Chen, Hai-Feng -AU - Chen HF -AD - Key Laboratory of Oil Crop Biology, Ministry of Agriculture, Wuhan, 430062, - China. -AD - Oil Crops Research Institute of Chinese Academy of Agriculture Sciences, Wuhan, - 430062, China. -FAU - Yang, Zhong-Lu -AU - Yang ZL -AD - Key Laboratory of Oil Crop Biology, Ministry of Agriculture, Wuhan, 430062, - China. -AD - Oil Crops Research Institute of Chinese Academy of Agriculture Sciences, Wuhan, - 430062, China. -FAU - Chen, Shui-Lian -AU - Chen SL -AD - Key Laboratory of Oil Crop Biology, Ministry of Agriculture, Wuhan, 430062, - China. -AD - Oil Crops Research Institute of Chinese Academy of Agriculture Sciences, Wuhan, - 430062, China. -FAU - Shan, Zhi-Hui -AU - Shan ZH -AD - Key Laboratory of Oil Crop Biology, Ministry of Agriculture, Wuhan, 430062, - China. -AD - Oil Crops Research Institute of Chinese Academy of Agriculture Sciences, Wuhan, - 430062, China. -FAU - Liu, Bao-Hong -AU - Liu BH -AD - Key Laboratory of Oil Crop Biology, Ministry of Agriculture, Wuhan, 430062, - China. -AD - Oil Crops Research Institute of Chinese Academy of Agriculture Sciences, Wuhan, - 430062, China. -FAU - Jing-Wang -AU - Jing-Wang -AD - Key Laboratory of Oil Crop Biology, Ministry of Agriculture, Wuhan, 430062, - China. -AD - Oil Crops Research Institute of Chinese Academy of Agriculture Sciences, Wuhan, - 430062, China. -FAU - Zhan, Yong -AU - Zhan Y -AD - Crop Research Institute, Xinjiang Academy of Agricultural and Reclamation - Science, Key Lab of Cereal Quality Research and Genetic Improvement, Xinjiang - Production and Construction Crops, 832000, Shihezi, China. -FAU - Zhang, Xiao-Juan -AU - Zhang XJ -AD - Key Laboratory of Oil Crop Biology, Ministry of Agriculture, Wuhan, 430062, - China. -AD - Oil Crops Research Institute of Chinese Academy of Agriculture Sciences, Wuhan, - 430062, China. -FAU - Qiu, De-Zhen -AU - Qiu DZ -AD - Key Laboratory of Oil Crop Biology, Ministry of Agriculture, Wuhan, 430062, - China. -AD - Oil Crops Research Institute of Chinese Academy of Agriculture Sciences, Wuhan, - 430062, China. -FAU - Li, Wen-Bin -AU - Li WB -AD - Key Laboratory of Soybean Biology in the Chinese Ministry of Education, Northeast - Agricultural University, Harbin, 150030, China. wenbinli@yahoo.com. -AD - Division of Soybean Breeding and Seed, Soybean Research & Development Center, - CARS (Key Laboratory of Biology and Genetics & Breeding for Soybean in Northeast - China, Ministry of Agriculture), Harbin, 150030, China. wenbinli@yahoo.com. -FAU - Zhou, Xin-An -AU - Zhou XA -AD - Key Laboratory of Oil Crop Biology, Ministry of Agriculture, Wuhan, 430062, - China. zhouocri@sina.com. -AD - Oil Crops Research Institute of Chinese Academy of Agriculture Sciences, Wuhan, - 430062, China. zhouocri@sina.com. -LA - eng -PT - Journal Article -PT - Research Support, Non-U.S. Gov't -DEP - 20190412 -PL - England -TA - Sci Rep -JT - Scientific reports -JID - 101563288 -RN - 0 (Qa-SNARE Proteins) -RN - 72S9A8J5GW (Abscisic Acid) -SB - IM -MH - Abscisic Acid/*metabolism -MH - Arabidopsis/cytology/genetics/metabolism/physiology -MH - *Droughts -MH - *Osmosis -MH - Phylogeny -MH - Plants, Genetically Modified -MH - Qa-SNARE Proteins/*genetics -MH - Salt Tolerance/*genetics -MH - Seeds/genetics -MH - Signal Transduction/*genetics -MH - Soybeans/genetics -MH - Up-Regulation -PMC - PMC6461667 -COIS- The authors declare no competing interests. -EDAT- 2019/04/14 06:00 -MHDA- 2020/10/08 06:00 -CRDT- 2019/04/14 06:00 -PHST- 2018/08/09 00:00 [received] -PHST- 2019/03/24 00:00 [accepted] -PHST- 2019/04/14 06:00 [entrez] -PHST- 2019/04/14 06:00 [pubmed] -PHST- 2020/10/08 06:00 [medline] -AID - 10.1038/s41598-019-42332-5 [pii] -AID - 42332 [pii] -AID - 10.1038/s41598-019-42332-5 [doi] -PST - epublish -SO - Sci Rep. 2019 Apr 12;9(1):5990. doi: 10.1038/s41598-019-42332-5. - - -##### PUB RECORD ##### -## 10.1007/s11248-019-00180-z 31673914 null Zhang, Luo, et al., 2020 "Zhang L, Luo Y, Liu B, Zhang L, Zhang W, Chen R, Wang L. Overexpression of the maize γ-tocopherol methyltransferase gene (ZmTMT) increases α-tocopherol content in transgenic Arabidopsis and maize seeds. Transgenic Res. 2020 Feb;29(1):95-104. doi: 10.1007/s11248-019-00180-z. Epub 2019 Oct 31. PMID: 31673914." ## - -PMID- 31673914 -OWN - NLM -STAT- MEDLINE -DCOM- 20210607 -LR - 20210607 -IS - 1573-9368 (Electronic) -IS - 0962-8819 (Linking) -VI - 29 -IP - 1 -DP - 2020 Feb -TI - Overexpression of the maize gamma-tocopherol methyltransferase gene (ZmTMT) increases - alpha-tocopherol content in transgenic Arabidopsis and maize seeds. -PG - 95-104 -LID - 10.1007/s11248-019-00180-z [doi] -AB - The vitamin E family includes tocopherols and tocotrienols, which are essential - lipid-soluble antioxidants necessary for human and livestock health. The seeds of - many plant species, including maize, have high gamma (gamma)-tocopherol but low alpha - (alpha)-tocopherol contents; however, alpha-tocopherol is the most effective antioxidant. - Therefore, it is necessary to optimize the tocopherol composition in plants. - alpha-Tocopherol is synthesized from gamma-tocopherol by gamma-tocopherol methyltransferase - (gamma-TMT, VTE4) in the final step of the tocopherol biosynthetic pathway. In the - present study, the full-length coding sequence (CDS) of gamma-TMT was isolated from - Zea mays, named ZmTMT. The ZmTMT CDS was 1059 bp in size, encoding 352 amino - acids. Recombinant ZmTMT was expressed in Escherichia coli and the purified - protein effectively converted gamma-tocopherol into alpha-tocopherol in vitro. A - comparison of enzyme activities showed that the activity of ZmTMT was higher than - that of GmTMT2a (Glycine max) and AtTMT (Arabidopsis thaliana). Overexpression of - ZmTMT increased the alpha-tocopherol content 4-5-fold in transgenic Arabidopsis and - around 6.5-fold in transgenic maize kernels, and increased the alpha-/gamma-tocopherol - ratio to approximately 15 and 17, respectively. These results show that it is - feasible to overexpress ZmTMT to optimize the tocopherol composition in maize; - such a corn product might be useful in the feed industry in the near future. -FAU - Zhang, Lan -AU - Zhang L -AUID- ORCID: 0000-0001-9372-2042 -AD - National Key Facility of Crop Gene Resources and Genetic Improvement, - Biotechnology Research Institute, Chinese Academy of Agricultural Sciences, - Beijing, 100081, China. -FAU - Luo, Yanzhong -AU - Luo Y -AD - National Key Facility of Crop Gene Resources and Genetic Improvement, - Biotechnology Research Institute, Chinese Academy of Agricultural Sciences, - Beijing, 100081, China. -FAU - Liu, Bin -AU - Liu B -AD - National Key Facility of Crop Gene Resources and Genetic Improvement, - Biotechnology Research Institute, Chinese Academy of Agricultural Sciences, - Beijing, 100081, China. -FAU - Zhang, Liang -AU - Zhang L -AD - National Key Facility of Crop Gene Resources and Genetic Improvement, - Biotechnology Research Institute, Chinese Academy of Agricultural Sciences, - Beijing, 100081, China. -FAU - Zhang, Wei -AU - Zhang W -AD - National Key Facility of Crop Gene Resources and Genetic Improvement, - Biotechnology Research Institute, Chinese Academy of Agricultural Sciences, - Beijing, 100081, China. -FAU - Chen, Rumei -AU - Chen R -AD - National Key Facility of Crop Gene Resources and Genetic Improvement, - Biotechnology Research Institute, Chinese Academy of Agricultural Sciences, - Beijing, 100081, China. -FAU - Wang, Lei -AU - Wang L -AD - National Key Facility of Crop Gene Resources and Genetic Improvement, - Biotechnology Research Institute, Chinese Academy of Agricultural Sciences, - Beijing, 100081, China. wanglei01@caas.cn. -LA - eng -GR - 2016ZX08003-002/Earmarked Fund for China Agriculture Research - System/International -PT - Journal Article -PT - Research Support, Non-U.S. Gov't -DEP - 20191031 -PL - Netherlands -TA - Transgenic Res -JT - Transgenic research -JID - 9209120 -RN - EC 2.1.1.- (Methyltransferases) -RN - EC 2.1.1.95 (gamma-tocopherol methyltransferase) -RN - H4N855PNZ1 (alpha-Tocopherol) -SB - IM -MH - Arabidopsis/genetics/*metabolism -MH - Methyltransferases/genetics/*metabolism -MH - Plants, Genetically Modified/genetics/*metabolism -MH - Seeds/genetics/*metabolism -MH - Zea mays/*enzymology -MH - alpha-Tocopherol/*metabolism -OTO - NOTNLM -OT - Zea mays -OT - alpha-/gamma-Tocopherol ratio -OT - alpha-Tocopherol -OT - gamma-Tocopherol methyltransferase (gamma-TMT) -EDAT- 2019/11/02 06:00 -MHDA- 2021/06/08 06:00 -CRDT- 2019/11/02 06:00 -PHST- 2019/08/12 00:00 [received] -PHST- 2019/10/22 00:00 [accepted] -PHST- 2019/11/02 06:00 [pubmed] -PHST- 2021/06/08 06:00 [medline] -PHST- 2019/11/02 06:00 [entrez] -AID - 10.1007/s11248-019-00180-z [pii] -AID - 10.1007/s11248-019-00180-z [doi] -PST - ppublish -SO - Transgenic Res. 2020 Feb;29(1):95-104. doi: 10.1007/s11248-019-00180-z. Epub 2019 - Oct 31. - - -##### PUB RECORD ##### -## 10.1371/journal.pone.0222469 31518373 PMC6743760 Sugawara, Umehara et al., 2019 "Sugawara M, Umehara Y, Kaga A, Hayashi M, Ishimoto M, Sato S, Mitsui H, Minamisawa K. Symbiotic incompatibility between soybean and Bradyrhizobium arises from one amino acid determinant in soybean Rj2 protein. PLoS One. 2019 Sep 13;14(9):e0222469. doi: 10.1371/journal.pone.0222469. PMID: 31518373; PMCID: PMC6743760." ## - -PMID- 31518373 -OWN - NLM -STAT- MEDLINE -DCOM- 20200310 -LR - 20200310 -IS - 1932-6203 (Electronic) -IS - 1932-6203 (Linking) -VI - 14 -IP - 9 -DP - 2019 -TI - Symbiotic incompatibility between soybean and Bradyrhizobium arises from one - amino acid determinant in soybean Rj2 protein. -PG - e0222469 -LID - 10.1371/journal.pone.0222469 [doi] -LID - e0222469 -AB - Cultivated soybean (Glycine max) carrying the Rj2 allele restricts nodulation - with specific Bradyrhizobium strains via host immunity, mediated by rhizobial - type III secretory protein NopP and the host resistance protein Rj2. Here we - found that the single isoleucine residue I490 in Rj2 is required for induction of - symbiotic incompatibility. Furthermore, we investigated the geographical - distribution of the Rj2-genotype soybean in a large set of germplasm by single - nucleotide polymorphism (SNP) genotyping using a SNP marker for I490. By allelic - comparison of 79 accessions in the Japanese soybean mini-core collection, we - suggest substitution of a single amino acid residue (R490 to I490) in Rj2 induces - symbiotic incompatibility with Bradyrhizobium diazoefficiens USDA 122. The - importance of I490 was verified by complementation of rj2-soybean by the dominant - allele encoding the Rj2 protein containing I490 residue. The Rj2 allele was also - found in Glycine soja, the wild progenitor of G. max, and their single amino acid - polymorphisms were associated with the Rj2-nodulation phenotype. By SNP - genotyping against 1583 soybean accessions, we detected the Rj2-genotype in 5.4% - of G. max and 7.7% of G. soja accessions. Distribution of the Rj2-genotype - soybean plants was relatively concentrated in the temperate Asian region. These - results provide important information about the mechanism of host - genotype-specific symbiotic incompatibility mediated by host immunity and suggest - that the Rj2 gene has been maintained by environmental conditions during the - process of soybean domestication. -FAU - Sugawara, Masayuki -AU - Sugawara M -AUID- ORCID: 0000-0002-3058-4348 -AD - Graduate School of Life Sciences, Tohoku University, Sendai, Miyagi, Japan. -FAU - Umehara, Yosuke -AU - Umehara Y -AD - Institute of Agrobiological Sciences, National Agriculture and Food Research - Organization, Tsukuba, Ibaraki, Japan. -FAU - Kaga, Akito -AU - Kaga A -AD - National Institute of Crop Science, National Agriculture and Food Research - Organization, Tsukuba, Ibaraki, Japan. -FAU - Hayashi, Masaki -AU - Hayashi M -AD - Institute of Agrobiological Sciences, National Agriculture and Food Research - Organization, Tsukuba, Ibaraki, Japan. -FAU - Ishimoto, Masao -AU - Ishimoto M -AD - National Institute of Crop Science, National Agriculture and Food Research - Organization, Tsukuba, Ibaraki, Japan. -FAU - Sato, Shusei -AU - Sato S -AD - Graduate School of Life Sciences, Tohoku University, Sendai, Miyagi, Japan. -FAU - Mitsui, Hisayuki -AU - Mitsui H -AD - Graduate School of Life Sciences, Tohoku University, Sendai, Miyagi, Japan. -FAU - Minamisawa, Kiwamu -AU - Minamisawa K -AD - Graduate School of Life Sciences, Tohoku University, Sendai, Miyagi, Japan. -LA - eng -PT - Journal Article -PT - Research Support, Non-U.S. Gov't -DEP - 20190913 -PL - United States -TA - PLoS One -JT - PloS one -JID - 101285081 -RN - 0 (Amino Acids) -RN - 0 (Soybean Proteins) -RN - 0 (Type III Secretion Systems) -SB - IM -MH - Alleles -MH - Amino Acids/*genetics -MH - Bradyrhizobium/*genetics -MH - Genotype -MH - Phenotype -MH - Plant Root Nodulation/genetics -MH - Plant Roots/genetics/microbiology -MH - Polymorphism, Single Nucleotide/genetics -MH - Rhizobium/genetics -MH - Soybean Proteins/*genetics -MH - Soybeans/*genetics/*microbiology -MH - Symbiosis/*genetics -MH - Type III Secretion Systems/*genetics -PMC - PMC6743760 -COIS- The authors have declared that no competing interests exist. -EDAT- 2019/09/14 06:00 -MHDA- 2020/03/11 06:00 -CRDT- 2019/09/14 06:00 -PHST- 2019/06/27 00:00 [received] -PHST- 2019/08/29 00:00 [accepted] -PHST- 2019/09/14 06:00 [entrez] -PHST- 2019/09/14 06:00 [pubmed] -PHST- 2020/03/11 06:00 [medline] -AID - PONE-D-19-18174 [pii] -AID - 10.1371/journal.pone.0222469 [doi] -PST - epublish -SO - PLoS One. 2019 Sep 13;14(9):e0222469. doi: 10.1371/journal.pone.0222469. - eCollection 2019. - - -##### PUB RECORD ##### -## 10.1038/ncomms5340 25004933 PMC4104456 Qi, Li et al., 2014 "Qi X, Li MW, Xie M, Liu X, Ni M, Shao G, Song C, Kay-Yuen Yim A, Tao Y, Wong FL, Isobe S, Wong CF, Wong KS, Xu C, Li C, Wang Y, Guan R, Sun F, Fan G, Xiao Z, Zhou F, Phang TH, Liu X, Tong SW, Chan TF, Yiu SM, Tabata S, Wang J, Xu X, Lam HM. Identification of a novel salt tolerance gene in wild soybean by whole-genome sequencing. Nat Commun. 2014 Jul 9;5:4340. doi: 10.1038/ncomms5340. PMID: 25004933; PMCID: PMC4104456." ## - -PMID- 25004933 -OWN - NLM -STAT- MEDLINE -DCOM- 20151116 -LR - 20220331 -IS - 2041-1723 (Electronic) -IS - 2041-1723 (Linking) -VI - 5 -DP - 2014 Jul 9 -TI - Identification of a novel salt tolerance gene in wild soybean by whole-genome - sequencing. -PG - 4340 -LID - 10.1038/ncomms5340 [doi] -LID - 4340 -AB - Using a whole-genome-sequencing approach to explore germplasm resources can serve - as an important strategy for crop improvement, especially in investigating wild - accessions that may contain useful genetic resources that have been lost during - the domestication process. Here we sequence and assemble a draft genome of wild - soybean and construct a recombinant inbred population for - genotyping-by-sequencing and phenotypic analyses to identify multiple QTLs - relevant to traits of interest in agriculture. We use a combination of de novo - sequencing data from this work and our previous germplasm re-sequencing data to - identify a novel ion transporter gene, GmCHX1, and relate its sequence - alterations to salt tolerance. Rapid gain-of-function tests show the protective - effects of GmCHX1 towards salt stress. This combination of whole-genome de novo - sequencing, high-density-marker QTL mapping by re-sequencing and functional - analyses can serve as an effective strategy to unveil novel genomic information - in wild soybean to facilitate crop improvement. -FAU - Qi, Xinpeng -AU - Qi X -AD - 1] School of Life Sciences and Center for Soybean Research of the State Key - Laboratory of Agrobiotechnology, The Chinese University of Hong Kong, Shatin - HKSAR, Hong Kong [2]. -FAU - Li, Man-Wah -AU - Li MW -AD - 1] School of Life Sciences and Center for Soybean Research of the State Key - Laboratory of Agrobiotechnology, The Chinese University of Hong Kong, Shatin - HKSAR, Hong Kong [2]. -FAU - Xie, Min -AU - Xie M -AD - 1] BGI-Shenzhen, Shenzhen 518083, PR China [2]. -FAU - Liu, Xin -AU - Liu X -AD - BGI-Shenzhen, Shenzhen 518083, PR China. -FAU - Ni, Meng -AU - Ni M -AD - School of Life Sciences and Center for Soybean Research of the State Key - Laboratory of Agrobiotechnology, The Chinese University of Hong Kong, Shatin - HKSAR, Hong Kong. -FAU - Shao, Guihua -AU - Shao G -AD - Institute of Crop Sciences, The Chinese Academy of Agricultural Sciences, Beijing - 100081, PR China. -FAU - Song, Chi -AU - Song C -AD - BGI-Shenzhen, Shenzhen 518083, PR China. -FAU - Kay-Yuen Yim, Aldrin -AU - Kay-Yuen Yim A -AD - School of Life Sciences and Center for Soybean Research of the State Key - Laboratory of Agrobiotechnology, The Chinese University of Hong Kong, Shatin - HKSAR, Hong Kong. -FAU - Tao, Ye -AU - Tao Y -AD - BGI-Shenzhen, Shenzhen 518083, PR China. -FAU - Wong, Fuk-Ling -AU - Wong FL -AD - School of Life Sciences and Center for Soybean Research of the State Key - Laboratory of Agrobiotechnology, The Chinese University of Hong Kong, Shatin - HKSAR, Hong Kong. -FAU - Isobe, Sachiko -AU - Isobe S -AD - Kazusa DNA Research Institute, Chiba 292-0818, Japan. -FAU - Wong, Chi-Fai -AU - Wong CF -AD - School of Life Sciences and Center for Soybean Research of the State Key - Laboratory of Agrobiotechnology, The Chinese University of Hong Kong, Shatin - HKSAR, Hong Kong. -FAU - Wong, Kwong-Sen -AU - Wong KS -AD - School of Life Sciences and Center for Soybean Research of the State Key - Laboratory of Agrobiotechnology, The Chinese University of Hong Kong, Shatin - HKSAR, Hong Kong. -FAU - Xu, Chunyan -AU - Xu C -AD - BGI-Shenzhen, Shenzhen 518083, PR China. -FAU - Li, Chunqing -AU - Li C -AD - BGI-Shenzhen, Shenzhen 518083, PR China. -FAU - Wang, Ying -AU - Wang Y -AD - BGI-Shenzhen, Shenzhen 518083, PR China. -FAU - Guan, Rui -AU - Guan R -AD - BGI-Shenzhen, Shenzhen 518083, PR China. -FAU - Sun, Fengming -AU - Sun F -AD - BGI-Shenzhen, Shenzhen 518083, PR China. -FAU - Fan, Guangyi -AU - Fan G -AD - BGI-Shenzhen, Shenzhen 518083, PR China. -FAU - Xiao, Zhixia -AU - Xiao Z -AD - School of Life Sciences and Center for Soybean Research of the State Key - Laboratory of Agrobiotechnology, The Chinese University of Hong Kong, Shatin - HKSAR, Hong Kong. -FAU - Zhou, Feng -AU - Zhou F -AD - School of Life Sciences and Center for Soybean Research of the State Key - Laboratory of Agrobiotechnology, The Chinese University of Hong Kong, Shatin - HKSAR, Hong Kong. -FAU - Phang, Tsui-Hung -AU - Phang TH -AD - School of Life Sciences and Center for Soybean Research of the State Key - Laboratory of Agrobiotechnology, The Chinese University of Hong Kong, Shatin - HKSAR, Hong Kong. -FAU - Liu, Xuan -AU - Liu X -AD - Department of Computer Science, The University of Hong Kong, Pokfulam HKSAR, Hong - Kong. -FAU - Tong, Suk-Wah -AU - Tong SW -AD - School of Life Sciences and Center for Soybean Research of the State Key - Laboratory of Agrobiotechnology, The Chinese University of Hong Kong, Shatin - HKSAR, Hong Kong. -FAU - Chan, Ting-Fung -AU - Chan TF -AD - School of Life Sciences and Center for Soybean Research of the State Key - Laboratory of Agrobiotechnology, The Chinese University of Hong Kong, Shatin - HKSAR, Hong Kong. -FAU - Yiu, Siu-Ming -AU - Yiu SM -AD - Department of Computer Science, The University of Hong Kong, Pokfulam HKSAR, Hong - Kong. -FAU - Tabata, Satoshi -AU - Tabata S -AD - Kazusa DNA Research Institute, Chiba 292-0818, Japan. -FAU - Wang, Jian -AU - Wang J -AD - BGI-Shenzhen, Shenzhen 518083, PR China. -FAU - Xu, Xun -AU - Xu X -AD - BGI-Shenzhen, Shenzhen 518083, PR China. -FAU - Lam, Hon-Ming -AU - Lam HM -AD - School of Life Sciences and Center for Soybean Research of the State Key - Laboratory of Agrobiotechnology, The Chinese University of Hong Kong, Shatin - HKSAR, Hong Kong. -LA - eng -SI - GENBANK/AZNC00000000 -SI - GENBANK/KF879911 -SI - GENBANK/KF879912 -SI - SRA/SRR1185321 -SI - SRA/SRR1185322 -SI - SRA/SRR1185323 -SI - SRA/SRR1185926 -SI - SRA/SRR1185927 -SI - SRA/SRR1185928 -SI - SRA/SRR1185929 -PT - Journal Article -PT - Research Support, Non-U.S. Gov't -DEP - 20140709 -PL - England -TA - Nat Commun -JT - Nature communications -JID - 101528555 -RN - 0 (Ion Pumps) -RN - 0 (Plant Proteins) -RN - 451W47IQ8X (Sodium Chloride) -SB - IM -MH - Chromosome Mapping -MH - *Genome, Plant -MH - Genotype -MH - Ion Pumps/*genetics/metabolism -MH - Molecular Sequence Data -MH - Plant Proteins/*genetics -MH - Quantitative Trait Loci -MH - *Salt Tolerance -MH - Sodium Chloride/metabolism -MH - Soybeans/*genetics/physiology -PMC - PMC4104456 -EDAT- 2014/07/10 06:00 -MHDA- 2015/11/17 06:00 -CRDT- 2014/07/10 06:00 -PHST- 2014/03/01 00:00 [received] -PHST- 2014/06/09 00:00 [accepted] -PHST- 2014/07/10 06:00 [entrez] -PHST- 2014/07/10 06:00 [pubmed] -PHST- 2015/11/17 06:00 [medline] -AID - ncomms5340 [pii] -AID - 10.1038/ncomms5340 [doi] -PST - epublish -SO - Nat Commun. 2014 Jul 9;5:4340. doi: 10.1038/ncomms5340. - - -##### PUB RECORD ##### -## 10.1534/g3.116.038596 28235823 PMC5386870 Dobbels, Michno et al., 2017 "Dobbels AA, Michno JM, Campbell BW, Virdi KS, Stec AO, Muehlbauer GJ, Naeve SL, Stupar RM. An Induced Chromosomal Translocation in Soybean Disrupts a KASI Ortholog and Is Associated with a High-Sucrose and Low-Oil Seed Phenotype. G3 (Bethesda). 2017 Apr 3;7(4):1215-1223. doi: 10.1534/g3.116.038596. PMID: 28235823; PMCID: PMC5386870." ## - -PMID- 28235823 -OWN - NLM -STAT- MEDLINE -DCOM- 20180710 -LR - 20181113 -IS - 2160-1836 (Electronic) -IS - 2160-1836 (Linking) -VI - 7 -IP - 4 -DP - 2017 Apr 3 -TI - An Induced Chromosomal Translocation in Soybean Disrupts a KASI Ortholog and Is - Associated with a High-Sucrose and Low-Oil Seed Phenotype. -PG - 1215-1223 -LID - 10.1534/g3.116.038596 [doi] -AB - Mutagenesis is a useful tool in many crop species to induce heritable genetic - variability for trait improvement and gene discovery. In this study, forward - screening of a soybean fast neutron (FN) mutant population identified an - individual that produced seed with nearly twice the amount of sucrose (8.1% on - dry matter basis) and less than half the amount of oil (8.5% on dry matter basis) - as compared to wild type. Bulked segregant analysis (BSA), comparative genomic - hybridization, and genome resequencing were used to associate the seed - composition phenotype with a reciprocal translocation between chromosomes 8 and - 13. In a backcross population, the translocation perfectly cosegregated with the - seed composition phenotype and exhibited non-Mendelian segregation patterns. We - hypothesize that the translocation is responsible for the altered seed - composition by disrupting a beta-ketoacyl-[acyl carrier protein] synthase 1 (KASI) - ortholog. KASI is a core fatty acid synthesis enzyme that is involved in the - conversion of sucrose into oil in developing seeds. This finding may lead to new - research directions for developing soybean cultivars with modified carbohydrate - and oil seed composition. -CI - Copyright (c) 2017 Dobbels et al. -FAU - Dobbels, Austin A -AU - Dobbels AA -AD - Department of Agronomy and Plant Genetics, University of Minnesota, St. Paul, - Minnesota 55108. -FAU - Michno, Jean-Michel -AU - Michno JM -AUID- ORCID: 0000-0003-3723-2246 -AD - Department of Agronomy and Plant Genetics, University of Minnesota, St. Paul, - Minnesota 55108. -FAU - Campbell, Benjamin W -AU - Campbell BW -AUID- ORCID: 0000-0002-5510-8583 -AD - Department of Agronomy and Plant Genetics, University of Minnesota, St. Paul, - Minnesota 55108. -FAU - Virdi, Kamaldeep S -AU - Virdi KS -AD - Department of Agronomy and Plant Genetics, University of Minnesota, St. Paul, - Minnesota 55108. -FAU - Stec, Adrian O -AU - Stec AO -AD - Department of Agronomy and Plant Genetics, University of Minnesota, St. Paul, - Minnesota 55108. -FAU - Muehlbauer, Gary J -AU - Muehlbauer GJ -AUID- ORCID: 0000-0001-9320-2629 -AD - Department of Agronomy and Plant Genetics, University of Minnesota, St. Paul, - Minnesota 55108. -AD - Department of Plant Biology, University of Minnesota, St. Paul, Minnesota 55108. -FAU - Naeve, Seth L -AU - Naeve SL -AD - Department of Agronomy and Plant Genetics, University of Minnesota, St. Paul, - Minnesota 55108. -FAU - Stupar, Robert M -AU - Stupar RM -AUID- ORCID: 0000-0002-8836-2924 -AD - Department of Agronomy and Plant Genetics, University of Minnesota, St. Paul, - Minnesota 55108 stup0004@umn.edu. -LA - eng -PT - Journal Article -PT - Research Support, Non-U.S. Gov't -PT - Research Support, U.S. Gov't, Non-P.H.S. -DEP - 20170403 -PL - England -TA - G3 (Bethesda) -JT - G3 (Bethesda, Md.) -JID - 101566598 -RN - 0 (Plant Proteins) -RN - 57-50-1 (Sucrose) -RN - 8001-22-7 (Soybean Oil) -SB - IM -MH - Chromosome Mapping -MH - Chromosomes, Plant/*genetics -MH - Genes, Plant -MH - Heterozygote -MH - Homozygote -MH - Mutation/genetics -MH - Phenotype -MH - Plant Proteins/*genetics -MH - Reproducibility of Results -MH - Seeds/*genetics -MH - *Sequence Homology, Nucleic Acid -MH - Soybean Oil/*metabolism -MH - Soybeans/*genetics -MH - Sucrose/*metabolism -MH - *Translocation, Genetic -PMC - PMC5386870 -OTO - NOTNLM -OT - fast neutron -OT - oil -OT - soybean -OT - sucrose -OT - translocation -EDAT- 2017/02/27 06:00 -MHDA- 2018/07/11 06:00 -CRDT- 2017/02/26 06:00 -PHST- 2017/02/27 06:00 [pubmed] -PHST- 2018/07/11 06:00 [medline] -PHST- 2017/02/26 06:00 [entrez] -AID - g3.116.038596 [pii] -AID - GGG_038596 [pii] -AID - 10.1534/g3.116.038596 [doi] -PST - epublish -SO - G3 (Bethesda). 2017 Apr 3;7(4):1215-1223. doi: 10.1534/g3.116.038596. - - -##### PUB RECORD ##### -## 10.3389/fpls.2017.01604 28979275 PMC5611487 Manan, Ahmad et al., 2017 "Manan S, Ahmad MZ, Zhang G, Chen B, Haq BU, Yang J, Zhao J. Soybean LEC2 Regulates Subsets of Genes Involved in Controlling the Biosynthesis and Catabolism of Seed Storage Substances and Seed Development. Front Plant Sci. 2017 Sep 20;8:1604. doi: 10.3389/fpls.2017.01604. PMID: 28979275; PMCID: PMC5611487." ## - -PMID- 28979275 -OWN - NLM -STAT- PubMed-not-MEDLINE -LR - 20220331 -IS - 1664-462X (Print) -IS - 1664-462X (Electronic) -IS - 1664-462X (Linking) -VI - 8 -DP - 2017 -TI - Soybean LEC2 Regulates Subsets of Genes Involved in Controlling the Biosynthesis - and Catabolism of Seed Storage Substances and Seed Development. -PG - 1604 -LID - 10.3389/fpls.2017.01604 [doi] -LID - 1604 -AB - Soybean is an important oilseed crop and major dietary protein resource, yet the - molecular processes and regulatory mechanisms involved in biosynthesis of seed - storage substances are not fully understood. The B3 domain transcription factor - (TF) LEC2 essentially regulates embryo development and seed maturation in other - plants, but is not functionally characterized in soybean. Here, we characterize - the function of a soybean LEC2 homolog, GmLEC2a, in regulating carbohydrate - catabolism, triacylglycerol (TAG) biosynthesis, and seed development. The - experimental analysis showed that GmLEC2a complemented Arabidopsis atlec2 mutant - defects in seedling development and TAG accumulation. Over-expression of GmLEC2a - in Arabidopsis seeds increased the TAG contents by 34% and the composition of - long chain fatty acids by 4% relative to the control seeds. Transcriptome - analysis showed that ectopic expression of GmLEC2a in soybean hairy roots - up-regulated several sets of downstream TF genes GmLEC1, GmFUS3, GmABI3, GmDof11 - and GmWRI1 that regulate the seed development and production of seed storage - substances. GmLEC2a regulated the lipid transporter genes and oil body protein - gene OLEOSIN (OLE1). The genes involved in carbohydrate biosynthesis and storage, - such as sucrose synthesis, and catabolism of TAG, such as lipases in GmLEC2a - hairy roots were down-regulated. GmLEC2a targeted metabolic genes for seed - protein in soybean. -FAU - Manan, Sehrish -AU - Manan S -AD - National Key Laboratory of Crop Genetic Improvement, Huazhong Agricultural - UniversityWuhan, China. -FAU - Ahmad, Muhammad Z -AU - Ahmad MZ -AD - National Key Laboratory of Crop Genetic Improvement, Huazhong Agricultural - UniversityWuhan, China. -AD - State Key Lab of Tea Plant Biology and Utilization, College of Tea and Food - Science and Technology, Anhui Agricultural UniversityHefei, China. -FAU - Zhang, Gaoyang -AU - Zhang G -AD - National Key Laboratory of Crop Genetic Improvement, Huazhong Agricultural - UniversityWuhan, China. -AD - State Key Lab of Tea Plant Biology and Utilization, College of Tea and Food - Science and Technology, Anhui Agricultural UniversityHefei, China. -FAU - Chen, Beibei -AU - Chen B -AD - National Key Laboratory of Crop Genetic Improvement, Huazhong Agricultural - UniversityWuhan, China. -FAU - Haq, Basir U -AU - Haq BU -AD - National Key Laboratory of Crop Genetic Improvement, Huazhong Agricultural - UniversityWuhan, China. -FAU - Yang, Jihong -AU - Yang J -AD - State Key Lab of Tea Plant Biology and Utilization, College of Tea and Food - Science and Technology, Anhui Agricultural UniversityHefei, China. -FAU - Zhao, Jian -AU - Zhao J -AD - National Key Laboratory of Crop Genetic Improvement, Huazhong Agricultural - UniversityWuhan, China. -AD - State Key Lab of Tea Plant Biology and Utilization, College of Tea and Food - Science and Technology, Anhui Agricultural UniversityHefei, China. -LA - eng -PT - Journal Article -DEP - 20170920 -PL - Switzerland -TA - Front Plant Sci -JT - Frontiers in plant science -JID - 101568200 -PMC - PMC5611487 -OTO - NOTNLM -OT - LEAFY COTYLEDON2 -OT - carbohydrate catabolism -OT - protein biosynthesis -OT - seed storage substances -OT - transcription factor -OT - triacylglycerol -EDAT- 2017/10/06 06:00 -MHDA- 2017/10/06 06:01 -CRDT- 2017/10/06 06:00 -PHST- 2017/06/20 00:00 [received] -PHST- 2017/08/31 00:00 [accepted] -PHST- 2017/10/06 06:00 [entrez] -PHST- 2017/10/06 06:00 [pubmed] -PHST- 2017/10/06 06:01 [medline] -AID - 10.3389/fpls.2017.01604 [doi] -PST - epublish -SO - Front Plant Sci. 2017 Sep 20;8:1604. doi: 10.3389/fpls.2017.01604. eCollection - 2017. - - -##### PUB RECORD ##### -## 10.1007/s11103-013-0133-1 24072327 null RojasRodas, Rodriguez et al., 2013 "Rojas Rodas F, Rodriguez TO, Murai Y, Iwashina T, Sugawara S, Suzuki M, Nakabayashi R, Yonekura-Sakakibara K, Saito K, Kitajima J, Toda K, Takahashi R. Linkage mapping, molecular cloning and functional analysis of soybean gene Fg2 encoding flavonol 3-O-glucoside (1 → 6) rhamnosyltransferase. Plant Mol Biol. 2014 Feb;84(3):287-300. doi: 10.1007/s11103-013-0133-1. Epub 2013 Sep 27. PMID: 24072327." ## - -PMID- 24072327 -OWN - NLM -STAT- MEDLINE -DCOM- 20140227 -LR - 20220309 -IS - 1573-5028 (Electronic) -IS - 0167-4412 (Linking) -VI - 84 -IP - 3 -DP - 2014 Feb -TI - Linkage mapping, molecular cloning and functional analysis of soybean gene Fg2 - encoding flavonol 3-O-glucoside (1 --> 6) rhamnosyltransferase. -PG - 287-300 -LID - 10.1007/s11103-013-0133-1 [doi] -AB - There are substantial genotypic differences in the levels of flavonol glycosides - (FGs) in soybean leaves. The first objective of this study was to identify and - locate genes responsible for FG biosynthesis in the soybean genome. The second - objective was to clone and verify the function of these candidate genes. - Recombinant inbred lines (RILs) were developed by crossing the Kitakomachi and - Koganejiro cultivars. The FGs were separated by high performance liquid - chromatography (HPLC) and identified. The FGs of Koganejiro had rhamnose at the - 6''-position of the glucose or galactose bound to the 3-position of kaempferol, - whereas FGs of Kitakomachi were devoid of rhamnose. Among the 94 RILs, 53 RILs - had HPLC peaks classified as Koganejiro type, and 41 RILs had peaks classified as - Kitakomachi type. The segregation fitted a 1:1 ratio, suggesting that a single - gene controls FG composition. SSR analysis, linkage mapping and genome database - survey revealed a candidate gene in the molecular linkage group O (chromosome - 10). The coding region of the gene from Koganejiro, designated as GmF3G6''Rt-a, is - 1,392 bp long and encodes 464 amino acids, whereas the gene of Kitakomachi, - GmF3G6''Rt-b, has a two-base deletion resulting in a truncated polypeptide - consisting of 314 amino acids. The recombinant GmF3G6''Rt-a protein converted - kaempferol 3-O-glucoside to kaempferol 3-O-rutinoside and utilized - 3-O-glucosylated/galactosylated flavonols and UDP-rhamnose as substrates. - GmF3G6''Rt-b protein had no activity. These results indicate that GmF3G6''Rt - encodes a flavonol 3-O-glucoside (1 --> 6) rhamnosyltransferase and it probably - corresponds to the Fg2 gene. GmF3G6''Rt was designated as UGT79A6 by the UGT - Nomenclature Committee. -FAU - Rojas Rodas, Felipe -AU - Rojas Rodas F -AD - Graduate School of Life and Environmental Sciences, University of Tsukuba, - Tsukuba, Ibaraki, 305-8518, Japan. -FAU - Rodriguez, Tito O -AU - Rodriguez TO -FAU - Murai, Yoshinori -AU - Murai Y -FAU - Iwashina, Tsukasa -AU - Iwashina T -FAU - Sugawara, Satoko -AU - Sugawara S -FAU - Suzuki, Makoto -AU - Suzuki M -FAU - Nakabayashi, Ryo -AU - Nakabayashi R -FAU - Yonekura-Sakakibara, Keiko -AU - Yonekura-Sakakibara K -FAU - Saito, Kazuki -AU - Saito K -FAU - Kitajima, Junichi -AU - Kitajima J -FAU - Toda, Kyoko -AU - Toda K -FAU - Takahashi, Ryoji -AU - Takahashi R -LA - eng -PT - Journal Article -PT - Research Support, Non-U.S. Gov't -DEP - 20130927 -PL - Netherlands -TA - Plant Mol Biol -JT - Plant molecular biology -JID - 9106343 -RN - 0 (DNA Primers) -RN - 0 (DNA, Complementary) -RN - 0 (Recombinant Proteins) -RN - 0 (Soybean Proteins) -RN - EC 2.4.1.- (Hexosyltransferases) -RN - EC 2.4.1.- (flavonol 3-O-glucoside (1-6) rhamnosyltransferase, soybean) -SB - IM -MH - Amino Acid Sequence -MH - Base Sequence -MH - Chromatography, High Pressure Liquid -MH - *Chromosome Mapping -MH - Cloning, Molecular -MH - DNA Primers -MH - DNA, Complementary/genetics -MH - Gene Expression Regulation, Plant -MH - *Genes, Plant -MH - Hexosyltransferases/chemistry/*genetics/isolation & purification -MH - Molecular Sequence Data -MH - Recombinant Proteins/chemistry/genetics/isolation & purification -MH - Sequence Homology, Amino Acid -MH - Soybean Proteins/chemistry/*genetics/isolation & purification -MH - Soybeans/*genetics -EDAT- 2013/09/28 06:00 -MHDA- 2014/02/28 06:00 -CRDT- 2013/09/28 06:00 -PHST- 2013/07/10 00:00 [received] -PHST- 2013/09/17 00:00 [accepted] -PHST- 2013/09/28 06:00 [entrez] -PHST- 2013/09/28 06:00 [pubmed] -PHST- 2014/02/28 06:00 [medline] -AID - 10.1007/s11103-013-0133-1 [doi] -PST - ppublish -SO - Plant Mol Biol. 2014 Feb;84(3):287-300. doi: 10.1007/s11103-013-0133-1. Epub 2013 - Sep 27. - - -##### PUB RECORD ##### -## 10.1016/j.plantsci.2019.110298 31779909 null Bai, Jing et al., 2021 "Bai Y, Jing G, Zhou J, Li S, Bi R, Zhao J, Jia Q, Zhang Q, Zhang W. Overexpression of soybean GmPLDγ enhances seed oil content and modulates fatty acid composition in transgenic Arabidopsis. Plant Sci. 2020 Jan;290:110298. doi: 10.1016/j.plantsci.2019.110298. Epub 2019 Oct 6. Erratum in: Plant Sci. 2021 Jun;307:110881. PMID: 31779909." ## - -PMID- 31779909 -OWN - NLM -STAT- MEDLINE -DCOM- 20200323 -LR - 20210427 -IS - 1873-2259 (Electronic) -IS - 0168-9452 (Linking) -VI - 290 -DP - 2020 Jan -TI - Overexpression of soybean GmPLDgamma enhances seed oil content and modulates fatty - acid composition in transgenic Arabidopsis. -PG - 110298 -LID - S0168-9452(19)30840-4 [pii] -LID - 10.1016/j.plantsci.2019.110298 [doi] -AB - Phospholipase D (PLD) hydrolyzes the phosphodiester bond of glycerophospholipids - to yield phosphatidic acid (PA) and a free headgroup. PLDs are important for - plant growth, development, and responses to external stresses. However, their - roles in triacylglycerol (TAG) synthesis are still unclear. Here, we report that - a soybean (Glycine max) PLDgamma (GmPLDgamma) is involved in glycerolipid turnover and - seed oil production. GmPLDgamma was targeted to mitochondria and exhibited PLD - activity that was activated by oleate and phosphatidylinositol 4,5-bisphosphate - [PtdIns(4,5)P(2)]. Overexpression of GmPLDgamma (abbreviated GmPLDgamma-OE) in - Arabidopsis thaliana resulted in enhanced seed weight, elevated levels of TAGs - with 18-, 20-, and 22-carbon fatty acids (FAs), and altered oil-body morphology. - Furthermore, the levels of membrane lipids in vegetative tissues decreased - significantly, whereas no overt changes were found in mature seeds except for a - decrease in the digalactosyldiacylglycerol (DGDG) level in the GmPLDgamma-OE lines. - Additionally, the expression of genes involved in glycerolipid metabolism was - significantly upregulated in developing siliques in GmPLDgamma-OE lines. Together, - our data indicate a regulatory role for GmPLDgamma in TAG synthesis and fatty-acid - remodeling, highlighting the importance of mitochondria-directed - glycerophospholipid homeostasis in seed oil accumulation. -CI - Copyright (c) 2019 Elsevier B.V. All rights reserved. -FAU - Bai, Yang -AU - Bai Y -AD - College of Life Sciences, State Key Laboratory of Crop Genetics and Germplasm - Enhancement, Nanjing Agricultural University, Nanjing, 210095, PR China. -FAU - Jing, Guangqin -AU - Jing G -AD - College of Life Sciences, State Key Laboratory of Crop Genetics and Germplasm - Enhancement, Nanjing Agricultural University, Nanjing, 210095, PR China. -FAU - Zhou, Jing -AU - Zhou J -AD - College of Life Sciences, State Key Laboratory of Crop Genetics and Germplasm - Enhancement, Nanjing Agricultural University, Nanjing, 210095, PR China. -FAU - Li, Shuxiang -AU - Li S -AD - College of Life Sciences, State Key Laboratory of Crop Genetics and Germplasm - Enhancement, Nanjing Agricultural University, Nanjing, 210095, PR China. -FAU - Bi, Rongrong -AU - Bi R -AD - College of Life Sciences, State Key Laboratory of Crop Genetics and Germplasm - Enhancement, Nanjing Agricultural University, Nanjing, 210095, PR China. -FAU - Zhao, Jiangzhe -AU - Zhao J -AD - College of Life Sciences, State Key Laboratory of Crop Genetics and Germplasm - Enhancement, Nanjing Agricultural University, Nanjing, 210095, PR China. -FAU - Jia, Qianru -AU - Jia Q -AD - College of Life Sciences, State Key Laboratory of Crop Genetics and Germplasm - Enhancement, Nanjing Agricultural University, Nanjing, 210095, PR China. -FAU - Zhang, Qun -AU - Zhang Q -AD - College of Life Sciences, State Key Laboratory of Crop Genetics and Germplasm - Enhancement, Nanjing Agricultural University, Nanjing, 210095, PR China. - Electronic address: zhangqun@njau.edu.cn. -FAU - Zhang, Wenhua -AU - Zhang W -AD - College of Life Sciences, State Key Laboratory of Crop Genetics and Germplasm - Enhancement, Nanjing Agricultural University, Nanjing, 210095, PR China. - Electronic address: whzhang@njau.edu.cn. -LA - eng -PT - Journal Article -DEP - 20191006 -PL - Ireland -TA - Plant Sci -JT - Plant science : an international journal of experimental plant biology -JID - 9882015 -RN - 0 (Fatty Acids) -RN - 0 (Plant Oils) -RN - 0 (Plant Proteins) -RN - EC 3.1.4.4 (Phospholipase D) -SB - IM -EIN - Plant Sci. 2021 Jun;307:110881. PMID: 33902849 -MH - Arabidopsis/genetics/*metabolism -MH - Fatty Acids/*metabolism -MH - *Gene Expression Regulation, Plant -MH - Phospholipase D/*genetics/metabolism -MH - Plant Oils/*metabolism -MH - Plant Proteins/*genetics/metabolism -MH - Plants, Genetically Modified/genetics/metabolism -MH - Seeds/metabolism -MH - Soybeans/*genetics/metabolism -OTO - NOTNLM -OT - Mitochondria -OT - Oil synthesis -OT - Phospholipase Dgamma -OT - Soybean -OT - Transgenic Arabidopsis -EDAT- 2019/11/30 06:00 -MHDA- 2020/03/24 06:00 -CRDT- 2019/11/30 06:00 -PHST- 2019/06/18 00:00 [received] -PHST- 2019/09/23 00:00 [revised] -PHST- 2019/10/02 00:00 [accepted] -PHST- 2019/11/30 06:00 [entrez] -PHST- 2019/11/30 06:00 [pubmed] -PHST- 2020/03/24 06:00 [medline] -AID - S0168-9452(19)30840-4 [pii] -AID - 10.1016/j.plantsci.2019.110298 [doi] -PST - ppublish -SO - Plant Sci. 2020 Jan;290:110298. doi: 10.1016/j.plantsci.2019.110298. Epub 2019 - Oct 6. - - -##### PUB RECORD ##### -## 10.1007/s11248-013-9713-8 23645501 null Zhang, Luo et al., 2013 "Zhang L, Luo Y, Zhu Y, Zhang L, Zhang W, Chen R, Xu M, Fan Y, Wang L. GmTMT2a from soybean elevates the α-tocopherol content in corn and Arabidopsis. Transgenic Res. 2013 Oct;22(5):1021-8. doi: 10.1007/s11248-013-9713-8. Epub 2013 May 4. PMID: 23645501." ## - -PMID- 23645501 -OWN - NLM -STAT- MEDLINE -DCOM- 20140421 -LR - 20211021 -IS - 1573-9368 (Electronic) -IS - 0962-8819 (Linking) -VI - 22 -IP - 5 -DP - 2013 Oct -TI - GmTMT2a from soybean elevates the alpha-tocopherol content in corn and Arabidopsis. -PG - 1021-8 -LID - 10.1007/s11248-013-9713-8 [doi] -AB - Tocochromanol, or vitamin E, plays a crucial role in human and animal nutrition - and is synthesized only by photosynthetic organisms. gamma-Tocopherol - methyltransferase (gamma-TMT), one of the key enzymes in the tocopherol biosynthetic - pathway in plants, converts gamma, delta-tocopherols into alpha-, beta-tocopherols. Tocopherol - content was investigated in 15 soybean cultivars and GmTMT2 was isolated from - five varieties based on tocopherol content. GmTMT2a was expressed in E. coli and - the purified protein effectively converted gamma-tocopherol into alpha-tocopherol in - vitro. Overexpression of GmTMT2a enhanced alpha-tocopherol content 4-6-fold in - transgenic Arabidopsis, and alpha-tocopherol content increased 3-4.5-fold in - transgenic maize seed, which correlated with the accumulation of GmTMT2a. - Transgenic corn that is alpha-tocopherol-rich may be beneficial for animal health and - growth. -FAU - Zhang, Lan -AU - Zhang L -AD - Biotechnology Research Institute, National Key Facility of Crop Gene Resources - and Genetic Improvement, Chinese Academy of Agricultural Sciences, Beijing, - 100081, China. -FAU - Luo, Yanzhong -AU - Luo Y -FAU - Zhu, Yongxing -AU - Zhu Y -FAU - Zhang, Liang -AU - Zhang L -FAU - Zhang, Wei -AU - Zhang W -FAU - Chen, Rumei -AU - Chen R -FAU - Xu, Miaoyun -AU - Xu M -FAU - Fan, Yunliu -AU - Fan Y -FAU - Wang, Lei -AU - Wang L -LA - eng -PT - Journal Article -PT - Research Support, Non-U.S. Gov't -DEP - 20130504 -PL - Netherlands -TA - Transgenic Res -JT - Transgenic research -JID - 9209120 -RN - 0 (DNA Primers) -RN - EC 2.1.1.- (Methyltransferases) -RN - EC 2.1.1.95 (gamma-tocopherol methyltransferase) -RN - H4N855PNZ1 (alpha-Tocopherol) -SB - IM -MH - Arabidopsis/genetics/*metabolism -MH - Chromatography, High Pressure Liquid -MH - DNA Primers/genetics -MH - Enzyme-Linked Immunosorbent Assay -MH - Escherichia coli -MH - Methyltransferases/*genetics/metabolism -MH - Plants, Genetically Modified/genetics/*metabolism -MH - Soybeans/*genetics -MH - Zea mays/genetics/*metabolism -MH - alpha-Tocopherol/*metabolism -EDAT- 2013/05/07 06:00 -MHDA- 2014/04/22 06:00 -CRDT- 2013/05/07 06:00 -PHST- 2012/11/09 00:00 [received] -PHST- 2013/04/25 00:00 [accepted] -PHST- 2013/05/07 06:00 [entrez] -PHST- 2013/05/07 06:00 [pubmed] -PHST- 2014/04/22 06:00 [medline] -AID - 10.1007/s11248-013-9713-8 [doi] -PST - ppublish -SO - Transgenic Res. 2013 Oct;22(5):1021-8. doi: 10.1007/s11248-013-9713-8. Epub 2013 - May 4. - - -##### PUB RECORD ##### -## 10.1016/j.yrtph.2017.01.004 28132846 null Fang, Feng, et al., 2017 "Fang J, Feng Y, Zhi Y, Zhang L, Yu Z, Jia X. A 90-day toxicity study of GmTMT transgenic maize in Sprague-Dawley rats. Regul Toxicol Pharmacol. 2017 Apr;85:48-54. doi: 10.1016/j.yrtph.2017.01.004. Epub 2017 Jan 27. PMID: 28132846." ## - -PMID- 28132846 -OWN - NLM -STAT- MEDLINE -DCOM- 20170327 -LR - 20170327 -IS - 1096-0295 (Electronic) -IS - 0273-2300 (Linking) -VI - 85 -DP - 2017 Apr -TI - A 90-day toxicity study of GmTMT transgenic maize in Sprague-Dawley rats. -PG - 48-54 -LID - S0273-2300(17)30004-1 [pii] -LID - 10.1016/j.yrtph.2017.01.004 [doi] -AB - GmTMT transgenic maize is a genetically modified maize plant that overexpresses - the gamma-tocopherol methyltransferase (gamma-TMT) from Glycine max (Gm). The gamma-TMT gene - was introduced into maize line Zhen58 to encode the GmTMT2a protein which can - convert gamma-tocopherol into alpha-tocopherol. Overexpression of GmTMT2a significantly - increased the alpha-tocopherol content in transgenic maize. The present study was - designed to investigate any potential effects of GmTMT maize grain in a 90-day - subchronic rodent feeding study. Maize grains from GmTMT or Zhen58 were - incorporated into rodent diets at low (12.5%), medium (25%) or high (50%) - concentrations and administered to Sprague-Dawley rats (n = 10/sex/group) for 90 - days. The negative control group of rats (n = 10/sex/group) were fed with common - maize diets. Results from body weights, feed consumption, clinical chemistry, - hematology, absolute and relative organ weights indicated no treatment-related - side effects of GmTMT maize grain on rats in comparison with rats consuming diets - containing Zhen58 maize grain. In addition, no treatment-related changes were - found in necropsy and histopathology examinations. Altogether, our data indicates - that GmTMT transgenic maize is as safe and nutritious as its conventional - non-transgenic maize. -CI - Copyright (c) 2017 Elsevier Inc. All rights reserved. -FAU - Fang, Jin -AU - Fang J -AD - Key Laboratory of Food Safety Risk Assessment of Ministry of Health, National - Center for Food Safety Risk Assessment, Beijing 100021, China. -FAU - Feng, Yongquan -AU - Feng Y -AD - Key Laboratory of Food Safety Risk Assessment of Ministry of Health, National - Center for Food Safety Risk Assessment, Beijing 100021, China. -FAU - Zhi, Yuan -AU - Zhi Y -AD - Key Laboratory of Food Safety Risk Assessment of Ministry of Health, National - Center for Food Safety Risk Assessment, Beijing 100021, China. -FAU - Zhang, Lan -AU - Zhang L -AD - Biotechnology Research Institute, National Key Facility of Crop Gene Resources - and Genetic Improvement, Chinese Academy of Agricultural Sciences, Beijing - 100081, China. -FAU - Yu, Zhou -AU - Yu Z -AD - Key Laboratory of Food Safety Risk Assessment of Ministry of Health, National - Center for Food Safety Risk Assessment, Beijing 100021, China. Electronic - address: yuzhou310@163.com. -FAU - Jia, Xudong -AU - Jia X -AD - Key Laboratory of Food Safety Risk Assessment of Ministry of Health, National - Center for Food Safety Risk Assessment, Beijing 100021, China. Electronic - address: jiaxudong@cfsa.net.cn. -LA - eng -PT - Journal Article -DEP - 20170127 -PL - Netherlands -TA - Regul Toxicol Pharmacol -JT - Regulatory toxicology and pharmacology : RTP -JID - 8214983 -RN - 0 (Plant Proteins) -RN - EC 2.1.1.- (Methyltransferases) -RN - EC 2.1.1.95 (gamma-tocopherol methyltransferase) -SB - IM -MH - Animals -MH - Female -MH - Male -MH - Methyltransferases/*genetics -MH - Plant Proteins/*genetics -MH - Plants, Genetically Modified/*toxicity -MH - Rats, Sprague-Dawley -MH - Soybeans/*enzymology -MH - Toxicity Tests, Subchronic -MH - Zea mays/*genetics -OTO - NOTNLM -OT - Feeding study -OT - Rats -OT - Toxicity -OT - Transgenic maize -EDAT- 2017/01/31 06:00 -MHDA- 2017/03/28 06:00 -CRDT- 2017/01/31 06:00 -PHST- 2016/09/21 00:00 [received] -PHST- 2017/01/22 00:00 [revised] -PHST- 2017/01/24 00:00 [accepted] -PHST- 2017/01/31 06:00 [pubmed] -PHST- 2017/03/28 06:00 [medline] -PHST- 2017/01/31 06:00 [entrez] -AID - S0273-2300(17)30004-1 [pii] -AID - 10.1016/j.yrtph.2017.01.004 [doi] -PST - ppublish -SO - Regul Toxicol Pharmacol. 2017 Apr;85:48-54. doi: 10.1016/j.yrtph.2017.01.004. - Epub 2017 Jan 27. - - -##### PUB RECORD ##### -## 10.1038/s41467-022-34153-4 36307423 PMC9616897 Liang, Chen, et al., 2022 "Liang Q, Chen L, Yang X, Yang H, Liu S, Kou K, Fan L, Zhang Z, Duan Z, Yuan Y, Liang S, Liu Y, Lu X, Zhou G, Zhang M, Kong F, Tian Z. Natural variation of Dt2 determines branching in soybean. Nat Commun. 2022 Oct 28;13(1):6429. doi: 10.1038/s41467-022-34153-4. PMID: 36307423; PMCID: PMC9616897." ## - -PMID- 36307423 -OWN - NLM -STAT- MEDLINE -DCOM- 20221101 -LR - 20221223 -IS - 2041-1723 (Electronic) -IS - 2041-1723 (Linking) -VI - 13 -IP - 1 -DP - 2022 Oct 28 -TI - Natural variation of Dt2 determines branching in soybean. -PG - 6429 -LID - 10.1038/s41467-022-34153-4 [doi] -LID - 6429 -AB - Shoot branching is fundamentally important in determining soybean yield. Here, - through genome-wide association study, we identify one predominant association - locus on chromosome 18 that confers soybean branch number in the natural - population. Further analyses determine that Dt2 is the corresponding gene and the - natural variations in Dt2 result in significant differential transcriptional - levels between the two major haplotypes. Functional characterization reveals that - Dt2 interacts with GmAgl22 and GmSoc1a to physically bind to the promoters of - GmAp1a and GmAp1d and to activate their transcription. Population genetic - investigation show that the genetic differentiation of Dt2 display significant - geographic structure. Our study provides a predominant gene for soybean branch - number and may facilitate the breeding of high-yield soybean varieties. -CI - (c) 2022. The Author(s). -FAU - Liang, Qianjin -AU - Liang Q -AUID- ORCID: 0000-0002-7925-4593 -AD - State Key Laboratory of Plant Cell and Chromosome Engineering, Institute of - Genetics and Developmental Biology, Chinese Academy of Sciences, Beijing, China. -AD - University of Chinese Academy of Sciences, Beijing, China. -FAU - Chen, Liyu -AU - Chen L -AD - Guangdong Provincial Key Laboratory of Plant Adaptation and Molecular Design, - Innovative Center of Molecular Genetics and Evolution, School of Life Sciences, - Guangzhou University, Guangzhou, China. -FAU - Yang, Xia -AU - Yang X -AD - State Key Laboratory of Plant Cell and Chromosome Engineering, Institute of - Genetics and Developmental Biology, Chinese Academy of Sciences, Beijing, China. -AD - University of Chinese Academy of Sciences, Beijing, China. -FAU - Yang, Hui -AU - Yang H -AD - Guangdong Provincial Key Laboratory of Plant Adaptation and Molecular Design, - Innovative Center of Molecular Genetics and Evolution, School of Life Sciences, - Guangzhou University, Guangzhou, China. -FAU - Liu, Shulin -AU - Liu S -AUID- ORCID: 0000-0002-0154-2966 -AD - State Key Laboratory of Plant Cell and Chromosome Engineering, Institute of - Genetics and Developmental Biology, Chinese Academy of Sciences, Beijing, China. -FAU - Kou, Kun -AU - Kou K -AD - Guangdong Provincial Key Laboratory of Plant Adaptation and Molecular Design, - Innovative Center of Molecular Genetics and Evolution, School of Life Sciences, - Guangzhou University, Guangzhou, China. -FAU - Fan, Lei -AU - Fan L -AD - State Key Laboratory of Plant Cell and Chromosome Engineering, Institute of - Genetics and Developmental Biology, Chinese Academy of Sciences, Beijing, China. -FAU - Zhang, Zhifang -AU - Zhang Z -AD - State Key Laboratory of Plant Cell and Chromosome Engineering, Institute of - Genetics and Developmental Biology, Chinese Academy of Sciences, Beijing, China. -FAU - Duan, Zongbiao -AU - Duan Z -AD - State Key Laboratory of Plant Cell and Chromosome Engineering, Institute of - Genetics and Developmental Biology, Chinese Academy of Sciences, Beijing, China. -FAU - Yuan, Yaqin -AU - Yuan Y -AD - State Key Laboratory of Plant Cell and Chromosome Engineering, Institute of - Genetics and Developmental Biology, Chinese Academy of Sciences, Beijing, China. -AD - University of Chinese Academy of Sciences, Beijing, China. -FAU - Liang, Shan -AU - Liang S -AD - State Key Laboratory of Plant Cell and Chromosome Engineering, Institute of - Genetics and Developmental Biology, Chinese Academy of Sciences, Beijing, China. -AD - University of Chinese Academy of Sciences, Beijing, China. -FAU - Liu, Yucheng -AU - Liu Y -AD - State Key Laboratory of Plant Cell and Chromosome Engineering, Institute of - Genetics and Developmental Biology, Chinese Academy of Sciences, Beijing, China. -FAU - Lu, Xingtong -AU - Lu X -AD - State Key Laboratory of Plant Cell and Chromosome Engineering, Institute of - Genetics and Developmental Biology, Chinese Academy of Sciences, Beijing, China. -AD - University of Chinese Academy of Sciences, Beijing, China. -FAU - Zhou, Guoan -AU - Zhou G -AD - State Key Laboratory of Plant Cell and Chromosome Engineering, Institute of - Genetics and Developmental Biology, Chinese Academy of Sciences, Beijing, China. -FAU - Zhang, Min -AU - Zhang M -AD - State Key Laboratory of Plant Cell and Chromosome Engineering, Institute of - Genetics and Developmental Biology, Chinese Academy of Sciences, Beijing, China. -FAU - Kong, Fanjiang -AU - Kong F -AUID- ORCID: 0000-0001-7138-1478 -AD - Guangdong Provincial Key Laboratory of Plant Adaptation and Molecular Design, - Innovative Center of Molecular Genetics and Evolution, School of Life Sciences, - Guangzhou University, Guangzhou, China. kongfj@gzhu.edu.cn. -FAU - Tian, Zhixi -AU - Tian Z -AUID- ORCID: 0000-0001-6051-9670 -AD - State Key Laboratory of Plant Cell and Chromosome Engineering, Institute of - Genetics and Developmental Biology, Chinese Academy of Sciences, Beijing, China. - zxtian@genetics.ac.cn. -AD - University of Chinese Academy of Sciences, Beijing, China. zxtian@genetics.ac.cn. -LA - eng -PT - Journal Article -PT - Research Support, Non-U.S. Gov't -DEP - 20221028 -PL - England -TA - Nat Commun -JT - Nature communications -JID - 101528555 -SB - IM -MH - *Soybeans/genetics -MH - *Genome-Wide Association Study -MH - Plant Breeding -MH - Haplotypes -MH - Polymorphism, Single Nucleotide -PMC - PMC9616897 -COIS- The authors declare no competing interests. -EDAT- 2022/10/29 06:00 -MHDA- 2022/11/02 06:00 -CRDT- 2022/10/28 23:20 -PHST- 2022/05/26 00:00 [received] -PHST- 2022/10/16 00:00 [accepted] -PHST- 2022/10/29 06:00 [pubmed] -PHST- 2022/11/02 06:00 [medline] -PHST- 2022/10/28 23:20 [entrez] -AID - 10.1038/s41467-022-34153-4 [pii] -AID - 34153 [pii] -AID - 10.1038/s41467-022-34153-4 [doi] -PST - epublish -SO - Nat Commun. 2022 Oct 28;13(1):6429. doi: 10.1038/s41467-022-34153-4. - - -##### PUB RECORD ##### -## 10.1105/tpc.114.126938 25005919 PMC4145117 Ping, Liu, et al., 2014 "Ping J, Liu Y, Sun L, Zhao M, Li Y, She M, Sui Y, Lin F, Liu X, Tang Z, Nguyen H, Tian Z, Qiu L, Nelson RL, Clemente TE, Specht JE, Ma J. Dt2 is a gain-of-function MADS-domain factor gene that specifies semideterminacy in soybean. Plant Cell. 2014 Jul;26(7):2831-42. doi: 10.1105/tpc.114.126938. Epub 2014 Jul 8. PMID: 25005919; PMCID: PMC4145117." ## - -PMID- 25005919 -OWN - NLM -STAT- MEDLINE -DCOM- 20150714 -LR - 20211021 -IS - 1532-298X (Electronic) -IS - 1040-4651 (Print) -IS - 1040-4651 (Linking) -VI - 26 -IP - 7 -DP - 2014 Jul -TI - Dt2 is a gain-of-function MADS-domain factor gene that specifies semideterminacy - in soybean. -PG - 2831-42 -LID - 10.1105/tpc.114.126938 [doi] -AB - Similar to Arabidopsis thaliana, the wild soybeans (Glycine soja) and many - cultivars exhibit indeterminate stem growth specified by the shoot identity gene - Dt1, the functional counterpart of Arabidopsis TERMINAL FLOWER1 (TFL1). Mutations - in TFL1 and Dt1 both result in the shoot apical meristem (SAM) switching from - vegetative to reproductive state to initiate terminal flowering and thus produce - determinate stems. A second soybean gene (Dt2) regulating stem growth was - identified, which, in the presence of Dt1, produces semideterminate plants with - terminal racemes similar to those observed in determinate plants. Here, we report - positional cloning and characterization of Dt2, a dominant MADS domain factor - gene classified into the APETALA1/SQUAMOSA (AP1/SQUA) subfamily that includes - floral meristem (FM) identity genes AP1, FUL, and CAL in Arabidopsis. Unlike AP1, - whose expression is limited to FMs in which the expression of TFL1 is repressed, - Dt2 appears to repress the expression of Dt1 in the SAMs to promote early - conversion of the SAMs into reproductive inflorescences. Given that Dt2 is not - the gene most closely related to AP1 and that semideterminacy is rarely seen in - wild soybeans, Dt2 appears to be a recent gain-of-function mutation, which has - modified the genetic pathways determining the stem growth habit in soybean. -CI - (c) 2014 American Society of Plant Biologists. All rights reserved. -FAU - Ping, Jieqing -AU - Ping J -AD - Department of Agronomy, Purdue University, West Lafayette, Indiana 47907. -FAU - Liu, Yunfeng -AU - Liu Y -AD - Department of Agronomy, Purdue University, West Lafayette, Indiana 47907. -FAU - Sun, Lianjun -AU - Sun L -AD - Department of Agronomy, Purdue University, West Lafayette, Indiana 47907. -FAU - Zhao, Meixia -AU - Zhao M -AD - Department of Agronomy, Purdue University, West Lafayette, Indiana 47907. -FAU - Li, Yinghui -AU - Li Y -AD - Institute of Crop Sciences, Chinese Academy of Agricultural Sciences, Beijing - 100081, China. -FAU - She, Maoyun -AU - She M -AD - Department of Agronomy, Purdue University, West Lafayette, Indiana 47907. -FAU - Sui, Yi -AU - Sui Y -AD - Department of Agronomy, Purdue University, West Lafayette, Indiana 47907. -FAU - Lin, Feng -AU - Lin F -AD - Department of Agronomy, Purdue University, West Lafayette, Indiana 47907. -FAU - Liu, Xiaodong -AU - Liu X -AD - Department of Agronomy, Purdue University, West Lafayette, Indiana 47907. -FAU - Tang, Zongxiang -AU - Tang Z -AD - Department of Agronomy, Purdue University, West Lafayette, Indiana 47907. -FAU - Nguyen, Hanh -AU - Nguyen H -AD - Department of Agronomy and Horticulture/Center for Plant Science Innovation, - University of Nebraska, Lincoln, Nebraska 68583. -FAU - Tian, Zhixi -AU - Tian Z -AD - Department of Agronomy, Purdue University, West Lafayette, Indiana 47907. -FAU - Qiu, Lijuan -AU - Qiu L -AD - Institute of Crop Sciences, Chinese Academy of Agricultural Sciences, Beijing - 100081, China. -FAU - Nelson, Randall L -AU - Nelson RL -AD - Soybean/Maize Germplasm, Pathology, and Genetics Research Unit, U.S. Department - of Agriculture-Agricultural Research Service, Department of Crop Sciences, - University of Illinois, Urbana, Illinois 61801. -FAU - Clemente, Thomas E -AU - Clemente TE -AD - Department of Agronomy and Horticulture/Center for Plant Science Innovation, - University of Nebraska, Lincoln, Nebraska 68583. -FAU - Specht, James E -AU - Specht JE -AD - Department of Agronomy and Horticulture/Center for Plant Science Innovation, - University of Nebraska, Lincoln, Nebraska 68583. -FAU - Ma, Jianxin -AU - Ma J -AD - Department of Agronomy, Purdue University, West Lafayette, Indiana 47907 - maj@purdue.edu. -LA - eng -SI - GENBANK/KF908014 -SI - GENBANK/KF908015 -PT - Journal Article -PT - Research Support, Non-U.S. Gov't -PT - Research Support, U.S. Gov't, Non-P.H.S. -DEP - 20140708 -PL - England -TA - Plant Cell -JT - The Plant cell -JID - 9208688 -RN - 0 (MADS Domain Proteins) -RN - 0 (Plant Proteins) -SB - IM -MH - Arabidopsis/genetics -MH - Base Sequence -MH - Chromosome Mapping -MH - Chromosomes, Plant/*genetics -MH - Flowers/genetics/growth & development -MH - Gene Expression Regulation, Developmental -MH - *Gene Expression Regulation, Plant -MH - Genetic Linkage -MH - Genetic Loci -MH - MADS Domain Proteins/*genetics/metabolism -MH - Meristem/genetics/growth & development -MH - Molecular Sequence Data -MH - Mutation -MH - Phenotype -MH - Phylogeny -MH - Plant Proteins/genetics/metabolism -MH - Plant Stems/genetics/growth & development -MH - Plants, Genetically Modified -MH - Sequence Analysis, DNA -MH - Soybeans/*genetics/growth & development -PMC - PMC4145117 -EDAT- 2014/07/10 06:00 -MHDA- 2015/07/15 06:00 -CRDT- 2014/07/10 06:00 -PHST- 2014/07/10 06:00 [entrez] -PHST- 2014/07/10 06:00 [pubmed] -PHST- 2015/07/15 06:00 [medline] -AID - tpc.114.126938 [pii] -AID - 126938 [pii] -AID - 10.1105/tpc.114.126938 [doi] -PST - ppublish -SO - Plant Cell. 2014 Jul;26(7):2831-42. doi: 10.1105/tpc.114.126938. Epub 2014 Jul 8. - - -##### PUB RECORD ##### -## 10.1016/j.plantsci.2019.110386 32005391 null Tian, Liu et al., 2019 "Tian SN, Liu DD, Zhong CL, Xu HY, Yang S, Fang Y, Ran J, Liu JZ. Silencing GmFLS2 enhances the susceptibility of soybean to bacterial pathogen through attenuating the activation of GmMAPK signaling pathway. Plant Sci. 2020 Mar;292:110386. doi: 10.1016/j.plantsci.2019.110386. Epub 2019 Dec 24. PMID: 32005391." ## - -PMID- 32005391 -OWN - NLM -STAT- MEDLINE -DCOM- 20200831 -LR - 20200930 -IS - 1873-2259 (Electronic) -IS - 0168-9452 (Linking) -VI - 292 -DP - 2020 Mar -TI - Silencing GmFLS2 enhances the susceptibility of soybean to bacterial pathogen - through attenuating the activation of GmMAPK signaling pathway. -PG - 110386 -LID - S0168-9452(19)31559-6 [pii] -LID - 10.1016/j.plantsci.2019.110386 [doi] -AB - The plasma membrane (PM)-localized receptor-like kinases (RLKs) play important - roles in pathogen defense. One of the first cloned RLKs is the Arabidopsis - receptor kinase FLAGELLIN SENSING 2 (FLS2), which specifically recognizes a - conserved 22 amino acid N-terminal sequence of Pseudomonas syringae pv.tomato - DC3000 (Pst) flagellin protein (flg22). Although extensively studied in - Arabidopsis, the functions of RLKs in crop plants remain largely uninvestigated. - To understand the roles of RLKs in soybean (Glycine max), GmFLS2 was silenced via - virus induced gene silencing (VIGS) mediated by Bean pod mottle virus (BPMV). No - significant morphological differences were observed between GmFLS2-silenced - plants and the vector control plants. However, silencing GmFLS2 significantly - enhanced the susceptibility of the soybean plants to Pseudomonas syringae - pv.glycinea (Psg). Kinase activity assay showed that silencing GmFLS2 - significantly reduced the phosphorylation level of GmMPK6 in response to flg22 - treatment. However, reduced phosphorylation level of both GmMPK3 and GmMPK6 in - response to Psg infection was observed in GmFLS2-silenced plants, implying that - defense response is likely transduced through activation of the downstream GmMAPK - signaling pathway upon recognition of bacterial pathogen by GmFLS2. The core - peptides of flg22 from Pst and Psg were highly conserved and only 4 amino acid - differences were seen at their N-termini. Interestingly, it appeared that the - Psg-flg22 was more effective in activating soybean MAPKs than activating - Arabidopsis MAPKs, and conversely, Pst-flg22 was more effective in activating - Arabidopsis MAPKs than activating soybean MAPKs, suggesting that the cognate - recognition is more potent than heterologous recognition in activating downstream - signaling. Taken together, our results suggest that the function of FLS2 is - conserved in immunity against bacteria pathogens across different plant species. -CI - Copyright (c) 2019. Published by Elsevier B.V. -FAU - Tian, Sheng-Nan -AU - Tian SN -AD - College of Chemistry and Life Sciences, Zhejiang Normal University, Jinhua, - Zhejiang Province, 321004, China. -FAU - Liu, Dan-Dan -AU - Liu DD -AD - College of Chemistry and Life Sciences, Zhejiang Normal University, Jinhua, - Zhejiang Province, 321004, China. -FAU - Zhong, Chen-Li -AU - Zhong CL -AD - College of Chemistry and Life Sciences, Zhejiang Normal University, Jinhua, - Zhejiang Province, 321004, China. -FAU - Xu, Hui-Yang -AU - Xu HY -AD - College of Chemistry and Life Sciences, Zhejiang Normal University, Jinhua, - Zhejiang Province, 321004, China. -FAU - Yang, Shuo -AU - Yang S -AD - College of Chemistry and Life Sciences, Zhejiang Normal University, Jinhua, - Zhejiang Province, 321004, China. -FAU - Fang, Yuan -AU - Fang Y -AD - College of Chemistry and Life Sciences, Zhejiang Normal University, Jinhua, - Zhejiang Province, 321004, China. -FAU - Ran, Jie -AU - Ran J -AD - College of Chemistry and Life Sciences, Zhejiang Normal University, Jinhua, - Zhejiang Province, 321004, China. -FAU - Liu, Jian-Zhong -AU - Liu JZ -AD - College of Chemistry and Life Sciences, Zhejiang Normal University, Jinhua, - Zhejiang Province, 321004, China. Electronic address: jzliu@zjnu.cn. -LA - eng -PT - Journal Article -DEP - 20191224 -PL - Ireland -TA - Plant Sci -JT - Plant science : an international journal of experimental plant biology -JID - 9882015 -RN - 0 (Plant Proteins) -RN - EC 2.7.- (Protein Kinases) -RN - Bean pod mottle virus -SB - IM -MH - Comovirus -MH - *Gene Silencing -MH - Plant Diseases/*genetics/microbiology -MH - Plant Proteins/*genetics/metabolism -MH - Protein Kinases/*genetics/metabolism -MH - Pseudomonas syringae/*physiology -MH - Soybeans/*genetics/*microbiology -OTO - NOTNLM -OT - FLAGELLIN SENSING 2 (FLS2) -OT - MAPK -OT - Soybean -OT - Virus-induced gene silencing (VIGS) -OT - flg22 -COIS- Declaration of Competing Interest The authors declare that they have no known - competing financial interests or personal relationships that could have appeared - to influence the work reported in this paper. -EDAT- 2020/02/02 06:00 -MHDA- 2020/09/01 06:00 -CRDT- 2020/02/02 06:00 -PHST- 2019/10/13 00:00 [received] -PHST- 2019/12/16 00:00 [revised] -PHST- 2019/12/21 00:00 [accepted] -PHST- 2020/02/02 06:00 [entrez] -PHST- 2020/02/02 06:00 [pubmed] -PHST- 2020/09/01 06:00 [medline] -AID - S0168-9452(19)31559-6 [pii] -AID - 10.1016/j.plantsci.2019.110386 [doi] -PST - ppublish -SO - Plant Sci. 2020 Mar;292:110386. doi: 10.1016/j.plantsci.2019.110386. Epub 2019 - Dec 24. - - -##### PUB RECORD ##### -## 10.1104/pp.114.242495 24872380 PMC4081336 Wang, Shine et al., 2014 "Wang J, Shine MB, Gao QM, Navarre D, Jiang W, Liu C, Chen Q, Hu G, Kachroo A. Enhanced Disease Susceptibility1 Mediates Pathogen Resistance and Virulence Function of a Bacterial Effector in Soybean. Plant Physiol. 2014 Jul;165(3):1269-1284. doi: 10.1104/pp.114.242495. Epub 2014 May 28. PMID: 24872380; PMCID: PMC4081336." ## - -PMID- 24872380 -OWN - NLM -STAT- PubMed-not-MEDLINE -LR - 20220331 -IS - 1532-2548 (Electronic) -IS - 0032-0889 (Print) -IS - 0032-0889 (Linking) -VI - 165 -IP - 3 -DP - 2014 Jul -TI - Enhanced Disease Susceptibility1 Mediates Pathogen Resistance and Virulence - Function of a Bacterial Effector in Soybean. -PG - 1269-1284 -AB - Enhanced disease susceptibility1 (EDS1) and phytoalexin deficient4 (PAD4) are - well-known regulators of both basal and resistance (R) protein-mediated plant - defense. We identified two EDS1-like (GmEDS1a/GmEDS1b) proteins and one PAD4-like - (GmPAD4) protein that are required for resistance signaling in soybean (Glycine - max). Consistent with their significant structural conservation to Arabidopsis - (Arabidopsis thaliana) counterparts, constitutive expression of GmEDS1 or GmPAD4 - complemented the pathogen resistance defects of Arabidopsis eds1 and pad4 - mutants, respectively. Interestingly, however, the GmEDS1 and GmPAD4 did not - complement pathogen-inducible salicylic acid accumulation in the eds1/pad4 - mutants. Furthermore, the GmEDS1a/GmEDS1b proteins were unable to complement the - turnip crinkle virus coat protein-mediated activation of the Arabidopsis R - protein Hypersensitive reaction to Turnip crinkle virus (HRT), even though both - interacted with HRT. Silencing GmEDS1a/GmEDS1b or GmPAD4 reduced basal and - pathogen-inducible salicylic acid accumulation and enhanced soybean - susceptibility to virulent pathogens. The GmEDS1a/GmEDS1b and GmPAD4 genes were - also required for Resistance to Pseudomonas syringae pv glycinea2 (Rpg2)-mediated - resistance to Pseudomonas syringae. Notably, the GmEDS1a/GmEDS1b proteins - interacted with the cognate bacterial effector AvrA1 and were required for its - virulence function in rpg2 plants. Together, these results show that despite - significant structural similarities, conserved defense signaling components from - diverse plants can differ in their functionalities. In addition, we demonstrate a - role for GmEDS1 in regulating the virulence function of a bacterial effector. -CI - (c) 2014 American Society of Plant Biologists. All Rights Reserved. -FAU - Wang, Jialin -AU - Wang J -AD - College of Agriculture, Northeast Agricultural University, Harbin 150030, China - (J.W., W.J., Q.C., G.H.);Department of Plant Pathology, University of Kentucky, - Lexington, Kentucky 40546 (J.W., M.B.S., Q.-M.G., A.K.);United States Department - of Agriculture-Agricultural Research Service, Washington State University, - Prosser, Washington 99350 (D.N.); andLand Reclamation Research and Breeding - Centre of Heilongjiang, Harbin 150090, China (C.L., G.H.). -FAU - Shine, M B -AU - Shine MB -AD - College of Agriculture, Northeast Agricultural University, Harbin 150030, China - (J.W., W.J., Q.C., G.H.);Department of Plant Pathology, University of Kentucky, - Lexington, Kentucky 40546 (J.W., M.B.S., Q.-M.G., A.K.);United States Department - of Agriculture-Agricultural Research Service, Washington State University, - Prosser, Washington 99350 (D.N.); andLand Reclamation Research and Breeding - Centre of Heilongjiang, Harbin 150090, China (C.L., G.H.). -FAU - Gao, Qing-Ming -AU - Gao QM -AD - College of Agriculture, Northeast Agricultural University, Harbin 150030, China - (J.W., W.J., Q.C., G.H.);Department of Plant Pathology, University of Kentucky, - Lexington, Kentucky 40546 (J.W., M.B.S., Q.-M.G., A.K.);United States Department - of Agriculture-Agricultural Research Service, Washington State University, - Prosser, Washington 99350 (D.N.); andLand Reclamation Research and Breeding - Centre of Heilongjiang, Harbin 150090, China (C.L., G.H.). -FAU - Navarre, Duroy -AU - Navarre D -AD - College of Agriculture, Northeast Agricultural University, Harbin 150030, China - (J.W., W.J., Q.C., G.H.);Department of Plant Pathology, University of Kentucky, - Lexington, Kentucky 40546 (J.W., M.B.S., Q.-M.G., A.K.);United States Department - of Agriculture-Agricultural Research Service, Washington State University, - Prosser, Washington 99350 (D.N.); andLand Reclamation Research and Breeding - Centre of Heilongjiang, Harbin 150090, China (C.L., G.H.). -FAU - Jiang, Wei -AU - Jiang W -AD - College of Agriculture, Northeast Agricultural University, Harbin 150030, China - (J.W., W.J., Q.C., G.H.);Department of Plant Pathology, University of Kentucky, - Lexington, Kentucky 40546 (J.W., M.B.S., Q.-M.G., A.K.);United States Department - of Agriculture-Agricultural Research Service, Washington State University, - Prosser, Washington 99350 (D.N.); andLand Reclamation Research and Breeding - Centre of Heilongjiang, Harbin 150090, China (C.L., G.H.). -FAU - Liu, Chunyan -AU - Liu C -AD - College of Agriculture, Northeast Agricultural University, Harbin 150030, China - (J.W., W.J., Q.C., G.H.);Department of Plant Pathology, University of Kentucky, - Lexington, Kentucky 40546 (J.W., M.B.S., Q.-M.G., A.K.);United States Department - of Agriculture-Agricultural Research Service, Washington State University, - Prosser, Washington 99350 (D.N.); andLand Reclamation Research and Breeding - Centre of Heilongjiang, Harbin 150090, China (C.L., G.H.). -FAU - Chen, Qingshan -AU - Chen Q -AD - College of Agriculture, Northeast Agricultural University, Harbin 150030, China - (J.W., W.J., Q.C., G.H.);Department of Plant Pathology, University of Kentucky, - Lexington, Kentucky 40546 (J.W., M.B.S., Q.-M.G., A.K.);United States Department - of Agriculture-Agricultural Research Service, Washington State University, - Prosser, Washington 99350 (D.N.); andLand Reclamation Research and Breeding - Centre of Heilongjiang, Harbin 150090, China (C.L., G.H.). -FAU - Hu, Guohua -AU - Hu G -AD - College of Agriculture, Northeast Agricultural University, Harbin 150030, China - (J.W., W.J., Q.C., G.H.);Department of Plant Pathology, University of Kentucky, - Lexington, Kentucky 40546 (J.W., M.B.S., Q.-M.G., A.K.);United States Department - of Agriculture-Agricultural Research Service, Washington State University, - Prosser, Washington 99350 (D.N.); andLand Reclamation Research and Breeding - Centre of Heilongjiang, Harbin 150090, China (C.L., G.H.) apkach2@uky.edu - hugh757@vip.163.com. -FAU - Kachroo, Aardra -AU - Kachroo A -AD - College of Agriculture, Northeast Agricultural University, Harbin 150030, China - (J.W., W.J., Q.C., G.H.);Department of Plant Pathology, University of Kentucky, - Lexington, Kentucky 40546 (J.W., M.B.S., Q.-M.G., A.K.);United States Department - of Agriculture-Agricultural Research Service, Washington State University, - Prosser, Washington 99350 (D.N.); andLand Reclamation Research and Breeding - Centre of Heilongjiang, Harbin 150090, China (C.L., G.H.) apkach2@uky.edu - hugh757@vip.163.com. -LA - eng -PT - Journal Article -DEP - 20140528 -PL - United States -TA - Plant Physiol -JT - Plant physiology -JID - 0401224 -PMC - PMC4081336 -EDAT- 2014/05/30 06:00 -MHDA- 2014/05/30 06:01 -CRDT- 2014/05/30 06:00 -PHST- 2014/05/30 06:00 [entrez] -PHST- 2014/05/30 06:00 [pubmed] -PHST- 2014/05/30 06:01 [medline] -AID - pp.114.242495 [pii] -AID - 242495 [pii] -AID - 10.1104/pp.114.242495 [doi] -PST - ppublish -SO - Plant Physiol. 2014 Jul;165(3):1269-1284. doi: 10.1104/pp.114.242495. Epub 2014 - May 28. - - -##### PUB RECORD ##### -## 10.1016/j.pbi.2005.05.010 15939664 null Weirmer, Feys et al., 2005 "Wiermer M, Feys BJ, Parker JE. Plant immunity: the EDS1 regulatory node. Curr Opin Plant Biol. 2005 Aug;8(4):383-9. doi: 10.1016/j.pbi.2005.05.010. PMID: 15939664." ## - -PMID- 15939664 -OWN - NLM -STAT- MEDLINE -DCOM- 20050817 -LR - 20220317 -IS - 1369-5266 (Print) -IS - 1369-5266 (Linking) -VI - 8 -IP - 4 -DP - 2005 Aug -TI - Plant immunity: the EDS1 regulatory node. -PG - 383-9 -AB - ENHANCED DISEASE SUSCEPTIBILITY 1 (EDS1) and its interacting partner, PHYTOALEXIN - DEFICIENT 4 (PAD4), constitute a regulatory hub that is essential for basal - resistance to invasive biotrophic and hemi-biotrophic pathogens. EDS1 and PAD4 - are also recruited by Toll-Interleukin-1 receptor (TIR)-type nucleotide - binding-leucine rich repeat (NB-LRR) proteins to signal isolate-specific pathogen - recognition. Recent work points to a fundamental role of EDS1 and PAD4 in - transducing redox signals in response to certain biotic and abiotic stresses. - These intracellular proteins are important activators of salicylic acid (SA) - signaling and also mediate antagonism between the jasmonic acid (JA) and ethylene - (ET) defense response pathways. EDS1 forms several molecularly and spatially - distinct complexes with PAD4 and a newly discovered in vivo signaling partner, - SENESCENCE ASSOCIATED GENE 101 (SAG101). Together, EDS1, PAD4 and SAG101 provide - a major barrier to infection by both host-adapted and non-host pathogens. -FAU - Wiermer, Marcel -AU - Wiermer M -AD - Max Planck Institute for Plant Breeding Research, Department of Plant-Microbe - Interactions, Carl-von-Linne-Weg 10, D-50829 Cologne, Germany. -FAU - Feys, Bart J -AU - Feys BJ -FAU - Parker, Jane E -AU - Parker JE -LA - eng -PT - Journal Article -PT - Research Support, Non-U.S. Gov't -PT - Review -PL - England -TA - Curr Opin Plant Biol -JT - Current opinion in plant biology -JID - 100883395 -RN - 0 (Arabidopsis Proteins) -RN - 0 (DNA-Binding Proteins) -RN - 0 (EDS1 protein, Arabidopsis) -RN - EC 3.1.1.- (Carboxylic Ester Hydrolases) -RN - EC 3.1.1.- (PAD4 protein, Arabidopsis) -SB - IM -MH - Arabidopsis/*immunology/metabolism -MH - Arabidopsis Proteins/metabolism/*physiology -MH - Carboxylic Ester Hydrolases/metabolism/*physiology -MH - DNA-Binding Proteins/metabolism/*physiology -MH - Gene Expression Regulation, Plant -MH - Oxidative Stress -MH - *Plant Diseases -MH - Signal Transduction -RF - 45 -EDAT- 2005/06/09 09:00 -MHDA- 2005/08/18 09:00 -CRDT- 2005/06/09 09:00 -PHST- 2005/04/18 00:00 [received] -PHST- 2005/05/19 00:00 [accepted] -PHST- 2005/06/09 09:00 [pubmed] -PHST- 2005/08/18 09:00 [medline] -PHST- 2005/06/09 09:00 [entrez] -AID - S1369-5266(05)00071-3 [pii] -AID - 10.1016/j.pbi.2005.05.010 [doi] -PST - ppublish -SO - Curr Opin Plant Biol. 2005 Aug;8(4):383-9. doi: 10.1016/j.pbi.2005.05.010. - - -##### PUB RECORD ##### -## 10.3389/fpls.2021.629069 33841461 PMC8029582 Yang, Zhang et al., 2021 "Yang X, Zhang Y, Shan J, Sun J, Li D, Zhang X, Li W, Zhao L. GmIDD Is Induced by Short Days in Soybean and May Accelerate Flowering When Overexpressed in Arabidopsis via Inhibiting AGAMOUS-LIKE 18. Front Plant Sci. 2021 Feb 26;12:629069. doi: 10.3389/fpls.2021.629069. PMID: 33841461; PMCID: PMC8029582." ## - -PMID- 33841461 -OWN - NLM -STAT- PubMed-not-MEDLINE -LR - 20210413 -IS - 1664-462X (Print) -IS - 1664-462X (Electronic) -IS - 1664-462X (Linking) -VI - 12 -DP - 2021 -TI - GmIDD Is Induced by Short Days in Soybean and May Accelerate Flowering When - Overexpressed in Arabidopsis via Inhibiting AGAMOUS-LIKE 18. -PG - 629069 -LID - 10.3389/fpls.2021.629069 [doi] -LID - 629069 -AB - Photoperiod is one of the main climatic factors that determine flowering time and - yield. Some members of the INDETERMINATE DOMAIN (IDD) transcription factor family - have been reported to be involved in regulation of flowering time in Arabidopsis, - maize, and rice. In this study, the domain analysis showed that GmIDD had a - typical ID domain and was a member of the soybean IDD transcription factor - family. Quantitative real-time PCR analysis showed that GmIDD was induced by - short day conditions in leaves and regulated by circadian clock. Under long day - conditions, transgenic Arabidopsis overexpressing GmIDD flowered earlier than - wild-type, and idd mutants flowered later, while the overexpression of GmIDD - rescued the late-flowering phenotype of idd mutants. Chromatin - immunoprecipitation sequencing assays of GmIDD binding sites in - GmIDD-overexpression (GmIDD-ox) Arabidopsis further identified potential direct - targets, including a transcription factor, AGAMOUS-like 18 (AGL18). GmIDD might - inhibit the transcriptional activity of flower repressor AGL18 by binding to the - TTTTGGTCC motif of AGL18 promoter. Furthermore, the results also showed that - GmIDD overexpression increased the transcription levels of flowering time-related - genes FLOWERING LOCUS T (FT), SUPPRESSOR OF OVEREXPRESSION OF CONSTANS1 (SOC1), - LEAFY (LFY) and APETALA1 (AP1) in Arabidopsis. Taken together, GmIDD appeared to - inhibit the transcriptional activity of AGL18 and induced the expression of FT - gene to promote Arabidopsis flowering. -CI - Copyright (c) 2021 Yang, Zhang, Shan, Sun, Li, Zhang, Li and Zhao. -FAU - Yang, Xue -AU - Yang X -AD - Key Laboratory of Soybean Biology of Ministry of Education, China (Key Laboratory - of Biology and Genetics and Breeding for Soybean in Northeast China), Northeast - Agricultural University, Harbin, China. -FAU - Zhang, Yuntong -AU - Zhang Y -AD - Key Laboratory of Soybean Biology of Ministry of Education, China (Key Laboratory - of Biology and Genetics and Breeding for Soybean in Northeast China), Northeast - Agricultural University, Harbin, China. -FAU - Shan, Jinming -AU - Shan J -AD - Key Laboratory of Soybean Biology of Ministry of Education, China (Key Laboratory - of Biology and Genetics and Breeding for Soybean in Northeast China), Northeast - Agricultural University, Harbin, China. -FAU - Sun, Jingzhe -AU - Sun J -AD - Key Laboratory of Soybean Biology of Ministry of Education, China (Key Laboratory - of Biology and Genetics and Breeding for Soybean in Northeast China), Northeast - Agricultural University, Harbin, China. -FAU - Li, Dongmei -AU - Li D -AD - Key Laboratory of Soybean Biology of Ministry of Education, China (Key Laboratory - of Biology and Genetics and Breeding for Soybean in Northeast China), Northeast - Agricultural University, Harbin, China. -FAU - Zhang, Xiaoming -AU - Zhang X -AD - Key Laboratory of Soybean Biology of Ministry of Education, China (Key Laboratory - of Biology and Genetics and Breeding for Soybean in Northeast China), Northeast - Agricultural University, Harbin, China. -FAU - Li, Wenbin -AU - Li W -AD - Key Laboratory of Soybean Biology of Ministry of Education, China (Key Laboratory - of Biology and Genetics and Breeding for Soybean in Northeast China), Northeast - Agricultural University, Harbin, China. -FAU - Zhao, Lin -AU - Zhao L -AD - Key Laboratory of Soybean Biology of Ministry of Education, China (Key Laboratory - of Biology and Genetics and Breeding for Soybean in Northeast China), Northeast - Agricultural University, Harbin, China. -LA - eng -PT - Journal Article -DEP - 20210226 -PL - Switzerland -TA - Front Plant Sci -JT - Frontiers in plant science -JID - 101568200 -PMC - PMC8029582 -OTO - NOTNLM -OT - AGL18 -OT - GmIDD -OT - flowering -OT - photoperiod -OT - soybean -COIS- The authors declare that the research was conducted in the absence of any - commercial or financial relationships that could be construed as a potential - conflict of interest. -EDAT- 2021/04/13 06:00 -MHDA- 2021/04/13 06:01 -CRDT- 2021/04/12 06:17 -PHST- 2020/12/07 00:00 [received] -PHST- 2021/01/22 00:00 [accepted] -PHST- 2021/04/12 06:17 [entrez] -PHST- 2021/04/13 06:00 [pubmed] -PHST- 2021/04/13 06:01 [medline] -AID - 10.3389/fpls.2021.629069 [doi] -PST - epublish -SO - Front Plant Sci. 2021 Feb 26;12:629069. doi: 10.3389/fpls.2021.629069. - eCollection 2021. - - -##### PUB RECORD ##### -## 10.1534/g3.114.015255 25452420 PMC4291463 Campbell, Mani et al., 2014 "Campbell BW, Mani D, Curtin SJ, Slattery RA, Michno JM, Ort DR, Schaus PJ, Palmer RG, Orf JH, Stupar RM. Identical substitutions in magnesium chelatase paralogs result in chlorophyll-deficient soybean mutants. G3 (Bethesda). 2014 Dec 1;5(1):123-31. doi: 10.1534/g3.114.015255. PMID: 25452420; PMCID: PMC4291463." ## - -PMID- 25452420 -OWN - NLM -STAT- MEDLINE -DCOM- 20150917 -LR - 20220408 -IS - 2160-1836 (Electronic) -IS - 2160-1836 (Linking) -VI - 5 -IP - 1 -DP - 2014 Dec 1 -TI - Identical substitutions in magnesium chelatase paralogs result in - chlorophyll-deficient soybean mutants. -PG - 123-31 -LID - 10.1534/g3.114.015255 [doi] -AB - The soybean [Glycine max (L.) Merr.] chlorophyll-deficient line MinnGold is a - spontaneous mutant characterized by yellow foliage. Map-based cloning and - transgenic complementation revealed that the mutant phenotype is caused by a - nonsynonymous nucleotide substitution in the third exon of a Mg-chelatase subunit - gene (ChlI1a) on chromosome 13. This gene was selected as a candidate for a - different yellow foliage mutant, T219H (Y11y11), that had been previously mapped - to chromosome 13. Although the phenotypes of MinnGold and T219H are clearly - distinct, sequencing of ChlI1a in T219H identified a different nonsynonymous - mutation in the third exon, only six base pairs from the MinnGold mutation. This - information, along with previously published allelic tests, were used to identify - and clone a third yellow foliage mutation, CD-5, which was previously mapped to - chromosome 15. This mutation was identified in the ChlI1b gene, a paralog of - ChlI1a. Sequencing of the ChlI1b allele in CD-5 identified a nonsynonymous - substitution in the third exon that confers an identical amino acid change as the - T219H substitution at ChlI1a. Protein sequence alignments of the two Mg-chelatase - subunits indicated that the sites of amino acid modification in MinnGold, T219H, - and CD-5 are highly conserved among photosynthetic species. These results suggest - that amino acid alterations in this critical domain may create competitive - inhibitory interactions between the mutant and wild-type ChlI1a and ChlI1b - proteins. -CI - Copyright (c) 2015 Campbell et al. -FAU - Campbell, Benjamin W -AU - Campbell BW -AD - Department of Agronomy and Plant Genetics, University of Minnesota, St. Paul, - Minnesota 55108. -FAU - Mani, Dhananjay -AU - Mani D -AD - Department of Agronomy and Plant Genetics, University of Minnesota, St. Paul, - Minnesota 55108. -FAU - Curtin, Shaun J -AU - Curtin SJ -AD - Department of Agronomy and Plant Genetics, University of Minnesota, St. Paul, - Minnesota 55108. -FAU - Slattery, Rebecca A -AU - Slattery RA -AD - Department of Plant Biology, University of Illinois, Urbana, Illinois 61801. -FAU - Michno, Jean-Michel -AU - Michno JM -AD - Department of Agronomy and Plant Genetics, University of Minnesota, St. Paul, - Minnesota 55108. -FAU - Ort, Donald R -AU - Ort DR -AD - Department of Plant Biology, University of Illinois, Urbana, Illinois 61801 US - Department of Agriculture/Agricultural Research Service, Global Change and - Photosynthesis Research Unit, Urbana, Illinois 61801. -FAU - Schaus, Philip J -AU - Schaus PJ -AD - Department of Agronomy and Plant Genetics, University of Minnesota, St. Paul, - Minnesota 55108. -FAU - Palmer, Reid G -AU - Palmer RG -AD - Department of Agronomy, Iowa State University, Ames, Iowa 50011. -FAU - Orf, James H -AU - Orf JH -AD - Department of Agronomy and Plant Genetics, University of Minnesota, St. Paul, - Minnesota 55108. -FAU - Stupar, Robert M -AU - Stupar RM -AD - Department of Agronomy and Plant Genetics, University of Minnesota, St. Paul, - Minnesota 55108 rstupar@umn.edu. -LA - eng -PT - Journal Article -PT - Research Support, Non-U.S. Gov't -DEP - 20141201 -PL - England -TA - G3 (Bethesda) -JT - G3 (Bethesda, Md.) -JID - 101566598 -RN - 0 (Protein Subunits) -RN - 1406-65-1 (Chlorophyll) -RN - EC 4.- (Lyases) -RN - EC 4.99.1- (magnesium chelatase) -SB - IM -MH - Amino Acid Sequence -MH - Chlorophyll/*deficiency -MH - Lyases/*genetics -MH - Mutation -MH - Plant Leaves -MH - Protein Subunits/genetics -MH - Soybeans/*genetics -PMC - PMC4291463 -OTO - NOTNLM -OT - chlorophyll -OT - duplication -OT - paralog -OT - photosynthesis -OT - soybean -EDAT- 2014/12/03 06:00 -MHDA- 2015/09/18 06:00 -CRDT- 2014/12/03 06:00 -PHST- 2014/12/03 06:00 [entrez] -PHST- 2014/12/03 06:00 [pubmed] -PHST- 2015/09/18 06:00 [medline] -AID - g3.114.015255 [pii] -AID - GGG_015255 [pii] -AID - 10.1534/g3.114.015255 [doi] -PST - epublish -SO - G3 (Bethesda). 2014 Dec 1;5(1):123-31. doi: 10.1534/g3.114.015255. - - -##### PUB RECORD ##### -## 10.1186/1471-2229-14-154 24893844 PMC4074861 Zhou, He et al., 2014 "Zhou L, He H, Liu R, Han Q, Shou H, Liu B. Overexpression of GmAKT2 potassium channel enhances resistance to soybean mosaic virus. BMC Plant Biol. 2014 Jun 3;14:154. doi: 10.1186/1471-2229-14-154. PMID: 24893844; PMCID: PMC4074861." ## - -PMID- 24893844 -OWN - NLM -STAT- MEDLINE -DCOM- 20150116 -LR - 20220331 -IS - 1471-2229 (Electronic) -IS - 1471-2229 (Linking) -VI - 14 -DP - 2014 Jun 3 -TI - Overexpression of GmAKT2 potassium channel enhances resistance to soybean mosaic - virus. -PG - 154 -LID - 10.1186/1471-2229-14-154 [doi] -AB - BACKGROUND: Soybean mosaic virus (SMV) is the most prevalent viral disease in - many soybean production areas. Due to a large number of SMV resistant loci and - alleles, SMV strains and the rapid evolution in avirulence/effector genes, - traditional breeding for SMV resistance is complex. Genetic engineering is an - effective alternative method for improving SMV resistance in soybean. Potassium - (K+) is the most abundant inorganic solute in plant cells, and is involved in - plant responses to abiotic and biotic stresses. Studies have shown that altering - the level of K+ status can reduce the spread of the viral diseases. Thus K+ - transporters are putative candidates to target for soybean virus resistance. - RESULTS: The addition of K+ fertilizer significantly reduced SMV incidence. - Analysis of K+ channel gene expression indicated that GmAKT2, the ortholog of - Arabidopsis K+ weak channel encoding gene AKT2, was significantly induced by SMV - inoculation in the SMV highly-resistant genotype Rsmv1, but not in the - susceptible genotype Ssmv1. Transgenic soybean plants overexpressing GmAKT2 were - produced and verified by Southern blot and RT-PCR analysis. Analysis of K+ - concentrations on different leaves of both the transgenic and the wildtype - (Williams 82) plants revealed that overexpression of GmAKT2 significantly - increased K+ concentrations in young leaves of plants. In contrast, K+ - concentrations in the old leaves of the GmAKT2-Oe plants were significantly lower - than those in WT plants. These results indicated that GmAKT2 acted as a K+ - transporter and affected the distribution of K+ in soybean plants. Starting from - 14 days after inoculation (DAI) of SMV G7, severe mosaic symptoms were observed - on the WT leaves. In contrast, the GmAKT2-Oe plants showed no symptom of SMV - infection. At 14 and 28 DAI, the amount of SMV RNA in WT plants increased 200- - and 260- fold relative to GmAKT2-Oe plants at each time point. Thus, SMV - development was significantly retarded in GmAKT2-overexpressing transgenic - soybean plants. CONCLUSIONS: Overexpression of GmAKT2 significantly enhanced SMV - resistance in transgenic soybean. Thus, alteration of K+ transporter expression - is a novel molecular approach for enhancing SMV resistance in soybean. -FAU - Zhou, Lian -AU - Zhou L -FAU - He, Hongli -AU - He H -FAU - Liu, Ruifang -AU - Liu R -FAU - Han, Qiang -AU - Han Q -FAU - Shou, Huixia -AU - Shou H -AD - State Key Laboratory of Plant Physiology and Biochemistry, College of Life - Sciences, Zhejiang University, Hangzhou 310058, P, R, China. huixia@zju.edu.cn. -FAU - Liu, Bao -AU - Liu B -LA - eng -PT - Journal Article -PT - Research Support, Non-U.S. Gov't -DEP - 20140603 -PL - England -TA - BMC Plant Biol -JT - BMC plant biology -JID - 100967807 -RN - 0 (Plant Proteins) -RN - 0 (Potassium Channels) -RN - RWP5GA015D (Potassium) -SB - IM -MH - *Disease Resistance/drug effects/genetics -MH - Gene Expression Regulation, Plant/drug effects -MH - Genotype -MH - Mosaic Viruses/drug effects/*physiology -MH - Plant Diseases/genetics/*virology -MH - Plant Leaves/drug effects/metabolism -MH - Plant Proteins/genetics/*metabolism -MH - Plants, Genetically Modified -MH - Potassium/metabolism/pharmacology -MH - Potassium Channels/genetics/*metabolism -MH - Reproducibility of Results -MH - Soybeans/drug effects/genetics/growth & development/*virology -PMC - PMC4074861 -EDAT- 2014/06/05 06:00 -MHDA- 2015/01/17 06:00 -CRDT- 2014/06/05 06:00 -PHST- 2014/02/25 00:00 [received] -PHST- 2014/05/27 00:00 [accepted] -PHST- 2014/06/05 06:00 [entrez] -PHST- 2014/06/05 06:00 [pubmed] -PHST- 2015/01/17 06:00 [medline] -AID - 1471-2229-14-154 [pii] -AID - 10.1186/1471-2229-14-154 [doi] -PST - epublish -SO - BMC Plant Biol. 2014 Jun 3;14:154. doi: 10.1186/1471-2229-14-154. - - -##### PUB RECORD ##### -## 10.1007/s11103-013-0062-z 23636865 null Zhao, Wang et al., 2013 "Zhao L, Wang Z, Lu Q, Wang P, Li Y, Lv Q, Song X, Li D, Gu Y, Liu L, Li W. Overexpression of a GmGBP1 ortholog of soybean enhances the responses to flowering, stem elongation and heat tolerance in transgenic tobaccos. Plant Mol Biol. 2013 Jun;82(3):279-99. doi: 10.1007/s11103-013-0062-z. Epub 2013 May 1. PMID: 23636865." ## - -PMID- 23636865 -OWN - NLM -STAT- MEDLINE -DCOM- 20130821 -LR - 20211021 -IS - 1573-5028 (Electronic) -IS - 0167-4412 (Linking) -VI - 82 -IP - 3 -DP - 2013 Jun -TI - Overexpression of a GmGBP1 ortholog of soybean enhances the responses to - flowering, stem elongation and heat tolerance in transgenic tobaccos. -PG - 279-99 -LID - 10.1007/s11103-013-0062-z [doi] -AB - Soybean is a typical short-day crop, and its photoperiodic and gibberellin (GA) - responses for the control of flowering are critical to seed yield. The GmGBP1 - mRNA abundance in leaves was dramatically increased in short-days (SDs) compared - to that in long-days in which it was consistently low at all time points from 0 - to 6 days (days after transfer to SDs). GmGBP1 was highly expressed in leaves and - exhibited a circadian rhythm in SDs. Ectopic overexpression of GmGBP1 in tobaccos - caused photoperiod-insensitive early flowering by increasing NtCO mRNA levels. - GmGBP1 mRNA abundance was also increased by GAs. Transgenic GmGBP1 overexpressing - (-ox) tobacco plants exhibited increased GA signaling-related phenotypes - including flowering and plant height promotion. Furthermore, the hypocotyl - elongation, early-flowering and longer internode phenotypes were largely - accelerated by GA3 application in the GmGBP1-ox tobacco seedlings. Being - consistent, overexpression of GmGBP1 resulted in significantly enhanced GA - signaling (evidenced suppressed expression of NtGA20ox) both with and without GA - treatments. GmGBP1 was a positive regulator of both photoperiod and GA-mediated - flowering responses. In addition, GmGBP1-ox tobaccos were hypersensitive to ABA, - salt and osmotic stresses during seed germination. Heat-inducible GmGBP1 also - enhanced thermotolerance in transgenic GmGBP1-ox tobaccos during seed germination - and growth. GmGBP1 protein was localized in the nucleus. Analyses of a series of - 5'-deletions of the GmGBP1 promoter suggested that several cis-acting elements, - including P-BOX, TCA-motif and three HSE elements necessary to induce gene - expression by GA, salicic acid and heat stress, were specifically localized in - the GmGBP1 promoter region. -FAU - Zhao, Lin -AU - Zhao L -AD - Key Laboratory of Soybean Biology of Chinese Education Ministry (Key Laboratory - of Biology and Genetics & Breeding for Soybean in Northeast China), Northeast - Agricultural University, Harbin 150030, China. zlhappy1981@yahoo.com.cn -FAU - Wang, Zhixin -AU - Wang Z -FAU - Lu, Qingyao -AU - Lu Q -FAU - Wang, Pengpeng -AU - Wang P -FAU - Li, Yongguang -AU - Li Y -FAU - Lv, Qingxue -AU - Lv Q -FAU - Song, Xianping -AU - Song X -FAU - Li, Dongmei -AU - Li D -FAU - Gu, Yuejiao -AU - Gu Y -FAU - Liu, Lixue -AU - Liu L -FAU - Li, Wenbin -AU - Li W -LA - eng -PT - Journal Article -PT - Research Support, Non-U.S. Gov't -DEP - 20130501 -PL - Netherlands -TA - Plant Mol Biol -JT - Plant molecular biology -JID - 9106343 -RN - 0 (Gibberellins) -RN - 0 (Plant Growth Regulators) -RN - 0 (Plant Proteins) -RN - 0 (Soybean Proteins) -RN - 147336-22-9 (Green Fluorescent Proteins) -RN - 451W47IQ8X (Sodium Chloride) -SB - IM -MH - Adaptation, Physiological/genetics -MH - Arabidopsis/genetics/growth & development -MH - Base Sequence -MH - Cell Nucleus -MH - Flowers/*genetics/growth & development -MH - Gene Expression Regulation, Developmental/drug effects/radiation effects -MH - Gene Expression Regulation, Plant/drug effects/radiation effects -MH - Gibberellins/pharmacology -MH - Green Fluorescent Proteins/genetics/metabolism -MH - *Hot Temperature -MH - Microscopy, Electron, Scanning -MH - Microscopy, Fluorescence -MH - Molecular Sequence Data -MH - Photoperiod -MH - Plant Growth Regulators/pharmacology -MH - Plant Proteins/*genetics/metabolism -MH - Plant Stems/*genetics/growth & development/ultrastructure -MH - Plants, Genetically Modified -MH - Promoter Regions, Genetic/genetics -MH - Reverse Transcriptase Polymerase Chain Reaction -MH - Sodium Chloride/pharmacology -MH - Soybean Proteins/*genetics/metabolism -MH - Soybeans/*genetics/metabolism -MH - Tobacco/*genetics/growth & development -EDAT- 2013/05/03 06:00 -MHDA- 2013/08/22 06:00 -CRDT- 2013/05/03 06:00 -PHST- 2013/01/16 00:00 [received] -PHST- 2013/04/14 00:00 [accepted] -PHST- 2013/05/03 06:00 [entrez] -PHST- 2013/05/03 06:00 [pubmed] -PHST- 2013/08/22 06:00 [medline] -AID - 10.1007/s11103-013-0062-z [doi] -PST - ppublish -SO - Plant Mol Biol. 2013 Jun;82(3):279-99. doi: 10.1007/s11103-013-0062-z. Epub 2013 - May 1. - - -##### PUB RECORD ##### -## 10.1093/pcp/pcy215 30418611 null Li, Liu et al., 2019 "Li MW, Liu W, Lam HM, Gendron JM. Characterization of Two Growth Period QTLs Reveals Modification of PRR3 Genes During Soybean Domestication. Plant Cell Physiol. 2019 Feb 1;60(2):407-420. doi: 10.1093/pcp/pcy215. PMID: 30418611." ## - -PMID- 30418611 -OWN - NLM -STAT- MEDLINE -DCOM- 20190820 -LR - 20190820 -IS - 1471-9053 (Electronic) -IS - 0032-0781 (Linking) -VI - 60 -IP - 2 -DP - 2019 Feb 1 -TI - Characterization of Two Growth Period QTLs Reveals Modification of PRR3 Genes - During Soybean Domestication. -PG - 407-420 -LID - 10.1093/pcp/pcy215 [doi] -AB - Soybean yield is largely dependent on growth period. We characterized two growth - period quantitative trait loci, Gp11 and Gp12, from a recombinant inbred - population generated from a cross of wild (W05) and cultivated (C08) soybean. - Lines carrying Gp11C08 and Gp12C08 tend to have a shorter growth period and - higher expression of GmFT2a and GmFT5a. Furthermore, multiple interval mapping - suggests that Gp11 and Gp12 may be genetically interacting with the E2 locus. - This is consistent with the observation that GmFT2a and GmFT5a are activated by - Gp11C08 and Gp12C08 at ZT4 in the recessive e2 but not the dominant E2 - background. Gp11 and Gp12 are duplicated genomic regions each containing a copy - of the soybean ortholog of PSEUDO RESPONSE REGULATOR 3 (GmPRR3A and GmPRR3B). - GmPRR3A and GmPRR3B from C08 carry mutations that delete the CCT domain in the - encoded proteins. These mutations were selected during soybean improvement and - they alter the subcellular localization of GmPRR3A and GmPRR3B. Furthermore, - GmPRR3A and GmPRR3B can interact with TOPLESS-related transcription factors, - suggesting that they function in a transcription repressor complex. This study - addresses previously unexplored components of the genetic network that probably - controls the growth period of soybean and puts these loci into context with the - well-characterized growth period-regulating E loci. -CI - i inverted question mark(1/2) The Author(s) 2018. Published by Oxford University Press on behalf of - Japanese Society of Plant Physiologists. All rights reserved. For permissions, - please email: journals.permissions@oup.com. -FAU - Li, Man-Wah -AU - Li MW -AD - Department of Molecular, Cellular and Developmental Biology, Yale University, New - Haven, CT, USA. -FAU - Liu, Wei -AU - Liu W -AD - Department of Molecular, Cellular and Developmental Biology, Yale University, New - Haven, CT, USA. -FAU - Lam, Hon-Ming -AU - Lam HM -AD - Centre for Soybean Research of the State Key Laboratory of Agrobiotechnology and - School of Life Sciences, The Chinese University of Hong Kong, Shatin, New - Territories, Hong Kong SAR. -FAU - Gendron, Joshua M -AU - Gendron JM -AD - Department of Molecular, Cellular and Developmental Biology, Yale University, New - Haven, CT, USA. -LA - eng -PT - Journal Article -PL - Japan -TA - Plant Cell Physiol -JT - Plant & cell physiology -JID - 9430925 -RN - 0 (Plant Proteins) -RN - 0 (Transcription Factors) -MH - *Domestication -MH - Gene Expression Regulation, Plant -MH - Genes, Plant/*genetics/physiology -MH - Phylogeny -MH - Plant Proteins/*genetics/physiology -MH - Quantitative Trait Loci/*genetics -MH - Soybeans/*genetics/growth & development -MH - Transcription Factors/*genetics/physiology -OTO - NOTNLM -OT - Domestication -OT - Flowering -OT - Growth period -OT - Pseudo-response regulator -OT - Soybean -EDAT- 2018/11/13 06:00 -MHDA- 2019/08/21 06:00 -CRDT- 2018/11/13 06:00 -PHST- 2018/06/19 00:00 [received] -PHST- 2018/11/01 00:00 [accepted] -PHST- 2018/11/13 06:00 [pubmed] -PHST- 2019/08/21 06:00 [medline] -PHST- 2018/11/13 06:00 [entrez] -AID - 5168116 [pii] -AID - 10.1093/pcp/pcy215 [doi] -PST - ppublish -SO - Plant Cell Physiol. 2019 Feb 1;60(2):407-420. doi: 10.1093/pcp/pcy215. - - -##### PUB RECORD ##### -## 10.1111/tpj.15414 34245624 null Wang, Li et al., 2021 "Wang X, Li MW, Wong FL, Luk CY, Chung CY, Yung WS, Wang Z, Xie M, Song S, Chung G, Chan TF, Lam HM. Increased copy number of gibberellin 2-oxidase 8 genes reduced trailing growth and shoot length during soybean domestication. Plant J. 2021 Sep;107(6):1739-1755. doi: 10.1111/tpj.15414. Epub 2021 Jul 29. PMID: 34245624." ## - -PMID- 34245624 -OWN - NLM -STAT- MEDLINE -DCOM- 20220126 -LR - 20220126 -IS - 1365-313X (Electronic) -IS - 0960-7412 (Linking) -VI - 107 -IP - 6 -DP - 2021 Sep -TI - Increased copy number of gibberellin 2-oxidase 8 genes reduced trailing growth - and shoot length during soybean domestication. -PG - 1739-1755 -LID - 10.1111/tpj.15414 [doi] -AB - Copy number variations (CNVs) play important roles in crop domestication. - However, there is only very limited information on the involvement of CNVs in - soybean domestication. Trailing growth and long shoots are soybean adaptations - for natural habitats but cause lodging that hampers yield in cultivation. - Previous studies have focused on Dt1/2 affecting the indeterminate/determinate - growth habit, whereas the possible role of the gibberellin pathway remained - unclear. In the present study, quantitative trait locus (QTL) mapping of a - recombinant inbred population of 460 lines revealed a - trailing-growth-and-shoot-length QTL. A CNV region within this QTL was - identified, featuring the apical bud-expressed gibberellin 2-oxidase 8A/B, the - copy numbers of which were positively correlated with expression levels and - negatively with trailing growth and shoot length, and their effects were - demonstrated by transgenic soybean and Arabidopsis thaliana. Based on the - fixation index, this CNV region underwent intense selection during the initial - domestication process. -CI - (c) 2021 Society for Experimental Biology and John Wiley & Sons Ltd. -FAU - Wang, Xin -AU - Wang X -AD - School of Life Sciences and the Centre for Soybean Research of the State Key - Laboratory of Agrobiotechnology, The Chinese University of Hong Kong, Shatin, - Hong Kong, China. -FAU - Li, Man-Wah -AU - Li MW -AUID- ORCID: 0000-0003-4859-5683 -AD - School of Life Sciences and the Centre for Soybean Research of the State Key - Laboratory of Agrobiotechnology, The Chinese University of Hong Kong, Shatin, - Hong Kong, China. -FAU - Wong, Fuk-Ling -AU - Wong FL -AD - School of Life Sciences and the Centre for Soybean Research of the State Key - Laboratory of Agrobiotechnology, The Chinese University of Hong Kong, Shatin, - Hong Kong, China. -FAU - Luk, Ching-Yee -AU - Luk CY -AD - School of Life Sciences and the Centre for Soybean Research of the State Key - Laboratory of Agrobiotechnology, The Chinese University of Hong Kong, Shatin, - Hong Kong, China. -FAU - Chung, Claire Yik-Lok -AU - Chung CY -AD - School of Life Sciences and the Centre for Soybean Research of the State Key - Laboratory of Agrobiotechnology, The Chinese University of Hong Kong, Shatin, - Hong Kong, China. -FAU - Yung, Wai-Shing -AU - Yung WS -AD - School of Life Sciences and the Centre for Soybean Research of the State Key - Laboratory of Agrobiotechnology, The Chinese University of Hong Kong, Shatin, - Hong Kong, China. -FAU - Wang, Zhili -AU - Wang Z -AD - School of Life Sciences and the Centre for Soybean Research of the State Key - Laboratory of Agrobiotechnology, The Chinese University of Hong Kong, Shatin, - Hong Kong, China. -FAU - Xie, Min -AU - Xie M -AD - School of Life Sciences and the Centre for Soybean Research of the State Key - Laboratory of Agrobiotechnology, The Chinese University of Hong Kong, Shatin, - Hong Kong, China. -FAU - Song, Shikui -AU - Song S -AD - FAFU-UCR Joint Center for Horticultural Biology and Metabolomics, Haixia - Institute of Science and Technology, Fujian Agriculture and Forestry University, - Fuzhou, China. -FAU - Chung, Gyuhwa -AU - Chung G -AD - Department of Biotechnology, Chonnam National University, Yeosu, South Korea. -FAU - Chan, Ting-Fung -AU - Chan TF -AUID- ORCID: 0000-0002-0489-3884 -AD - School of Life Sciences and the Centre for Soybean Research of the State Key - Laboratory of Agrobiotechnology, The Chinese University of Hong Kong, Shatin, - Hong Kong, China. -AD - Shenzhen Research Institute, The Chinese University of Hong Kong, Shenzhen, - 518000, China. -FAU - Lam, Hon-Ming -AU - Lam HM -AUID- ORCID: 0000-0002-6673-8740 -AD - School of Life Sciences and the Centre for Soybean Research of the State Key - Laboratory of Agrobiotechnology, The Chinese University of Hong Kong, Shatin, - Hong Kong, China. -AD - Shenzhen Research Institute, The Chinese University of Hong Kong, Shenzhen, - 518000, China. -LA - eng -PT - Journal Article -PT - Research Support, Non-U.S. Gov't -DEP - 20210729 -PL - England -TA - Plant J -JT - The Plant journal : for cell and molecular biology -JID - 9207397 -RN - 0 (Gibberellins) -RN - 0 (Soybean Proteins) -RN - EC 1.- (Mixed Function Oxygenases) -RN - EC 1.14.11.13 (gibberellin 2-dioxygenase) -SB - IM -MH - Arabidopsis/genetics -MH - Chromosome Mapping -MH - DNA Copy Number Variations -MH - *Domestication -MH - Gene Expression Regulation, Plant -MH - Gene Knockdown Techniques -MH - Gene Knockout Techniques -MH - Gibberellins/metabolism -MH - Mixed Function Oxygenases/*genetics -MH - Plant Shoots/genetics/*growth & development -MH - Plants, Genetically Modified -MH - Quantitative Trait Loci -MH - Soybean Proteins/*genetics -MH - Soybeans/*genetics/growth & development -OTO - NOTNLM -OT - domestication -OT - gene copy number -OT - gibberellin 2-oxdase -OT - growth habit -OT - shoot length -OT - soybean -EDAT- 2021/07/11 06:00 -MHDA- 2022/01/27 06:00 -CRDT- 2021/07/10 17:08 -PHST- 2021/06/28 00:00 [revised] -PHST- 2021/03/04 00:00 [received] -PHST- 2021/07/06 00:00 [accepted] -PHST- 2021/07/11 06:00 [pubmed] -PHST- 2022/01/27 06:00 [medline] -PHST- 2021/07/10 17:08 [entrez] -AID - 10.1111/tpj.15414 [doi] -PST - ppublish -SO - Plant J. 2021 Sep;107(6):1739-1755. doi: 10.1111/tpj.15414. Epub 2021 Jul 29. - - -##### PUB RECORD ##### -## 10.1186/1471-2229-13-21 23388059 PMC3571917 Zhang, Zhao et al., 2013 "Zhang Y, Zhao L, Li H, Gao Y, Li Y, Wu X, Teng W, Han Y, Zhao X, Li W. GmGBP1, a homolog of human ski interacting protein in soybean, regulates flowering and stress tolerance in Arabidopsis. BMC Plant Biol. 2013 Feb 6;13:21. doi: 10.1186/1471-2229-13-21. PMID: 23388059; PMCID: PMC3571917." ## - -PMID- 23388059 -OWN - NLM -STAT- MEDLINE -DCOM- 20130621 -LR - 20211021 -IS - 1471-2229 (Electronic) -IS - 1471-2229 (Linking) -VI - 13 -DP - 2013 Feb 6 -TI - GmGBP1, a homolog of human ski interacting protein in soybean, regulates - flowering and stress tolerance in Arabidopsis. -PG - 21 -LID - 10.1186/1471-2229-13-21 [doi] -AB - BACKGROUND: SKIP is a transcription cofactor in many eukaryotes. It can regulate - plant stress tolerance in rice and Arabidopsis. But the homolog of SKIP protein - in soybean has been not reported up to now. RESULTS: In this study, the - expression patterns of soybean GAMYB binding protein gene (GmGBP1) encoding a - homolog of SKIP protein were analyzed in soybean under abiotic stresses and - different day lengths. The expression of GmGBP1 was induced by polyethyleneglycol - 6000, NaCl, gibberellin, abscisic acid and heat stress. GmGBP1 had - transcriptional activity in C-terminal. GmGBP1 could interact with R2R3 domain of - GmGAMYB1 in SKIP domain to take part in gibberellin flowering pathway. In - long-day (16 h-light) condition, transgenic Arabidopsis with the ectopic - overexpression of GmGBP1 exhibited earlier flowering and less number of rosette - leaves; Suppression of AtSKIP in Arabidopsis resulted in growth arrest, flowering - delay and down-regulation of many flowering-related genes (CONSTANS, FLOWERING - LOCUS T, LEAFY); Arabidopsis myb33 mutant plants with ectopic overexpression of - GmGBP1 showed the same flowering phenotype with wild type. In short-day (8 - h-light) condition, transgenic Arabidopsis plants with GmGBP1 flowered later and - showed a higher level of FLOWERING LOCUS C compared with wild type. When treated - with abiotic stresses, transgenic Arabidopsis with the ectopic overexpression of - GmGBP1 enhanced the tolerances to heat and drought stresses but reduced the - tolerance to high salinity, and affected the expressions of several - stress-related genes. CONCLUSIONS: In Arabidopsis, GmGBP1 might positively - regulate the flowering time by affecting CONSTANS, FLOWERING LOCUS T, LEAFY and - GAMYB directly or indirectly in photoperiodic and gibberellin pathways in LDs, - but GmGBP1 might represse flowering by affecting FLOWERING LOCUS C and SHORT - VEGETATIVE PHASE in autonomous pathway in SDs. GmGBP1 might regulate the activity - of ROS-eliminating to improve the resistance to heat and drought but reduce the - high-salinity tolerance. -FAU - Zhang, Yanwei -AU - Zhang Y -AD - Key Laboratory of Soybean Biology in Chinese Education Ministry, College of - Agronomy, Northeast Agricultural University, Harbin, 150030, China. -FAU - Zhao, Lin -AU - Zhao L -FAU - Li, Haiyan -AU - Li H -FAU - Gao, Yang -AU - Gao Y -FAU - Li, Yongguang -AU - Li Y -FAU - Wu, Xiaoxia -AU - Wu X -FAU - Teng, Weili -AU - Teng W -FAU - Han, Yingpeng -AU - Han Y -FAU - Zhao, Xue -AU - Zhao X -FAU - Li, Wenbin -AU - Li W -LA - eng -PT - Journal Article -PT - Research Support, Non-U.S. Gov't -DEP - 20130206 -PL - England -TA - BMC Plant Biol -JT - BMC plant biology -JID - 100967807 -RN - 0 (Soybean Proteins) -SB - IM -MH - Arabidopsis/genetics/*metabolism/*physiology -MH - Droughts -MH - Flowers/genetics/*metabolism/*physiology -MH - Gene Expression Regulation, Plant -MH - Hot Temperature -MH - Humans -MH - Plants, Genetically Modified/genetics/metabolism/physiology -MH - Soybean Proteins/genetics/*metabolism -MH - Soybeans/genetics/*metabolism -PMC - PMC3571917 -EDAT- 2013/02/08 06:00 -MHDA- 2013/06/25 06:00 -CRDT- 2013/02/08 06:00 -PHST- 2012/11/06 00:00 [received] -PHST- 2013/01/28 00:00 [accepted] -PHST- 2013/02/08 06:00 [entrez] -PHST- 2013/02/08 06:00 [pubmed] -PHST- 2013/06/25 06:00 [medline] -AID - 1471-2229-13-21 [pii] -AID - 10.1186/1471-2229-13-21 [doi] -PST - epublish -SO - BMC Plant Biol. 2013 Feb 6;13:21. doi: 10.1186/1471-2229-13-21. - - -##### PUB RECORD ##### -## 10.1111/tpj.14025 30004144 null Zhao, Li et al., 2018 "Zhao L, Li M, Xu C, Yang X, Li D, Zhao X, Wang K, Li Y, Zhang X, Liu L, Ding F, Du H, Wang C, Sun J, Li W. Natural variation in GmGBP1 promoter affects photoperiod control of flowering time and maturity in soybean. Plant J. 2018 Oct;96(1):147-162. doi: 10.1111/tpj.14025. Epub 2018 Aug 16. PMID: 30004144." ## - -PMID- 30004144 -OWN - NLM -STAT- MEDLINE -DCOM- 20190625 -LR - 20190625 -IS - 1365-313X (Electronic) -IS - 0960-7412 (Linking) -VI - 96 -IP - 1 -DP - 2018 Oct -TI - Natural variation in GmGBP1 promoter affects photoperiod control of flowering - time and maturity in soybean. -PG - 147-162 -LID - 10.1111/tpj.14025 [doi] -AB - The present study screened for polymorphisms in coding and non-coding regions of - the GmGBP1 gene in 278 soybean accessions with variable maturity and growth habit - characteristics under natural field conditions in three different latitudes in - China. The results showed that the promoter region was highly diversified - compared with the coding sequence of GmGBP1. Five polymorphisms and four - haplotypes were closely related to soybean flowering time and maturity through - association and linkage disequilibrium analyses. Varieties with the polymorphisms - SNP_-796G, SNP_-770G, SNP_-307T, InDel_-242normal, SNP_353A, or haplotypes Hap-3 - and Hap-4 showed earlier flowering time and maturity in different environments. - The shorter growth period might be largely due to higher GmGBP1 expression levels - in soybean that were caused by the TCT-motif with SNP_-796G in the promoter. In - contrast, the lower expression level of GmGBP1 in soybean caused by RNAi - interference of GmGBP1 resulted in a longer growth period under different day - lengths. Furthermore, the gene interference of GmGBP1 also caused a reduction in - photoperiod response sensitivity (PRS) before flowering in soybean. RNA-seq - analysis on GmGBP1 underexpression in soybean showed that 94 and 30 predicted - genes were significantly upregulated and downregulated, respectively. Of these, - the diurnal photoperiod-specific expression pattern of three significant - flowering time genes GmFT2a, GmFT5a, and GmFULc also showed constantly lower mRNA - levels in GmGBP1-i soybean than in wild type, especially under short day - conditions. Together, the results showed that GmGBP1 functioned as a positive - regulator upstream of GmFT2a and GmFT5a to activate the expression of GmFULc to - promote flowering on short days. -CI - (c) 2018 The Authors The Plant Journal (c) 2018 John Wiley & Sons Ltd. -FAU - Zhao, Lin -AU - Zhao L -AD - Key Laboratory of Soybean Biology of Ministry of Education China (Key Laboratory - of Biology and Genetics & Breeding for Soybean in Northeast China), Northeast - Agricultural University, Harbin, 150030, China. -FAU - Li, Minmin -AU - Li M -AD - Key Laboratory of Soybean Biology of Ministry of Education China (Key Laboratory - of Biology and Genetics & Breeding for Soybean in Northeast China), Northeast - Agricultural University, Harbin, 150030, China. -FAU - Xu, Chongjing -AU - Xu C -AD - Key Laboratory of Soybean Biology of Ministry of Education China (Key Laboratory - of Biology and Genetics & Breeding for Soybean in Northeast China), Northeast - Agricultural University, Harbin, 150030, China. -FAU - Yang, Xue -AU - Yang X -AD - Key Laboratory of Soybean Biology of Ministry of Education China (Key Laboratory - of Biology and Genetics & Breeding for Soybean in Northeast China), Northeast - Agricultural University, Harbin, 150030, China. -FAU - Li, Dongmei -AU - Li D -AD - Key Laboratory of Soybean Biology of Ministry of Education China (Key Laboratory - of Biology and Genetics & Breeding for Soybean in Northeast China), Northeast - Agricultural University, Harbin, 150030, China. -FAU - Zhao, Xue -AU - Zhao X -AD - Key Laboratory of Soybean Biology of Ministry of Education China (Key Laboratory - of Biology and Genetics & Breeding for Soybean in Northeast China), Northeast - Agricultural University, Harbin, 150030, China. -FAU - Wang, Kuo -AU - Wang K -AD - Key Laboratory of Soybean Biology of Ministry of Education China (Key Laboratory - of Biology and Genetics & Breeding for Soybean in Northeast China), Northeast - Agricultural University, Harbin, 150030, China. -FAU - Li, Yinghua -AU - Li Y -AD - Key Laboratory of Soybean Biology of Ministry of Education China (Key Laboratory - of Biology and Genetics & Breeding for Soybean in Northeast China), Northeast - Agricultural University, Harbin, 150030, China. -FAU - Zhang, Xiaoming -AU - Zhang X -AD - Key Laboratory of Soybean Biology of Ministry of Education China (Key Laboratory - of Biology and Genetics & Breeding for Soybean in Northeast China), Northeast - Agricultural University, Harbin, 150030, China. -FAU - Liu, Lixue -AU - Liu L -AD - Key Laboratory of Soybean Biology of Ministry of Education China (Key Laboratory - of Biology and Genetics & Breeding for Soybean in Northeast China), Northeast - Agricultural University, Harbin, 150030, China. -FAU - Ding, Fuquan -AU - Ding F -AD - Key Laboratory of Soybean Biology of Ministry of Education China (Key Laboratory - of Biology and Genetics & Breeding for Soybean in Northeast China), Northeast - Agricultural University, Harbin, 150030, China. -FAU - Du, Hailong -AU - Du H -AD - Key Laboratory of Soybean Biology of Ministry of Education China (Key Laboratory - of Biology and Genetics & Breeding for Soybean in Northeast China), Northeast - Agricultural University, Harbin, 150030, China. -FAU - Wang, Chunsheng -AU - Wang C -AD - Key Laboratory of Soybean Biology of Ministry of Education China (Key Laboratory - of Biology and Genetics & Breeding for Soybean in Northeast China), Northeast - Agricultural University, Harbin, 150030, China. -FAU - Sun, Jingzhe -AU - Sun J -AD - Key Laboratory of Soybean Biology of Ministry of Education China (Key Laboratory - of Biology and Genetics & Breeding for Soybean in Northeast China), Northeast - Agricultural University, Harbin, 150030, China. -FAU - Li, Wenbin -AU - Li W -AD - Key Laboratory of Soybean Biology of Ministry of Education China (Key Laboratory - of Biology and Genetics & Breeding for Soybean in Northeast China), Northeast - Agricultural University, Harbin, 150030, China. -LA - eng -PT - Journal Article -PT - Research Support, Non-U.S. Gov't -DEP - 20180816 -PL - England -TA - Plant J -JT - The Plant journal : for cell and molecular biology -JID - 9207397 -RN - 0 (Plant Proteins) -SB - IM -MH - Flowers/*growth & development -MH - Gene Expression Regulation, Plant -MH - Haplotypes -MH - Linkage Disequilibrium -MH - *Photoperiod -MH - Plant Proteins/genetics/*physiology -MH - Polymorphism, Single Nucleotide/genetics/physiology -MH - Promoter Regions, Genetic/genetics/*physiology -MH - Soybeans/genetics/growth & development/*physiology -OTO - NOTNLM -OT - SNP -OT - GmGBP1 gene -OT - photoperiod -OT - promoter -OT - soybean maturity -EDAT- 2018/07/14 06:00 -MHDA- 2019/06/27 06:00 -CRDT- 2018/07/14 06:00 -PHST- 2018/01/31 00:00 [received] -PHST- 2018/06/21 00:00 [revised] -PHST- 2018/06/26 00:00 [accepted] -PHST- 2018/07/14 06:00 [pubmed] -PHST- 2019/06/27 06:00 [medline] -PHST- 2018/07/14 06:00 [entrez] -AID - 10.1111/tpj.14025 [doi] -PST - ppublish -SO - Plant J. 2018 Oct;96(1):147-162. doi: 10.1111/tpj.14025. Epub 2018 Aug 16. - - -##### PUB RECORD ##### -## 10.1111/j.1365-313x.2010.04214.x 20345602 null Yi, Jinxin et al., 2010 "Yi J, Derynck MR, Li X, Telmer P, Marsolais F, Dhaubhadel S. A single-repeat MYB transcription factor, GmMYB176, regulates CHS8 gene expression and affects isoflavonoid biosynthesis in soybean. Plant J. 2010 Jun 1;62(6):1019-34. doi: 10.1111/j.1365-313X.2010.04214.x. Epub 2010 Mar 25. PMID: 20345602." ## - -PMID- 20345602 -OWN - NLM -STAT- MEDLINE -DCOM- 20100927 -LR - 20220310 -IS - 1365-313X (Electronic) -IS - 0960-7412 (Linking) -VI - 62 -IP - 6 -DP - 2010 Jun 1 -TI - A single-repeat MYB transcription factor, GmMYB176, regulates CHS8 gene - expression and affects isoflavonoid biosynthesis in soybean. -PG - 1019-34 -LID - 10.1111/j.1365-313X.2010.04214.x [doi] -AB - Here we demonstrate that GmMYB176 regulates CHS8 expression and affects - isoflavonoid synthesis in soybean. We previously established that CHS8 expression - determines the isoflavonoid level in soybean seeds by comparing the transcript - profiles of cultivars with different isoflavonoid contents. In the present study, - a functional genomic approach was used to identify the factor that regulates CHS8 - expression and isoflavonoid synthesis. Candidate genes were cloned, and - co-transfection assays were performed in Arabidopsis leaf protoplasts. The - results showed that GmMYB176 can trans-activate the CHS8 promoter with maximum - activity. Transient expression of GmMYB176 in soybean embryo protoplasts - increased endogenous CHS8 transcript levels up to 169-fold after 48 h. GmMYB176 - encodes an R1 MYB protein, and is expressed in soybean seed during maturation. - Furthermore, GmMYB176 recognizes a 23 bp motif containing a TAGT(T/A)(A/T) - sequence within the CHS8 promoter. A subcellular localization study confirmed - nuclear localization of GmMYB176. A predicted pST binding site for 14-3-3 protein - is required for subcellular localization of GmMYB176. RNAi silencing of GmMYB176 - in hairy roots resulted in reduced levels of isoflavonoids, showing that GmMYB176 - is necessary for isoflavonoid biosynthesis. However, over-expression of GmMYB176 - was not sufficient to increase CHS8 transcript and isoflavonoid levels in hairy - roots. We conclude that an R1 MYB transcription factor, GmMYB176, regulates CHS8 - expression and isoflavonoid synthesis in soybean. -FAU - Yi, Jinxin -AU - Yi J -AD - Southern Crop Protection and Food Research Center, Agriculture and Agri-Food - Canada, London, Ontario, N5V 4T3, Canada. -FAU - Derynck, Michael R -AU - Derynck MR -FAU - Li, Xuyan -AU - Li X -FAU - Telmer, Patrick -AU - Telmer P -FAU - Marsolais, Frederic -AU - Marsolais F -FAU - Dhaubhadel, Sangeeta -AU - Dhaubhadel S -LA - eng -PT - Journal Article -PT - Research Support, Non-U.S. Gov't -DEP - 20100325 -PL - England -TA - Plant J -JT - The Plant journal : for cell and molecular biology -JID - 9207397 -RN - 0 (Flavonoids) -RN - 0 (Plant Proteins) -RN - 0 (RNA, Plant) -RN - 0 (Transcription Factors) -SB - IM -CIN - Plant Signal Behav. 2010 Jul;5(7):921-3. PMID: 20622511 -MH - Amino Acid Sequence -MH - Flavonoids/*biosynthesis -MH - Gene Expression Profiling -MH - Gene Expression Regulation, Plant -MH - Molecular Sequence Data -MH - Mutagenesis, Site-Directed -MH - Phylogeny -MH - Plant Proteins/genetics/*metabolism -MH - Plant Roots/metabolism -MH - Promoter Regions, Genetic -MH - RNA Interference -MH - RNA, Plant/genetics -MH - Seeds/*metabolism -MH - Sequence Alignment -MH - Sequence Analysis, DNA -MH - Soybeans/genetics/metabolism -MH - Transcription Factors/genetics/*metabolism -EDAT- 2010/03/30 06:00 -MHDA- 2010/09/29 06:00 -CRDT- 2010/03/30 06:00 -PHST- 2010/03/30 06:00 [entrez] -PHST- 2010/03/30 06:00 [pubmed] -PHST- 2010/09/29 06:00 [medline] -AID - TPJ4214 [pii] -AID - 10.1111/j.1365-313X.2010.04214.x [doi] -PST - ppublish -SO - Plant J. 2010 Jun 1;62(6):1019-34. doi: 10.1111/j.1365-313X.2010.04214.x. Epub - 2010 Mar 25. - - -##### PUB RECORD ##### -## 10.1038/s42003-021-01889-6 33742087 null Vadivel, Anguraj AK, et al., 2021 "Anguraj Vadivel AK, McDowell T, Renaud JB, Dhaubhadel S. A combinatorial action of GmMYB176 and GmbZIP5 controls isoflavonoid biosynthesis in soybean (Glycine max). Commun Biol. 2021 Mar 19;4(1):356. doi: 10.1038/s42003-021-01889-6. PMID: 33742087; PMCID: PMC7979867." ## - -PMID- 33742087 -OWN - NLM -STAT- MEDLINE -DCOM- 20210811 -LR - 20210811 -IS - 2399-3642 (Electronic) -IS - 2399-3642 (Linking) -VI - 4 -IP - 1 -DP - 2021 Mar 19 -TI - A combinatorial action of GmMYB176 and GmbZIP5 controls isoflavonoid biosynthesis - in soybean (Glycine max). -PG - 356 -LID - 10.1038/s42003-021-01889-6 [doi] -LID - 356 -AB - GmMYB176 is an R1 MYB transcription factor that regulates multiple genes in the - isoflavonoid biosynthetic pathway, thereby affecting their levels in soybean - roots. While GmMYB176 is important for isoflavonoid synthesis, it is not - sufficient for the function and requires additional cofactor(s). The aim of this - study was to identify the GmMYB176 interactome for the regulation of isoflavonoid - biosynthesis in soybean. Here, we demonstrate that a bZIP transcription factor - GmbZIP5 co-immunoprecipitates with GmMYB176 and shows protein-protein interaction - in planta. RNAi silencing of GmbZIP5 reduced the isoflavonoid level in soybean - hairy roots. Furthermore, co-overexpression of GmMYB176 and GmbZIP5 enhanced the - level of multiple isoflavonoid phytoallexins including glyceollin, isowighteone - and a unique O-methylhydroxy isoflavone in soybean hairy roots. These findings - could be utilized to develop biotechnological strategies to manipulate the - metabolite levels either to enhance plant defense mechanisms or for human health - benefits in soybean or other economically important crops. -FAU - Anguraj Vadivel, Arun Kumaran -AU - Anguraj Vadivel AK -AUID- ORCID: 0000-0002-6384-6316 -AD - London Research and Development Centre, Agriculture and Agri-Food Canada, London, - ON, Canada. -AD - Department of Biology, University of Western Ontario, London, ON, Canada. -FAU - McDowell, Tim -AU - McDowell T -AUID- ORCID: 0000-0001-5334-1923 -AD - London Research and Development Centre, Agriculture and Agri-Food Canada, London, - ON, Canada. -FAU - Renaud, Justin B -AU - Renaud JB -AD - London Research and Development Centre, Agriculture and Agri-Food Canada, London, - ON, Canada. -FAU - Dhaubhadel, Sangeeta -AU - Dhaubhadel S -AUID- ORCID: 0000-0003-2582-5503 -AD - London Research and Development Centre, Agriculture and Agri-Food Canada, London, - ON, Canada. sangeeta.dhaubhadel@canada.ca. -AD - Department of Biology, University of Western Ontario, London, ON, Canada. - sangeeta.dhaubhadel@canada.ca. -LA - eng -PT - Journal Article -PT - Research Support, Non-U.S. Gov't -DEP - 20210319 -PL - England -TA - Commun Biol -JT - Communications biology -JID - 101719179 -RN - 0 (Basic-Leucine Zipper Transcription Factors) -RN - 0 (Isoflavones) -RN - 0 (Pterocarpans) -RN - 0 (Soybean Proteins) -RN - 0 (Transcription Factors) -RN - 6461TV6UCH (glyceollin) -SB - IM -MH - Basic-Leucine Zipper Transcription Factors/genetics/metabolism -MH - Gene Expression Regulation, Plant -MH - Isoflavones/*biosynthesis -MH - Plant Roots -MH - Protein Binding -MH - Pterocarpans/biosynthesis -MH - Soybean Proteins/genetics/*metabolism -MH - Soybeans/genetics/*metabolism -MH - Transcription Factors/genetics/*metabolism -PMC - PMC7979867 -COIS- The authors declare no competing interests. -EDAT- 2021/03/21 06:00 -MHDA- 2021/08/12 06:00 -CRDT- 2021/03/20 06:33 -PHST- 2020/09/03 00:00 [received] -PHST- 2021/02/19 00:00 [accepted] -PHST- 2021/03/20 06:33 [entrez] -PHST- 2021/03/21 06:00 [pubmed] -PHST- 2021/08/12 06:00 [medline] -AID - 10.1038/s42003-021-01889-6 [pii] -AID - 1889 [pii] -AID - 10.1038/s42003-021-01889-6 [doi] -PST - epublish -SO - Commun Biol. 2021 Mar 19;4(1):356. doi: 10.1038/s42003-021-01889-6. - - diff --git a/Glycine/max/gene_functions/glyma.traits.yml b/Glycine/max/gene_functions/glyma.traits.yml index fe84e15..8481250 100644 --- a/Glycine/max/gene_functions/glyma.traits.yml +++ b/Glycine/max/gene_functions/glyma.traits.yml @@ -1,317 +1,518 @@ ## DOCUMENT 1 ## --- -classical_locus: E9 +scientific_name: Glycine max gene_symbols: - - GmFT2a -gene_symbol_long: Flowering Time 2a -gene_model_pub_name: Glyma.16g150700 -gene_model_full_id: glyma.Wm82.gnm4.ann1.Glyma.16G150700 + - GmPLDγ +gene_symbol_long: Phospholipase D gamma +gene_model_pub_name: Glyma.01G215100 +gene_model_full_id: glyma.Wm82.gnm2.ann1.Glyma.01G215100 confidence: 5 curators: - - Steven Cannon -phenotype_synopsis: Photoperiodic flowering time regulation + - Greg Murrell + - Scott Kalberer +phenotype_summary: Overexpression of GmPLDγ introduced from soybean results in higher seed oil content and fatty-acid remodeling in Arabidopsis. traits: - - entity_name: flowering time - entity: TO:0002616 - relation_name: positively regulates + - entity_name: seed oil content + entity: CO_336:0000048 + - relation_name: positively regulates relation: RO:0002213 - - entity_name: days to maturity - entity: TO:0000469 - relation_name: positively regulates + - entity_name: fat and essential oil composition related trait + entity: TO:0000491 + - entity_name: seed weight + entity: TO:0000181 + - relation_name: positively regulates + relation: RO:0002213 + - entity_name: triglyceride metabolic process + entity: GO:0006641 + - relation_name: positively regulates relation: RO:0002213 references: - - citation: Kong, Liu et al., 2010 - doi: 10.1104/pp.110.160796 - pmid: 20864544 - - citation: Kong, Nan et al., 2014 - doi: 10.2135/cropsci2014.03.0228 - - citation: Takeshima, Hayashi et al., 2016 - doi: 10.1093/jxb/erw283 - pmid: 27422993 - - citation: Zhao, Takeshima et al., 2016 - doi: 10.1186/s12870-016-0704-9 - pmid: 26786479 - - citation: Dietz, Chan et al., 2023 - doi: 10.3389/fpls.2022.889066 - pmid: 35574141 - - citation: Lin, Liu et al., 2021 - doi: 10.1111/jipb.13021 - pmid: 33090664 + - citation: Bai, Jing et al., 2020 + doi: 10.1016/j.plantsci.2019.110298 + pmid: 31779909 ## DOCUMENT 2 ## --- +scientific_name: Glycine max gene_symbols: - - GmFT5a - - FT5a - - FTL4 -gene_symbol_long: Flowering Time 5a -gene_model_pub_name: Glyma.16G044100 -gene_model_full_id: glyma.Wm82.gnm4.ann1.Glyma.16G044100 + - GmTIR1A +gene_symbol_long: Transport Inhibitor Response 1A +gene_model_pub_name: Glyma.02G152800 +gene_model_full_id: glyma.Wm82.gnm2.ann1.Glyma.02G152800 confidence: 5 curators: - - Steven Cannon - - Greg Murrell -phenotype_synopsis: Control of flowering time and shoot determinacy + - Marlene Dorneich-Hayes + - Scott Kalberer +comments: + - TIR1A is strongly expressed in developing nodules, main and lateral roots, and especially in main root tips and lateral root primordia. + - Expression in roots decreases as nodulation progresses. + - TIR1A is upregulated by auxin. +phenotype_synopsis: TIR1A is an auxin receptor which positively regulates root growth and nodulation. traits: - - entity_name: photoperiod-sensitive flowering time trait - entity: TO:0000934 - - entity_name: plant height - entity: TO:0000207 - - entity_name: flowering time - entity: TO:0002616 - relation_name: positively regulates + - entity_name: auxin receptor activity + entity: GO:0038198 + - entity_name: regulation of biological process involved in symbiotic interaction + entity: GO:0043903 + - entity_name: nodulation + entity: GO:0009877 + - relation_name: positively regulates relation: RO:0002213 - - entity_name: days to maturity - entity: TO:0000469 - relation_name: positively regulates + - entity_name: root development + entity: GO:0048364 + - relation_name: positively regulates relation: RO:0002213 + - entity_name: positive regulation of lateral root development + entity: GO:1901333 references: - - citation: Yue, Li et al., 2021 - doi: 10.1111/jipb.13070 - pmid: 33458938 - - citation: Nan, Cao et al., 2014 - doi: 10.1371/journal.pone.0097669 - pmid: 24845624 - - citation: Takeshima, Hayashi et al., 2016 - doi: 10.1093/jxb/erw283 - pmid: 27422993 - - citation: Zhao, Takeshima et al., 2016 - doi: 10.1186/s12870-016-0704-9 - pmid: 26786479 - - citation: Dietz, Chan et al., 2023 - doi: 10.3389/fpls.2022.889066 - pmid: 35574141 - - citation: Cai, Wang et al., 2020 - doi: 10.1111/pbi.13199 - pmid: 31240772 - - citation: Jiang, Zhang et al., 2019 - doi: 10.1186/s12864-019-5577-5 - pmid: 30894121 - - citation: Liu, Jiang et al., 2018 - doi: 10.1111/nph.14884 - pmid: 29120038 - - citation: Cao, Takeshima et al., 2017 - doi: 10.1093/jxb/erw394 - pmid: 28338712 - - citation: Kong, Liu et al., 2010 - doi: 10.1104/pp.110.160796 - pmid: 20864544 - + - citation: Cai, Wang et al., 2017 + doi: 10.1111/nph.14632 + pmid: 28598036 + - citation: Yang, Lan et al., 2022 + doi: 10.1111/jipb.13207 + pmid: 34962095 ## DOCUMENT 3 ## --- -classical_locus: E1 +scientific_name: Glycine max gene_symbols: - - E1 -gene_symbol_long: Earliness 1 -gene_model_pub_name: Glyma.06G207800 -gene_model_full_id: glyma.Wm82.gnm4.ann1.Glyma.06G207800 -confidence: 5 + - GmTIR1B +gene_symbol_long: Transport Inhibitor Response 1B +gene_model_pub_name: Glyma.10G021500 +gene_model_full_id: glyma.Wm82.gnm2.ann1.Glyma.10G021500 +confidence: 4 curators: - - Steven Cannon -phenotype_synopsis: Photoperiodic flowering time regulation + - Marlene Dorneich-Hayes + - Scott Kalberer +comments: + - TIR1B is most strongly expressed in developing nodules and main and lateral roots. + - Expression in roots decreases as nodulation progresses. + - RNAi knockdowns of TIR1B have reduced nodulation. +phenotype_synopsis: TIR1B is an auxin receptor which positively regulates root growth and nodulation. traits: - - entity_name: flowering time - entity: TO:0002616 - relation_name: negatively regulates - relation: RO:0002212 - - entity_name: days to maturity - entity: TO:0000469 - relation_name: negatively regulates - relation: RO:0002212 + - entity_name: auxin receptor activity + entity: GO:0038198 + - entity_name: regulation of biological process involved in symbiotic interaction + entity: GO:0043903 + - entity_name: nodulation + entity: GO:0009877 + - relation_name: positively regulates + relation: RO:0002213 + - entity_name: root development + entity: GO:0048364 + - relation_name: positively regulates + relation: RO:0002213 + - entity_name: positive regulation of lateral root development + entity: GO:1901333 references: - - citation: Xia, Zhai et al., 2012 - doi: 10.3389/fpls.2021.632754 - pmid: 33995435 - - citation: Watanabe, Xia et al., 2011 - doi: 10.1534/genetics.110.125062 - pmid: 21406680 - - citation: Dietz, Chan et al., 2023 - doi: 10.3389/fpls.2022.889066 - pmid: 35574141 - - citation: Lin, Liu et al., 2021 - doi: 10.1111/jipb.13021 - pmid: 33090664 + - citation: Cai, Wang et al., 2017 + doi: 10.1111/nph.14632 + pmid: 28598036 + - citation: Yang, Lan et al., 2022 + doi: 10.1111/jipb.13207 + pmid: 34962095 ## DOCUMENT 4 ## --- -classical_locus: E2 +scientific_name: Glycine max gene_symbols: - - GmGI -gene_symbol_long: Earliness 2 -gene_model_pub_name: Glyma.10G221500 -gene_model_full_id: glyma.Wm82.gnm2.ann1.Glyma.10G221500 + - GmTIR1C +gene_symbol_long: Transport Inhibitor Response 1C +gene_model_pub_name: Glyma.19G206800 +gene_model_full_id: glyma.Wm82.gnm2.ann1.Glyma.19G206800 confidence: 5 curators: - - Steven Cannon -phenotype_synopsis: Photoperiodic flowering time regulation + - Marlene Dorneich-Hayes + - Scott Kalberer +comments: + - TIR1C is most strongly expressed in developing nodules and root meristems. + - Expression in roots is upregulated by Bradyrhizobium japonicum and auxin but downregulated by miR393d. +phenotype_synopsis: TIR1C is an auxin receptor which positively regulates root growth and nodulation. traits: - - entity_name: flowering time - entity: TO:0002616 - relation_name: negatively regulates - relation: RO:0002212 - - entity_name: days to maturity - entity: TO:0000469 - relation_name: negatively regulates - relation: RO:0002212 + - entity_name: auxin receptor activity + entity: GO:0038198 + - entity_name: regulation of biological process involved in symbiotic interaction + entity: GO:0043903 + - entity_name: nodulation + entity: GO:0009877 + - relation_name: positively regulates + relation: RO:0002213 + - entity_name: root development + entity: GO:0048364 + - relation_name: positively regulates + relation: RO:0002213 + - entity_name: regulation of root meristem growth + entity: GO:0010082 + - relation_name: positively regulates + relation: RO:0002213 references: - - citation: Tsubokura, Watanabe et al., 2013 - doi: 10.1093/aob/mct269 - pmid: 24284817 - - citation: Dietz, Chan et al., 2023 - doi: 10.3389/fpls.2022.889066 - pmid: 35574141 - - citation: Lin, Liu et al., 2021 - doi: 10.1111/jipb.13021 - pmid: 33090664 - - citation: Watanabe, Xia et al., 2011 - doi: 10.1534/genetics.110.125062 - pmid: 21406680 - - citation: Xu, Yamagishi et al., 2015 - doi: 10.1104/pp.15.00763 - pmid: 26134161 + - citation: Cai, Wang et al., 2017 + doi: 10.1111/nph.14632 + pmid: 28598036 + - citation: Yang, Lan et al., 2022 + doi: 10.1111/jipb.13207 + pmid: 34962095 ## DOCUMENT 5 ## --- +scientific_name: Glycine max gene_symbols: - - Tof11 - - PRR3a -gene_symbol_long: Time of Flowering 11 -gene_model_pub_name: SoyZH13_11G141200 -gene_model_full_id: glyma.Zh13.gnm1.ann1.SoyZH13_11G141200 -confidence: 5 + - GmTIR1D +gene_symbol_long: Transport Inhibitor Response 1D +gene_model_pub_name: Glyma.03G209400 +gene_model_full_id: glyma.Wm82.gnm2.ann1.Glyma.03G209400 +confidence: 4 curators: - - Steven Cannon -phenotype_synopsis: Photoperiodic flowering time regulation + - Marlene Dorneich-Hayes + - Scott Kalberer +comments: + - TIR1D is most strongly expressed in developing nodules, main and lateral root tips, and lateral root primordia. + - RNAi knockdowns of TIR1D have reduced nodulation. +phenotype_synopsis: TIR1D is an auxin receptor which positively regulates root growth and nodulation. traits: - - entity_name: flowering time - entity: TO:0002616 - relation_name: negatively regulates - relation: RO:0002212 - - entity_name: days to maturity - entity: TO:0000469 - relation_name: negatively regulates - relation: RO:0002212 + - entity_name: auxin receptor activity + entity: GO:0038198 + - entity_name: regulation of biological process involved in symbiotic interaction + entity: GO:0043903 + - entity_name: nodulation + entity: GO:0009877 + - relation_name: positively regulates + relation: RO:0002213 + - entity_name: root development + entity: GO:0048364 + - relation_name: positively regulates + relation: RO:0002213 + - entity_name: positive regulation of lateral root development + entity: GO:1901333 references: - - citation: Lu, Dong et al., 2020 - doi: 10.1038/s41588-020-0604-7 - pmid: 32231277 - - citation: Lin, Liu et al., 2021 - doi: 10.1111/jipb.13021 - pmid: 33090664 + - citation: Cai, Wang et al., 2017 + doi: 10.1111/nph.14632 + pmid: 28598036 + - citation: Yang, Lan et al., 2022 + doi: 10.1111/jipb.13207 + pmid: 34962095 ## DOCUMENT 6 ## --- +scientific_name: Glycine max gene_symbols: - - Tof12 - - PRR3b -gene_symbol_long: Time of Flowering 12 -gene_model_pub_name: SoyZH13_12G067700 -gene_model_full_id: glyma.Zh13.gnm1.ann1.SoyZH13_12G067700 + - GmAFB3A +gene_symbol_long: Auxin-Signaling F-Box 3A +gene_model_pub_name: Glyma.19G100200 +gene_model_full_id: glyma.Wm82.gnm2.ann1.Glyma.19G100200 confidence: 5 curators: - - Steven Cannon -phenotype_synopsis: Photoperiodic flowering time regulation + - Marlene Dorneich-Hayes + - Scott Kalberer +comments: + - AFB3A is most strongly expressed in developing nodules, main and lateral roots, and especially in main root tips and lateral root primordia. + - AFB3A is upregulated by the presence of auxin but downregulated by miR393d. + - RNAi knockdowns of AFB3A have reduced nodulation. + - Transgenic overexpression of AFB3A did not increase nodulation. +phenotype_synopsis: AFB3A is an auxin receptor which has a minor role in the positive regulation of root growth and nodulation. traits: - - entity_name: flowering time - entity: TO:0002616 - relation_name: negatively regulates - relation: RO:0002212 - - entity_name: days to maturity - entity: TO:0000469 - relation_name: negatively regulates - relation: RO:0002212 + - entity_name: auxin receptor activity + entity: GO:0038198 + - entity_name: regulation of biological process involved in symbiotic interaction + entity: GO:0043903 + - entity_name: nodulation + entity: GO:0009877 + - relation_name: positively regulates + relation: RO:0002213 + - entity_name: root development + entity: GO:0048364 + - relation_name: positively regulates + relation: RO:0002213 + - entity_name: positive regulation of lateral root development + entity: GO:1901333 references: - - citation: Lu, Dong et al., 2020 - doi: 10.1038/s41588-020-0604-7 - pmid: 32231277 - - citation: Lin, Liu et al., 2021 - doi: 10.1111/jipb.13021 - pmid: 33090664 + - citation: Cai, Wang et al., 2017 + doi: 10.1111/nph.14632 + pmid: 28598036 + - citation: Yang, Lan et al., 2022 + doi: 10.1111/jipb.13207 + pmid: 34962095 ## DOCUMENT 7 ## --- +scientific_name: Glycine max gene_symbols: - - GmSWN -gene_symbol_long: Swinger -gene_model_pub_name: Glyma.03G224300 -gene_model_full_id: glyma.Wm82.gnm2.ann1.Glyma.03G224300 -confidence: 5 + - GmAFB3B +gene_symbol_long: Auxin-Signaling F-Box 3B +gene_model_pub_name: Glyma.16G050500 +gene_model_full_id: glyma.Wm82.gnm2.ann1.Glyma.16G050500 +confidence: 4 curators: - - Steven Cannon -phenotype_synopsis: Photoperiodic flowering time regulation + - Marlene Dorneich-Hayes + - Scott Kalberer +comments: + - Expression of AFB3B is barely detectable in roots and developing nodules. + - It is likely involved in shoot development rather than in root growth and nodulation. + - RNAi knockdowns of AFB3B have reduced nodulation. +phenotype_synopsis: AFB3B is an auxin receptor. traits: - - entity_name: flowering time - entity: TO:0002616 - - entity_name: days to maturity - entity: TO:0000469 + - entity_name: auxin receptor activity + entity: GO:0038198 + - relation_name: positively regulates + relation: RO:0002213 + - entity_name: shoot system development + entity: GO:0048367 references: - - citation: Wu, Kang et al., 2019 - doi: 10.3389/fpls.2019.01221 - pmid: 31787988 - - citation: Dietz, Chan et al., 2023 - doi: 10.3389/fpls.2022.889066 - pmid: 35574141 + - citation: Cai, Wang et al., 2017 + doi: 10.1111/nph.14632 + pmid: 28598036 + - citation: Yang, Lan et al., 2022 + doi: 10.1111/jipb.13207 + pmid: 34962095 ## DOCUMENT 8 ## --- +scientific_name: Glycine max gene_symbols: - - GmELF5 -gene_symbol_long: Early Flowering 5 -gene_model_pub_name: Glyma.05G031100 -gene_model_full_id: glyma.Wm82.gnm2.ann1.Glyma.05G031100 -confidence: 5 + - GmChlI1a +gene_symbol_long: Mg-Chelatase Subunit Chl1a +gene_model_pub_name: Glyma.13G232500 +gene_model_full_id: glyma.Wm82.gnm2.ann1.Glyma.13G232500 +confidence: 4 curators: - - Steven Cannon -phenotype_synopsis: Photoperiodic flowering time regulation + - Marlene Dorneich-Hayes + - Scott Kalberer +comments: + - The MinnGold and T219H phenotypes cosegregate with ChlI1a. Transformation of WT ChlI1a into mutant soy reinstated normal phenotype. +phenotype_synopsis: Defective Mg-Chetelase is responsible for chlorophyll deficient MinnGold (y11-2) and T219H (y11) phenotypes. traits: - - entity_name: flowering time - entity: TO:0002616 - - entity_name: days to maturity - entity: TO:0000469 + - entity_name: magnesium chelatase activity + entity: GO:0016851 + - entity_name: leaf chlorophyll content + entity: TO:0012002 references: - - citation: Noh, Bizzell et al., 2004 - doi: 10.1111/j.1365-313x.2004.02072.x - pmid: 15125772 - - citation: Dietz, Chan et al., 2023 - doi: 10.3389/fpls.2022.889066 - pmid: 35574141 + - citation: Campbell, Mani et al., 2014 + doi: 10.1534/g3.114.015255 + pmid: 25452420 ## DOCUMENT 9 ## --- +scientific_name: Glycine max gene_symbols: - - GmTEM1a -gene_symbol_long: Tempranillo 1a -gene_model_pub_name: Glyma.20G186200 -gene_model_full_id: glyma.Wm82.gnm2.ann1.Glyma.20G186200 -confidence: 3 + - GmChlI1b +gene_symbol_long: Mg-Chelatase Subunit Chl1b +gene_model_pub_name: Glyma.15G080200 +gene_model_full_id: glyma.Wm82.gnm2.ann1.Glyma.15G080200 +confidence: 4 curators: - - Steven Cannon -phenotype_synopsis: Photoperiodic flowering time regulation -traits: - - entity_name: flowering time - entity: TO:0002616 - - entity_name: days to maturity - entity: TO:0000469 + - Marlene Dorneich-Hayes + - Scott Kalberer +comments: + - The CD-5 phenotype cosegregates with ChlI1b. +phenotype_synopsis: Defective Mg-chetelase is responsible for chlorophyll deficient CD-5 phenotype. +traits: + - entity_name: magnesium chelatase activity + entity: GO:0016851 + - entity_name: leaf chlorophyll content + entity: TO:0012002 references: - - citation: Noh, Bizzell et al., 2004 - doi: 10.1111/j.1365-313x.2004.02072.x - pmid: 15125772 - - citation: Dietz, Chan et al., 2023 - doi: 10.3389/fpls.2022.889066 - pmid: 35574141 + - citation: Campbell, Mani et al., 2014 + doi: 10.1534/g3.114.015255 + pmid: 25452420 ## DOCUMENT 10 ## --- +scientific_name: Glycine max +gene_symbols: + - GmFT2b +gene_symbol_long: Flowering Locus T-like Protein 2b +gene_model_pub_name: Glyma.16G151000 +gene_model_full_id: glyma.Wm82.gnm4.ann1.Glyma.16G151000 +confidence: 4 +curators: + - Greg Murrell + - Scott Kalberer +comments: + - Overexpression of GmFT2b upregulates expression of genes that are important in flowering time regulation. + - The major FT2b haplotype Hap3 is associated with significantly earlier flowering at higher latitudes. +phenotype_synopsis: GmFT2b promotes flowering under long-day conditions +traits: + - entity_name: photoperiod-sensitive flowering time trait + entity: TO:0000934 + - entity_name: positive regulation of long-day photoperiodism, flowering + entity: GO:0048578 +references: + - citation: Chen, Cai et al., 2020 + doi: 10.1111/pce.13695 + pmid: 31981430 + + +## DOCUMENT 11 ## +--- +scientific_name: Glycine max +gene_symbols: + - GmSYP24 + - GmLEA2-96 +gene_symbol_long: Syntaxin-24 +gene_model_pub_name: Glyma.19G198600 +gene_model_full_id: glyma.Wm82.gnm4.ann1.Glyma.19G198600 +confidence: 5 +curators: + - Greg Murrell + - Scott Kalberer +comments: + - GmSYP24 was identified as a dehydration-responsive gene with the expressed protein located on the cell membrane. + - Overexpression of SYP24 in soybean and heteroexpression in Arabidopsis produced insensitivity to osmotic/drought stress and high salinity levels. + - SYP24-transgenic soybeans had greater water content and higher activities of peroxidase and superoxide dismutase compared with non-transgenic controls following exposure to abiotic stresses. + - SYP24-transgenic soybeans showed altered expression of some aquaporins under osmotic/drought, salt, or ABA treatment. + - Leaf stomatal density and opening were reduced in SYP24-transgenic Arabidopsis, and ABA-responsive genes were up-regulated. + - Sensitivity to ABA was decreased during seed germination of both SYP24-transgenic soybean and Arabidopsis. +phenotype_synopsis: GmSYP24 plays an important role to enhance drought response and salt tolerance as part of the ABA signaling pathway. +traits: + - entity_name: drought tolerance + entity: TO:0000276 + - relation_name: positively regulates + relation: RO:0002213 + - entity_name: salt tolerance + entity: TO:0006001 + - relation_name: positively regulates + relation: RO:0002213 + - entity_name: abscisic acid-activated signaling pathway + entity: GO:0009738 + - entity_name: seed germination + entity: GO:0009845 +references: + - citation: Chen, Fang et al., 2019 + doi: 10.1038/s41598-019-42332-5 + pmid: 30979945 + + +## DOCUMENT 12 ## +--- +scientific_name: Glycine max +gene_symbols: + - GmDGAT1A +gene_symbol_long: Diacylglycerol Acyltransferase 1A +gene_model_pub_name: Glyma.13G106100 +gene_model_full_id: glyma.Wm82.gnm2.ann1.Glyma.13G106100 +confidence: 3 +curators: + - Marlene Dorneich-Hayes + - Scott Kalberer +comments: + - Overexpression of DGAT1A enhances triacylglycerol biosynthesis in seeds (and in other tissues to a lesser extent). + - It is involved in stress response and downregulated by stressors like cold, insect bites, and jasmonate. + - DGAT1A produces similar results when transformed into other species. +phenotype_synopsis: DGAT1A controls synthesis of many triacylglycerols, using 18:3 acyl CoA as an acyl donor. Oil mostly accumulates in seeds. +traits: + - entity_name: regulation of triglyceride biosynthetic process + entity: GO:0010866 + - entity_name: seed development + entity: GO:0048316 +references: + - citation: Chen, Wang et al., 2016 + doi: 10.1038/srep28541 + pmid: 27345221 + - citation: Li, Hatanaka et al., 2013 + doi: 10.1007/s10142-012-0306-z + pmid: 23322364 + - citation: Zhau, Bi et al., 2019 + doi: 10.1016/j.jplph.2019.153019 + pmid: 31437808 + - citation: Zuo, Ikram et al., 2022 + doi: 10.1016/j.csbj.2022.06.014 + pmid: 35782726 + + +## DOCUMENT 13 ## +--- +scientific_name: Glycine max +gene_symbols: + - GmDGAT2D +gene_symbol_long: Diacylglycerol Acyltransferase 2D +gene_model_pub_name: Glyma.01G156000 +gene_model_full_id: glyma.Wm82.gnm2.ann1.Glyma.01G156000 +confidence: 3 +curators: + - Marlene Dorneich-Hayes + - Scott Kalberer +comments: + - Overexpression of DGAT2D enhances triacylglycerol biosynthesis in flower tissues. + - DGAT2D is upregulated by temperature stress but downregulated by insect bites and jasmonate. + - DGAT2D produces similar results when transformed into other species. +phenotype_synopsis: DGAT2D controls synthesis of many triacylglycerols, using 18:1 and 18:2 acyl CoA as acyl donors. Oil accumulates most in flowers. +traits: + - entity_name: regulation of triglyceride biosynthetic process + entity: GO:0010866 + - entity_name: seed development + entity: GO:0048316 +references: + - citation: Chen, Wang et al., 2016 + doi: 10.1038/srep28541 + pmid: 27345221 + + +## DOCUMENT 14 ## +--- +scientific_name: Glycine max +gene_symbols: + - GmLHY2a + - GmLCL3 + - GmMYB156 +gene_symbol_long: Late Elongated Hypocotyl 2a +gene_model_pub_name: Glyma.19G260900 +gene_model_full_id: glyma.Wm82.gnm4.ann1.Glyma.19G260900 +confidence: 5 +curators: + - Greg Murrell + - Scott Kalberer +phenotype_synopsis: GmLHY2a encodes a MYB transciption factor that affects plant height through mediating the gibberellin pathway in soybean. +traits: + - entity_name: plant height + entity: TO:0000207 + - relation_name: negatively regulates + relation: RO:0002212 + - entity_name: gibberellin metabolic process + entity: GO:0009685 +references: + - citation: Cheng, Dong et al., 2019 + doi: 10.1186/s12870-019-2145-8 + pmid: 31852439 + + +## DOCUMENT 15 ## +--- +scientific_name: Glycine max +gene_symbols: + - GmbHLHm1 + - GmSAT1 +gene_symbol_long: bHLH transcription factor +gene_model_pub_name: Glyma08g06880 +gene_model_full_id: glyma.gnm2.ann1.Glyma.07g184900 +confidence: 5 +phenotype_synopsis: GmbHLHm1 is important to the soybean rhizobium symbiosis because loss of activity results in a reduction of nodule fitness and growth. Transcriptional changes in nodules highlight downstream signaling pathways involving circadian clock regulation, nutrient transport, hormone signaling, and cell wall modification. +comments: + - Established using mutation, expression, and related functional tests. + - Originally named GmSAT1 (Symbiotic Ammonium Transporter 1) by Kaiser et al., 1998, but does not encode an NH4+ transporter. +traits: + - entity_name: plant organ growth and development trait + entity: TO:0000927 + - entity_name: root nodule + entity: PO:0003023 +references: + - citation: Chiasson, Loughlin et al., 2014 + doi: 10.1073/pnas.1312801111 + pmid: 24707045 + - citation: Kaiser, Finnegan et al., 1998 + doi: 10.1126/science.281.5380.1202 + pmid: 9712587 + + +## DOCUMENT 16 ## +--- gene_symbols: - GmPHYE1 gene_symbol_long: Phytochrome E1 @@ -332,7 +533,7 @@ references: pmid: 35574141 -## DOCUMENT 11 ## +## DOCUMENT 17 ## --- gene_symbols: - GmTOC1 @@ -354,7 +555,7 @@ references: pmid: 35574141 -## DOCUMENT 12 ## +## DOCUMENT 18 ## --- gene_symbols: - GmGA2OX5 @@ -376,7 +577,7 @@ references: pmid: 35574141 -## DOCUMENT 13 ## +## DOCUMENT 19 ## --- gene_symbols: - GmGA2OX6 @@ -398,7 +599,7 @@ references: pmid: 35574141 -## DOCUMENT 14 ## +## DOCUMENT 20 ## --- gene_symbols: - GmMSI1 @@ -423,72 +624,103 @@ references: pmid: 35574141 -## DOCUMENT 15 ## +## DOCUMENT 21 ## --- +scientific_name: Glycine max gene_symbols: - - E1La -gene_symbol_long: E1-like-a -gene_model_pub_name: Glyma.04G156400 -gene_model_full_id: glyma.Wm82.gnm2.ann1.Glyma.04G156400 -confidence: 5 + - GmKASI +gene_symbol_long: Beta-Ketoacyl-Acyl Carrier Protein Synthase I +gene_model_pub_name: Glyma.08G084300 +gene_model_full_id: glyma.Wm82.gnm4.ann1.Glyma.08G084300 +confidence: 4 curators: - - Steven Cannon -phenotype_synopsis: Photoperiodic flowering time regulation + - Greg Murrell + - Scott Kalberer +comments: + - GmKASI is a fatty acid synthesis enzyme involved in the conversion of sucrose into oil during seed development via elongation of ACP-bound acyl species. +phenotype_synopsis: Soybean seeds from a mutagenized plant exhibited doubled sucrose and halved oil content relative to wild type because of disruption to a Beta-Ketoacyl-Acyl Carrier Protein Synthase ortholog (GmKASI) by chromosomal translocation. traits: - - entity_name: flowering time - entity: TO:0002616 - relation_name: negatively regulates - relation: RO:0002212 - - entity_name: days to maturity - entity: TO:0000469 - relation_name: negatively regulates + - entity_name: sucrose content + entity: TO:0000328 + - relation_name: negatively regulates relation: RO:0002212 + - entity_name: fat & essential oil content + entity: TO:0000604 + - relation_name: positively regulates + relation: RO:0002213 + - entity_name: fatty acid biosynthetic process + entity: GO:0006633 references: - - citation: Xu, Yamagishi et al., 2015 - doi: 10.1104/pp.15.00763 - pmid: 26134161 - - citation: Lin, Liu et al., 2021 - doi: 10.1111/jipb.13021 - pmid: 33090664 + - citation: Dobbels, Michno et al., 2017 + doi: 10.1534/g3.116.038596 + pmid: 28235823 -## DOCUMENT 16 ## +## DOCUMENT 22 ## --- +scientific_name: Glycine max gene_symbols: - - E1Lb -gene_symbol_long: E1-like-b -gene_model_pub_name: Glyma.04G143300 -gene_model_full_id: glyma.Wm82.gnm2.ann1.Glyma.04G143300 + - GmMYB118 +gene_model_pub_name: GLYMA_17G094400 +gene_model_full_id: glyma.Wm82.gnm2.ann1.Glyma.17G094400 +confidence: 4 +curators: + - William Hardison +comments: + - The accession number of the maker gene located in the nucleus is At2g30250 + - also known as glyma.Wm82.gnm4.ann1.Glyma.17G094400.1 +phenotype_synopsis: improved tolerance to drought and salt stress +traits: + - entity_name: drought tolerance + entity: TO:0000276 + - entity_name: stress trait + entity: TO:0000164 +references: + - citation: Du, Zhao, et al., 2018 + doi: 10.1186/s12870-018-1551-7 + pmid: 30509166 + + +## DOCUMENT 23 ## +--- +gene_symbols: + - GmFT2b +gene_symbol_long: Flowering Time 2b +gene_model_pub_name: Glyma.16G151000 +gene_model_full_id: glyma.Wm82.gnm2.ann1.Glyma.16G151000 confidence: 5 curators: - Steven Cannon + - Greg Murrell phenotype_synopsis: Photoperiodic flowering time regulation traits: - entity_name: flowering time entity: TO:0002616 - relation_name: negatively regulates - relation: RO:0002212 + - relation_name: positively regulates + relation: RO:0002213 - entity_name: days to maturity entity: TO:0000469 - relation_name: negatively regulates - relation: RO:0002212 + - relation_name: positively regulates + relation: RO:0002213 references: - - citation: Watanabe, Xia et al., 2011 - doi: 10.1534/genetics.110.125062 - pmid: 21406680 + - citation: Fan, Hu et al., 2014 + doi: 10.1186/1471-2229-14-9 + pmid: 24397545 - citation: Lin, Liu et al., 2021 doi: 10.1111/jipb.13021 pmid: 33090664 + - citation: Chen, Cai et al., 2020 + doi: 10.1111/pce.13695 + pmid: 31981430 -## DOCUMENT 17 ## +## DOCUMENT 24 ## --- -classical_locus: E3 gene_symbols: - - GmphyA3 -gene_symbol_long: Earliness 3 -gene_model_pub_name: Glyma.19G224200 -gene_model_full_id: glyma.Wm82.gnm2.ann1.Glyma.19G224200 + - GmFT3a +gene_symbol_long: Flowering Time 3a +gene_model_pub_name: Glyma.16G044200 +gene_model_full_id: glyma.Wm82.gnm2.ann1.Glyma.16G044200 confidence: 5 curators: - Steven Cannon @@ -496,29 +728,28 @@ phenotype_synopsis: Photoperiodic flowering time regulation traits: - entity_name: flowering time entity: TO:0002616 - relation_name: negatively regulates - relation: RO:0002212 + - relation_name: positively regulates + relation: RO:0002213 - entity_name: days to maturity entity: TO:0000469 - relation_name: negatively regulates - relation: RO:0002212 + - relation_name: positively regulates + relation: RO:0002213 references: - - citation: Watanabe, Hideshima et al., 2009 - doi: 10.1534/genetics.108.098772 - pmid: 19474204 + - citation: Fan, Hu et al., 2014 + doi: 10.1186/1471-2229-14-9 + pmid: 24397545 - citation: Lin, Liu et al., 2021 doi: 10.1111/jipb.13021 pmid: 33090664 -## DOCUMENT 18 ## +## DOCUMENT 25 ## --- -classical_locus: E4 gene_symbols: - - GmphyA2 -gene_symbol_long: Earliness 4 -gene_model_pub_name: Glyma.20G090000 -gene_model_full_id: glyma.Wm82.gnm2.ann1.Glyma.20G090000 + - GmFT3b +gene_symbol_long: Flowering Time 3b +gene_model_pub_name: Glyma.19G108100 +gene_model_full_id: glyma.Wm82.gnm2.ann1.Glyma.19G108100 confidence: 5 curators: - Steven Cannon @@ -526,29 +757,28 @@ phenotype_synopsis: Photoperiodic flowering time regulation traits: - entity_name: flowering time entity: TO:0002616 - relation_name: negatively regulates - relation: RO:0002212 + - relation_name: positively regulates + relation: RO:0002213 - entity_name: days to maturity entity: TO:0000469 - relation_name: negatively regulates - relation: RO:0002212 + - relation_name: positively regulates + relation: RO:0002213 references: - - citation: Liu, Jiang et al., 2008a - doi: 10.1111/nph.14884 - pmid: 29120038 + - citation: Fan, Hu et al., 2014 + doi: 10.1186/1471-2229-14-9 + pmid: 24397545 - citation: Lin, Liu et al., 2021 doi: 10.1111/jipb.13021 pmid: 33090664 -## DOCUMENT 19 ## +## DOCUMENT 26 ## --- -classical_locus: E10 gene_symbols: - - GmFT4 -gene_symbol_long: Earliness 10 -gene_model_pub_name: Glyma.08G363100 -gene_model_full_id: glyma.Wm82.gnm2.ann1.Glyma.08G363100 + - GmFT5b +gene_symbol_long: Flowering Time 5b +gene_model_pub_name: Glyma.19G108200 +gene_model_full_id: glyma.Wm82.gnm2.ann1.Glyma.19G108200 confidence: 5 curators: - Steven Cannon @@ -556,94 +786,117 @@ phenotype_synopsis: Photoperiodic flowering time regulation traits: - entity_name: flowering time entity: TO:0002616 - relation_name: negatively regulates - relation: RO:0002212 + - relation_name: positively regulates + relation: RO:0002213 - entity_name: days to maturity entity: TO:0000469 - relation_name: negatively regulates - relation: RO:0002212 + - relation_name: positively regulates + relation: RO:0002213 references: - - citation: Zhai et al., 2014 - doi: 10.1371/journal.pone.0089030 - pmid: 24586488 - - citation: Samanfar et al., 2017 - doi: 10.1007/s00122-016-2819-7 - pmid: 27832313 + - citation: Fan, Hu et al., 2014 + doi: 10.1186/1471-2229-14-9 + pmid: 24397545 - citation: Lin, Liu et al., 2021 doi: 10.1111/jipb.13021 pmid: 33090664 -## DOCUMENT 20 ## +## DOCUMENT 27 ## --- -classical_locus: J +scientific_name: Glycine max +classical_locus: D1 gene_symbols: - - GmELF3 -gene_symbol_long: Early Flowering 3 -gene_model_pub_name: Glyma.04G050200 -gene_model_full_id: glyma.Wm82.gnm2.ann1.Glyma.04G050200 + - GmD1 +gene_model_pub_name: Glyma01g42390 +gene_model_full_id: glyma.Wm82.gnm1.ann1.Glyma11g02980 confidence: 5 curators: - - Steven Cannon -phenotype_synopsis: Photoperiodic flowering time regulation + - William Hardison +phenotype_synopsis: chlorophyll retention in mature tissues traits: - - entity_name: flowering time - entity: TO:0002616 - relation_name: positively regulates - relation: RO:0002213 - - entity_name: days to maturity - entity: TO:0000469 - relation_name: positively regulates - relation: RO:0002213 + - entity_name: negative regulation of chlorophyll catabolic process + entity: GO:1903647 references: - - citation: Lu, Zhao et al., 2017 - doi: 10.1038/ng.3819 - pmid: 28319089 - - citation: Yue et al., 2017 - doi: 10.1016/j.molp.2016.12.004 - pmid: 27979775 - - citation: Lin, Liu et al., 2021 - doi: 10.1111/jipb.13021 - pmid: 33090664 + - citation: Fang, Li et al., 2014 + doi: 10.1111/tpj.12419 + pmid: 24372721 + - citation: Schmutz et al., 2010 + doi: 10.1038/nature08670 + pmid: 20075913 + - citation: Chao et al., 1995 + doi: 10.1104/pp.107.1.253 + pmid: 12228359 -## DOCUMENT 21 ## +## DOCUMENT 28 ## --- +scientific_name: Glycine max +classical_locus: D2 gene_symbols: - - GmFT5a -gene_symbol_long: Flowering Time 5a -gene_model_pub_name: Gyma.16G044100 -gene_model_full_id: glyma.Wm82.gnm2.ann1.Gyma.16G044100 -confidence: 5 + - GmD2 +gene_model_pub_name: Glyma11g02980 +gene_model_full_id: glyma.Wm82.gnm1.ann1.Glyma11g02980 +confidence: 4 curators: - - Steven Cannon -phenotype_synopsis: Photoperiodic flowering time regulation + - William Hardison +phenotype_synopsis: chlorophyll retention in mature tissues traits: - - entity_name: flowering time - entity: TO:0002616 - relation_name: positively regulates - relation: RO:0002213 - - entity_name: days to maturity - entity: TO:0000469 - relation_name: positively regulates - relation: RO:0002213 + - entity_name: negative regulation of chlorophyll catabolic process + entity: GO:1903647 references: - - citation: Kong, Liu et al., 2010 - doi: 10.1104/pp.110.160796 - pmid: 20864544 - - citation: Fan, Hu et al., 2014 - doi: 10.1186/1471-2229-14-9 - pmid: 24397545 - - citation: Lin, Liu et al., 2021 - doi: 10.1111/jipb.13021 - pmid: 33090664 + - citation: Fang, Li et al., 2014 + doi: 10.1111/tpj.12419 + pmid: 24372721 + - citation: Schmutz et al., 2010 + doi: 10.1038/nature08670 + pmid: 20075913 + - citation: Chao et al., 1995 + doi: 10.1104/pp.107.1.253 + pmid: 12228359 -## DOCUMENT 22 ## +## DOCUMENT 29 ## +--- +scientific_name: Glycine max +gene_symbols: + - GmBS1 +gene_symbol_long: Big Seeds 1 +gene_model_pub_name: Glyma10G38970 +gene_model_full_id: glyma.Wm82.gnm1.ann1.Glyma10G38970 +confidence: 4 +curators: + - Marlene Dorneich-Hayes + - Scott Kalberer +comments: + - Downregulation of BS1 increases seed size, weight, and amino acid content. +phenotype_synopsis: BS1 negatively regulates the size of seeds, seed pods, and leaves. +traits: + - entity_name: regulation of seed growth + entity: GO:0080113 + - entity_name: seed development + entity: GO:0048316 + - entity_name: seed size + entity: TO:0000391 + - relation_name: negatively regulates + relation: RO:0002212 + - entity_name: fat and essential oil content + entity: TO:0000604 + - relation_name: negatively regulates + relation: RO:0002212 +references: + - citation: Ge, Yu et al., 2016 + doi: 10.1073/pnas.1611763113 + pmid: 27791139 + - citation: Zuo, Ikram et al., 2022 + doi: 10.1016/j.csbj.2022.06.014 + pmid: 35782726 + + +## DOCUMENT 30 ## --- gene_symbols: - GmFT1a -gene_symbol_long: Flowering Timne 1a +gene_symbol_long: Flowering Time 1a gene_model_pub_name: Glyma.18G298900 gene_model_full_id: glyma.Wm82.gnm2.ann1.Glyma.18G298900 confidence: 5 @@ -653,11 +906,11 @@ phenotype_synopsis: Photoperiodic flowering time regulation traits: - entity_name: flowering time entity: TO:0002616 - relation_name: negatively regulates + - relation_name: negatively regulates relation: RO:0002212 - entity_name: days to maturity entity: TO:0000469 - relation_name: negatively regulates + - relation_name: negatively regulates relation: RO:0002212 references: - citation: Guo, Xu et al., 2015 @@ -668,7 +921,7 @@ references: pmid: 33090664 -## DOCUMENT 23 ## +## DOCUMENT 31 ## --- gene_symbols: - GmFT1b @@ -682,11 +935,11 @@ phenotype_synopsis: Photoperiodic flowering time regulation traits: - entity_name: flowering time entity: TO:0002616 - relation_name: negatively regulates + - relation_name: negatively regulates relation: RO:0002212 - entity_name: days to maturity entity: TO:0000469 - relation_name: negatively regulates + - relation_name: negatively regulates relation: RO:0002212 references: - citation: Guo, Xu et al., 2015 @@ -697,75 +950,258 @@ references: pmid: 33090664 -## DOCUMENT 24 ## +## DOCUMENT 32 ## --- +scientific_name: Glycine max gene_symbols: - - GmFT2b -gene_symbol_long: Flowering Time 2b -gene_model_pub_name: Glyma.16G151000 -gene_model_full_id: glyma.Wm82.gnm2.ann1.Glyma.16G151000 -confidence: 5 + - GmKASII-A +gene_symbol_long: beta-ketoacyl-ACP synthase II +gene_model_pub_name: Glyma17g05200 +gene_model_full_id: glyma.Wm82.gnm1.ann1.Glyma17g05200 +confidence: 3 curators: - - Steven Cannon - - Greg Murrell -phenotype_synopsis: Photoperiodic flowering time regulation + - Wei Huang +comments: + - Mutations in the soybean 3-ketoacyl-ACP synthase gene are correlated with high levels of seed palmitic acid +phenotype_synopsis: Palmitic acid levels were significantly higher in the mutants than in the Williams-82 wild type control traits: - - entity_name: flowering time + - entity_name: beta-ketoacyl-acyl-carrier-protein synthase II activity + entity: GO:0033817 +references: + - citation: Head, Katie, et al., 2012 + doi: 10.1007/s11032-012-9707-x + pmid: null + + +## DOCUMENT 33 ## +--- +scientific_name: Glycine max +gene_symbols: + - GmKASII-B +gene_symbol_long: plastid 3-keto-acyl-ACP synthase II-B +gene_model_pub_name: Glyma13g17290 +gene_model_full_id: glyma.Wm82.gnm1.ann1.Glyma13g17290 +confidence: 3 +curators: + - Wei Huang +phenotype_synopsis: Palmitic acid levels were significantly higher in the mutants than in the Williams-82 wild type control +traits: + - entity_name: beta-ketoacyl-acyl-carrier-protein synthase II activity + entity: GO:0033817 +references: + - citation: Head, Katie, et al., 2012 + doi: 10.1007/s11032-012-9707-x + pmid: null + + +## DOCUMENT 34 ## +--- +scientific_name: Glycine max +classical_locus: D1 +gene_symbols: + - GmFLD +gene_symbol_long: Flowering Locus D +gene_model_pub_name: Glyma02g18610 +gene_model_full_id: glyma.Wm82.gnm1.ann1.Glyma02g18610 +confidence: 4 +curators: + - William Hardison +phenotype_synopsis: early flowering time +traits: + - entity_name: flowering time trait entity: TO:0002616 - relation_name: positively regulates - relation: RO:0002213 - - entity_name: days to maturity - entity: TO:0000469 - relation_name: positively regulates +references: + - citation: Hu, Jin et al., 2014 + doi: 10.1186/s12870-014-0263-x + pmid: 25287450 + + +## DOCUMENT 35 ## +--- +scientific_name: Glycine max +gene_symbols: + - GmNFR1α +gene_symbol_long: Nod Factor Receptor 1α +gene_model_pub_name: Glyma.02G270800 +gene_model_full_id: glyma.Wm82.gnm2.ann1.Glyma.02G270800 +confidence: 5 +curators: + - Marlene Dorneich-Hayes + - Scott Kalberer +comments: + - Mutants lacking NFR1α don't form nodules. + - Transgenic overexpression increased the number of nodules per plant and allowed plants to form nodules in unfavorable conditions. +phenotype_synopsis: NFR1α codes for a receptor kinase which positively regulates nodule number. +traits: + - entity_name: regulation of biological process involved in symbiotic interaction + entity: GO:0043903 + - entity_name: nodulation + entity: GO:0009877 + - relation_name: positively regulates relation: RO:0002213 references: - - citation: Fan, Hu et al., 2014 - doi: 10.1186/1471-2229-14-9 - pmid: 24397545 - - citation: Lin, Liu et al., 2021 - doi: 10.1111/jipb.13021 - pmid: 33090664 - - citation: Chen, Cai et al., 2020 - doi: 10.1111/pce.13695 - pmid: 31981430 + - citation: Indrasumunar, Searle et al., 2011 + doi: 10.1111/j.1365-313x.2010.04398.x + pmid: 21175888 + - citation: Yang, Lan et al., 2022 + doi: 10.1111/jipb.13207 + pmid: 34962095 -## DOCUMENT 25 ## +## DOCUMENT 36 ## --- +scientific_name: Glycine max gene_symbols: - - GmFT3a -gene_symbol_long: Flowering Time 3a -gene_model_pub_name: Glyma.16G044200 -gene_model_full_id: glyma.Wm82.gnm2.ann1.Glyma.16G044200 + - GmNFR1β +gene_symbol_long: Nod Factor Receptor 1β +gene_model_pub_name: Glyma.14G046200 +gene_model_full_id: glyma.Wm82.gnm2.ann1.Glyma.14G046200 confidence: 5 curators: + - Marlene Dorneich-Hayes + - Scott Kalberer +comments: + - Mutants with functional NFR1β but nonfunctional NFR1α have very minimal nodulation. + - Overexpression of NFR1β did not increase nodule number. + - Expression of NFR1β is not sufficient to induce a healthy level of nodulation. +phenotype_synopsis: NFR1β codes for a redundant receptor kinase with unstable mRNA transcripts. +traits: + - entity_name: regulation of biological process involved in symbiotic interaction + entity: GO:0043903 + - entity_name: nodulation + entity: GO:0009877 +references: + - citation: Indrasumunar, Searle et al., 2011 + doi: 10.1111/j.1365-313x.2010.04398.x + pmid: 21175888 + - citation: Yang, Lan et al., 2022 + doi: 10.1111/jipb.13207 + pmid: 34962095 + + +## DOCUMENT 37 ## +--- +scientific_name: Glycine max +gene_symbols: + - GmERD15B +gene_symbol_long: Early Responsive to Dehydration 15B +gene_model_pub_name: Glyma.11G149900 +gene_model_full_id: glyma.Wm82.gnm4.ann1.Glyma.11G149900 +confidence: 4 +curators: + - Greg Murrell - Steven Cannon -phenotype_synopsis: Photoperiodic flowering time regulation + - Scott Kalberer +comments: + - Protein–protein interaction network analysis showed that five out of the top 10 potential interacting proteins of GmERD15B were GmPAB proteins. Two of the GmPAB genes, GmPAB-14G and GmPAB-17G, have annotations related to salt stress responses. +phenotype_summary: Gene overexpression in Glycine enhanced salt tolerance probably by increasing the expression levels of genes related to ABA-signalling, proline content, catalase peroxidase, dehydration response and cation transport. traits: - - entity_name: flowering time - entity: TO:0002616 - relation_name: positively regulates - relation: RO:0002213 - - entity_name: days to maturity - entity: TO:0000469 - relation_name: positively regulates + - entity_name: salt tolerance + entity: TO:0006001 + - relation_name: positively regulates relation: RO:0002213 references: - - citation: Fan, Hu et al., 2014 - doi: 10.1186/1471-2229-14-9 - pmid: 24397545 - - citation: Lin, Liu et al., 2021 - doi: 10.1111/jipb.13021 - pmid: 33090664 + - citation: Jin, Sun et al., 2021 + doi: 10.1111/pbi.13536 + pmid: 33368860 -## DOCUMENT 26 ## +## DOCUMENT 38 ## --- +scientific_name: Glycine max gene_symbols: - - GmFT3b -gene_symbol_long: Flowering Time 3b -gene_model_pub_name: Glyma.19G108100 -gene_model_full_id: glyma.Wm82.gnm2.ann1.Glyma.19G108100 + - GmDMI1-3 +gene_symbol_long: Doesn't Make Infections 1-3 +gene_model_pub_name: Glyma.19G263500 +gene_model_full_id: glyma.Wm82.gnm2.ann1.Glyma.19G263500 +confidence: 4 +curators: + - Marlene Dorneich-Hayes + - Scott Kalberer +comments: + - Transgenic overexpression of DMI1 reduces Heterodera glycines parasitism and increases nodulation. RNAi silencing of DMI1 increases suceptibility to H. glycines and reduces nodulation. +phenotype_synopsis: DMI genes confer resistance to H. glycines nematodes and are necessary for establishing symbiosis. DMI1 encodes a channel protein that controls the signalling pathway leading to nodulation. +traits: + - entity_name: biological process involved in symbiotic interaction + entity: GO:0044403 + - entity_name: nodulation + entity: GO:0009877 + - entity_name: defense response to nematode + entity: GO:0002215 +references: + - citation: Khatri, Pant et al., 2022 + doi: 10.3389/fpls.2022.842597 + pmid: 35599880 + + +## DOCUMENT 39 ## +--- +scientific_name: Glycine max +gene_symbols: + - GmDMI2-7 +gene_symbol_long: Doesn't Make Infections 2-7 +gene_model_pub_name: Glyma.11G246200 +gene_model_full_id: glyma.Wm82.gnm2.ann1.Glyma.11G246200 +confidence: 4 +curators: + - Marlene Dorneich-Hayes + - Scott Kalberer +comments: + - Transgenic overexpression of DMI2 reduces Heterodera glycines parasitism and increases nodulation even without rhizobia. RNAi silencing of DMI2 increases suceptibility to H. glycines and reduces nodulation. +phenotype_synopsis: DMI genes confer resistance to H. glycines nematodes and are necessary for establishing symbiosis. DMI2 encodes a kinase. +traits: + - entity_name: biological process involved in symbiotic interaction + entity: GO:0044403 + - entity_name: nodulation + entity: GO:0009877 + - entity_name: defense response to nematode + entity: GO:0002215 + - entity_name: protein kinase activity + entity: GO:0004672 +references: + - citation: Khatri, Pant et al., 2022 + doi: 10.3389/fpls.2022.842597 + pmid: 35599880 + + +## DOCUMENT 40 ## +--- +scientific_name: Glycine max +gene_symbols: + - GmDMI3-2 +gene_symbol_long: Doesn't Make Infections 3-2 +gene_model_pub_name: Glyma.15G222300 +gene_model_full_id: glyma.Wm82.gnm2.ann1.Glyma.15G222300 +confidence: 4 +curators: + - Marlene Dorneich-Hayes + - Scott Kalberer +comments: + - Transgenic overexpression of DMI3 reduces Heterodera glycines parasitism and increases nodulation even without rhizobia. RNAi silencing of DMI3 increases suceptibility to H. glycines and reduces nodulation. +phenotype_synopsis: DMI genes confer resistance to H. glycines nematodes and are necessary for establishing symbiosis. DMI3 encodes a kinase. +traits: + - entity_name: biological process involved in symbiotic interaction + entity: GO:0044403 + - entity_name: nodulation + entity: GO:0009877 + - entity_name: defense response to nematode + entity: GO:0002215 + - entity_name: protein kinase activity + entity: GO:0004672 +references: + - citation: Khatri, Pant et al., 2022 + doi: 10.3389/fpls.2022.842597 + pmid: 35599880 + + +## DOCUMENT 41 ## +--- +classical_locus: E9 +gene_symbols: + - GmFT2a +gene_symbol_long: Flowering Time 2a +gene_model_pub_name: Glyma.16g150700 +gene_model_full_id: glyma.Wm82.gnm4.ann1.Glyma.16G150700 confidence: 5 curators: - Steven Cannon @@ -773,28 +1209,40 @@ phenotype_synopsis: Photoperiodic flowering time regulation traits: - entity_name: flowering time entity: TO:0002616 - relation_name: positively regulates + - relation_name: positively regulates relation: RO:0002213 - entity_name: days to maturity entity: TO:0000469 - relation_name: positively regulates + - relation_name: positively regulates relation: RO:0002213 references: - - citation: Fan, Hu et al., 2014 - doi: 10.1186/1471-2229-14-9 - pmid: 24397545 + - citation: Kong, Liu et al., 2010 + doi: 10.1104/pp.110.160796 + pmid: 20864544 + - citation: Kong, Nan et al., 2014 + doi: 10.2135/cropsci2014.03.0228 + pmid: null + - citation: Takeshima, Hayashi et al., 2016 + doi: 10.1093/jxb/erw283 + pmid: 27422993 + - citation: Zhao, Takeshima et al., 2016 + doi: 10.1186/s12870-016-0704-9 + pmid: 26786479 + - citation: Dietz, Chan et al., 2023 + doi: 10.3389/fpls.2022.889066 + pmid: 35574141 - citation: Lin, Liu et al., 2021 doi: 10.1111/jipb.13021 pmid: 33090664 -## DOCUMENT 27 ## +## DOCUMENT 42 ## --- gene_symbols: - - GmFT5b -gene_symbol_long: Flowering Time 5b -gene_model_pub_name: Glyma.19G108200 -gene_model_full_id: glyma.Wm82.gnm2.ann1.Glyma.19G108200 + - GmFT5a +gene_symbol_long: Flowering Time 5a +gene_model_pub_name: Glyma.16G044100 +gene_model_full_id: glyma.Wm82.gnm2.ann1.Glyma.16G044100 confidence: 5 curators: - Steven Cannon @@ -802,13 +1250,16 @@ phenotype_synopsis: Photoperiodic flowering time regulation traits: - entity_name: flowering time entity: TO:0002616 - relation_name: positively regulates + - relation_name: positively regulates relation: RO:0002213 - entity_name: days to maturity entity: TO:0000469 - relation_name: positively regulates + - relation_name: positively regulates relation: RO:0002213 references: + - citation: Kong, Liu et al., 2010 + doi: 10.1104/pp.110.160796 + pmid: 20864544 - citation: Fan, Hu et al., 2014 doi: 10.1186/1471-2229-14-9 pmid: 24397545 @@ -817,855 +1268,2673 @@ references: pmid: 33090664 -## DOCUMENT 28 ## +## DOCUMENT 43 ## --- +scientific_name: Glycine max +classical_locus: Gp11 gene_symbols: - - GmFT6 -gene_symbol_long: Flowering Time 6 -gene_model_pub_name: Glyma.08G363200 -gene_model_full_id: glyma.Wm82.gnm2.ann1.Glyma.08G363200 -confidence: 5 -curators: - - Steven Cannon -phenotype_synopsis: Photoperiodic flowering time regulation + - GmPRR3A +gene_symbol_long: Pseudo Response Regulator 3A +gene_model_pub_name: Glyma11g15580 +gene_model_full_id: glyma.Wm82.gnm1.ann1.Glyma11g15580 +confidence: 3 +curators: + - William Hardison +comments: + - Glyma11g15580 pseudo-response regulator 3 + - Gp11 and Gp12 regulate the expression of GmFT2a and GmFT5a +phenotype_synopsis: Shorter growth period traits: - - entity_name: flowering time - entity: TO:0002616 - relation_name: negatively regulates - relation: RO:0002212 - entity_name: days to maturity entity: TO:0000469 - relation_name: negatively regulates - relation: RO:0002212 references: - - citation: Wang, Zhou et al., 2015 - doi: 10.1105/tpc.114.135103 - pmid: 25663621 - - citation: Lin, Liu et al., 2021 - doi: 10.1111/jipb.13021 - pmid: 33090664 + - citation: Li, Liu et al., 2019 + doi: 10.1093/pcp/pcy215 + pmid: 30418611 -## DOCUMENT 29 ## +## DOCUMENT 44 ## --- +scientific_name: Glycine max +classical_locus: Gp12 gene_symbols: - - LHY1a -gene_symbol_long: Leafy 1a -gene_model_pub_name: Glyma.16G017400 -gene_model_full_id: glyma.Wm82.gnm2.ann1.Glyma.16G017400 -confidence: 5 + - GmPRR3B +gene_symbol_long: Pseudo Response Regulator 3B +gene_model_pub_name: Glyma12g07861 +gene_model_full_id: glyma.Wm82.gnm1.ann1.Glyma12g07861 +confidence: 3 curators: - - Steven Cannon -phenotype_synopsis: Photoperiodic flowering time regulation + - William Hardison +comments: + - Gp11 and Gp12 regulate the expression of GmFT2a and GmFT5a + - Glyma12g07861 pseudo-response regulator 7 +phenotype_synopsis: Shorter growth period traits: - - entity_name: flowering time - entity: TO:0002616 - relation_name: positively regulates - relation: RO:0002213 - entity_name: days to maturity entity: TO:0000469 - relation_name: positively regulates - relation: RO:0002213 references: - - citation: Lu, Zhao et al., 2017 - doi: 10.1038/ng.3819 - pmid: 28319089 - - citation: Lin, Liu et al., 2021 - doi: 10.1111/jipb.13021 - pmid: 33090664 + - citation: Li, Liu et al., 2019 + doi: 10.1093/pcp/pcy215 + pmid: 30418611 -## DOCUMENT 30 ## +## DOCUMENT 45 ## --- +scientific_name: Glycine max +classical_locus: null gene_symbols: - - LHY1b -gene_symbol_long: Leafy 1b -gene_model_pub_name: Glyma.07G048500 -gene_model_full_id: glyma.Wm82.gnm2.ann1.Glyma.07G048500 + - GmDT2 +gene_symbol_long: Determinacy 2 +gene_model_pub_name: SoyZH13_18G242900 +gene_model_full_id: glyma.Wm82.gnm4.ann1.Glyma.18G273600 confidence: 5 curators: - - Steven Cannon -phenotype_synopsis: Photoperiodic flowering time regulation + - Brandon Jordan +phenotype_synopsis: In the presence of Dt1, Dt2 impacts determinacy, maturity, and branch number. +comments: + - knockout of SoyZH13_18g242900 produces plants with increased branch number and delayed flowering and maturity relative to wildtype. traits: - - entity_name: flowering time - entity: TO:0002616 - relation_name: positively regulates - relation: RO:0002213 - - entity_name: days to maturity - entity: TO:0000469 - relation_name: positively regulates - relation: RO:0002213 + - entity_name: shoot branching + entity: TO:0002639 + - relation_name: increased amount + relation: PATO:0000470 references: - - citation: Lu, Zhao et al., 2017 - doi: 10.1038/ng.3819 - pmid: 28319089 - - citation: Lin, Liu et al., 2021 - doi: 10.1111/jipb.13021 - pmid: 33090664 + - citation: Liang, Chen, et al., 2022 + doi: 10.1038/s41467-022-34153-4 + pmid: 36307423 + - citation: Ping, Liu, et al., 2014 + doi: 10.1105/tpc.114.126938 + pmid: 25005919 -## DOCUMENT 31 ## +## DOCUMENT 46 ## --- +classical_locus: E4 gene_symbols: - - LHY2a - - GmLHY2a - - LCL3 - - MYB156 -gene_symbol_long: Leafy 2a -gene_model_pub_name: Glyma.19G260900 -gene_model_full_id: glyma.Wm82.gnm2.ann1.Glyma.19G260900 + - GmphyA2 +gene_symbol_long: Earliness 4 +gene_model_pub_name: Glyma.20G090000 +gene_model_full_id: glyma.Wm82.gnm2.ann1.Glyma.20G090000 confidence: 5 curators: - Steven Cannon - - Greg Murrell phenotype_synopsis: Photoperiodic flowering time regulation -comments: Encodes a MYB transciption factor that affects plant height through mediating the GA pathway in soybean traits: - entity_name: flowering time entity: TO:0002616 - relation_name: positively regulates - relation: RO:0002213 + - relation_name: negatively regulates + relation: RO:0002212 - entity_name: days to maturity entity: TO:0000469 - relation_name: positively regulates - relation: RO:0002213 + - relation_name: negatively regulates + relation: RO:0002212 references: - - citation: Lu, Zhao et al., 2017 - doi: 10.1038/ng.3819 - pmid: 28319089 + - citation: Liu, Jiang et al., 2008 + doi: 10.1111/nph.14884 + pmid: 29120038 - citation: Lin, Liu et al., 2021 doi: 10.1111/jipb.13021 pmid: 33090664 - - citation: Chen, Cai et al., 2020 - doi: 10.1111/pce.13695 - pmid: 31981430 -## DOCUMENT 32 ## +## DOCUMENT 47 ## --- +scientific_name: Glycine max gene_symbols: - - LHY2b -gene_symbol_long: Leafy 2b -gene_model_pub_name: Glyma.03G261800 -gene_model_full_id: glyma.Wm82.gnm2.ann1.Glyma.03G261800 -confidence: 5 + - GmVTL1a +gene_symbol_long: Vacuolar Iron Transporter Like 1A +gene_model_pub_name: Glyma.05G121600 +gene_model_full_id: glyma.Wm82.gnm4.ann1.Glyma.05G121600 +confidence: 3 curators: - - Steven Cannon -phenotype_synopsis: Photoperiodic flowering time regulation + - William Hardison +comments: + - also known as glyma.Wm82.gnm2.ann1.Glyma.08G076300.1 + - iron import into symbiosomes from infected cell cytosol +phenotype_synopsis: Nitrogen fixation in the nodules traits: - - entity_name: flowering time - entity: TO:0002616 - relation_name: positively regulates - relation: RO:0002213 - - entity_name: days to maturity - entity: TO:0000469 - relation_name: positively regulates - relation: RO:0002213 + - entity_name: indeterminate root nodule nitrogen fixation zone + entity: ENVO:01000171 references: - - citation: Lu, Zhao et al., 2017 - doi: 10.1038/ng.3819 - pmid: 28319089 - - citation: Lin, Liu et al., 2021 - doi: 10.1111/jipb.13021 - pmid: 33090664 + - citation: Liu, Liao et al., 2020 + doi: 10.1111/nph.16506 + pmid: 32119117 -## DOCUMENT 33 ## +## DOCUMENT 48 ## --- -classical_locus: +scientific_name: Glycine max gene_symbols: - - GmDT2 -gene_symbol_long: Determinacy 2 -gene_model_pub_name: SoyZH13_18G242900 -gene_model_full_id: glyma.Wm82.gnm4.ann1.Glyma.18G273600 -confidence: 5 + - GmVTL1b +gene_symbol_long: Vacuolar Iron Transporter Like 1B +gene_model_pub_name: Glyma.08G076300 +gene_model_full_id: glyma.Wm82.gnm2.ann1.Glyma.08G076300 +confidence: 3 curators: - - Brandon Jordan -phenotype_synopsis: In the presence of Dt1, Dt2 impacts determinacy, maturity, and branch number. + - William Hardison comments: - - knockout of SoyZH13_18g242900 produces plants with increased branch number and delayed flowering and maturity relative to wildtype. + - Failed to keep wildtype phenotype +phenotype_synopsis: lack of iron homeostasis traits: - - entity_name: shoot branching - entity: TO:0002639 - relation_name: increased amount - relation: PATO:0000470 + - entity_name: indeterminate root nodule nitrogen fixation zone + entity: ENVO:01000171 references: - - citation: Liang, Chen et al., 2022 - doi: 10.1038/s41467-022-34153-4 - pmid: 36307423 - - citation: Ping, Liu et al., 2014 - doi: 10.1105/tpc.114.126938 - pmid: 25005919 + - citation: Liu, Liao et al., 2020 + doi: 10.1111/nph.16506 + pmid: 32119117 -## DOCUMENT 34 ## +## DOCUMENT 49 ## --- -classical_locus: +scientific_name: Glycine max gene_symbols: - GmDT1 - - TFL - - TFL1b - - TFL1.1 - - GmTFL1b gene_symbol_long: Determinacy 1 gene_model_pub_name: Glyma.19g194300 gene_model_full_id: glyma.Wm82.gnm2.ann1.Glyma.19G194300 confidence: 5 curators: - Brandon Jordan - - Greg Murrell -comments: - - Affects photoperiodic flowering time and determinacy -phenotype_synopsis: Modification of flowering time and determinacy +phenotype_synopsis: determinate stem growth habit traits: - - entity_name: photoperiod-sensitive flowering time trait - entity: TO:0000934 - - entity_name: plant height - entity: TO:0000207 - - entity_name: flowering time - entity: TO:0002616 - entity_name: meristem identity entity: TO:0006017 - relation_name: terminal + - relation_name: terminal relation: PATO:0002476 references: - citation: Liu, Watanabe et al., 2010 - doi: doi.org/10.1104/pp.109.150607 - pmid: 20219831 - - citation: Yue, Li et al., 2021 - doi: 10.1111/jipb.13070 - pmid: 33458938 - - citation: Tian, Wang et al., 2010 - doi: 10.1073/pnas.1000088107 - pmid: 20421496 - - citation: Langewisch, Zhang, 2014 - doi: 10.1371/journal.pone.0094150 - pmid: 24727730 + doi: null + pmid: null -## DOCUMENT 35 ## + +## DOCUMENT 50 ## --- +scientific_name: Glycine max gene_symbols: - - GmPLDγ -gene_symbol_long: Phospholipase D -gene_model_pub_name: Glyma.01g42420 -gene_model_full_id: Glyma.Wm82.gmn1.Glyma01g42420 -confidence: 5 + - GmPHR1 +gene_symbol_long: Phosphate Starvation Response 1 +gene_model_pub_name: Glyma.01G009600 +gene_model_full_id: glyma.Wm82.gnm2.ann1.Glyma.01G009600 +confidence: 4 curators: - - Greg Murrell -phenotype_summary: Overexpression of GmPLDγ from soybean results in higher seed oil content and fatty-acid remodeling in Arabidopsis. + - Marlene Dorneich-Hayes + - Scott Kalberer +comments: + - GmPHR1 is expressed throughout nodules and expression increases as nodules develop. + - Transgenic overexpression increased nodule size and increased the concentration of N and P. + - PHR1 and GmPHR4 promote each other's expression. + - When phosphorus is abundant, overexpression of PHR1 represses GmPHT1-4. + - PHR1 positively regulates GmPAP12 (see Wang, Yang et al., 2020). +phenotype_synopsis: GmPHR1 is a constitutively expressed transcription factor which induces expression of GmPHT1s to promote phosphate uptake. Together, PHRs and PHT1s maintain inorganic phosphate (Pi) homeostasis in nodules. traits: - - entity_name: seed oil content - entity: CO_336:0000048 - relation_name: positively regulates - relation: RO:0002213 - - entity_name: fat and essential oil composition related trait - entity: TO:0000491 - - entity_name: seed weight - entity: TO:0000181 - relation_name: positively regulates - relation: RO:0002213 - - entity_name: triglyceride metabolic process - entity: GO:0006641 - relation_name: positively regulates - relation: RO:0002213 + - entity_name: regulation of biological process involved in symbiotic interaction + entity: GO:0043903 + - entity_name: nodulation + entity: GO:0009877 references: - - citation: Bai, Jing et al., 2021 - doi: 10.1016/j.plantsci.2019.110298 - pmid: 31779909 + - citation: Lu, Cheng et al., 2020 + doi: 10.1104/pp.19.01209 + pmid: 32680974 + - citation: Isidra-Arellano, Pozas-Rodrguez et al., 2020 + doi: 10.1111/tpj.14789 + pmid: 32344464 + - citation: Wang, Yang et al., 2020 + doi: 10.3389/fpls.2020.00450 + pmid: 32499790 + - citation: Yang, Lan et al., 2022 + doi: 10.1111/jipb.13207 + pmid: 34962095 -## DOCUMENT 36 ## +## DOCUMENT 51 ## --- +scientific_name: Glycine max gene_symbols: - - GmSYP24 - - GmLEA2-96 - - SYP24 -gene_symbol_long: Putative Syntaxin Gene -gene_model_pub_name: Glyma.19G198600 -gene_model_full_id: glyma.Wm82.gnm4.ann1.Glyma.19G198600 -confidence: 5 + - GmPHR4 +gene_symbol_long: Phosphate Starvation Response 4 +gene_model_pub_name: Glyma.02G108500 +gene_model_full_id: glyma.Wm82.gnm2.ann1.Glyma.02G108500 +confidence: 4 curators: - - Greg Murrell -phenotype_synopsis: Dehydration response + - Marlene Dorneich-Hayes + - Scott Kalberer +comments: + - GmPHR4 is expressed in noninfected nodule tissues. Transgenic overexpression increased nodule size but decreased nodule number. + - PHR4 targets GmPHT1-1, GmPHT1-4, and GmPHT1-11. + - PHR4 and GmPHR1 promote each other's expression. + - When phosphorus is abundant, overexpression of PHR4 increases expression of PHT1-4. + - Silencing of PHR4 had no effect on PHT1-4 expression. +phenotype_synopsis: GmPHR4 is a constitutively expressed transcription factor which induces expression of GmPHT1s to promote phosphate uptake. Together, PHRs and PHT1s maintain inorganic phosphate (Pi) homeostasis in nodules. traits: - - entity_name: drought tolerance - entity: TO:0000276 - relation_name: positively regulates - relation: RO:0002213 - - entity_name: abscisic acid-activated signaling pathway - entity: GO:0009738 - - entity_name: seed germination - entity: GO:0009845 + - entity_name: regulation of biological process involved in symbiotic interaction + entity: GO:0043903 + - entity_name: nodulation + entity: GO:0009877 references: - - citation: Chen, Fang et al., 2019 - doi: 10.1038/s41598-019-42332-5 - pmid: 30979945 + - citation: Lu, Cheng et al., 2020 + doi: 10.1104/pp.19.01209 + pmid: 32680974 -## DOCUMENT 37 ## +## DOCUMENT 52 ## --- +scientific_name: Glycine max gene_symbols: - - KASI -gene_symbol_long: beta-ketoacyl-ACP synthetase I -gene_model_pub_name: Glyma.08G084300 -gene_model_full_id: glyma.Wm82.gnm4.ann1.Glyma.08G084300 -confidence: 4 + - GmPHT1-1 +gene_symbol_long: Phosphate Transporter 1-1 +gene_model_pub_name: Glyma10G33030 +gene_model_full_id: glyma.Wm82.gnm1.ann1.Glyma10G33030 +confidence: 3 curators: - - Greg Murrell -phenotype_synopsis: Altered seed sucrose & oil content due to due to disruption of a core fatty acid synthase. + - Marlene Dorneich-Hayes + - Scott Kalberer +comments: + - Expression is enhanced by GmPHR1 in N2-fixing regions. + - Expression is enhanced in non N2-fixing regions by both PHR1 and GmPHR4. + - Expression of GmPHT1-1 is positively correlated with nitrogen fixation. +phenotype_synopsis: GmPHT1-1 is a target of GmPHR1 and GmPHR4. It encodes a plasma membrane phosphate transporter. traits: - - entity_name: sucrose content - entity: TO:0000328 - relation_name: positively regulates - relation: RO:0002213 - - entity_name: fat & essential oil content - entity: TO:0000604 - relation_name: negatively regulates - relation: RO:0002212 + - entity_name: inorganic phosphate transmembrane transporter activity + entity: GO:0005315 + - entity_name: regulation of biological process involved in symbiotic interaction + entity: GO:0043903 + - entity_name: nodulation + entity: GO:0009877 references: - - citation: Dobbels, Michno et al., 2017 - doi: 10.1534/g3.116.038596 - pmid: 28235823 + - citation: Lu, Cheng et al., 2020 + doi: 10.1104/pp.19.01209 + pmid: 32680974 + - citation: Yang, Lan et al., 2022 + doi: 10.1111/jipb.13207 + pmid: 34962095 -## DOCUMENT 38 ## +## DOCUMENT 53 ## --- +scientific_name: Glycine max gene_symbols: - - GmLEC2a - - GmLEC2 - - LEC2 -gene_symbol_long: Leafy Cotyledon 2 -gene_model_pub_name: Glyma.20G035700 -gene_model_full_id: glyma.Wm82.gnm4.ann1.Glyma.20G035700 -confidence: 4 + - GmPHT1-4 +gene_symbol_long: Phosphate Transporter 1-4 +gene_model_pub_name: Glyma.10G036800 +gene_model_full_id: glyma.Wm82.gnm4.ann1.Glyma.10G036800 +confidence: 3 curators: - - Greg Murrell -phenotype_synopsis: Regulation of genes involved in biosynthesis and catabolism of seed storage and development. -traits: - - entity_name: seed growth and development trait - entity: TO:0000653 - - entity_name: triglyceride catabolic process - entity: GO:0019433 - relation_name: negatively regulates + - Marlene Dorneich-Hayes + - Scott Kalberer +comments: + - GmPHR1 and GmPHR4 enhance expression of GmPHT1-4 in non N2-fixing regions. + - When phosphorus concentration is low, PHR4 enhances PHT1-4 expression. + - When phosphorus is readily available, overexpression of PHR1 represses PHT1-4. + - Expression of GmPHT1-1 is positively correlated with nitrogen fixation. +phenotype_synopsis: GmPHT1-4 is a target of GmPHR1 and GmPHR4. It encodes a plasma membrane phosphate transporter. +traits: + - entity_name: inorganic phosphate transmembrane transporter activity + entity: GO:0005315 + - entity_name: regulation of biological process involved in symbiotic interaction + entity: GO:0043903 + - entity_name: nodulation + entity: GO:0009877 +references: + - citation: Lu, Cheng et al., 2020 + doi: 10.1104/pp.19.01209 + pmid: 32680974 + - citation: Yang, Lan et al., 2022 + doi: 10.1111/jipb.13207 + pmid: 34962095 + + +## DOCUMENT 54 ## +--- +scientific_name: Glycine max +gene_symbols: + - GmPHT1-11 +gene_symbol_long: Phosphate Transporter 1-11 +gene_model_pub_name: Glyma.14G188000 +gene_model_full_id: glyma.Wm82.gnm2.ann1.Glyma.14G188000 +confidence: 4 +curators: + - Marlene Dorneich-Hayes + - Scott Kalberer +comments: + - GmPHT1-11 is expressed in noninfected nodule tissues. + - RNAi silencing of PHT1-11 increased nodule number but decreased nodule size and nitrogenase activity. + - Transgenic overexpression of PHT1-11 enhanced nitrogenase activity. + - Expression of PHT1-11 is enhanced by GmPHR1, except in N2-fixing regions, where PHR1 represses PHT1-11. + - PHT1-11 is repressed by GmPHR4. + - Overexpression of PHT1-11 represses GmPHT1-4. +phenotype_synopsis: GmPHT1-11 is targeted by GmPHR1 and GmPHR4. It encodes a plasma membrane phosphate transporter. +traits: + - entity_name: inorganic phosphate transmembrane transporter activity + entity: GO:0005315 + - entity_name: regulation of biological process involved in symbiotic interaction + entity: GO:0043903 + - entity_name: nodulation + entity: GO:0009877 +references: + - citation: Lu, Cheng et al., 2020 + doi: 10.1104/pp.19.01209 + pmid: 32680974 + - citation: Yang, Lan et al., 2022 + doi: 10.1111/jipb.13207 + pmid: 34962095 + + +## DOCUMENT 55 ## +--- +gene_symbols: + - Tof11 + - PRR3a +gene_symbol_long: Time of Flowering 11 +gene_model_pub_name: SoyZH13_11G141200 +gene_model_full_id: glyma.Zh13.gnm1.ann1.SoyZH13_11G141200 +confidence: 5 +curators: + - Steven Cannon +phenotype_synopsis: Photoperiodic flowering time regulation +traits: + - entity_name: flowering time + entity: TO:0002616 + - relation_name: negatively regulates relation: RO:0002212 - - entity_name: carbohydrate biosynthetic process - entity: GO:0016051 - relation_name: negatively regulates + - entity_name: days to maturity + entity: TO:0000469 + - relation_name: negatively regulates relation: RO:0002212 - - entity_name: regulation of gene expression - entity: GO:0010468 references: - - citation: Manan, Ahmad et al., 2017 - doi: 10.3389/fpls.2017.01604 - pmid: 28979275 + - citation: Lu, Dong et al., 2020 + doi: 10.1038/s41588-020-0604-7 + pmid: 32231277 + - citation: Lin, Liu et al., 2021 + doi: 10.1111/jipb.13021 + pmid: 33090664 -## DOCUMENT 39 ## +## DOCUMENT 56 ## --- gene_symbols: - - GmCHX1 -gene_symbol_long: cation/H(+) antiporter 1 -gene_model_pub_name: Glyma.03G171600 -gene_model_full_id: glyma.Wm82.gnm4.ann1.Glyma.03G171600 -confidence: 4 + - Tof12 + - PRR3b +gene_symbol_long: Time of Flowering 12 +gene_model_pub_name: SoyZH13_12G067700 +gene_model_full_id: glyma.Zh13.gnm1.ann1.SoyZH13_12G067700 +confidence: 5 curators: - - Greg Murrell -phenotype_synopsis: Impacts salt tolerance + - Steven Cannon +phenotype_synopsis: Photoperiodic flowering time regulation +traits: + - entity_name: flowering time + entity: TO:0002616 + - relation_name: negatively regulates + relation: RO:0002212 + - entity_name: days to maturity + entity: TO:0000469 + - relation_name: negatively regulates + relation: RO:0002212 +references: + - citation: Lu, Dong et al., 2020 + doi: 10.1038/s41588-020-0604-7 + pmid: 32231277 + - citation: Lin, Liu et al., 2021 + doi: 10.1111/jipb.13021 + pmid: 33090664 + + +## DOCUMENT 57 ## +--- +scientific_name: Glycine max +gene_symbols: + - GmNFYA +gene_symbol_long: Nuclear Transcription Factor Y Subunit +gene_model_pub_name: Glyma.02G303800 +gene_model_full_id: glyma.Wm82.gnm2.ann1.Glyma.02G303800 +confidence: 3 +curators: + - Marlene Dorneich-Hayes + - Scott Kalberer +comments: + - Overexpression enhances seed oil content and salt tolerance. +phenotype_synopsis: NFYA is a transcription factor which is induced by salt stress and regulates seed oil metabolism by acting as a positive regulator of lipid biosynthesis. traits: - entity_name: salt tolerance entity: TO:0006001 - relation_name: positively regulates + - entity_name: fatty acid biosynthetic process + entity: GO:0006633 + - entity_name: regulation of metabolic process + entity: GO:0019222 +references: + - citation: Lu, Wei et al., 2021 + doi: 10.1111/pbi.13668 + pmid: 34265872 + - citation: Lu, Li et al., 2016 + doi: 10.1111/tpj.13181 + pmid: 27062090 + - citation: Zuo, Ikram et al., 2022 + doi: 10.1016/j.csbj.2022.06.014 + pmid: 35782726 + + +## DOCUMENT 58 ## +--- +classical_locus: J +gene_symbols: + - GmELF3 +gene_symbol_long: Early Flowering 3 +gene_model_pub_name: Glyma.04G050200 +gene_model_full_id: glyma.Wm82.gnm2.ann1.Glyma.04G050200 +confidence: 5 +curators: + - Steven Cannon +phenotype_synopsis: Photoperiodic flowering time regulation +traits: + - entity_name: flowering time + entity: TO:0002616 + - relation_name: positively regulates + relation: RO:0002213 + - entity_name: days to maturity + entity: TO:0000469 + - relation_name: positively regulates relation: RO:0002213 references: - - citation: Qi, Li et al., 2014 - doi: 10.1038/ncomms5340 - pmid: 25004933 + - citation: Lu, Zhao et al., 2017 + doi: 10.1038/ng.3819 + pmid: 28319089 + - citation: Yue, Liu et al., 2017 + doi: 10.1016/j.molp.2016.12.004 + pmid: 27979775 + - citation: Lin, Liu et al., 2021 + doi: 10.1111/jipb.13021 + pmid: 33090664 -## DOCUMENT 40 ## +## DOCUMENT 59 ## --- gene_symbols: - - Fg2 - - GmF3G6R-b - - GmF3G6_Rt-b -gene_symbol_long: flavonol glycoside 2 mRNA for flavonol 3-O-glucoside (1->6) rhamnosyltransferase -gene_model_pub_name: Glyma.10G194000 -gene_model_full_id: glyma.Wm82.gnm4.ann1.Glyma.10G194000 -confidence: 4 + - LHY1a +gene_symbol_long: Leafy 1a +gene_model_pub_name: Glyma.16G017400 +gene_model_full_id: glyma.Wm82.gnm2.ann1.Glyma.16G017400 +confidence: 5 curators: - - Greg Murrell -phenotype_synopsis: Encodes a flavonol 3-O-glucoside (1 -> 6) rhamnosyltransferase. + - Steven Cannon +phenotype_synopsis: Photoperiodic flowering time regulation traits: - - entity_name: glycoside biosynthetic process - entity: GO:0016138 + - entity_name: flowering time + entity: TO:0002616 + - relation_name: positively regulates + relation: RO:0002213 + - entity_name: days to maturity + entity: TO:0000469 + - relation_name: positively regulates + relation: RO:0002213 references: - - citation: RojasRodas, Rodriguez et al., 2013 - doi: 10.1007/s11103-013-0133-1 - pmid: 24072327 + - citation: Lu, Zhao et al., 2017 + doi: 10.1038/ng.3819 + pmid: 28319089 + - citation: Lin, Liu et al., 2021 + doi: 10.1111/jipb.13021 + pmid: 33090664 -## DOCUMENT 41 ## +## DOCUMENT 60 ## --- gene_symbols: - - Rj2 -gene_symbol_long: Restriction of nodulation 2 -gene_model_pub_name: Glyma16g33780 -gene_model_full_id: glyma.Wm82.gnm1.ann1.Glyma16g33780 + - LHY1b +gene_symbol_long: Leafy 1b +gene_model_pub_name: Glyma.07G048500 +gene_model_full_id: glyma.Wm82.gnm2.ann1.Glyma.07G048500 +confidence: 5 +curators: + - Steven Cannon +phenotype_synopsis: Photoperiodic flowering time regulation +traits: + - entity_name: flowering time + entity: TO:0002616 + - relation_name: positively regulates + relation: RO:0002213 + - entity_name: days to maturity + entity: TO:0000469 + - relation_name: positively regulates + relation: RO:0002213 +references: + - citation: Lu, Zhao et al., 2017 + doi: 10.1038/ng.3819 + pmid: 28319089 + - citation: Lin, Liu et al., 2021 + doi: 10.1111/jipb.13021 + pmid: 33090664 + + +## DOCUMENT 61 ## +--- +gene_symbols: + - LHY2a + - GmLHY2a + - LCL3 + - MYB156 +gene_symbol_long: Leafy 2a +gene_model_pub_name: Glyma.19G260900 +gene_model_full_id: glyma.Wm82.gnm2.ann1.Glyma.19G260900 +confidence: 5 +curators: + - Steven Cannon +phenotype_synopsis: Photoperiodic flowering time regulation +comments: + - Encodes a MYB transciption factor that affects plant height through mediating the GA pathway in soybean +traits: + - entity_name: flowering time + entity: TO:0002616 + - relation_name: positively regulates + relation: RO:0002213 + - entity_name: days to maturity + entity: TO:0000469 + - relation_name: positively regulates + relation: RO:0002213 +references: + - citation: Lu, Zhao et al., 2017 + doi: 10.1038/ng.3819 + pmid: 28319089 + - citation: Lin, Liu et al., 2021 + doi: 10.1111/jipb.13021 + pmid: 33090664 + - citation: Chen, Cai et al., 2020 + doi: 10.1111/pce.13695 + pmid: 31981430 + + +## DOCUMENT 62 ## +--- +gene_symbols: + - LHY2b +gene_symbol_long: Leafy 2b +gene_model_pub_name: Glyma.03G261800 +gene_model_full_id: glyma.Wm82.gnm2.ann1.Glyma.03G261800 +confidence: 5 +curators: + - Steven Cannon +phenotype_synopsis: Photoperiodic flowering time regulation +traits: + - entity_name: flowering time + entity: TO:0002616 + - relation_name: positively regulates + relation: RO:0002213 + - entity_name: days to maturity + entity: TO:0000469 + - relation_name: positively regulates + relation: RO:0002213 +references: + - citation: Lu, Zhao et al., 2017 + doi: 10.1038/ng.3819 + pmid: 28319089 + - citation: Lin, Liu et al., 2021 + doi: 10.1111/jipb.13021 + pmid: 33090664 + + +## DOCUMENT 63 ## +--- +scientific_name: Glycine max +gene_symbols: + - GmLEC2a + - GmLEC2 +gene_symbol_long: Leafy Cotyledon 2 +gene_model_pub_name: Glyma.20G035700 +gene_model_full_id: glyma.Wm82.gnm4.ann1.Glyma.20G035700 confidence: 4 curators: - - Greg Murrell -phenotype_synopsis: Some alleles of Rj2 restrict nodulation to specific rhizobial strains. + - Greg Murrell +phenotype_synopsis: Regulation of genes involved in biosynthesis and catabolism of seed storage and development. +traits: + - entity_name: seed growth and development trait + entity: TO:0000653 + - entity_name: triglyceride catabolic process + entity: GO:0019433 + - relation_name: negatively regulates + relation: RO:0002212 + - entity_name: carbohydrate biosynthetic process + entity: GO:0016051 + - relation_name: negatively regulates + relation: RO:0002212 + - entity_name: regulation of gene expression + entity: GO:0010468 +references: + - citation: Manan, Ahmad et al., 2017 + doi: 10.3389/fpls.2017.01604 + pmid: 28979275 + + +## DOCUMENT 64 ## +--- +gene_symbols: + - GmELF5 +gene_symbol_long: Early Flowering 5 +gene_model_pub_name: Glyma.05G031100 +gene_model_full_id: glyma.Wm82.gnm2.ann1.Glyma.05G031100 +confidence: 5 +curators: + - Steven Cannon +phenotype_synopsis: Photoperiodic flowering time regulation +traits: + - entity_name: flowering time + entity: TO:0002616 + - entity_name: days to maturity + entity: TO:0000469 +references: + - citation: Noh, Bizzell et al., 2004 + doi: 10.1111/j.1365-313x.2004.02072.x + pmid: 15125772 + - citation: Dietz, Chan et al., 2023 + doi: 10.3389/fpls.2022.889066 + pmid: 35574141 + + +## DOCUMENT 65 ## +--- +gene_symbols: + - GmTEM1a +gene_symbol_long: Tempranillo 1a +gene_model_pub_name: Glyma.20G186200 +gene_model_full_id: glyma.Wm82.gnm2.ann1.Glyma.20G186200 +confidence: 3 +curators: + - Steven Cannon +phenotype_synopsis: Photoperiodic flowering time regulation +traits: + - entity_name: flowering time + entity: TO:0002616 + - entity_name: days to maturity + entity: TO:0000469 +references: + - citation: Noh, Bizzell et al., 2004 + doi: 10.1111/j.1365-313x.2004.02072.x + pmid: 15125772 + - citation: Dietz, Chan et al., 2023 + doi: 10.3389/fpls.2022.889066 + pmid: 35574141 + + +## DOCUMENT 66 ## +--- +scientific_name: Glycine max +gene_symbols: + - GmCAMTA12 +gene_symbol_long: Calmodulin Binding Transcription Activator 12 +gene_model_pub_name: Glyma.17G031900 +gene_model_full_id: glyma.Wm82.gnm2.ann1.Glyma.17G031900 +confidence: 4 +curators: + - Marlene Dorneich-Hayes + - Scott Kalberer +comments: + - Overexpression of GmCAMTA12 increases drought tolerance in Glycine max and Arabidopsis thaliana. +phenotype_synopsis: GmCAMTA12 affects the expression of many genes involved in stress tolerance. +traits: + - entity_name: abiotic plant stress trait + entity: TO:0000168 + - entity_name: drought tolerance + entity: TO:0000276 + - entity_name: calmodulin binding + entity: GO:0005516 +references: + - citation: Noman, Jameel et al., 2019 + doi: 10.3390/ijms20194849 + pmid: 31569565 + - citation: Wang, Zeng et al., 2015 + doi: 10.1007/s11104-014-2267-6 + pmid: null + + +## DOCUMENT 67 ## +--- +scientific_name: Glycine max +gene_symbols: + - GmABCC8 +gene_symbol_long: ATP-Binding Cassette Transporter 8 +gene_model_pub_name: Glyma.07G011600 +gene_model_full_id: glyma.Wm82.gnm2.ann1.Glyma.07G011600 +confidence: 5 +curators: + - Marlene Dorneich-Hayes + - Scott Kalberer +comments: + - Overexpression of GmABCC8 in transgenic plants created glyphosate resistance. ABCC8 knockout plants had decreased resistance to glyphosate. +phenotype_synopsis: GmABCC8 codes for an efflux pump that extrudes the herbicide glyphosate out of a cell's cytoplasm, making the plant glyphosate resistant. +traits: + - entity_name: glyphosate sensitivity + entity: TO:0005006 + - entity_name: herbicide resistance + entity: OMIT:0025284 + - entity_name: ABC-type transporter activity + entity: GO:0140359 +references: + - citation: Pan, Yu et al., 2021 + doi: 10.1073/pnas.2100136118 + pmid: 33846264 + + +## DOCUMENT 68 ## +--- +scientific_name: Glycine max +gene_symbols: + - GmFAD2-1A +gene_symbol_long: Fatty Acid Desaturase 2-1A +gene_model_pub_name: Glyma.10G278000 +gene_model_full_id: glyma.Wm82.gnm2.ann1.Glyma.10G278000 +confidence: 4 +curators: + - Marlene Dorneich-Hayes + - Scott Kalberer +comments: + - If GmFAD2-1A and GmFAD2-1B are both downregulated or have loss-of-function mutations, seeds will have high oleic acid content. + - Knockout studies confirm that functional FAD2-1A decreases accumulation of oleic acid in seeds. +phenotype_synopsis: GmFAD2-1A converts the precursors of oleic acid into linoleic acid. +traits: + - entity_name: lipid metabolic process + entity: GO:0006629 + - entity_name: regulation of triglyceride biosynthetic process + entity: GO:0010866 + - entity_name: fat and essential oil content + entity: TO:0000604 +references: + - citation: Pham, Lee et al., 2010 + doi: 10.1186/1471-2229-10-195 + pmid: 20828382 + - citation: Combs, Bilyeu, 2019 + doi: 10.1007/s11032-019-0972-9 + pmid: null + - citation: Zuo, Ikram et al., 2022 + doi: 10.1016/j.csbj.2022.06.014 + pmid: 35782726 + + +## DOCUMENT 69 ## +--- +scientific_name: Glycine max +gene_symbols: + - GmFAD2-1B +gene_symbol_long: Fatty Acid Desaturase 2-1B +gene_model_pub_name: Glyma.20G111000 +gene_model_full_id: glyma.Wm82.gnm4.ann1.Glyma.20G111000 +confidence: 4 +curators: + - Marlene Dorneich-Hayes + - Scott Kalberer +comments: + - If GmFAD2-1A and GmFAD2-1B are both downregulated or have loss-of-function mutations, seeds will have high oleic acid content. + - FAD2-1B is more active at low temperatures. + - Knockout studies confirm that functional FAD2-1B decreases accumulation of oleic acid in seeds. +phenotype_synopsis: Normal GmFAD2-1B converts the precursors of oleic acid into linoleic acid. +traits: + - entity_name: lipid metabolic process + entity: GO:0006629 + - entity_name: regulation of triglyceride biosynthetic process + entity: GO:0010866 + - entity_name: fat and essential oil content + entity: TO:0000604 +references: + - citation: Pham, Lee et al., 2010 + doi: 10.1186/1471-2229-10-195 + pmid: 20828382 + - citation: Combs, Bilyeu, 2019 + doi: 10.1007/s11032-019-0972-9 + pmid: null + + +## DOCUMENT 70 ## +--- +scientific_name: Glycine max +gene_symbols: + - GmCHX1 +gene_symbol_long: cation/H(+) antiporter 1 +gene_model_pub_name: Glyma.03G171600 +gene_model_full_id: glyma.Wm82.gnm4.ann1.Glyma.03G171600 +confidence: 4 +curators: + - Greg Murrell +phenotype_synopsis: Impacts salt tolerance +traits: + - entity_name: salt tolerance + entity: TO:0006001 + - relation_name: positively regulates + relation: RO:0002213 +references: + - citation: Qi, Li et al., 2014 + doi: 10.1038/ncomms5340 + pmid: 25004933 + + +## DOCUMENT 71 ## +--- +scientific_name: Glycine max +gene_symbols: + - GmMIPS +gene_symbol_long: Myo-Inositol-Phosphate Synthase +gene_model_pub_name: Glyma.11G238800 +gene_model_full_id: glyma.Wm82.gnm2.ann1.Glyma.11G238800 +confidence: 3 +curators: + - Marlene Dorneich-Hayes + - Scott Kalberer +comments: + - Silencing of GmMIPS in transgenic lines (with RNAi and antisense) reduces accumulation of phytic acid in seeds. +phenotype_synopsis: GmMIPS codes for the rate-limiting enzyme in phytic acid biosynthesis. Supression of MIPS reduces the phytic acid concentration in seeds which improves their nutritional value, but also reduces their germination rate. +traits: + - entity_name: biosynthetic process + entity: GO:0009058 +references: + - citation: Redekar, Glover et al., 2020 + doi: 10.1371/journal.pone.0235120 + pmid: 32584851 + - citation: Kumar, Kumar et al., 2019 + doi: 10.1038/s41598-019-44255-7 + pmid: 31123331 + - citation: Yu, Jin et al., 2019 + doi: 10.1186/s12870-019-2201-4 + pmid: 31856712 + - citation: Nunes, Vianna et al., 2006 + doi: 10.1007/s00425-005-0201-0 + pmid: 16395584 + - citation: Hegeman, Good et al., 2001 + doi: 10.1104/pp.125.4.1941 + pmid: 11299373 + + +## DOCUMENT 72 ## +--- +scientific_name: Glycine max +gene_symbols: + - GmRIC1 +gene_symbol_long: Rhizobia-Induced CLE 1 +gene_model_pub_name: Glyma13G36830 +gene_model_full_id: glyma.Wm82.gnm2.ann1.Glyma.13G292300 +confidence: 5 +curators: + - Marlene Dorneich-Hayes + - Scott Kalberer +comments: + - RT-qPCR studies conducted on tissue injected with Bradyrhizobium nodulation factor showed that GmRIC1 is upregulated hours after injection. + - Introduction of plasmids carrying an extra dose of RIC1 inhibited nodulation. +phenotype_synopsis: GmRIC1 reduces nodulation in Lotus japonicus and Medicago truncatula. It is induced by Bradyrhizobium nodulation factor. +traits: + - entity_name: plant organ growth and development trait + entity: TO:0000927 + - entity_name: root nodule morphology trait + entity: TO:0000898 + - entity_name: root nodule + entity: PO:0003023 +references: + - citation: Reid, Ferguson et al., 2011 + doi: 10.1094/mpmi-09-10-0207 + pmid: 21198362 + + +## DOCUMENT 73 ## +--- +scientific_name: Glycine max +gene_symbols: + - GmRIC2 +gene_symbol_long: Rhizobia-Induced CLE 2 +gene_model_pub_name: Glyma06G43680 +gene_model_full_id: glyma.Wm82.gnm2.ann1.Glyma.06G284100 +confidence: 5 +curators: + - Marlene Dorneich-Hayes + - Scott Kalberer +comments: + - RT-qPCR studies conducted on tissue injected with Bradyrhizobium nodulation factor showed that GmRIC2 is upregulated a few days after injection. + - Introduction of plasmids carrying an extra dose of RIC2 inhibited nodulation. +phenotype_synopsis: GmRIC2 reduces nodulation in Lotus japonicus and Medicago truncatula. It is induced by Bradyrhizobium nodulation factor. +traits: + - entity_name: plant organ growth and development trait + entity: TO:0000927 + - entity_name: root nodule morphology trait + entity: TO:0000898 + - entity_name: root nodule + entity: PO:0003023 +references: + - citation: Reid, Ferguson et al., 2011 + doi: 10.1094/mpmi-09-10-0207 + pmid: 21198362 + + +## DOCUMENT 74 ## +--- +scientific_name: Glycine max +gene_symbols: + - GmNIC1 +gene_symbol_long: Nitrate-Induced CLE 1 +gene_model_pub_name: Glyma12G33660 +gene_model_full_id: glyma.Wm82.gnm1.ann1.Glyma12G33660 +confidence: 5 +curators: + - Marlene Dorneich-Hayes + - Scott Kalberer +comments: + - RT-qPCR conducted on root tissue exposed to varying concentrations of nitrate showed that GmNIC1 expression is induced when roots are exposed to nitrate. + - Introduction of plasmids carrying an extra dose of NIC1 inhibited nodulation. +phenotype_synopsis: GmNIC1 reduces nodulation in Lotus japonicus and Medicago truncatula. It is induced by nitrate but inhibited by Bradyrhizobium nodulation factor. +traits: + - entity_name: plant organ growth and development trait + entity: TO:0000927 + - entity_name: root nodule morphology trait + entity: TO:0000898 + - entity_name: root nodule + entity: PO:0003023 +references: + - citation: Reid, Ferguson et al., 2011 + doi: 10.1094/mpmi-09-10-0207 + pmid: 21198362 + + +## DOCUMENT 75 ## +--- +scientific_name: Glycine max +gene_symbols: + - GmFg2 + - GmF3G6R-b + - GmF3G6_Rt-b +gene_symbol_long: flavonol glycoside 2 mRNA for flavonol 3-O-glucoside (1->6) rhamnosyltransferase +gene_model_pub_name: Glyma.10G194000 +gene_model_full_id: glyma.Wm82.gnm4.ann1.Glyma.10G194000 +confidence: 4 +curators: + - Greg Murrell +phenotype_synopsis: Encodes a flavonol 3-O-glucoside (1 -> 6) rhamnosyltransferase. +traits: + - entity_name: glycoside biosynthetic process + entity: GO:0016138 +references: + - citation: RojasRodas, Rodriguez et al., 2013 + doi: 10.1007/s11103-013-0133-1 + pmid: 24072327 + + +## DOCUMENT 76 ## +--- +scientific_name: Glycine max +gene_symbols: + - GmNARK +gene_symbol_long: Nodule Autoregulation Receptor Kinase +gene_model_pub_name: Glyma.12G040000 +gene_model_full_id: glyma.Wm82.gnm2.ann1.Glyma.12G040000 +confidence: 4 +curators: + - Marlene Dorneich-Hayes + - Scott Kalberer +comments: + - All these studies identified the implicated gene by comparing mutant strains to each other and to wild type. + - GmNARK is a negative regulator of miR172c, which affects the activity of nodulation gene GmNNC1 (see Wang, Wang et al., 2014). + - NARK is expressed in roots, leaves, and shoots. + - If the kinase domain of NARK is nonfunctional, most plants produce huge numbers of extra nodules, extra lateral roots, and more symbiotic interactions. + - If NARK is less severely compromised, fewer extra nodules form. +phenotype_synopsis: GmNARK exerts long-distance control on nodule proliferation by activating nodulation-suppressing genes. +traits: + - entity_name: kinase activity + entity: GO:0016301 + - entity_name: regulation of biological process involved in symbiotic interaction + entity: GO:0043903 + - entity_name: nodulation + entity: GO:0009877 + - entity_name: root development + entity: GO:0048364 +references: + - citation: Searle, Men et al., 2003 + doi: 10.1126/science.1077937 + pmid: 12411574 + - citation: Kim, Van et al., 2005 + doi: 10.1007/s00122-004-1887-2 + pmid: 15731930 + - citation: Meixner, Vegvari et al., 2007 + doi: 10.1111/j.1399-3054.2007.00903.x + pmid: null + - citation: Wang, Wang et al., 2014 + doi: 10.1105/tpc.114.131607 + pmid: 25549672 + - citation: Yang, Lan et al., 2022 + doi: 10.1111/jipb.13207 + pmid: 34962095 + + +## DOCUMENT 77 ## +--- +scientific_name: Glycine max +gene_symbols: + - GmDRR1 +gene_symbol_long: Disease Resistance Responsive 1 +gene_model_pub_name: Glyma.11G150400 +gene_model_full_id: glyma.Wm82.gnm2.ann1.Glyma.11G150400 +confidence: 3 +curators: + - Marlene Dorneich-Hayes + - Scott Kalberer +comments: + - The importance of GmDRR1 in nodule formation was established through its overexpression in soybean, which increased the number of nodules relative to the wild-type. RNA interference had no effect on nodule number. + - DRR1 is homologous with other dirigent proteins such as GmDRR2 and GmDRR3. + - DRR1 promotes the synthesis of (+)-pinoresinol which is needed to increase lignin biosynthesis. Higher levels of lignin content and secondary cell wall deposition function as a physical barrier and inhibit the ability of Phytophthora sojae to infect soybeans. + - The GmNAC1 transcription factor may bind to the DRR1 promoter to upregulate DRR1 expression and enhance Phytophthora sojae resistance. +phenotype_synopsis: GmDRR1 was induced in soybean roots by the presence of rhizobia and helped establish a symbiotic relationship that resulted in development of root nodules and nitrogen fixation. Additionally, DRR1 expression increased the resistance of soybean to Phytophthora sojae. +traits: + - entity_name: nodulation + entity: GO:0009877 + - entity_name: biological process involved in symbiotic interaction + entity: GO:0044403 + - entity_name: microbial disease response + entity: TO:0000112 + - entity_name: nitrogen fixation + entity: GO:0009399 +references: + - citation: Shi, Zhang et al., 2020 + doi: 10.1094/mpmi-01-20-0017-r + pmid: 32186464 + - citation: Yu, Zou et al., 2021 + doi: 10.1016/j.cj.2021.08.009 + pmid: null + + +## DOCUMENT 78 ## +--- +scientific_name: Glycine max +gene_symbols: + - GmDRR2 +gene_symbol_long: Disease Resistance Responsive 2 +gene_model_pub_name: Glyma.11G150300 +gene_model_full_id: glyma.Wm82.gnm2.ann1.Glyma.11G150300 +confidence: 3 +curators: + - Marlene Dorneich-Hayes + - Scott Kalberer +comments: + - GmDRR1 and GmDRR2 are homologous dirigent proteins. The function of DRR1 may depend on dimer formation with DRR2. +phenotype_synopsis: GmDRR2 promoted a symbiotic relationship with rhizobia that resulted in development of root nodules and nitrogen fixation in soybeans. +traits: + - entity_name: nodulation + entity: GO:0009877 + - entity_name: biological process involved in symbiotic interaction + entity: GO:0044403 + - entity_name: microbial disease response + entity: TO:0000112 + - entity_name: nitrogen fixation + entity: GO:0009399 +references: + - citation: Shi, Zhang et al., 2020 + doi: 10.1094/mpmi-01-20-0017-r + pmid: 32186464 + - citation: Yu, Zou et al., 2021 + doi: 10.1016/j.cj.2021.08.009 + pmid: null + + +## DOCUMENT 79 ## +--- +scientific_name: Glycine max +gene_symbols: + - GmbZIP123 +gene_symbol_long: Basic Leucine Zipper 123 +gene_model_pub_name: Glyma06G01240 +gene_model_full_id: glyma.Wm82.gnm1.ann1.Glyma06G01240 +confidence: 3 +curators: + - Marlene Dorneich-Hayes + - Scott Kalberer +comments: + - The effect of GmbZIP123 was studied in transgenic Arabidopsis thaliana rather than in Glycine max. + - Overexpression of bZIP123 increased lipid content in seeds of transgenic Arabidopsis. + - The transcription factor bZIP123 bound to the promoters and upregulated Arabidopis genes for two sucrose transporters (SUC1 and SUC5) and three cell-wall invertases (cwINV1, cwINV3, and cwINV6). + - Cell-wall invertase activity and sugar translocation were consequently boosted in Arabidopsis siliques. The result was greater levels of the sugars glucose, fructose, and sucrose within seeds. +phenotype_synopsis: GmbZIP123 is a transcription factor which promotes expression of sucrose transporter and cell-wall invertase genes. Regulation of lipid accumulation in soybean seeds may be mediated by controlling transport of sugar into seeds from photoautotrophic tissues. +traits: + - entity_name: lipid metabolic process + entity: GO:0006629 + - entity_name: regulation of triglyceride biosynthetic process + entity: GO:0010866 + - entity_name: fat and essential oil content + entity: TO:0000604 + - entity_name: seed development + entity: GO:0048316 +references: + - citation: Song, Li et al., 2013 + doi: 10.1093/jxb/ert238 + pmid: 23963672 + - citation: Zuo, Ikram et al., 2022 + doi: 10.1016/j.csbj.2022.06.014 + pmid: 35782726 + + +## DOCUMENT 80 ## +--- +scientific_name: Glycine max +gene_symbols: + - GmGA20ox_a +gene_symbol_long: Gibberellic Acid 20-Oxidase a +gene_model_pub_name: Glyma.04G244200 +gene_model_full_id: glyma.Wm82.gnm4.ann1.Glyma.04G244200 +confidence: 3 +curators: + - Marlene Dorneich-Hayes + - Scott Kalberer +comments: + - GmGA20ox_a is induced by inoculation with compatible rhizobia (e.g., Bradyrhizobium japonicum) in soybean root cortical cells during nodule primordia establishment. Mutant rhizobia (nodC-) that lack a chitin synthase gene, and thus cannot produce the Nod factor, don't induce nodulation and concomitant GA20ox_a gene expression. + - GA20ox_a is expressed at the beginning of nodule development, with levels peaking at 12 hours after inoculation and then decreasing substantially by 48 hours post-inoculation. + - GA20ox_a gene expression was substantially higher in newly-developing nodules than in other plant structures and is probably nodulation-specific. +phenotype_synopsis: GmGA20ox_a is a gibberellic acid biosynthesis gene that increases levels of gibberellin during early nodulation. +traits: + - entity_name: gibberellin biosynthetic process + entity: GO:0009686 + - entity_name: regulation of biological process involved in symbiotic interaction + entity: GO:0043903 + - entity_name: nodulation + entity: GO:0009877 +references: + - citation: Song, Montes-Luz et al., 2022 + doi: 10.3389/fpls.2022.820348 + pmid: 35498680 + - citation: Hayashi, Gresshoff et al., 2014 + doi: 10.1111/jipb.12201 + pmid: 24673766 + - citation: Hayashi, Reid et al., 2012 + doi: 10.1111/j.1467-7652.2012.00729.x + pmid: 22863334 + - citation: Yang, Lan et al., 2022 + doi: 10.1111/jipb.13207 + pmid: 34962095 + + +## DOCUMENT 81 ## +--- +scientific_name: Glycine max +gene_symbols: + - GmGA3ox_1a +gene_symbol_long: ARRAY(0x83213b6d8) +gene_model_pub_name: Glyma.15G012100 +gene_model_full_id: glyma.Wm82.gnm4.ann1.Glyma.15G012100 +confidence: 4 +curators: + - Marlene Dorneich-Hayes + - Scott Kalberer +comments: + - GmGA3ox_1a is induced by inoculation with compatible rhizobia (e.g., Bradyrhizobium japonicum) in soybean root cortical cells during nodule primordia establishment. + - GA3ox_1a is expressed at the beginning of nodule development, with levels peaking at 12 hours after inoculation and then decreasing substantially by 48 hours post-inoculation. + - GA3ox_1a expression is not exclusive to nodule development, appearing in multiple tissues, and likely serves general roles. + - Nodulation was reduced by RNAi silencing of GA3ox_1a in transgenic soybean hairy roots. +phenotype_synopsis: GmGA3ox_1a is a gibberellic acid biosynthesis gene that increases levels of gibberellin during early nodulation. +traits: + - entity_name: gibberellin biosynthetic process + entity: GO:0009686 + - entity_name: regulation of biological process involved in symbiotic interaction + entity: GO:0043903 + - entity_name: nodulation + entity: GO:0009877 +references: + - citation: Song, Montes-Luz et al., 2022 + doi: 10.3389/fpls.2022.820348 + pmid: 35498680 + - citation: Hayashi, Gresshoff et al., 2014 + doi: 10.1111/jipb.12201 + pmid: 24673766 + - citation: Hayashi, Reid et al., 2012 + doi: 10.1111/j.1467-7652.2012.00729.x + pmid: 22863334 + - citation: Yang, Lan et al., 2022 + doi: 10.1111/jipb.13207 + pmid: 34962095 + + +## DOCUMENT 82 ## +--- +scientific_name: Glycine max +gene_symbols: + - GmGA20ox_b +gene_symbol_long: Gibberellic Acid 20-Oxidase b +gene_model_pub_name: Glyma.06G119100 +gene_model_full_id: glyma.Wm82.gnm2.ann1.Glyma.06G119100 +confidence: 2 +curators: + - Scott Kalberer +comments: + - GmGA20ox_b is induced by inoculation with compatible rhizobia (e.g., Bradyrhizobium japonicum) in soybean root cortical cells during nodule primordia establishment. +phenotype_synopsis: GmGA20ox_b is a gibberellic acid biosynthesis gene that increases levels of gibberellin during early nodulation. +traits: + - entity_name: gibberellin biosynthetic process + entity: GO:0009686 + - entity_name: regulation of biological process involved in symbiotic interaction + entity: GO:0043903 + - entity_name: nodulation + entity: GO:0009877 +references: + - citation: Song, Montes-Luz et al., 2022 + doi: 10.3389/fpls.2022.820348 + pmid: 35498680 + + +## DOCUMENT 83 ## +--- +scientific_name: Glycine max +gene_symbols: + - GmRj2 +gene_symbol_long: Restriction of nodulation 2 +gene_model_pub_name: Glyma16g33780 +gene_model_full_id: glyma.Wm82.gnm1.ann1.Glyma16g33780 +confidence: 4 +curators: + - Greg Murrell +phenotype_synopsis: Some alleles of Rj2 restrict nodulation to specific rhizobial strains. +traits: + - entity_name: root nodule + entity: PO:0003023 +references: + - citation: Sugawara, Umehara et al., 2019 + doi: 10.1371/journal.pone.0222469 + pmid: 31518373 + + +## DOCUMENT 84 ## +--- +scientific_name: Glycine max +gene_symbols: + - GmCIF1 +gene_symbol_long: Cell Wall Invertase Inhibitor +gene_model_pub_name: Glyma17G036300 +gene_model_full_id: glyma.Wm82.gnm2.ann1.Glyma.17G036300 +confidence: 4 +curators: + - Marlene Dorneich-Hayes +comments: + - Ectopic expression and RNAi silencing show that CIF1 has a role in suppressing extracellular invertases. + - Silencing of CIF1 increases seed weight as well as protein and starch content. + - CIF1 is strongly expressed in flowers, mature leaves, and developing seeds. + - CIF1 is activated by ABA signaling, draught, and senescence. +phenotype_synopsis: CIF1 is an invertase inhibitor which represses CWI (cell wall invertase). +traits: + - entity_name: regulation of seed growth + entity: GO:0080113 + - entity_name: seed development + entity: GO:0048316 + - entity_name: seed size + entity: TO:0000391 + - entity_name: protein content + entity: TO:0000598 + - entity_name: starch content + entity: TO:0000696 +references: + - citation: Tang, Su et. al., 2017 + doi: 10.1093/jxb/erw425 + pmid: 28204559 + - citation: Su, Han et. al., 2018 + doi: 10.3390/ijms19082395 + pmid: 30110937 + - citation: Zuo, Ikram et. al., 2022 + doi: 10.1016/j.csbj.2022.06.014 + pmid: 35782726 + + +## DOCUMENT 85 ## +--- +scientific_name: Glycine max +gene_symbols: + - GmC/VIF2 +gene_symbol_long: Cell Wall or Vacuolar Inhibitor of β-Fructosidase 2 +gene_model_pub_name: Glyma17G036400 +gene_model_full_id: glyma.Wm82.gnm2.ann1.Glyma.17G036400 +confidence: 4 +curators: + - Marlene Dorneich-Hayes +comments: + - Ectopic expression and RNAi silencing show that C/VIF2 has a role in suppressing extracellular invertases. + - Silencing of C/VIF2 increases seed weight as well as protein and starch content. + - C/VIF2 is most strongly expressed in flowers, roots, and developing seeds. + - C/VIF2 is activated by ABA signaling, draught, and senescence but suppressed by fungal infections. +phenotype_synopsis: C/VIF2 is an invertase inhibitor which represses CWI (cell wall invertase). +traits: + - entity_name: regulation of seed growth + entity: GO:0080113 + - entity_name: seed development + entity: GO:0048316 + - entity_name: seed size + entity: TO:0000391 + - entity_name: protein content + entity: TO:0000598 + - entity_name: starch content + entity: TO:0000696 +references: + - citation: Tang, Su et. al., 2017 + doi: 10.1093/jxb/erw425 + pmid: 28204559 + - citation: Su, Han et. al., 2018 + doi: 10.3390/ijms19082395 + pmid: 30110937 + + +## DOCUMENT 86 ## +--- +scientific_name: Glycine max +gene_symbols: + - GmFLS2a +gene_symbol_long: flagellin sensing 2 +gene_model_pub_name: glyma.08g083300 +gene_model_full_id: glyma.Wm82.gnm2.ann1.Glyma.08G083300 +confidence: 4 +curators: + - Marlene Dorneich-Hayes +comments: + - GmFLS2a and GmFLS2b are likely redundant. They are not distinguishable by the VIGS knockout approach. When both of these genes are silenced, soy plants became much more suceptible to bacterial pathogens (Pseudomonas syringae pv. glycinea), but resistance to viral pathogens (Soybean mosaic virus) is not affected. +phenotype_synopsis: GmFLS2a and GmFLS2b kinases start a phosphorylation cascade that activates GmMPK3 and GmMPK6, which are involved in the plant's response to bacterial infection. +traits: + - entity_name: bacterial disease resistance + entity: TO:0000315 + - entity_name: kinase activity + entity: GO:0016301 +references: + - citation: Tian, Liu et al., 2019 + doi: 10.1016/j.plantsci.2019.110386 + pmid: 32005391 + + +## DOCUMENT 87 ## +--- +scientific_name: Glycine max +gene_symbols: + - GmFLS2b +gene_symbol_long: flagellin sensing 2 +gene_model_pub_name: glyma.05g128200 +gene_model_full_id: glyma.Wm82.gnm2.ann1.Glyma.05G128200 +confidence: 4 +curators: + - Marlene Dorneich-Hayes +comments: + - GmFLS2a and GmFLS2b are likely redundant. They are not distinguishable by the VIGS knockout approach. When both are silenced, soy plants became much more suceptible to bacterial pathogens (Pseudomonas syringae pv. glycinea), but resistance to viral pathogens (Soybean mosaic virus) is not affected. +phenotype_synopsis: GmFLS2a and GmFLS2b kinases start a phosphorylation cascade that activates GmMPK3 and GmMPK6, which are involved in the plant's response to bacterial infection. +traits: + - entity_name: bacterial disease resistance + entity: TO:0000315 + - entity_name: kinase activity + entity: GO:0016301 +references: + - citation: Tian, Liu et al., 2019 + doi: 10.1016/j.plantsci.2019.110386 + pmid: 32005391 + + +## DOCUMENT 88 ## +--- +classical_locus: E2 +gene_symbols: + - GmGI +gene_symbol_long: Earliness 2 +gene_model_pub_name: Glyma.10G221500 +gene_model_full_id: glyma.Wm82.gnm2.ann1.Glyma.10G221500 +confidence: 5 +curators: + - Steven Cannon +phenotype_synopsis: Photoperiodic flowering time regulation +traits: + - entity_name: flowering time + entity: TO:0002616 + - relation_name: negatively regulates + relation: RO:0002212 + - entity_name: days to maturity + entity: TO:0000469 + - relation_name: negatively regulates + relation: RO:0002212 +references: + - citation: Tsubokura, Watanabe et al., 2013 + doi: 10.1093/aob/mct269 + pmid: 24284817 + - citation: Dietz, Chan et al., 2023 + doi: 10.3389/fpls.2022.889066 + pmid: 35574141 + - citation: Lin, Liu et al., 2021 + doi: 10.1111/jipb.13021 + pmid: 33090664 + - citation: Watanabe, Xia et al., 2011 + doi: 10.1534/genetics.110.125062 + pmid: 21406680 + - citation: Xu, Yamagishi et al., 2015 + doi: 10.1104/pp.15.00763 + pmid: 26134161 + + +## DOCUMENT 89 ## +--- +scientific_name: Glycine max +gene_symbols: + - GmMYB176 +gene_symbol_long: GmMYB176 +gene_model_pub_name: Glyma.05g032200 +gene_model_full_id: glyma.Wm82.gnm4.ann1.Glyma.05g032200 +confidence: 4 +curators: + - Wei Huang +comments: + - A combinatorial action of GmMYB176 and GmbZIP5 controls isoflavonoid biosynthesis in soybean (Glycine max) +phenotype_synopsis: GmMYB176 regulates multiple genes in the isoflavonoid biosynthetic pathway, thereby affecting their levels in soybean roots. +traits: + - entity_name: isoflavonoid biosynthetic process + entity: GO:0009717 + - entity_name: isoflavonoid phytoalexin metabolic process + entity: GO:0046289 +references: + - citation: Vadivel, Anguraj AK, et al., 2021 + doi: 10.1038/s42003-021-01889-6 + pmid: 33742087 + - citation: Yi, Jinxin et al., 2010 + doi: 10.1111/j.1365-313x.2010.04214.x + pmid: 20345602 + + +## DOCUMENT 90 ## +--- +scientific_name: Glycine max +gene_symbols: + - Gmbzip5 +gene_symbol_long: GmbZIP5 +gene_model_pub_name: Glyma.15g014800 +gene_model_full_id: glyma.Wm82.gnm4.ann1.Glyma.15g014800 +confidence: 4 +curators: + - Wei Huang +phenotype_synopsis: RNAi silencing of GmbZIP5 reduced the isoflavonoid level in soybean hairy roots. +traits: + - entity_name: isoflavonoid biosynthetic process + entity: GO:0009717 + - entity_name: isoflavonoid phytoalexin metabolic process + entity: GO:0046289 +references: + - citation: Vadivel, Anguraj AK, et al., 2021 + doi: 10.1038/s42003-021-01889-6 + pmid: 33742087 + + +## DOCUMENT 91 ## +--- +scientific_name: Glycine max +gene_symbols: + - GmSTF3 +gene_symbol_long: Soybean TGACG-motif Binding Factor 3 +gene_model_pub_name: Glyma.14G088300 +gene_model_full_id: glyma.Wm82.gnm2.ann1.Glyma.14G088300 +confidence: 5 +curators: + - Marlene Dorneich-Hayes + - Scott Kalberer +comments: + - Overexpression of STF3 increased nodulation, RNAi knockdown decreased nodulation. + - STF3 is induced by the blue light activated transcription factor CRY1 and expressed mainly in leaves. + - The protein product of STF3 migrates from shoots to roots. + - After migration, it is phosphorylated by calcium/calmodulin dependent protein kinase (CCaMK), which is activated by rhizobial infection. + - Phosphorylation causes STF3 and FT2a to form a complex. +phenotype_synopsis: STF3 promotes nodulation by inducing expression of nodule signalling pathway 1 (NSP1), nodule inception (NIN), and nuclear factor Y (NFY) genes. +traits: + - entity_name: regulation of biological process involved in symbiotic interaction + entity: GO:0043903 + - entity_name: nodulation + entity: GO:0009877 + - relation_name: positively regulates + relation: RO:0002213 + - entity_name: positive regulation of lateral root development + entity: GO:1901333 +references: + - citation: Wang, Guo et al., 2021 + doi: 10.1126/science.abh2890 + pmid: 34591638 + - citation: Hasan, Corpas et al., 2022 + doi: 10.1016/j.tplants.2022.07.002 + pmid: 35840482 + - citation: Yang, Lan et al., 2022 + doi: 10.1111/jipb.13207 + pmid: 34962095 + - citation: Kong, Liu et al., 2010 + doi: 10.1104/pp.110.160796 + pmid: 20864544 + - citation: Kong, Nan et al., 2014 + doi: 10.2135/cropsci2014.03.0228 + pmid: null + - citation: Takeshima, Hayashi et al., 2016 + doi: 10.1093/jxb/erw283 + pmid: 27422993 + - citation: Zhao, Takeshima et al., 2016 + doi: 10.1186/s12870-016-0704-9 + pmid: 26786479 + - citation: Dietz, Chan et al., 2023 + doi: 10.3389/fpls.2022.889066 + pmid: 35574141 + - citation: Lin, Liu et al., 2021 + doi: 10.1111/jipb.13021 + pmid: 33090664 + + +## DOCUMENT 92 ## +--- +scientific_name: Glycine max +classical_locus: E9 +gene_symbols: + - GmFT2a +gene_symbol_long: Flowering Locus T2a +gene_model_pub_name: Glyma.16G150700 +gene_model_full_id: glyma.Wm82.gnm2.ann1.Glyma.16G150700 +confidence: 5 +curators: + - Marlene Dorneich-Hayes + - Scott Kalberer +comments: + - Overexpression of FT2a increased nodulation while RNAi knockdown decreased nodulation. + - FT2a is induced by the transcription factors GmCRY1 and CONSTANS. + - It is mainly expressed in leaves and migrates from shoots to roots. + - In the shoots, the product of FT2a forms a complex with the phosphorylated product of STF3. +phenotype_synopsis: FT2a is known for stimulating flowering but it also positivley regulates nodulation. +traits: + - entity_name: regulation of biological process involved in symbiotic interaction + entity: GO:0043903 + - entity_name: nodulation + entity: GO:0009877 + - relation_name: positively regulates + relation: RO:0002213 + - entity_name: positive regulation of lateral root development + entity: GO:1901333 +references: + - citation: Wang, Guo et al., 2021 + doi: 10.1126/science.abh2890 + pmid: 34591638 + - citation: Hasan, Corpas et al., 2022 + doi: 10.1016/j.tplants.2022.07.002 + pmid: 35840482 + - citation: Yang, Lan et al., 2022 + doi: 10.1111/jipb.13207 + pmid: 34962095 + - citation: Kong, Liu et al., 2010 + doi: 10.1104/pp.110.160796 + pmid: 20864544 + - citation: Kong, Nan et al., 2014 + doi: 10.2135/cropsci2014.03.0228 + pmid: null + - citation: Takeshima, Hayashi et al., 2016 + doi: 10.1093/jxb/erw283 + pmid: 27422993 + - citation: Zhao, Takeshima et al., 2016 + doi: 10.1186/s12870-016-0704-9 + pmid: 26786479 + - citation: Dietz, Chan et al., 2023 + doi: 10.3389/fpls.2022.889066 + pmid: 35574141 + - citation: Lin, Liu et al., 2021 + doi: 10.1111/jipb.13021 + pmid: 33090664 + + +## DOCUMENT 93 ## +--- +scientific_name: Glycine max +gene_symbols: + - GmGA2ox8A +gene_symbol_long: Gibberellin 2-Oxidase 8A +gene_model_pub_name: Glyma.13G287600 +gene_model_full_id: glyma.Wm82.gnm4.ann1.Glyma.13G287600 +confidence: 3 +curators: + - William Hardison +comments: + - ncbi says the locus for gibberellin 2-beta-dioxygenase 8 [Glycine max] -> "LOCUS NP_001242439" + - Cannot find plant trait ontology for trailing growth and shoot length -> "shoot height (related)" is for plant height + - glyma.Wm82.gnm2.ann1.Glyma.13G287600.1 also works + - +phenotype_synopsis: Negatively correlated with shoot length and trailing growth +traits: + - entity_name: plant height + entity: TO:0000207 +references: + - citation: Wang, Li et al., 2021 + doi: 10.1111/tpj.15414 + pmid: 34245624 + + +## DOCUMENT 94 ## +--- +scientific_name: Glycine max +gene_symbols: + - GmGA2ox8B +gene_symbol_long: Gibberellin 2-Oxidase 8B +gene_model_pub_name: Glyma.13G288000 +gene_model_full_id: glyma.Wm82.gnm4.ann1.Glyma.13G288000 +confidence: 5 +curators: + - William Hardison +comments: + - Cannot find plant trait ontology for trailing growth and shoot length -> "shoot height (related)" is for plant height + - glyma.Wm82.gnm2.ann1.Glyma.13G288000.1 also works +phenotype_synopsis: Negatively correlated with shoot length and trailing growth +traits: + - entity_name: plant height + entity: TO:0000207 +references: + - citation: Wang, Li et al., 2021 + doi: 10.1111/tpj.15414 + pmid: 34245624 + + +## DOCUMENT 95 ## +--- +scientific_name: Glycine max +gene_symbols: + - GmEDS1a +gene_symbol_long: enhanced disease susceptibility 1a +gene_model_pub_name: Glyma04g34800 +gene_model_full_id: glyma.Wm82.gnm1.ann1.Glyma04g34800 +confidence: 4 +curators: + - Marlene Dorneich-Hayes +comments: + - Silencing of GmEDS1a/b and GmPAD4 stopped accumulation of salicylic acid and increased the plant's suceptibility to Pseudomonas syringae pv glycinea and soybean mosaic virus infection. The phenotype is only altered if all three genes are silenced. +phenotype_synopsis: responsible for basal and pathogen-inducible accumulation of salicylic acid, which helps the plant resist bacterial, oomycete, and viral infection. Gene activity is induced by infection. +traits: + - entity_name: defense response to bacterium + entity: GO:0042742 + - enitity_name: defense response to virus + entity: GO:0051607 +references: + - citation: Wang, Shine et al., 2014 + doi: 10.1104/pp.114.242495 + pmid: 24872380 + - citation: Weirmer, Feys et al., 2005 + doi: 10.1016/j.pbi.2005.05.010 + pmid: 15939664 + + +## DOCUMENT 96 ## +--- +scientific_name: Glycine max +gene_symbols: + - GmEDS1b +gene_symbol_long: enhanced disease suceptibility 1b +gene_model_pub_name: Glyma06g19920 +gene_model_full_id: glyma.Wm82.gnm1.ann1.Glyma06g19920 +confidence: 4 +curators: + - Marlene Dorneich-Hayes +comments: + - Silencing of GmEDS1a/b and GmPAD4 stopped accumulation of salicylic acid and increased the plant's suceptibility to Pseudomonas syringae pv glycinea and soybean mosaic virus infection. The phenotype is only altered if all three genes are silenced. +phenotype_synopsis: responsible for basal and pathogen-inducible accumulation of salicylic acid, which helps the plant resist bacterial, oomycete, and viral infection. Gene activity is induced by infection. +traits: + - entity_name: defense response to bacterium + entity: GO:0042742 + - enitity_name: defense response to virus + entity: GO:0051607 +references: + - citation: Wang, Shine et al., 2014 + doi: 10.1104/pp.114.242495 + pmid: 24872380 + - citation: Weirmer, Feys et al., 2005 + doi: 10.1016/j.pbi.2005.05.010 + pmid: 15939664 + + +## DOCUMENT 97 ## +--- +scientific_name: Glycine max +gene_symbols: + - GmPAD4 +gene_symbol_long: phytoalexin deficient 4 +gene_model_pub_name: Glyma08g00420 +gene_model_full_id: glyma.Wm82.gnm1.ann1.Glyma08g00420 +confidence: 4 +curators: + - Marlene Dorneich-Hayes +comments: + - Silencing of GmEDS1a/b and GmPAD4 stopped accumulation of salicylic acid and increased the plant's suceptibility to Pseudomonas syringae pv glycinea and soybean mosaic virus infection. The phenotype is only altered if all three genes are silenced. +phenotype_synopsis: responsible for basal and pathogen-inducible accumulation of salicylic acid, which helps the plant resist bacterial, oomycete, and viral infection. Gene activity is induced by infection. +traits: + - entity_name: defense response to bacterium + entity: GO:0042742 + - enitity_name: defense response to virus + entity: GO:0051607 +references: + - citation: Wang, Shine et al., 2014 + doi: 10.1104/pp.114.242495 + pmid: 24872380 + - citation: Weirmer, Feys et al., 2005 + doi: 10.1016/j.pbi.2005.05.010 + pmid: 15939664 + + +## DOCUMENT 98 ## +--- +scientific_name: Glycine max +gene_symbols: + - GmNNC1 +gene_symbol_long: Nodule Number Control 1 +gene_model_pub_name: Glyma12g07800 +gene_model_full_id: glyma.Wm82.gnm2.ann1.Glyma.12G078000 +confidence: 5 +curators: + - Marlene Dorneich-Hayes +comments: + - Expression patterns of NNC1 were studied with GAL4/UAS, GUS, and GFP reporter systems. + - Its function was confirmed with RNAi knockdown and transgenic overexpression studies. + - The activity of NNC1 is modulated by miR172c to fine-tune nodulation and symbiosis. + - miR172c cleaves the protein product of NNC1, allowing ENOD40 to be transcribed. + - miR172c is, in turn, negatively regulated by NARK (see Searle, Men et. al., 2003). +phenotype_synopsis: NNC1 is a transcription factor that negatively regulates nodule number by repressing GmENOD40. +traits: + - entity_name: DNA-binding transcription factor activity + entity: GO:0003700 + - entity_name: regulation of biological process involved in symbiotic interaction + entity: GO:0043903 + - entity_name: nodulation + entity: GO:0009877 + - relation_name: negatively regulates + relation: RO:0002212 +references: + - citation: Wang, Wang et. al., 2014 + doi: 10.1105/tpc.114.131607 + pmid: 25549672 + - citation: Searle, Men et. al., 2003 + doi: 10.1126/science.1077937 + pmid: 12411574 + - citation: Yang, Lan et. al., 2022 + doi: 10.1111/jipb.13207 + pmid: 34962095 + + +## DOCUMENT 99 ## +--- +scientific_name: Glycine max +gene_symbols: + - GmVSPβ +gene_model_pub_name: Glyma08g21410 +gene_model_full_id: glyma.Wm82.gnm1.ann1.Glyma08g21410 +confidence: 3 +curators: + - William Hardison +comments: + - increased resistance to CCW (Common cutworm) +phenotype_synopsis: increased resistance to insect infestations +traits: + - entity_name: insect damage resistance + entity: TO:0000261 +references: + - citation: Wang, Wang et al., 2015 + doi: null + pmid: null + + +## DOCUMENT 100 ## +--- +scientific_name: Glycine max +gene_symbols: + - GmN:IFR +gene_model_pub_name: Glyma01g37810 +gene_model_full_id: glyma.Wm82.gnm1.ann1.Glyma01g37810 +confidence: 3 +curators: + - William Hardison +comments: + - increased resistance to CCW (Common cutworm) +phenotype_synopsis: increased resistance to insect infestations +traits: + - entity_name: insect damage resistance + entity: TO:0000261 +references: + - citation: Wang, Wang et al., 2015 + doi: 10.1007/s11240-015-0837-9 + pmid: null + + +## DOCUMENT 101 ## +--- +scientific_name: Glycine max +gene_symbols: + - GmPAP12 +gene_symbol_long: Purple Acid Phosphatase 12 +gene_model_pub_name: Glyma06G170300 +gene_model_full_id: glyma.Wm82.gnm2.ann1.Glyma.06G170300 +confidence: 5 +curators: + - Marlene Dorneich-Hayes +comments: + - When phosphate (P) is abuntant, overexpression of PAP12 increases nodule number, nitrogenase and phytase activity, and alkaline phosphatase (APase) activity. + - When PAP12 is silenced, nodule number and APase activity are reduced. + - PAP12 is induced by low-P conditions. + - PAP12 is induced by transcription factor PHR1 (see Lu, Cheng et. al., 2020). +phenotype_synopsis: ARRAY(0x83237f2a0) +traits: + - entity_name: nodulation + entity: GO:0009877 + - entity_name: nitrogen fixation + entity: GO:0009399 + - entity_name: phosphate ion homeostasis + entity: GO:0055062 +references: + - citation: Wang, Yang et. al., 2020 + doi: 10.3389/fpls.2020.00450 + pmid: 32499790 + - citation: Yang, Lan et. al., 2022 + doi: 10.1111/jipb.13207 + pmid: 34962095 + - citation: Lu, Cheng et. al., 2020 + doi: 10.1104/pp.19.01209 + pmid: 32680974 + + +## DOCUMENT 102 ## +--- +scientific_name: Glycine max +gene_symbols: + - GmLCLb2 +gene_symbol_long: LHY/CCA1-like b2 +gene_model_pub_name: Glyma19g45030 +gene_model_full_id: glyma.Wm82.gnm1.ann1.Glyma19g45030 +confidence: 4 +curators: + - Marlene Dorneich-Hayes +comments: + - Transgenic expression of LCLb2 shows that the gene maintains rhythmicity, is expressed most strongly at dawn, and is influenced by light/dark and temperature cycles. + - The circadian cycle speeds up when the transgenic plant is exposed to higher intensity red or blue light. + - Knockout of transcription factors LCLa1, LCLa2, LCLb1, and LCLb2 produces short circadian rhythms and delayed flowering time. + - GmLCL genes share homology with AtCCA1, AtLHY, and VrCCA1L26 genes (see Liu_Zhang_2022.yml) +phenotype_synopsis: Positive regulation of circadian clock. +traits: + - entity_name: transcription factor binding + entity: GO:0008134 + - entity_name: positive regulation of circadian rhythm + entity: GO:0042753 +references: + - citation: Wang, Yuan, et. al., 2019 + doi: 10.1111/pce.13678 + pmid: 31724182 + + +## DOCUMENT 103 ## +--- +gene_symbols: + - GmFT6 +gene_symbol_long: Flowering Time 6 +gene_model_pub_name: Glyma.08G363200 +gene_model_full_id: glyma.Wm82.gnm2.ann1.Glyma.08G363200 +confidence: 5 +curators: + - Steven Cannon +phenotype_synopsis: Photoperiodic flowering time regulation +traits: + - entity_name: flowering time + entity: TO:0002616 + - relation_name: negatively regulates + relation: RO:0002212 + - entity_name: days to maturity + entity: TO:0000469 + - relation_name: negatively regulates + relation: RO:0002212 +references: + - citation: Wang, Zhou et al., 2015 + doi: 10.1105/tpc.114.135103 + pmid: 25663621 + - citation: Lin, Liu et al., 2021 + doi: 10.1111/jipb.13021 + pmid: 33090664 + + +## DOCUMENT 104 ## +--- +classical_locus: E3 +gene_symbols: + - GmphyA3 +gene_symbol_long: Earliness 3 +gene_model_pub_name: Glyma.19G224200 +gene_model_full_id: glyma.Wm82.gnm2.ann1.Glyma.19G224200 +confidence: 5 +curators: + - Steven Cannon +phenotype_synopsis: Photoperiodic flowering time regulation +traits: + - entity_name: flowering time + entity: TO:0002616 + - relation_name: negatively regulates + relation: RO:0002212 + - entity_name: days to maturity + entity: TO:0000469 + - relation_name: negatively regulates + relation: RO:0002212 +references: + - citation: Watanabe, Hideshima et al., 2009 + doi: 10.1534/genetics.108.098772 + pmid: 19474204 + - citation: Lin, Liu et al., 2021 + doi: 10.1111/jipb.13021 + pmid: 33090664 + + +## DOCUMENT 105 ## +--- +gene_symbols: + - E1Lb +gene_symbol_long: E1-like-b +gene_model_pub_name: Glyma.04G143300 +gene_model_full_id: glyma.Wm82.gnm2.ann1.Glyma.04G143300 +confidence: 5 +curators: + - Steven Cannon +phenotype_synopsis: Photoperiodic flowering time regulation +traits: + - entity_name: flowering time + entity: TO:0002616 + - relation_name: negatively regulates + relation: RO:0002212 + - entity_name: days to maturity + entity: TO:0000469 + - relation_name: negatively regulates + relation: RO:0002212 +references: + - citation: Watanabe, Xia et al., 2011 + doi: 10.1534/genetics.110.125062 + pmid: 21406680 + - citation: Lin, Liu et al., 2021 + doi: 10.1111/jipb.13021 + pmid: 33090664 + + +## DOCUMENT 106 ## +--- +gene_symbols: + - GmSWN +gene_symbol_long: Swinger +gene_model_pub_name: Glyma.03G224300 +gene_model_full_id: glyma.Wm82.gnm2.ann1.Glyma.03G224300 +confidence: 5 +curators: + - Steven Cannon +phenotype_synopsis: Photoperiodic flowering time regulation +traits: + - entity_name: flowering time + entity: TO:0002616 + - entity_name: days to maturity + entity: TO:0000469 +references: + - citation: Wu, Kang et al., 2019 + doi: 10.3389/fpls.2019.01221 + pmid: 31787988 + - citation: Dietz, Chan et al., 2023 + doi: 10.3389/fpls.2022.889066 + pmid: 35574141 + + +## DOCUMENT 107 ## +--- +scientific_name: Glycine max +gene_symbols: + - GmCOL1a +gene_symbol_long: CONSTANS-Like 1a +gene_model_pub_name: Glyma08g28370 +gene_model_full_id: glyma.Wm82.gnm1.ann1.Glyma08g28370 +confidence: 5 +curators: + - William Hardison +comments: + - Phylogenetic analysis of full-length amino acid sequences -> "Clade I, GmCOL1a, GmCOL1b, GmCOL2a and GmCOL2b clustered together with Arabidopsis CO and rice CO (Hd1), well-characterized flowering inducers" + - gene_model_pub_name found in Awal Khan, Mohammad, et al., 2022 -> https://doi.org/10.3389/fpls.2022.817544 +phenotype_synopsis: late long day flowering and early short day flowering +traits: + - entity_name: photoperiod-sensitive flowering time trait + entity: TO:0000934 +references: + - citation: Wu, Price et al., 2014 + doi: 10.1371/journal.pone.0085754 + pmid: 24465684 + - citation: Awal Khan, Mohammad, et al., 2022 + doi: 10.3389/fpls.2022.817544 + pmid: 35371153 + + +## DOCUMENT 108 ## +--- +scientific_name: Glycine max +gene_symbols: + - GmCOL1b +gene_symbol_long: CONSTANS-Like 1b +gene_model_pub_name: Glyma18g51320 +gene_model_full_id: glyma.Wm82.gnm1.ann1.Glyma18g51320 +confidence: 3 +curators: + - William Hardison +comments: + - gene_model_pub_name found in Awal Khan, Mohammad, et al., 2022 -> https://doi.org/10.3389/fpls.2022.817544 +phenotype_synopsis: late long day flowering and early short day flowering +traits: + - entity_name: photoperiod-sensitive flowering time trait + entity: TO:0000934 +references: + - citation: Wu, Price et al., 2014 + doi: 10.1371/journal.pone.0085754 + pmid: 24465684 + - citation: Awal Khan, Mohammad, et al., 2022 + doi: 10.3389/fpls.2022.817544 + pmid: 35371153 + + +## DOCUMENT 109 ## +--- +classical_locus: E1 +gene_symbols: + - E1 +gene_symbol_long: Earliness 1 +gene_model_pub_name: Glyma.06G207800 +gene_model_full_id: glyma.Wm82.gnm4.ann1.Glyma.06G207800 +confidence: 5 +curators: + - Steven Cannon +phenotype_synopsis: Photoperiodic flowering time regulation +traits: + - entity_name: flowering time + entity: TO:0002616 + - relation_name: negatively regulates + relation: RO:0002212 + - entity_name: days to maturity + entity: TO:0000469 + - relation_name: negatively regulates + relation: RO:0002212 +references: + - citation: Xia, Zhai et al., 2012 + doi: 10.3389/fpls.2021.632754 + pmid: 33995435 + - citation: Watanabe, Xia et al., 2011 + doi: 10.1534/genetics.110.125062 + pmid: 21406680 + - citation: Dietz, Chan et al., 2023 + doi: 10.3389/fpls.2022.889066 + pmid: 35574141 + - citation: Lin, Liu et al., 2021 + doi: 10.1111/jipb.13021 + pmid: 33090664 + + +## DOCUMENT 110 ## +--- +gene_symbols: + - E1La +gene_symbol_long: E1-like-a +gene_model_pub_name: Glyma.04G156400 +gene_model_full_id: glyma.Wm82.gnm2.ann1.Glyma.04G156400 +confidence: 5 +curators: + - Steven Cannon +phenotype_synopsis: Photoperiodic flowering time regulation traits: - - entity_name: root nodule - entity: PO:0003023 + - entity_name: flowering time + entity: TO:0002616 + - relation_name: negatively regulates + relation: RO:0002212 + - entity_name: days to maturity + entity: TO:0000469 + - relation_name: negatively regulates + relation: RO:0002212 references: - - citation: Sugawara, Umehara et al., 2019 - doi: 10.1371/journal.pone.0222469 - pmid: 31518373 + - citation: Xu, Yamagishi et al., 2015 + doi: 10.1104/pp.15.00763 + pmid: 26134161 + - citation: Lin, Liu et al., 2021 + doi: 10.1111/jipb.13021 + pmid: 33090664 -## DOCUMENT 42 ## +## DOCUMENT 111 ## --- +scientific_name: Glycine max gene_symbols: - - GmTMT2a -gene_symbol_long: glyma.Wm82.gnm1.ann1.Glyma12g01690 -gene_model_pub_name: Glyma12g01690 -gene_model_full_id: glyma.Wm82.gnm1.ann1.Glyma12g01690 + - GmBEHL1 + - GmBES1-5 +gene_symbol_long: BES1/BZR1 Homolog-Like protein 1 +gene_model_pub_name: Glyma01G178000 +gene_model_full_id: glyma.Wm82.gnm2.ann1.Glyma.01G178000 confidence: 5 curators: - - Greg Murrell -phenotype_synopsis: Catalyzes the conversion of γ-tocopherol to α-tocopherol. + - Marlene Dorneich-Hayes +comments: + - Overexpression of BEHL1 decreases nodulation, RNAi knockdown of BEHL1 increases nodulation. + - BEHL1 interacts with the nodulation factor (NF) pathway as well as the brassinosteroid signalling (BR) pathway. + - The product of BEHL1 binds to BR-responsive Responsive Elements (BRRE) and the gene GmBIN2 to regulate BR signalling. +phenotype_synopsis: BEHL1 is a corepressor. It works with NNC1 (see Wang, Wang et. al., 2014) as a negative regulator of nodulation. traits: - - entity_name: vitamin E biosynthetic process - entity: GO:0010189 - relation_name: positively regulates - relation: RO:0002213 + - entity_name: regulation of biological process involved in symbiotic interaction + entity: GO:0043903 + - entity_name: nodulation + entity: GO:0009877 + - relation_name: negatively regulates + relation: RO:0002212 references: - - citation: Zhang, Luo et al., 2013 - doi: 10.1007/s11248-013-9713-8 - pmid: 23645501 - - citation: Fang, Feng et al., 2017 - doi: 10.1016/j.yrtph.2017.01.004 - pmid: 28132846 - - citation: Zhang, Luo et al., 2020 - doi: 10.1007/s11248-019-00180-z - pmid: 31673914 + - citation: Yan, Wang et. al., 2018 + doi: 10.1038/s41598-018-25910-x + pmid: 29769571 + - citation: Li, Guo et. al., 2019 + doi: 10.1016/j.heliyon.2019.e01868 + pmid: 31206092 + - citation: Wang, Wang et. al., 2014 + doi: 10.1105/tpc.114.131607 + pmid: 25549672 + - citation: Yang, Lan et. al., 2022 + doi: 10.1111/jipb.13207 + pmid: 34962095 -## DOCUMENT 43 ## +## DOCUMENT 112 ## --- +scientific_name: Glycine max gene_symbols: - - ChlI1a -gene_symbol_long: Mg-chelatase subunit Chl1 -gene_model_pub_name: Glyma.13G232500 -gene_model_full_id: glyma.Wm82.gnm2.ann1.Glyma.13G232500 -confidence: 4 + - GmIDD +gene_symbol_long: soybean indeterminate domain transcription factor +gene_model_pub_name: Glyma.14G095900 +gene_model_full_id: glyma.Wm82.gnm2.ann1.Glyma.14G095900 +confidence: 5 +curators: + - Marlene Dorneich-Hayes comments: - - The MinnGold and T219H phenotypes cosegregate with ChlI1a. Transformation of WT ChlI1a into mutant soy reinstated normal phenotype. -phenotype_synopsis: defective Mg-chetelase is responsible for chlorophyll deficient MinnGold (y11-2) and T219H (y11) phenotypes + - Comparisons between plants exposed to different day lengths indicated that GmIDD was induced by short days. Overexpression of GmIDD induces early flowering in WT Arabidopsis plants and restores normal flowering time to late-flowering Arabidopsis mutants. Genes acted on by the GmIDD-endcoded transcription factor identified by ChIP-Seq. +phenotype_synopsis: GmIDD is induced by short days and promotes flowering in soy, maize, rice, and Arabidopsis. traits: - - entity_name: magnesium chelatase activity - entity: GO:0016851 - - entity_name: leaf chlorophyll content - entity: TO:0012002 + - entity_name: photoperiod sensitive flowering time + entity: TO:0000934 + - entity_name: flowering time + entity: TO:0002616 + - entity_name: short day length exposure + entity: PECO:0007200 references: - - citation: Campbell, Mani et al., 2014 - doi: 10.1534/g3.114.015255 - pmid: 25452420 + - citation: Yang, Zhang et al., 2021 + doi: 10.3389/fpls.2021.629069 + pmid: 33841461 -## DOCUMENT 44 ## +## DOCUMENT 113 ## --- +scientific_name: Glycine max gene_symbols: - - ChlI1b -gene_symbol_long: null -gene_model_pub_name: Glyma.15g08680 -gene_model_full_id: glyma.Wm82.gnm2.ann1.Glyma.15G086800 -confidence: 4 + - GmSFT +gene_symbol_long: Seed-Flooding Tolerance +gene_model_pub_name: Glyma.13g248000 +gene_model_full_id: glyma.Wm82.gnm4.ann1.Glyma.13G248000 +confidence: 3 +curators: + - William Hardison comments: - - The CD-5 phenotype cosegregates with ChlI1b. -phenotype_synopsis: defective Mg-chetelase is responsible for chlorophyll deficient CD-5 phenotype + - Genome-Wide Association Study (GWAS) + - also known as glyma.Wm82.gnm2.ann1.Glyma.13G248000.1 + - condifence is 4 because further functional validation is required to determine its [Glyma.13g248000] roles in seed-flooding tolerance of soybean + - GmSFT(Glyma.13g248000) was considered to be the most likely candidate gene regulating seed-flooding tolerance in soybean +phenotype_synopsis: Ability to grow in seed flooding conditions traits: - - entity_name: magnesium chelatase activity - entity: GO:0016851 - - entity_name: leaf chlorophyll content - entity: TO:0012002 + - entity_name: flooding related trait + entity: TO:0000114 references: - - citation: Campbell, Mani et al., 2014 - doi: 10.1534/g3.114.015255 - pmid: 25452420 + - citation: Yu, Chang et al., 2019 + doi: 10.3390/genes10120957 + pmid: 31766569 -## DOCUMENT 45 ## +## DOCUMENT 114 ## --- +scientific_name: Glycine max gene_symbols: - - GmCAMTA12 -gene_symbol_long: Glycine max calmodulin binding transcription activator -gene_model_pub_name: Glyma.17G031900 -gene_model_full_id: glyma.Wm82.gnm2.ann1.Glyma.17G031900 -confidence: 4 + - GmFT5a + - GmFTL4 +gene_symbol_long: Flowering Locus T +gene_model_pub_name: Glyma.16G044100 +gene_model_full_id: glyma.Wm82.gnm4.ann1.Glyma.16G044100 +confidence: 5 curators: - - Marlene Dorneich-Hayes -comments: - - Overexpression of GmCAMTA12 increases drought tolerance in Glycine max and Arabidopsis. -phenotype_synopsis: GmCAMTA12 affects the expression of many genes involved in stress tolerance. + - Greg Murrell +phenotype_synopsis: Control of flowering time and shoot determinacy traits: - - entity_name: abiotic stress trait - entity: TO:0000168 - - entity_name: drought tolerance - entity: TO:0000276 - - entity_name: calmodulin binding - entity: GO:0005516 + - entity_name: photoperiod-sensitive flowering time trait + entity: TO:0000934 + - entity_name: plant height + entity: TO:0000207 + - entity_name: transcription factor AP-1 complex + entity: GO:0035976 + - relation_name: positively regulates + relation: RO:0002213 references: - - citation: Noman, Jameel et al., 2019 - doi: 10.3390/ijms20194849 - pmid: null - - citation: Wang, Zeng et al., 2015 - doi: 10.1007/s11104-014-2267-6 - pmid: null + - citation: Yue, Li et al., 2021 + doi: 10.1111/jipb.13070 + pmid: 33458938 + - citation: Takeshima, Hayashi, et al., 2016 + doi: 10.1093/jxb/erw283 + pmid: 27422993 + - citation: Cai, Wang, et al., 2020 + doi: 10.1111/pbi.13199 + pmid: 31240772 + - citation: Takeshima, Nan, et al., 2019 + doi: 10.1093/jxb/erz199 + pmid: 31035293 + - citation: Nan, Cao, et al., 2014 + doi: 10.1371/journal.pone.0097669 + pmid: 24845624 + - citation: Jiang, Zhang, et al., 2019 + doi: 10.1186/s12864-019-5577-5 + pmid: 30894121 + - citation: Liu, Jiang, et al., 2018 + doi: 10.1111/nph.14884 + pmid: 29120038 + - citation: Cao, Takeshima, et al., 2017 + doi: 10.1093/jxb/erw394 + pmid: 28338712 + - citation: Kong, Liu, et al., 2010 + doi: 10.1104/pp.110.160796 + pmid: 20864544 -## DOCUMENT 46 ## +## DOCUMENT 115 ## --- +scientific_name: Glycine max gene_symbols: - - GmFLS2a -gene_symbol_long: Glycine max flagellin sensing 2 -gene_model_pub_name: glyma.08g083300 -gene_model_full_id: glyma.Wm82.gnm2.ann1.Glyma.08G083300 -confidence: 4 -curators: - - Marlene Dorneich-Hayes + - GmDT1 + - GmTFL + - GmTFL1b + - GmTFL1.1 + - GmTFL1b +gene_symbol_long: Terminal Flower 1-Like +gene_model_pub_name: Glyma.19G194300 +gene_model_full_id: glyma.Wm82.gnm4.ann1.Glyma.19G194300 +confidence: 5 comments: - - GmFLS2a and GmFLS2b are likely redundant. They are not distinguishable by the VIGS knockout approach. When both of these genes are silenced, soy plants became much more suceptible to bacterial pathogens (Pseudomonas syringae pv. glycinea), but resistance to viral pathogens (Soybean mosaic virus) is not affected. -phenotype_synopsis: GmFLS2a and GmFLS2b kinases start a phosphorylation cascade that activates GmMPK3 and GmMPK6, which are involved in the plant's response to bacterial infection. + - photoperiodic flowering time +phenotype_synopsis: Modification of flowering time and determinacy traits: - - entity_name: bacterial disease resistance - entity: TO:0000315 - - entity_name: kinase activity - entity: GO:0016301 + - entity_name: soybean flowering time trait + entity: CO_336:0000000 + - entity_name: soybean plant height trait + entity: CO_336:0000027 references: - - citation: Tian, Liu et al., 2019 - doi: 10.1016/j.plantsci.2019.110386 - pmid: 32005391 + - citation: Yue, Li et al., 2021 + doi: 10.1111/jipb.13070 + pmid: 33458938 + - citation: Tian, Wang, et al., 2010 + doi: 10.1073/pnas.1000088107 + pmid: 20421496 + - citation: Liu, Watanabe, et al., 2010 + doi: 10.1104/pp.109.150607 + pmid: 20219831 + - citation: Langewisch, Zhang, 2014 + doi: 10.1371/journal.pone.0094150 + pmid: 24727730 -## DOCUMENT 47 ## +## DOCUMENT 116 ## --- +classical_locus: E10 gene_symbols: - - GmFLS2b -gene_symbol_long: Glycine max flagellin sensing 2 -gene_model_pub_name: glyma.05g128200 -gene_model_full_id: glyma.Wm82.gnm2.ann1.Glyma.05G128200 -confidence: 4 + - GmFT4 +gene_symbol_long: Earliness 10 +gene_model_pub_name: Glyma.08G363100 +gene_model_full_id: glyma.Wm82.gnm2.ann1.Glyma.08G363100 +confidence: 5 curators: - - Marlene Dorneich-Hayes -comments: - - GmFLS2a and GmFLS2b are likely redundant. They are not distinguishable by the VIGS knockout approach. When both are silenced, soy plants became much more suceptible to bacterial pathogens (Pseudomonas syringae pv. glycinea), but resistance to viral pathogens (Soybean mosaic virus) is not affected. -phenotype_synopsis: GmFLS2a and GmFLS2b kinases start a phosphorylation cascade that activates GmMPK3 and GmMPK6, which are involved in the plant's response to bacterial infection. + - Steven Cannon +phenotype_synopsis: Photoperiodic flowering time regulation traits: - - entity_name: bacterial disease resistance - entity: TO:0000315 - - entity_name: kinase activity - entity: GO:0016301 + - entity_name: flowering time + entity: TO:0002616 + - relation_name: negatively regulates + relation: RO:0002212 + - entity_name: days to maturity + entity: TO:0000469 + - relation_name: negatively regulates + relation: RO:0002212 references: - - citation: Tian, Liu et al., 2019 - doi: 10.1016/j.plantsci.2019.110386 - pmid: 32005391 + - citation: Zhai, Lu et al., 2014 + doi: 10.1371/journal.pone.0089030 + pmid: 24586488 + - citation: Samanfar, Molnar et al., 2017 + doi: 10.1007/s00122-016-2819-7 + pmid: 27832313 + - citation: Lin, Liu et al., 2021 + doi: 10.1111/jipb.13021 + pmid: 33090664 -## DOCUMENT 48 ## +## DOCUMENT 117 ## --- +scientific_name: Glycine max +classical_locus: ARRAY(0x8323f76f0) gene_symbols: - - GmEDS1a -gene_symbol_long: Glycine max enhanced disease susceptibility 1a -gene_model_pub_name: Glyma04g34800 -gene_model_full_id: glyma.Wm82.gnm1.ann1.Glyma04g34800 -confidence: 4 + - SACPD-C +gene_symbol_long: delta-9-Stearoyl-Acyl Carrier Protein Desaturase-C +gene_model_pub_name: Glyma14g27990 +gene_model_full_id: glyma.Wm82.gnm1.ann1.Glyma14g27990 +confidence: 3 curators: - Marlene Dorneich-Hayes comments: - - Silencing of GmEDS1a/b and GmPAD4 stopped accumulation of salicylic acid and increased the plant's suceptibility to Pseudomonas syringae pv glycinea and soybean mosaic virus infection. The phenotype is only altered if all three genes are silenced. -phenotype_synopsis: responsible for basal and pathogen-inducible accumulation of salicylic acid, which helps the plant resist bacterial, oomycete, and viral infection. Gene activity is induced by infection. + - Mutants with defective SACPD-C produce seeds with high stearic acid content. + - Plants with defective or silent SACPD-C produce seeds high in stearic acid. + - SACPD-C also has pleiotropic effects on nodule structure. +phenotype_synopsis: SACPD-C codes for a seed-specific enzyme that converts stearic acid into oleic acid. traits: - - entity_name: defense response to bacterium - entity: GO:0042742 - - enitity_name: defense response to virus - entity: GO:0051607 + - entity_name: seed development + entity: GO:0048316 + - entity_name: lipid metabolic process + entity: GO:0006629 + - entity_name: regulation of triglyceride biosynthetic process + entity: GO:0010866 + - entity_name: fat and essential oil content + entity: TO:0000604 references: - - citation: Wang, Shine et al., 2014 - doi: 10.1104/pp.114.242495 - pmid: 24872380 - - citation: Weirmer, Feys et al., 2005 - doi: 10.1016/j.pbi.2005.05.010 - pmid: 15939664 + - citation: Zhang, Burton et. al., 2008 + doi: null + pmid: null + - citation: Gillman, Stacey et. al., 2014 + doi: 10.1186/1471-2229-14-143 + pmid: 24886084 + - citation: Carrero-Colon, Abshire et. al., 2014 + doi: 10.1371/journal.pone.0097891 + pmid: 24846334 + - citation: Zuo, Ikram et. al., 2022 + doi: 10.1016/j.csbj.2022.06.014 + pmid: 35782726 -## DOCUMENT 49 ## +## DOCUMENT 118 ## --- +scientific_name: Glycine max gene_symbols: - - GmEDS1b -gene_symbol_long: Glycine max enhanced disease suceptibility 1b -gene_model_pub_name: Glyma06g19920 -gene_model_full_id: glyma.Wm82.gnm1.ann1.Glyma06g19920 + - GmBTB/POZ +gene_symbol_long: Broad Complex Tramtrack Bric-a-brac Pox Virus and Zinc finger +gene_model_pub_name: XP_006578952 +gene_model_full_id: glyma.Wm82.gnm4.ann1.Glyma.04G244900 confidence: 4 curators: - Marlene Dorneich-Hayes + - Steven Cannon comments: - - Silencing of GmEDS1a/b and GmPAD4 stopped accumulation of salicylic acid and increased the plant's suceptibility to Pseudomonas syringae pv glycinea and soybean mosaic virus infection. The phenotype is only altered if all three genes are silenced. -phenotype_synopsis: responsible for basal and pathogen-inducible accumulation of salicylic acid, which helps the plant resist bacterial, oomycete, and viral infection. Gene activity is induced by infection. + - Overexpression of GmBTB/POZ increases resistance to Phytophthora sojae in GmLHP1 overexpressing plants. +phenotype_synopsis: the product of GmBTB/POZ positively regulates the plant's response to Phytophthora sojae infection by marking the product of GmLHP1 for degradation, thus activating the transcription factor GmWRKY40. traits: - - entity_name: defense response to bacterium - entity: GO:0042742 - - enitity_name: defense response to virus - entity: GO:0051607 + - entity_name: defence response to fungus + entity: GO:0050832 references: - - citation: Wang, Shine et al., 2014 - doi: 10.1104/pp.114.242495 - pmid: 24872380 - - citation: Weirmer, Feys et al., 2005 - doi: 10.1016/j.pbi.2005.05.010 - pmid: 15939664 + - citation: Zhang, Cheng et al., 2021 + doi: 10.1038/s42003-021-01907-7 + pmid: 33742112 + - citation: Zhang, Gao et al., 2018 + doi: 10.1111/mpp.12741 + pmid: 30113770 -## DOCUMENT 50 ## +## DOCUMENT 119 ## --- +scientific_name: Glycine max gene_symbols: - - GmPAD4 -gene_symbol_long: Glycine max phytoalexin deficient 4 -gene_model_pub_name: Glyma08g00420 -gene_model_full_id: glyma.Wm82.gnm1.ann1.Glyma08g00420 + - GmSWEET39 +gene_symbol_long: Sugars Will Eventually be Exported Transporter 39 +gene_model_pub_name: Glyma.15G049200 +gene_model_full_id: glyma.Wm82.gnm2.ann1.Glyma.15G049200 confidence: 4 curators: - Marlene Dorneich-Hayes comments: - - Silencing of GmEDS1a/b and GmPAD4 stopped accumulation of salicylic acid and increased the plant's suceptibility to Pseudomonas syringae pv glycinea and soybean mosaic virus infection. The phenotype is only altered if all three genes are silenced. -phenotype_synopsis: responsible for basal and pathogen-inducible accumulation of salicylic acid, which helps the plant resist bacterial, oomycete, and viral infection. Gene activity is induced by infection. -traits: - - entity_name: defense response to bacterium - entity: GO:0042742 - - enitity_name: defense response to virus - entity: GO:0051607 -references: - - citation: Wang, Shine et al., 2014 - doi: 10.1104/pp.114.242495 - pmid: 24872380 - - citation: Weirmer, Feys et al., 2005 - doi: 10.1016/j.pbi.2005.05.010 - pmid: 15939664 + - Expression positively correlates to seed oil content and negatively correlates to seed protein content. +phenotype_synopsis: SWEET39 codes for a sucrose efflux transporter in the plasma membrane which produces a pleiotropic affect on seed protein and oil content. +traits: + - entity_name: protein content + entity: TO:0000598 + - entity_name: fat and essential oil content + entity: TO:0000604 + - entity_name: efflux transmembrane transporter activity + entity: GO:0015562 +references: + - citation: Zhang, Goettel et. al., 2020 + doi: 10.1371/journal.pgen.1009114 + pmid: 33175845 + - citation: Miao, Yang et. al., 2020 + doi: 10.1111/nph.16250 + pmid: 31596499 + - citation: Zuo, Ikram et. al., 2022 + doi: 10.1016/j.csbj.2022.06.014 + pmid: 35782726 -## DOCUMENT 51 ## +## DOCUMENT 120 ## --- +scientific_name: Glycine max gene_symbols: - - GmIDD -gene_symbol_long: soybean indeterminate domain transcription factor -gene_model_pub_name: Glyma.14G095900 -gene_model_full_id: glyma.Wm82.gnm2.ann1.Glyma.14G095900 + - GmTMT2a +gene_symbol_long: glyma.Wm82.gnm1.ann1.Glyma12g01690 +gene_model_pub_name: Glyma12g01690 +gene_model_full_id: glyma.Wm82.gnm1.ann1.Glyma12g01690 confidence: 5 curators: - - Marlene Dorneich-Hayes -comments: - - Comparisons between plants exposed to different day lengths indicated that GmIDD was induced by short days. Overexpression of GmIDD induces early flowering in WT Arabidopsis plants and restores normal flowering time to late-flowering Arabidopsis mutants. Genes acted on by the GmIDD-endcoded transcription factor identified by ChIP-Seq. -phenotype_synopsis: GmIDD is induced by short days and promotes flowering in soy, maize, rice, and Arabidopsis. + - Greg Murrell +phenotype_synopsis: Catalyzes the conversion of γ-tocopherol to α-tocopherol. traits: - - entity_name: photoperiod sensitive flowering time - entity: TO:0000934 - - entity_name: flowering time - entity: TO:0002616 - - entity_name: short day length exposure - entity: PECO:0007200 + - entity_name: vitamin E biosynthetic process + entity: GO:0010189 + - relation_name: positively regulates + relation: RO:0002213 references: - - citation: Yang, Zhang et al., 2021 - doi: 10.3389/fpls.2021.629069 - pmid: 33841461 + - citation: Zhang, Luo et al., 2013 + doi: 10.1007/s11248-013-9713-8 + pmid: 23645501 + - citation: Fang, Feng, et al., 2017 + doi: 10.1016/j.yrtph.2017.01.004 + pmid: 28132846 + - citation: Zhang, Luo, et al., 2020 + doi: 10.1007/s11248-019-00180-z + pmid: 31673914 -## DOCUMENT 52 ## +## DOCUMENT 121 ## --- +scientific_name: Glycine max gene_symbols: - - GmAKT2 -gene_symbol_long: soybean potassium transporter gene 2 -gene_model_pub_name: Glym08g20030 -gene_model_full_id: glyma.Wm82.gnm2.ann1.Glym08g20030 -confidence: 5 + - GmB1 +gene_symbol_long: Bloom 1 +gene_model_pub_name: Glyma13g31540 +gene_model_full_id: glyma.Wm82.gnm1.ann1.Glyma13g31540 +confidence: 4 curators: - Marlene Dorneich-Hayes comments: - - Overexpression of GmAKT2 in transgenic SMV-susceptible soy plants increases resistance to SMV relative to WT -phenotype_synopsis: GmAKT2 increases a soy plant's resistance to SMV by affecting distribution of potassium ions in the leaves. + - Expression of B1 in transgenic plants negatively correlates with the accumuation of oil and positively correlates with the amount of bloom. + - Overexpression of B1 reduced fatty acid content in seed pods and increased bloom on the seed coat. +phenotype_synopsis: ARRAY(0x832513348) traits: - - entity_name: soybean mosaic virus - entity: NCBITaxon:12222 - - entity_name: viral disease resistance - entity: TO:0000148 - - entity_name: mineral and ion transportation - entity: TO:0020096 - - entity_name: postassium ion concentration - entity: TO:0000513 + - entity_name: regulation of seed growth + entity: GO:0080113 + - entity_name: seed development + entity: GO:0048316 + - entity_name: fat and essential oil content + entity: TO:0000604 + - entity_name: seed coat luster + entity: TO:0000888 references: - - citation: Zhou, He et al., 2014 - doi: 10.1186/1471-2229-14-154 - pmid: 24893844 + - citation: Zhang, Sun et. al., 2017 + doi: 10.1038/s41477-017-0084-7 + pmid: 29292374 + - citation: Zuo, Ikram et. al., 2022 + doi: 10.1016/j.csbj.2022.06.014 + pmid: 35782726 -## DOCUMENT 53 ## +## DOCUMENT 122 ## --- -classical_locus: Gp11 +scientific_name: Glycine max gene_symbols: - - GmPRR3A -gene_symbol_long: null -gene_model_pub_name: Glyma11g15580 -gene_model_full_id: glyma.Wm82.gnm1.ann1.Glyma11g15580.3 + - GmNNL1 +gene_symbol_long: Nodule Number Locus 1 +gene_model_pub_name: Glyma.02G076900 +gene_model_full_id: glyma.Wm82.gnm2.ann1.Glyma.02G076900 confidence: 5 curators: - - William Hardison + - Marlene Dorneich-Hayes comments: - - Glyma11g15580 pseudo-response regulator 3 - - Gp11 and Gp12 regulate the expression of GmFT2a and GmFT5a -phenotype_synopsis: Shorter growth period + - NNL1 encodes an R protein that interacts with nodulation outer protein P (NopP) of Bradyrhizobium japonicum to prevent symbiosis. + - Different NNL1 alleles provide immunity to different B. japonicum symbionts. + - GmSINE1 may be inserted into NNL1, producing an inactive truncated protein. Infection proceeds normally when NNL1 is nonfunctional. + - NNL1 is induced by innoculation with B. japonicum and expressed in root hairs. +phenotype_synopsis: NNL1 gives soy plants immunity to root hair infection by B. japonicum, which inhibits nodulation and reduces nitrogen fixation. traits: - - entity_name: days to maturity - entity: TO:0000469 + - entity_name: regulation of biological process involved in symbiotic interaction + entity: GO:0043903 + - entity_name: nodulation + entity: GO:0009877 + - relation_name: negatively regulates + entity: RO:0002212 references: - - citation: Li, Liu et al., 2019 - doi: 10.1093/pcp/pcy215 - pmid: 30418611 + - citation: Zhang, Wang et. al, 2021 + doi: 10.1038/s41477-020-00832-7 + pmid: 33452487 + - citation: Yang, Lan et. al., 2022 + doi: 10.1111/jipb.13207 + pmid: 34962095 -## DOCUMENT 54 ## +## DOCUMENT 123 ## --- -classical_locus: Gp12 +scientific_name: Glycine max gene_symbols: - - GmPRR3B -gene_symbol_long: null -gene_model_pub_name: Glyma12g07861 -gene_model_full_id: glyma.Wm82.gnm1.ann1.Glyma12g07861.3 + - GmRj2 +gene_symbol_long: Resistance j2 +gene_model_pub_name: Glyma16g33780 +gene_model_full_id: glyma.Wm82.gnm2.ann1.Glyma.16G33780 confidence: 5 curators: - - William Hardison + - Marlene Dorneich-Hayes comments: - - Gp11 and Gp12 regulate the expression of GmFT2a and GmFT5a - - Glyma12g07861 pseudo-response regulator 7‡ -phenotype_synopsis: Shorter growth period + - Rj2 interacts with rhizobial NopP to determine compatibility of infecting rhizobia. + - Different Rj2 alleles provide immunity to different Bradyrhizobium symbionts. + - When invading NopP is incompatible with host Rj2, Rj2 activates defence gene PR-2 to prevent infection. + - Regardless of rhizobial compatibility, Rj2 induces ENOD40. + - Rj2 is expressed in nodules, root hairs, root tips, and shoot meristems. +phenotype_synopsis: Rj2 is a resistance gene involved in sensing compatibility between soy and Bradyrhizobium symbionts. traits: - - entity_name: days to maturity - entity: TO:0000469 + - entity_name: regulation of biological process involved in symbiotic interaction + entity: GO:0043903 + - entity_name: nodulation + entity: GO:0009877 + - relation_name: negatively regulates + entity: RO:0002212 references: - - citation: Li, Liu et al., 2019 - doi: 10.1093/pcp/pcy215 - pmid: 30418611 + - citation: Zhang, Wang et. al, 2021 + doi: 10.1038/s41477-020-00832-7 + pmid: 33452487 + - citation: Sugawara, Takahashi et. al., 2018 + doi: 10.1038/s41467-018-05663-x + pmid: 30087346 + - citation: Sugawara, Umehara et al., 2019 + doi: 10.1371/journal.pone.0222469 + pmid: 31518373 + - citation: Yang, Lan et. al., 2022 + doi: 10.1111/jipb.13207 + pmid: 34962095 -## DOCUMENT 55 ## +## DOCUMENT 124 ## --- -classical_locus: null +scientific_name: Glycine max gene_symbols: - - GA2ox8A -gene_symbol_long: gibberellin 2-oxidase 8A/B -gene_model_pub_name: Glyma.13G287600 -gene_model_full_id: glyma.Wm82.gnm4.ann1.Glyma.13G287600.1 -confidence: 5 + - GmDGAT1A +gene_symbol_long: Acyl-CoA:Diacylglycerol Acyltransferase 1A +gene_model_pub_name: Glyma13g16560 +gene_model_full_id: glyma.Wm82.gnm1.ann1.Glyma13g16560 +confidence: 3 curators: - William Hardison comments: - - ncbi says the locus for gibberellin 2-beta-dioxygenase 8 [Glycine max] -> LOCUS NP_001242439 - - Cannot find plant trait ontology for trailing growth and shoot length -> "shoot height (related)" is for plant height - - glyma.Wm82.gnm2.ann1.Glyma.13G287600.1 also works -phenotype_synopsis: Negatively correlated with shoot length and trailing growth + - soybean genome contains more DGAT genes -> duplicaiton events +phenotype_synopsis: increased fat content, reduced protein content, and increased response to temperature stress traits: - - entity_name: plant height - entity: TO:0000207 + - entity_name: fat and essential oil content + entity: TO:0000604 references: - - citation: Wang, Li et al., 2021 - doi: 10.1111/tpj.15414 - pmid: 34245624 + - citation: Zhao, Bi et al., 2019 + doi: 10.1016/j.jplph.2019.153019 + pmid: 31437808 -## DOCUMENT 56 ## +## DOCUMENT 125 ## --- -classical_locus: null +scientific_name: Glycine max gene_symbols: - - GA2ox8B -gene_symbol_long: gibberellin 2-oxidase 8A/B -gene_model_pub_name: Glyma.13G288000 -gene_model_full_id: glyma.Wm82.gnm4.ann1.Glyma.13G288000.1 -confidence: 5 + - GmDGAT1B +gene_symbol_long: Acyl-CoA:Diacylglycerol Acyltransferase 1B +gene_model_pub_name: Glyma17g06120 +gene_model_full_id: glyma.Wm82.gnm1.ann1.Glyma17g06120 +confidence: 3 curators: - William Hardison comments: - - Cannot find plant trait ontology for trailing growth and shoot length -> "shoot height (related)" is for plant height - - glyma.Wm82.gnm2.ann1.Glyma.13G288000.1 also works -phenotype_synopsis: Negatively correlated with shoot length and trailing growth + - soybean genome contains more DGAT genes -> duplicaiton events +phenotype_synopsis: increased fat content and reduced protein content traits: - - entity_name: plant height - entity: TO:0000207 + - entity_name: fat and essential oil content + entity: TO:0000604 + - entity_name: temperature response trait + entity: TO:0000432 references: - - citation: Wang, Li et al., 2021 - doi: 10.1111/tpj.15414 - pmid: 34245624 + - citation: Zhao, Bi et al., 2019 + doi: 10.1016/j.jplph.2019.153019 + pmid: 31437808 -## DOCUMENT 57 ## +## DOCUMENT 126 ## --- -classical_locus: null +scientific_name: Glycine max gene_symbols: - - GmVSPβ -gene_symbol_long: null -gene_model_pub_name: Glyma08g21410.1 -gene_model_full_id: glyma.Wm82.gnm1.ann1.Glyma08g21410.1 -confidence: 5 + - GmDGAT1C +gene_symbol_long: Acyl-CoA:Diacylglycerol Acyltransferase 1C +gene_model_pub_name: Glyma09g07520 +gene_model_full_id: glyma.Wm82.gnm1.ann1.Glyma09g07520 +confidence: 2 curators: - William Hardison comments: - - increased resistance to CCW (Common cutworm) -phenotype_synopsis: increased resistance to insect infestations + - transcriptional analysis -> similarity to GmDGAT1A and GmDGAT1B, no knockdowns or other experiments +phenotype_synopsis: increased fat content and reduced protein content traits: - - entity_name: insect damage resistance - entity: TO:0000261 + - entity_name: fat and essential oil content + entity: TO:0000604 references: - - citation: Wang, Wang et al., 2015 - doi: null - pmid: null + - citation: Zhao, Bi et al., 2019 + doi: 10.1016/j.jplph.2019.153019 + pmid: 31437808 -## DOCUMENT 58 ## +## DOCUMENT 127 ## --- -classical_locus: null +scientific_name: Glycine max gene_symbols: - - GmN:IFR -gene_symbol_long: null -gene_model_pub_name: Glyma01g37810.1 -gene_model_full_id: glyma.Wm82.gnm1.ann1.Glyma01g37810.1 -confidence: 5 + - GmDGAT2D +gene_symbol_long: Acyl-CoA:Diacylglycerol Acyltransferase 2D +gene_model_pub_name: Glyma01g36010 +gene_model_full_id: glyma.Wm82.gnm4.ann1.Glyma01g36010 +confidence: 3 curators: - William Hardison comments: - - increased resistance to CCW (Common cutworm) -phenotype_synopsis: increased resistance to insect infestations + - The gene model full id I pieced together from Information I found so it is probably wrong. (Williams 82, Glycine_Max_v4.0) + - soybean genome contains more DGAT genes -> duplicaiton events +phenotype_synopsis: increased response to temperature stress traits: - - entity_name: insect damage resistance - entity: TO:0000261 + - entity_name: temperature response trait + entity: TO:0000432 references: - - citation: Wang, Wang et al., 2015 + - citation: Zhao, Bi et al., 2019 + doi: 10.1016/j.jplph.2019.153019 + pmid: 31437808 + - citation: Zhao, Jiangzhe, et al. 2019 doi: null pmid: null -## DOCUMENT 59 ## +## DOCUMENT 128 ## --- -classical_locus: null +scientific_name: Glycine max gene_symbols: - GmGBP1 -gene_symbol_long: Glycine max GAMYB-binding protein gene +gene_symbol_long: GAMYB Binding Protein 1 gene_model_pub_name: DQ112540 -gene_model_full_id: glyma.Wm82.gnm4.ann1.Glyma.01G008600.1 -confidence: 5 +gene_model_full_id: glyma.Wm82.gnm2.ann1.Glyma.01G008600 +confidence: 4 curators: - William Hardison + - Steven Cannon comments: - - haplotype analysis, association analysis, phenotypic analysis, statistics analysis - - on ncbi -> GLYMA_01G008600v4, LOC732608, glyma.Wm82.gnm2.ann1.Glyma.01G008600.1 - - Zhang, Zhao et al., 2013 [doi 10.1186/1471-2229-13-21] identifies GmGBP1 as GenBank DQ112540 + - Could not determine the gene_model_pub_name from the paper. + - Zhang, Zhao et al., 2013 [doi 10.1186/1471-2229-13-21] identifies GmGBP1 as GenBank DQ112540. + - Zhao, Wang et al., 2013 [10.1007/s11103-013-0062-z] identifies GmGBP1 as Glyma16g08450. + - Sequence analysis indicates this is a SNW/SKIP transcription factor, equivalent to glyma.Wm82.gnm2.ann1.Glyma.01G008600 phenotype_synopsis: increased flowering on short days traits: - entity_name: photoperiod-sensitive flowering time trait @@ -1676,103 +3945,248 @@ references: - citation: Zhao, Li et al., 2018 doi: 10.1111/tpj.14025 pmid: 30004144 - - citation: Zhang, Zhao et al., 2013 - doi: 10.1186/1471-2229-13-21 - pmid: 23388059 - citation: Zhao, Wang et al., 2013 doi: 10.1007/s11103-013-0062-z pmid: 23636865 + - citation: Zhang, Zhao et al., 2013 + doi: 10.1186/1471-2229-13-21 + pmid: 23388059 -## DOCUMENT 60 ## +## DOCUMENT 129 ## --- +scientific_name: Glycine max gene_symbols: - - KASII-A -gene_symbol_long: beta-ketoacyl-ACP synthase II -gene_model_pub_name: Glyma17g05200 -gene_model_full_id: glyma.Wm82.gnm1.ann1.Glyma17g05200 -confidence: 3 + - GmAKT2 +gene_symbol_long: soybean potassium transporter gene 2 +gene_model_pub_name: Glyma08g20030 +gene_model_full_id: glyma.Wm82.gnm1.ann1.Glyma08g20030 +confidence: 5 curators: - - Wei Huang + - Marlene Dorneich-Hayes comments: - - Mutations in the soybean 3-ketoacyl-ACP synthase gene are correlated with high levels of seed palmitic acid -phenotype_synopsis: Palmitic acid levels were significantly higher in the mutants than in the Williams-82 wild type control + - Overexpression of GmAKT2 in transgenic SMV-susceptible soy plants increases resistance to SMV relative to WT +phenotype_synopsis: GmAKT2 increases a soy plant's resistance to SMV by affecting distribution of potassium ions in the leaves. traits: - - entity_name: beta-ketoacyl-acyl-carrier-protein synthase II activity - entity: GO:0033817 + - entity_name: soybean mosaic virus + entity: NCBITaxon:12222 + - entity_name: viral disease resistance + entity: TO:0000148 + - entity_name: mineral and ion transportation + entity: TO:0020096 + - entity_name: postassium ion concentration + entity: TO:0000513 references: - - citation: Head, Katie et al., 2012 - doi: 10.1007/s11032-012-9707-x - pmid: null + - citation: Zhou, He et al., 2014 + doi: 10.1186/1471-2229-14-154 + pmid: 24893844 -## DOCUMENT 61 ## +## DOCUMENT 130 ## --- +scientific_name: Glycine max gene_symbols: - - KASII-B -gene_symbol_long: plastid 3-keto-acyl-ACP synthase II-B -gene_model_pub_name: Glyma13g17290 -gene_model_full_id: glyma.Wm82.gnm1.ann1.Glyma13g17290 + - GmFATA1a +gene_symbol_long: Fatty Acid Thioesterase A1a +gene_model_pub_name: Glyma18g36130 +gene_model_full_id: glyma.Wm82.gnm1.ann1.Glyma18g36130 confidence: 3 curators: - - Wei Huang -phenotype_synopsis: Palmitic acid levels were significantly higher in the mutants than in the Williams-82 wild type control + - Marlene Dorneich-Hayes +comments: + - Researchers studied the phenotypes of loss-of-function mutants and compared them to WT plants. + - GmFATA1a loss-of-function mutatants accumulate high concentrations of oleic acid in their seeds. +phenotype_synopsis: GmFATA1a is an acyl-acyl carrier protein thioesterase that hydrolizes 18:1 acyl-acyl carrier proteins. traits: - - entity_name: beta-ketoacyl-acyl-carrier-protein synthase II activity - entity: GO:0033817 + - entity_name: lipid metabolic process + entity: GO:0006629 + - entity_name: regulation of triglyceride biosynthetic process + entity: GO:0010866 + - entity_name: fat and essential oil content + entity: TO:0000604 + - entity_name: seed development + entity: GO:0048316 references: - - citation: Head, Katie et al., 2012 - doi: 10.1007/s11032-012-9707-x - pmid: null + - citation: Zhou, Lakhssassi et. al., 2021 + doi: 10.1007/s00122-021-03917-9 + pmid: 34319424 + - citation: Zuo, Ikram et. al., 2022 + doi: 10.1016/j.csbj.2022.06.014 + pmid: 35782726 -## DOCUMENT 62 ## +## DOCUMENT 131 ## --- +scientific_name: Glycine max +classical_locus: fap3 gene_symbols: - - MYB176 -gene_symbol_long: GmMYB176 -gene_model_pub_name: Glyma.05g032200 -gene_model_full_id: glyma.Wm82.gnm4.ann1.Glyma.05g032200 + - GmFATB1a +gene_symbol_long: Fatty Acid Thioesterase B1a +gene_model_pub_name: Glyma05G012300 +gene_model_full_id: glyma.Wm82.gnm2.ann1.Glyma.05G012300 confidence: 4 curators: - - Wei Huang + - Marlene Dorneich-Hayes comments: - - A combinatorial action of GmMYB176 and GmbZIP5 controls isoflavonoid biosynthesis in soybean (Glycine max) -phenotype_synopsis: GmMYB176 regulates multiple genes in the isoflavonoid biosynthetic pathway, thereby affecting their levels in soybean roots. + - CRISPR-Cas9 knockout study on genes identified in other species. + - FATB1a knockouts have low palmitic and stearic acid but high oleic and linoleic acid. + - FATB1a It is most strongly expressed in seeds and leaves. +phenotype_synopsis: FATB1a codes for an enzyme that hydrolizes saturated acyl-ACPs. traits: - - entity_name: isoflavonoid biosynthetic process - entity: GO:0009717 - - entity_name: isoflavonoid phytoalexin metabolic process - entity: GO:0046289 + - entity_name: lipid metabolic process + entity: GO:0006629 + - entity_name: regulation of triglyceride biosynthetic process + entity: GO:0010866 + - entity_name: fat and essential oil content + entity: TO:0000604 + - entity_name: seed development + entity: GO:0048316 references: - - citation: Vadivel, Anguraj AK et al., 2021 - doi: 10.1038/s42003-021-01889-6 - pmid: 33742087 - - citation: Yi, Jinxin et al., 2010 - doi: 10.1111/j.1365-313x.2010.04214.x - pmid: 20345602 + - citation: Zhou, Lakhssassi et. al., 2021 + doi: 10.1007/s00122-021-03917-9 + pmid: 34319424 + - citation: Ma, Sun et. al., 2021 + doi: 10.3390/ijms22083877 + pmid: 33918544 -## DOCUMENT 63 ## +## DOCUMENT 132 ## --- +scientific_name: Glycine max gene_symbols: - - bzip5 -gene_symbol_long: GmbZIP5 -gene_model_pub_name: Glyma.15g014800 -gene_model_full_id: glyma.Wm82.gnm4.ann1.Glyma.15g014800 + - GmFATB1b +gene_symbol_long: Fatty Acid Thioesterase B1b +gene_model_pub_name: Glyma.17G120400 +gene_model_full_id: glyma.Wm82.gnm2.ann1.Glyma.17G120400 confidence: 4 curators: - - Wei Huang -phenotype_synopsis: RNAi silencing of GmbZIP5 reduced the isoflavonoid level in soybean hairy roots. + - Marlene Dorneich-Hayes +comments: + - CRISPR-Cas9 knockout study on genes identified in other species. + - FATB1b knockouts have low palmitic and stearic acid but high oleic and linoleic acid. + - FATB1b is most strongly expressed in seeds and leaves. +phenotype_synopsis: FATB1b codes for an enzyme that hydrolizes saturated acyl-ACPs. traits: - - entity_name: isoflavonoid biosynthetic process - entity: GO:0009717 - - entity_name: isoflavonoid phytoalexin metabolic process - entity: GO:0046289 + - entity_name: lipid metabolic process + entity: GO:0006629 + - entity_name: regulation of triglyceride biosynthetic process + entity: GO:0010866 + - entity_name: fat and essential oil content + entity: TO:0000604 + - entity_name: seed development + entity: GO:0048316 references: - - citation: Vadivel, Anguraj AK et al., 2021 - doi: 10.1038/s42003-021-01889-6 - pmid: 33742087 + - citation: Zhou, Lakhssassi et. al., 2021 + doi: 10.1007/s00122-021-03917-9 + pmid: 34319424 + - citation: Ma, Sun et. al., 2021 + doi: 10.3390/ijms22083877 + pmid: 33918544 + - citation: Zuo, Ikram et. al., 2022 + doi: 10.1016/j.csbj.2022.06.014 + pmid: 35782726 +## DOCUMENT 133 ## +--- +scientific_name: Glycine max +gene_symbols: + - GmFATB2b +gene_symbol_long: Fatty Acid Thioesterase B2b +gene_model_pub_name: Glyma06g23560 +gene_model_full_id: glyma.Wm82.gnm1.ann1.Glyma06g23560 +confidence: 3 +curators: + - Marlene Dorneich-Hayes +comments: + - Researchers studied the phenotypes of loss-of-function mutants and compared them to WT plants. + - FATB2b knockouts have low palmitic acid but high oleic acid. + - FATB2b is most strongly expressed in flowers. +phenotype_synopsis: FATB2b codes for an enzyme that hydrolizes saturated acyl-ACPs. +traits: + - entity_name: lipid metabolic process + entity: GO:0006629 + - entity_name: regulation of triglyceride biosynthetic process + entity: GO:0010866 + - entity_name: fat and essential oil content + entity: TO:0000604 + - entity_name: seed development + entity: GO:0048316 +references: + - citation: Zhou, Lakhssassi et. al., 2021 + doi: 10.1007/s00122-021-03917-9 + pmid: 34319424 + - citation: Zuo, Ikram et. al., 2022 + doi: 10.1016/j.csbj.2022.06.014 + pmid: 35782726 + + +## DOCUMENT 134 ## +--- +scientific_name: Glycine max +gene_symbols: + - GmSPX5 +gene_symbol_long: SYG1/Pho81/Xpr1 5 +gene_model_pub_name: Glyma10g40820 +gene_model_full_id: glyma.Wm82.gnm1.ann1.Glyma10g40820 +confidence: 5 +curators: + - Marlene Dorneich-Hayes +comments: + - SPX5 is most strongly expressed in nodules. + - Phosphate deficiency promotes expression of SPX5 in nodules but decreases SPX5 expression in roots. Nitrogen deficiency decreased SPX5 expression in roots. + - SPX5 is upregulated by arbuscular mycorrhizal fungal infection in phosphate-deficient conditions. + - SPX5 promotes binding of NF-YC4 to the promoter of ASL6, increasing expression of ASL6 during nodule development. +phenotype_synopsis: SPX5 upregulates ASL genes to positively regulate nodule number. Unlike other SPX genes, SPX5 does not affect expression of PHR genes. +traits: + - entity_name: regulation of biological process involved in symbiotic interaction + entity: GO:0043903 + - entity_name: nodulation + entity: GO:0009877 + - relation_name: positively regulates + relation: RO:0002213 +references: + - citation: Zhuang, Xue et. al., 2021 + doi: 10.1111/tpj.15520 + pmid: 34587329 + - citation: Yao, Tian et. al., 2014 + doi: 10.1093/aob/mcu147 + pmid: 25074550 + - citation: Yang, Lan et. al., 2022 + doi: 10.1111/jipb.13207 + pmid: 34962095 + + +## DOCUMENT 135 ## +--- +scientific_name: Glycine max +gene_symbols: + - GmNF-YC4 +gene_symbol_long: Nuclear Factor Y subunit C4 +gene_model_pub_name: Glyma06g17780 +gene_model_full_id: glyma.Wm82.gnm1.ann1.Glyma06g17780 +confidence: 4 +curators: + - Marlene Dorneich-Hayes +comments: + - NF-YC4 positively regulates nodule number and nitrogenase activity. + - SPX5 promotes binding of NF-YC4 to the promoter of ASL6, increasing expression of ASL6 during nodule development. +phenotype_synopsis: NF-YC4 is a transcription factor which upregulates ASL genes to positively regulate nodule number. +traits: + - entity_name: DNA-binding transcription factor activity + entity: GO:0003700 + - entity_name: regulation of biological process involved in symbiotic interaction + entity: GO:0043903 + - entity_name: nodulation + entity: GO:0009877 + - relation_name: positively regulates + relation: RO:0002213 +references: + - citation: Zhuang, Xue et. al., 2021 + doi: 10.1111/tpj.15520 + pmid: 34587329 + - citation: Yang, Lan et. al., 2022 + doi: 10.1111/jipb.13207 + pmid: 34962095 + diff --git a/Glycine/soja/gene_functions/glyso.citations.txt b/Glycine/soja/gene_functions/glyso.citations.txt new file mode 100644 index 0000000..8485cc5 --- /dev/null +++ b/Glycine/soja/gene_functions/glyso.citations.txt @@ -0,0 +1,2 @@ +10.1111/pbi.13536 33368860 PMC8196659 Jin, Sun et al., 2021 "Jin T, Sun Y, Shan Z, He J, Wang N, Gai J, Li Y. Natural variation in the promoter of GsERD15B affects salt tolerance in soybean. Plant Biotechnol J. 2021 Jun;19(6):1155-1169. doi: 10.1111/pbi.13536. Epub 2021 Jan 19. PMID: 33368860; PMCID: PMC8196659." +10.1038/ncomms5340 25004933 PMC4104456 Qi, Li et al., 2014 "Qi X, Li MW, Xie M, Liu X, Ni M, Shao G, Song C, Kay-Yuen Yim A, Tao Y, Wong FL, Isobe S, Wong CF, Wong KS, Xu C, Li C, Wang Y, Guan R, Sun F, Fan G, Xiao Z, Zhou F, Phang TH, Liu X, Tong SW, Chan TF, Yiu SM, Tabata S, Wang J, Xu X, Lam HM. Identification of a novel salt tolerance gene in wild soybean by whole-genome sequencing. Nat Commun. 2014 Jul 9;5:4340. doi: 10.1038/ncomms5340. PMID: 25004933; PMCID: PMC4104456." diff --git a/Glycine/soja/gene_functions/glyso.traits.yml b/Glycine/soja/gene_functions/glyso.traits.yml new file mode 100644 index 0000000..1275914 --- /dev/null +++ b/Glycine/soja/gene_functions/glyso.traits.yml @@ -0,0 +1,60 @@ +## DOCUMENT 1 ## +--- +scientific_name: Glycine soja +gene_symbols: + - GsERD15B +gene_symbol_long: Early Responsive to Dehydration 15B +gene_model_pub_name: XP_028191281.1 +gene_model_full_id: glyso.PI483463.gnm1.ann1.GlysoPI483463.11G164100 +confidence: 4 +curators: + - Greg Murrell + - Steven Cannon + - Scott Kalberer +comments: + - A seven-base pair deletion in the GsERD15B promoter was discovered in the majority (42) of the 48 wild Glycine soja accessions with enhanced salt tolerance. + - Increased expression of GsERD15B in response to salt stress was associated with up-regulation of two GmPAB genes (GmPAB-14G and GmPAB-17G) and known stress-related genes including ABA-related genes (GmABI1, GmABI2, GmbZIP1), a proline synthesis-related gene (GmP5CS), a catalase peroxidase gene (GmCAT4), water loss-related genes (GmPIP1:6, GmMYB84), and an ion exchanger encoding gene (GmSOS1). + - GsERD15B overexpression enhanced the promoter activities of GmABI2, GmP5CS and GmbZIP1 in tobacco leaf assays. + - GsERD15B encodes an ERD15 protein with transcriptional activation function. The ERD15 contains a conserved PAM2 domain in the N-terminus that mediates its interaction with the PABC domain of poly(A)-binding (PAB) proteins. +phenotype_summary: Gene overexpression in Glycine enhanced salt tolerance probably by increasing the expression levels of genes related to ABA-signalling, proline content, catalase peroxidase, dehydration response and cation transport. +traits: + - entity_name: salt tolerance + entity: TO:0006001 + - relation_name: positively regulates + relation: RO:0002213 +references: + - citation: Jin, Sun et al., 2021 + doi: 10.1111/pbi.13536 + pmid: 33368860 + + +## DOCUMENT 2 ## +--- +scientific_name: Glycine soja +gene_symbols: + - GmCHX1 +gene_symbol_long: cation/H(+) antiporter 1 +gene_model_pub_name: Glysoja01g005509 +gene_model_full_id: glyso.PI483463.gnm1.ann1.GlysoPI483463.03G135400 +confidence: 4 +comments: + - Gene Glysoja01g005509 is newly sequenced from Glycine soja W05 and is not in the annotation glyso.W05.gnm1.ann1. + - The newly named gene Glysoja01g005509 has a different format than others in that annotation, which have a dot, e.g. Glysoja.01G001001 + - The gene GmCHX1 is associated with salt tolerance in Glycine soja W05 + - The gene glyso.PI483463.gnm1.ann1.GlysoPI483463.03G135400 has a full-length 100% match with the reported Glysoja01g005509 + - The reported sequence is >KF879911.1 Glycine soja CHX1 mRNA, complete cds ATGACGTTCAACGCGAGCACCATCACAACGGCGTCGGAAGGAGCCTGGCAGGGCGATAATCCCCTGAACC ACGCTCTTCCTTTGTTGATCGTTCAAACCATCCTCGTAGTCTTCGTGAGCCGCACACTCGCCTTTCTCCT CAAACCCTTTCGTCAACCTAAAGTTGTCGCCGAGATTATTGGTGGAATTTTGTTGGGGCCTTCTGCTATT GGGCGCAACAAGAAATTCATGCACATAGTGTTCCCAGCATGGAGCACTACCATGCTGGAATCAGTGGCAA GCTTCGGCCTCTTATTCTATCTATTTCTGGTGGGCCTAGAGCTCGACTTTCGCACCATTCGCCGGAGCGG CAAGCAAGCCTTCAACATCGCGGTGGCCGGAATAACCCTCCCCTTCATCTGCGCCGTGGGAGTAACGTTC CTTCTCCAGAGAGCCATCCGCTCTGAAAACCATAACATAGGGTACGTTCAGCACTTCGTGTTCTTAGGGG TATCTCTGTCCATCACGGCTTTCCCTGTGCTCGCGCGCATCTTAGCGGAGCTCAAACTGCTGACCACACG TGTGGGAGAAACCGCCATGGCGGCTGCAGCCTTCAACGACGTCGCTGCGTGGGTTTTGTTGGCCTTGGCG GTGGCTTTGGCTGGCCAGGGACACAAAAGCAGCTTGTTGACATCAATATGGGTGCTCTTCTCAGGGATGG CGTTTGTTGCAGCCATGATGATCCTGGTTCGACCGGTGATGAACCGTGTTGCTCGCAAGTGTTCTCACGA ACAAGACGTGTTACCCGAAATCTACATATGTTTAACTCTAGCGGGAGTAATGTTATCGGGGTTAGTGACA GACATGATAGGGTTACATTCAATTTTCGGGGGATTTGTTTTCGGGCTAACGATACCGAAAGGTGGCGAAT TTGCAAATAGAATGACGAGGAGGATTGAGGACTTCGTGTCCACGTTGTTCCTTCCCTTGTACTTTGCTGC CAGTGGTTTGAAAACTGACGTGACTAAGTTACGAAGCGTGGTGGATTGGGGGCTTCTTTTGCTGGTTACG TCCACCGCGAGCGTGGGGAAGATTTTGGGAACGTTTGCGGTGGCGATGATGTGCATGGTGCCGGTGAGAG AATCCTTGACGCTTGGAGTGTTAATGAACACCAAAGGGTTGGTGGAGCTAATCGTTCTCAATATTGGCAG AGAGAAGAAGGTGCTTAACGACGAGATGTTTACCATCCTAGTACTCATGGCTCTCTTCACCACCTTCATT ACAACTCCAATAGTCTTGGCCATATACAAACCCTCTCGTATAGTAAACTCCGGTTCGCAAAAACCGTCGC GGCTAACAGATTTGCAAGAGAAGCTTCGCATTCTTGCGTGCATCCATGGACCTGGCAACATACCCTCACT AATCAACTTCGTTGAATCAATTCGGGCCACCAACATGTCACGACTCAAACTCTACGTGATGCAACTTACC GAACTCACTGATAGCTCTTCCTCCATCTTGATGGTTCAACGCAGTCGAAAGAATGGTTTTCCCTTCATCA ACCGAATGAAGAGTGGACCAATGCATGAGCAAATTGCCACAGCATTCCAGGCTTATGGTGAAGTGGGTAA AGTTACTGTGCATCATTTAACATCTATCTCTCTATTGTCAACAATGCACGAGGACATATGCCACGTTGCA GAAAAGAAAGGTGTGGCAATGATTATATTGCCCTTCCACAAAAGGTGGGGAGGGGAAGATGAAGAGGTGA CAGAAGACTTAGGGCAGGGTTTGAGGGAAGTCAATCAAAGGGTGCTTCAAAATGCAGCCTGCTCTGTCGC AGTGCTAGTCAATCGTGGGGTTGCCAGAAGGTACGAACAAGAACCTGAGACAAGTGTTGCTGCAAGGAAA AGAGTGTGCATAATTTTCATTGGTGGACCACATGATCGCAAGGTTTTGGAGTTAGGTAGCAGAATGGCAG AGCATCCAGCAATTAGGTTGCTTTTAGTGAGATTCACTTCATACACAGAAGTTGGGGACGAGGGACCCAA ATATAACTCACCAACATCAACCACCAACTGGGAAAAAGAAAAGGAGTTGGATGAGGAAGCAGTAAACGAG TTCAAGGTTAAATGGCAGGAGACTGTGGAGTACATTGAAAAGAACGCAACCAACATAACAGAGGAGGTGT TATCAATTGGGAAAGCTAAGGATCACGACCTAGTAATTGTGGGGAAGCAACAACTTGAGACAACCATGTT GACAAACATAGATTTTCGTCACGGGAATGAAGAGCTGGGACCCATTGGAGATCTCTTTGTCTCTTCGGGT AACGGCATTACCAGTTCATTGCTCGTTATACAGGACCGATATTTTATAAATTCAAACGAAAGTAATCTCG TTAAGACATCAAGGGCCGAGAGTACTGTGATTAAAGATGCTATCGAAGAACTTTAA + - Protein product >AIG92838.1 CHX1 [Glycine soja] MTFNASTITTASEGAWQGDNPLNHALPLLIVQTILVVFVSRTLAFLLKPFRQPKVVAEIIGGILLGPSAI GRNKKFMHIVFPAWSTTMLESVASFGLLFYLFLVGLELDFRTIRRSGKQAFNIAVAGITLPFICAVGVTF LLQRAIRSENHNIGYVQHFVFLGVSLSITAFPVLARILAELKLLTTRVGETAMAAAAFNDVAAWVLLALA VALAGQGHKSSLLTSIWVLFSGMAFVAAMMILVRPVMNRVARKCSHEQDVLPEIYICLTLAGVMLSGLVT DMIGLHSIFGGFVFGLTIPKGGEFANRMTRRIEDFVSTLFLPLYFAASGLKTDVTKLRSVVDWGLLLLVT STASVGKILGTFAVAMMCMVPVRESLTLGVLMNTKGLVELIVLNIGREKKVLNDEMFTILVLMALFTTFI TTPIVLAIYKPSRIVNSGSQKPSRLTDLQEKLRILACIHGPGNIPSLINFVESIRATNMSRLKLYVMQLT ELTDSSSSILMVQRSRKNGFPFINRMKSGPMHEQIATAFQAYGEVGKVTVHHLTSISLLSTMHEDICHVA EKKGVAMIILPFHKRWGGEDEEVTEDLGQGLREVNQRVLQNAACSVAVLVNRGVARRYEQEPETSVAARK RVCIIFIGGPHDRKVLELGSRMAEHPAIRLLLVRFTSYTEVGDEGPKYNSPTSTTNWEKEKELDEEAVNE FKVKWQETVEYIEKNATNITEEVLSIGKAKDHDLVIVGKQQLETTMLTNIDFRHGNEELGPIGDLFVSSG NGITSSLLVIQDRYFINSNESNLVKTSRAESTVIKDAIEEL +curators: + - Greg Murrell, Steven Cannon +phenotype_summary: Raises salt tolerance. +traits: + - entity_name: salt tolerance + entity: TO:0006001 + - relation_name: positively regulates + relation: RO:0002213 +references: + - citation: Qi, Li et al., 2014 + doi: 10.1038/ncomms5340 + pmid: 25004933 + + diff --git a/Lotus/japonicus/gene_functions/lotja.citations.txt b/Lotus/japonicus/gene_functions/lotja.citations.txt new file mode 100644 index 0000000..0299db3 --- /dev/null +++ b/Lotus/japonicus/gene_functions/lotja.citations.txt @@ -0,0 +1,4 @@ +10.1093/pcp/pcu168 25416287 null Soyano, Shimoda et al., 2015 "Soyano T, Shimoda Y, Hayashi M. NODULE INCEPTION antagonistically regulates gene expression with nitrate in Lotus japonicus. Plant Cell Physiol. 2015 Feb;56(2):368-76. doi: 10.1093/pcp/pcu168. Epub 2014 Nov 20. PMID: 25416287." +10.1104/pp.113.233379 24722550 PMC4043699 Yoro, Suzaki et al., 2014 "Yoro E, Suzaki T, Toyokura K, Miyazawa H, Fukaki H, Kawaguchi M. A Positive Regulator of Nodule Organogenesis, NODULE INCEPTION, Acts as a Negative Regulator of Rhizobial Infection in Lotus japonicus. Plant Physiol. 2014 Jun;165(2):747-758. doi: 10.1104/pp.113.233379. Epub 2014 Apr 10. PMID: 24722550; PMCID: PMC4043699." +10.1073/pnas.1412716111 25246578 PMC4210044 Soyano, Hirakawa et al., 2014 "Soyano T, Hirakawa H, Sato S, Hayashi M, Kawaguchi M. Nodule Inception creates a long-distance negative feedback loop involved in homeostatic regulation of nodule organ production. Proc Natl Acad Sci U S A. 2014 Oct 7;111(40):14607-12. doi: 10.1073/pnas.1412716111. Epub 2014 Sep 22. PMID: 25246578; PMCID: PMC4210044." +10.1093/plcell/koab103 33826745 PMC8364233 Nishida, Nosaki et al., 2021 "" diff --git a/Lotus/japonicus/gene_functions/lotja.traits.yml b/Lotus/japonicus/gene_functions/lotja.traits.yml new file mode 100644 index 0000000..1957fe5 --- /dev/null +++ b/Lotus/japonicus/gene_functions/lotja.traits.yml @@ -0,0 +1,41 @@ +## DOCUMENT 1 ## +--- +scientific_name: Lotus japonicus +gene_symbols: + - LjNIN +gene_symbol_long: Nodule Inception +gene_model_pub_name: Lj2G3V3373110 +gene_model_full_id: lotja.MG20.gnm3.ann1.Lj2G3V3373110 +confidence: 4 +curators: + - Marlene Dorneich-Hayes + - Scott Kalberer +comments: + - Ectopic expression of Nodule Inception (LjNIN) produces nodule-like structures from the roots regardless of lack of rhizobia. Constitutive expression of NIN eventually leads to suppression of native NIN transcription in untransformed roots of the plant via effects on HAR1 receptor protein. The result is reduced nodulation and down-regulation of CLE-RS signal peptide expression. + - NIN codes for a transcription factor containing the RWP-RK domain that induces nodule primordia formation by promoting cortical cell division. + - NIN activates genes coding for the NIN-repressing signal proteins, Clavata3/Endosperm Surrounding Region Root Signal 1 (CLE-RS1) and CLE-RS2, that are expressed in the roots and travel long-distance to ultimately stop nodulation. They are perceived in the shoot by Hypernodulation Aberrant Root Formation 1 (HAR1) receptor proteins. +phenotype_synopsis: LjNIN is part of an autoregulatory negative feedback loop in Lotus japonicus that maintains healthy numbers of nodules containing nitrogen-fixing rhizobia. NIN positively regulates rhizobium infection by inducing the genes necessary to establish the symbiosis when nitrate is limited. +traits: + - entity_name: regulation of biological process involved in symbiotic interaction + entity: GO:0043903 + - relation_name: negatively regulates + relation: RO:0002212 + - entity_name: nodulation + entity: GO:0009877 + - relation_name: positively regulates + relation: RO:0002213 +references: + - citation: Soyano, Hirakawa et al., 2014 + doi: 10.1073/pnas.1412716111 + pmid: 25246578 + - citation: Soyano, Shimoda et al., 2015 + doi: 10.1093/pcp/pcu168 + pmid: 25416287 + - citation: Yoro, Suzaki et al., 2014 + doi: 10.1104/pp.113.233379 + pmid: 24722550 + - citation: Nishida, Nosaki et al., 2021 + doi: 10.1093/plcell/koab103 + pmid: 33826745 + + diff --git a/Medicago/truncatula/gene_functions/medtr.citations.txt b/Medicago/truncatula/gene_functions/medtr.citations.txt index 2f2a1fc..c844677 100644 --- a/Medicago/truncatula/gene_functions/medtr.citations.txt +++ b/Medicago/truncatula/gene_functions/medtr.citations.txt @@ -1,31 +1,34 @@ -10.1105/tpc.105.035394 16199614 PMC1276019 Ivashuta, Liu, et al., 2005 "Ivashuta S, Liu J, Liu J, Lohar DP, Haridas S, Bucciarelli B, VandenBosch KA, Vance CP, Harrison MJ, Gantt JS. RNA interference identifies a calcium-dependent protein kinase involved in Medicago truncatula root development. Plant Cell. 2005 Nov;17(11):2911-21. doi: 10.1105/tpc.105.035394. Epub 2005 Sep 30. PMID: 16199614; PMCID: PMC1276019." -10.1111/j.1469-8137.2011.03718.x 21679315 PMC3206218 Godiard, Lepage, et al., 2011 "Godiard L, Lepage A, Moreau S, Laporte D, Verdenaud M, Timmers T, Gamas P. MtbHLH1, a bHLH transcription factor involved in Medicago truncatula nodule vascular patterning and nodule to plant metabolic exchanges. New Phytol. 2011 Jul;191(2):391-404. doi: 10.1111/j.1469-8137.2011.03718.x. Epub 2011 Jun 17. PMID: 21679315; PMCID: PMC3206218." -10.1111/j.1365-313x.2009.04072.x 19912567 null Pumplin, Mondo, et al., 2009 "Pumplin N, Mondo SJ, Topp S, Starker CG, Gantt JS, Harrison MJ. Medicago truncatula Vapyrin is a novel protein required for arbuscular mycorrhizal symbiosis. Plant J. 2010 Feb 1;61(3):482-94. doi: 10.1111/j.1365-313X.2009.04072.x. Epub 2009 Nov 14. PMID: 19912567." -10.1105/tpc.15.00476 26410301 PMC4682322 Jun, Liu, et al., 2015 "Jun JH, Liu C, Xiao X, Dixon RA. The Transcriptional Repressor MYB2 Regulates Both Spatial and Temporal Patterns of Proanthocyandin and Anthocyanin Pigmentation in Medicago truncatula. Plant Cell. 2015 Oct;27(10):2860-79. doi: 10.1105/tpc.15.00476. Epub 2015 Sep 26. PMID: 26410301; PMCID: PMC4682322." -10.1104/pp.111.180182 21685176 PMC3149922 Laurie, Diwadkar, et al., 2011 "Laurie RE, Diwadkar P, Jaudal M, Zhang L, Hecht V, Wen J, Tadege M, Mysore KS, Putterill J, Weller JL, Macknight RC. The Medicago FLOWERING LOCUS T homolog, MtFTa1, is a key regulator of flowering time. Plant Physiol. 2011 Aug;156(4):2207-24. doi: 10.1104/pp.111.180182. Epub 2011 Jun 17. PMID: 21685176; PMCID: PMC3149922." -10.1094/mpmi-06-10-0144 20731530 null Miyahara, Richens, et al., 2010 "Miyahara A, Richens J, Starker C, Morieri G, Smith L, Long S, Downie JA, Oldroyd GE. Conservation in function of a SCAR/WAVE component during infection thread and root hair growth in Medicago truncatula. Mol Plant Microbe Interact. 2010 Dec;23(12):1553-62. doi: 10.1094/MPMI-06-10-0144. PMID: 20731530." -10.1111/j.1365-313x.2006.02910.x 17132148 null Gargantini, Gonzalez-Rizzo, et al., 2006 "Gargantini PR, Gonzalez-Rizzo S, Chinchilla D, Raices M, Giammaria V, Ulloa RM, Frugier F, Crespi MD. A CDPK isoform participates in the regulation of nodule number in Medicago truncatula. Plant J. 2006 Dec;48(6):843-56. doi: 10.1111/j.1365-313X.2006.02910.x. Epub 2006 Nov 21. PMID: 17132148." -10.1105/tpc.019406 15037734 PMC412876 Campalans, Kondorosi, et al., 2017 "Campalans A, Kondorosi A, Crespi M. Enod40, a short open reading frame-containing mRNA, induces cytoplasmic localization of a nuclear RNA binding protein in Medicago truncatula. Plant Cell. 2004 Apr;16(4):1047-59. doi: 10.1105/tpc.019406. Epub 2004 Mar 22. Erratum in: Plant Cell. 2017 Apr;29(4):912. PMID: 15037734; PMCID: PMC412876." -10.1073/pnas.0400595101 15070781 PMC384810 Mitra, Gleason, et al., 2004 "Mitra RM, Gleason CA, Edwards A, Hadfield J, Downie JA, Oldroyd GE, Long SR. A Ca2+/calmodulin-dependent protein kinase required for symbiotic nodule development: Gene identification by transcript-based cloning. Proc Natl Acad Sci U S A. 2004 Mar 30;101(13):4701-5. doi: 10.1073/pnas.0400595101. Epub 2004 Mar 1. PMID: 15070781; PMCID: PMC384810." -10.1104/pp.105.069054 16244141 PMC1283775 Isayenkov, Mrosk, et al., 2005 "Isayenkov S, Mrosk C, Stenzel I, Strack D, Hause B. Suppression of allene oxide cyclase in hairy roots of Medicago truncatula reduces jasmonate levels and the degree of mycorrhization with Glomus intraradices. Plant Physiol. 2005 Nov;139(3):1401-10. doi: 10.1104/pp.105.069054. Epub 2005 Oct 21. PMID: 16244141; PMCID: PMC1283775." -10.1093/jxb/erw474 28073951 PMC6055581 Herrbach, Chirinos, et al., 2017 "Herrbach V, Chirinos X, Rengel D, Agbevenou K, Vincent R, Pateyron S, Huguet S, Balzergue S, Pasha A, Provart N, Gough C, Bensmihen S. Nod factors potentiate auxin signaling for transcriptional regulation and lateral root formation in Medicago truncatula. J Exp Bot. 2017 Jan 1;68(3):569-583. doi: 10.1093/jxb/erw474. PMID: 28073951; PMCID: PMC6055581." -10.7554/elife.80741 36856086 PMC9991063 Lace, Su, et al., 2023 "Lace B, Su C, Invernot Perez D, Rodriguez-Franco M, Vernié T, Batzenschlager M, Egli S, Liu CW, Ott T. RPG acts as a central determinant for infectosome formation and cellular polarization during intracellular rhizobial infections. Elife. 2023 Mar 1;12:e80741. doi: 10.7554/eLife.80741. PMID: 36856086; PMCID: PMC9991063." -10.1104/pp.109.143024 19789288 PMC2773094 Kuppusamy, Ivashuta, et al., 2009 "Kuppusamy KT, Ivashuta S, Bucciarelli B, Vance CP, Gantt JS, Vandenbosch KA. Knockdown of CELL DIVISION CYCLE16 reveals an inverse relationship between lateral root and nodule numbers and a link to auxin in Medicago truncatula. Plant Physiol. 2009 Nov;151(3):1155-66. doi: 10.1104/pp.109.143024. Epub 2009 Sep 29. PMID: 19789288; PMCID: PMC2773094." -10.1105/tpc.107.053975 18156218 PMC2217646 Kevei, Lougnon, et al., 2007 "Kevei Z, Lougnon G, Mergaert P, Horváth GV, Kereszt A, Jayaraman D, Zaman N, Marcel F, Regulski K, Kiss GB, Kondorosi A, Endre G, Kondorosi E, Ané JM. 3-hydroxy-3-methylglutaryl coenzyme a reductase 1 interacts with NORK and is crucial for nodulation in Medicago truncatula. Plant Cell. 2007 Dec;19(12):3974-89. doi: 10.1105/tpc.107.053975. Epub 2007 Dec 21. PMID: 18156218; PMCID: PMC2217646." +10.1093/plphys/kiaa005 33631796 PMC8133602 Cheng, Li et al., 2021 "Cheng X, Li G, Krom N, Tang Y, Wen J. Genetic regulation of flowering time and inflorescence architecture by MtFDa and MtFTa1 in Medicago truncatula. Plant Physiol. 2021 Feb 25;185(1):161-178. doi: 10.1093/plphys/kiaa005. PMID: 33631796; PMCID: PMC8133602." +10.1111/j.1365-313x.2006.02910.x 17132148 null Gargantini, Gonzalez-Rizzo et al., 2006 "Gargantini PR, Gonzalez-Rizzo S, Chinchilla D, Raices M, Giammaria V, Ulloa RM, Frugier F, Crespi MD. A CDPK isoform participates in the regulation of nodule number in Medicago truncatula. Plant J. 2006 Dec;48(6):843-56. doi: 10.1111/j.1365-313X.2006.02910.x. Epub 2006 Nov 21. PMID: 17132148." +10.1105/tpc.107.053975 18156218 PMC2217646 Kevei, Lougnon et al., 2007 "Kevei Z, Lougnon G, Mergaert P, Horváth GV, Kereszt A, Jayaraman D, Zaman N, Marcel F, Regulski K, Kiss GB, Kondorosi A, Endre G, Kondorosi E, Ané JM. 3-hydroxy-3-methylglutaryl coenzyme a reductase 1 interacts with NORK and is crucial for nodulation in Medicago truncatula. Plant Cell. 2007 Dec;19(12):3974-89. doi: 10.1105/tpc.107.053975. Epub 2007 Dec 21. PMID: 18156218; PMCID: PMC2217646." +10.1105/tpc.15.00461 26672071 PMC4707452 Vernie, Kim et al., 2015 "" +10.1094/mpmi-06-10-0144 20731530 null Miyahara, Richens et al., 2010 "" +10.1111/j.1365-313x.2009.04072.x 19912567 null Pumplin, Mondo et al., 2009 "" +10.7554/elife.80741 36856086 PMC9991063 Lace, Su et al., 2023 "" +10.1073/pnas.0400595101 15070781 PMC384810 Mitra, Gleason et al., 2004 "Mitra RM, Gleason CA, Edwards A, Hadfield J, Downie JA, Oldroyd GE, Long SR. A Ca2+/calmodulin-dependent protein kinase required for symbiotic nodule development: Gene identification by transcript-based cloning. Proc Natl Acad Sci U S A. 2004 Mar 30;101(13):4701-5. doi: 10.1073/pnas.0400595101. Epub 2004 Mar 1. PMID: 15070781; PMCID: PMC384810." +10.1104/pp.108.125062 18790999 PMC2577242 Floss, Schliemann et al., 2008 "Floss DS, Schliemann W, Schmidt J, Strack D, Walter MH. RNA interference-mediated repression of MtCCD1 in mycorrhizal roots of Medicago truncatula causes accumulation of C27 apocarotenoids, shedding light on the functional role of CCD1. Plant Physiol. 2008 Nov;148(3):1267-82. doi: 10.1104/pp.108.125062. Epub 2008 Sep 12. PMID: 18790999; PMCID: PMC2577242." +10.1186/s12870-020-02619-6 32867687 null Jiao, Wang et al., 2020 "Jiao Z, Wang L, Du H, Wang Y, Wang W, Liu J, Huang J, Huang W, Ge L. Genome-wide study of C2H2 zinc finger gene family in Medicago truncatula. BMC Plant Biol. 2020 Aug 31;20(1):401. doi: 10.1186/s12870-020-02619-6. PMID: 32867687; PMCID: PMC7460785." +10.1111/j.1469-8137.2011.03718.x 21679315 PMC3206218 Godiard, Lepage et al., 2011 "" +10.1105/tpc.105.035394 16199614 PMC1276019 Ivashuta, Liu et al., 2005 "" +10.1104/pp.18.01588 30782966 PMC6501087 Laffont, Huault et al., 2019 "" +10.1111/nph.13162 25406544 null Carelli, Biazzi et al., 2014 "Carelli M, Biazzi E, Tava A, Losini I, Abbruscato P, Depedro C, Scotti C. Sapogenin content variation in Medicago inter-specific hybrid derivatives highlights some aspects of saponin synthesis and control. New Phytol. 2015 Apr;206(1):303-314. doi: 10.1111/nph.13162. Epub 2014 Nov 18. PMID: 25406544." +10.1105/tpc.019406 15037734 PMC412876 Campalans, Kondorosi et al., 2017 "Campalans A, Kondorosi A, Crespi M. Enod40, a short open reading frame-containing mRNA, induces cytoplasmic localization of a nuclear RNA binding protein in Medicago truncatula. Plant Cell. 2004 Apr;16(4):1047-59. doi: 10.1105/tpc.019406. Epub 2004 Mar 22. Erratum in: Plant Cell. 2017 Apr;29(4):912. doi: 10.1105/tpc.17.00245. PMID: 15037734; PMCID: PMC412876." +10.1104/pp.15.00164 25792252 PMC4577373 Weller, Foo et al., 2015 "Weller JL, Foo EM, Hecht V, Ridge S, Vander Schoor JK, Reid JB. Ethylene Signaling Influences Light-Regulated Development in Pea. Plant Physiol. 2015 Sep;169(1):115-24. doi: 10.1104/pp.15.00164. Epub 2015 Mar 19. PMID: 25792252; PMCID: PMC4577373." +10.3389/fpls.2016.00034 26858743 PMC4732000 Qiao, Pingault et al., 2016 "" +10.1104/pp.111.180182 21685176 PMC3149922 Laurie, Diwadkar et al., 2011 "" +10.1105/tpc.15.00476 26410301 PMC4682322 Jun, Liu et al., 2015 "" +10.3389/fpls.2015.00575 26284091 PMC4517396 Chen, Liu et al., 2015 "Chen DS, Liu CW, Roy S, Cousins D, Stacey N, Murray JD. Identification of a core set of rhizobial infection genes using data from single cell-types. Front Plant Sci. 2015 Jul 28;6:575. doi: 10.3389/fpls.2015.00575. PMID: 26284091; PMCID: PMC4517396." +10.1104/pp.105.069054 16244141 PMC1283775 Isayenkov, Mrosk et al., 2005 "Isayenkov S, Mrosk C, Stenzel I, Strack D, Hause B. Suppression of allene oxide cyclase in hairy roots of Medicago truncatula reduces jasmonate levels and the degree of mycorrhization with Glomus intraradices. Plant Physiol. 2005 Nov;139(3):1401-10. doi: 10.1104/pp.105.069054. Epub 2005 Oct 21. PMID: 16244141; PMCID: PMC1283775." +10.1007/s00425-023-04116-0 36928335 PMC10020325 Dvila-Delgado, Flores-Canl, et al., 2023 "Dávila-Delgado R, Flores-Canúl K, Juárez-Verdayes MA, Sánchez-López R. Rhizobia induce SYMRK endocytosis in Phaseolus vulgaris root hair cells. Planta. 2023 Mar 16;257(4):83. doi: 10.1007/s00425-023-04116-0. PMID: 36928335; PMCID: PMC10020325." +10.1038/s41477-018-0286-7 30397259 null Pecrix, Staton et al., 2018 "" +10.1111/nph.12198 23432463 null Rey, Nars et al., 2013 "" +10.1105/tpc.19.00609 32303662 PMC7268793 Ribeiro, Lacchini et al., 2020 "" +10.1094/mpmi.2000.13.7.763 10875337 null Salzer, Bonanomi et al., 2000 "" 10.1186/s13007-015-0053-y 25774204 PMC4359497 Oellrich, Walls et al., 2015 "Oellrich A, Walls RL, Cannon EK, Cannon SB, Cooper L, Gardiner J, Gkoutos GV, Harper L, He M, Hoehndorf R, Jaiswal P, Kalberer SR, Lloyd JP, Meinke D, Menda N, Moore L, Nelson RT, Pujar A, Lawrence CJ, Huala E. An ontology approach to comparative phenomics in plants. Plant Methods. 2015 Feb 25;11:10. doi: 10.1186/s13007-015-0053-y. PMID: 25774204; PMCID: PMC4359497." -10.1111/j.1469-8137.2012.04147.x 22530598 null Cheng, Peng, et al., 2012 "Cheng X, Peng J, Ma J, Tang Y, Chen R, Mysore KS, Wen J. NO APICAL MERISTEM (MtNAM) regulates floral organ identity and lateral organ separation in Medicago truncatula. New Phytol. 2012 Jul;195(1):71-84. doi: 10.1111/j.1469-8137.2012.04147.x. Epub 2012 Apr 24. PMID: 22530598." -10.3389/fpls.2015.00575 26284091 PMC4517396 Chen, Liu, et al., 2015 "Chen DS, Liu CW, Roy S, Cousins D, Stacey N, Murray JD. Identification of a core set of rhizobial infection genes using data from single cell-types. Front Plant Sci. 2015 Jul 28;6:575. doi: 10.3389/fpls.2015.00575. PMID: 26284091; PMCID: PMC4517396." -10.1105/tpc.15.00461 26672071 PMC4707452 Verni, Kim, et al., 2015 "Vernié T, Kim J, Frances L, Ding Y, Sun J, Guan D, Niebel A, Gifford ML, de Carvalho-Niebel F, Oldroyd GE. The NIN Transcription Factor Coordinates Diverse Nodulation Programs in Different Tissues of the Medicago truncatula Root. Plant Cell. 2015 Dec;27(12):3410-24. doi: 10.1105/tpc.15.00461. Epub 2015 Dec 15. PMID: 26672071; PMCID: PMC4707452." -10.1094/mpmi.2000.13.7.763 10875337 null Salzer, Bonanomi, et al., 2000 "Salzer P, Bonanomi A, Beyer K, Vögeli-Lange R, Aeschbacher RA, Lange J, Wiemken A, Kim D, Cook DR, Boller T. Differential expression of eight chitinase genes in Medicago truncatula roots during mycorrhiza formation, nodulation, and pathogen infection. Mol Plant Microbe Interact. 2000 Jul;13(7):763-77. doi: 10.1094/MPMI.2000.13.7.763. PMID: 10875337." -10.1104/pp.108.125062 18790999 PMC2577242 Floss, Schliemann, et al., 2008 "Floss DS, Schliemann W, Schmidt J, Strack D, Walter MH. RNA interference-mediated repression of MtCCD1 in mycorrhizal roots of Medicago truncatula causes accumulation of C27 apocarotenoids, shedding light on the functional role of CCD1. Plant Physiol. 2008 Nov;148(3):1267-82. doi: 10.1104/pp.108.125062. Epub 2008 Sep 12. PMID: 18790999; PMCID: PMC2577242." -10.1073/pnas.2205920119 35972963 PMC9407390 Liu, Lin, et al., 2022 "Liu H, Lin JS, Luo Z, Sun J, Huang X, Yang Y, Xu J, Wang YF, Zhang P, Oldroyd GED, Xie F. Constitutive activation of a nuclear-localized calcium channel complex in Medicago truncatula. Proc Natl Acad Sci U S A. 2022 Aug 23;119(34):e2205920119. doi: 10.1073/pnas.2205920119. Epub 2022 Aug 16. PMID: 35972963; PMCID: PMC9407390." -10.1111/nph.12198 23432463 null Rey, Nars, et al., 2013 "Rey T, Nars A, Bonhomme M, Bottin A, Huguet S, Balzergue S, Jardinaud MF, Bono JJ, Cullimore J, Dumas B, Gough C, Jacquet C. NFP, a LysM protein controlling Nod factor perception, also intervenes in Medicago truncatula resistance to pathogens. New Phytol. 2013 May;198(3):875-886. doi: 10.1111/nph.12198. Epub 2013 Feb 25. PMID: 23432463." -10.1104/pp.18.01588 30782966 PMC6501087 Laffont, Huault, et al., 2019 "Laffont C, Huault E, Gautrat P, Endre G, Kalo P, Bourion V, Duc G, Frugier F. Independent Regulation of Symbiotic Nodulation by the SUNN Negative and CRA2 Positive Systemic Pathways. Plant Physiol. 2019 May;180(1):559-570. doi: 10.1104/pp.18.01588. Epub 2019 Feb 19. PMID: 30782966; PMCID: PMC6501087." -10.3389/fpls.2016.00034 26858743 PMC4732000 Qiao, Pingault, et al., 2016 "Qiao Z, Pingault L, Nourbakhsh-Rey M, Libault M. Comprehensive Comparative Genomic and Transcriptomic Analyses of the Legume Genes Controlling the Nodulation Process. Front Plant Sci. 2016 Jan 29;7:34. doi: 10.3389/fpls.2016.00034. PMID: 26858743; PMCID: PMC4732000." -10.1186/s12870-020-02619-6 32867687 null Jiao, Wang, et al., 2020 "Jiao Z, Wang L, Du H, Wang Y, Wang W, Liu J, Huang J, Huang W, Ge L. Genome-wide study of C2H2 zinc finger gene family in Medicago truncatula. BMC Plant Biol. 2020 Aug 31;20(1):401. doi: 10.1186/s12870-020-02619-6. PMID: 32867687; PMCID: PMC7460785." -10.1038/s41477-018-0286-7 30397259 null Pecrix, Staton, et al., 2018 "Pecrix Y, Staton SE, Sallet E, Lelandais-Brière C, Moreau S, Carrère S, Blein T, Jardinaud MF, Latrasse D, Zouine M, Zahm M, Kreplak J, Mayjonade B, Satgé C, Perez M, Cauet S, Marande W, Chantry-Darmon C, Lopez-Roques C, Bouchez O, Bérard A, Debellé F, Muños S, Bendahmane A, Bergès H, Niebel A, Buitink J, Frugier F, Benhamed M, Crespi M, Gouzy J, Gamas P. Whole-genome landscape of Medicago truncatula symbiotic genes. Nat Plants. 2018 Dec;4(12):1017-1025. doi: 10.1038/s41477-018-0286-7. Epub 2018 Nov 5. PMID: 30397259." -10.1093/plphys/kiaa005 33631796 PMC8133602 Cheng, Li, et al., 2021 "Cheng X, Li G, Krom N, Tang Y, Wen J. Genetic regulation of flowering time and inflorescence architecture by MtFDa and MtFTa1 in Medicago truncatula. Plant Physiol. 2021 Feb 25;185(1):161-178. doi: 10.1093/plphys/kiaa005. PMID: 33631796; PMCID: PMC8133602." -10.1105/tpc.111.089128 22080596 PMC3246329 Peng, Yu, et al., 2011 "Peng J, Yu J, Wang H, Guo Y, Li G, Bai G, Chen R. Regulation of compound leaf development in Medicago truncatula by fused compound leaf1, a class M KNOX gene. Plant Cell. 2011 Nov;23(11):3929-43. doi: 10.1105/tpc.111.089128. Epub 2011 Nov 11. PMID: 22080596; PMCID: PMC3246329." -10.1104/pp.15.00164 25792252 null Weller, Foo, et al., 2015 "Weller JL, Foo EM, Hecht V, Ridge S, Vander Schoor JK, Reid JB. Ethylene Signaling Influences Light-Regulated Development in Pea. Plant Physiol. 2015 Sep;169(1):115-24. doi: 10.1104/pp.15.00164. Epub 2015 Mar 19. PMID: 25792252; PMCID: PMC4577373." -10.1105/tpc.19.00609 32303662 PMC7268793 Ribeiro, Lacchini, et al., 2020 "Ribeiro B, Lacchini E, Bicalho KU, Mertens J, Arendt P, Vanden Bossche R, Calegario G, Gryffroy L, Ceulemans E, Buitink J, Goossens A, Pollier J. A Seed-Specific Regulator of Triterpene Saponin Biosynthesis in Medicago truncatula. Plant Cell. 2020 Jun;32(6):2020-2042. doi: 10.1105/tpc.19.00609. Epub 2020 Apr 17. PMID: 32303662; PMCID: PMC7268793." -10.1111/nph.13162 25406544 null Carelli, Biazzi, et al., 2014 "Carelli M, Biazzi E, Tava A, Losini I, Abbruscato P, Depedro C, Scotti C. Sapogenin content variation in Medicago inter-specific hybrid derivatives highlights some aspects of saponin synthesis and control. New Phytol. 2015 Apr;206(1):303-314. doi: 10.1111/nph.13162. Epub 2014 Nov 18. PMID: 25406544." +10.1073/pnas.2205920119 35972963 PMC9407390 Liu, Lin et al., 2022 "Liu H, Lin JS, Luo Z, Sun J, Huang X, Yang Y, Xu J, Wang YF, Zhang P, Oldroyd GED, Xie F. Constitutive activation of a nuclear-localized calcium channel complex in Medicago truncatula. Proc Natl Acad Sci U S A. 2022 Aug 23;119(34):e2205920119. doi: 10.1073/pnas.2205920119. Epub 2022 Aug 16. PMID: 35972963; PMCID: PMC9407390." +10.1093/jxb/erac112 35294003 PMC9232208 Wang, Lu et al., 2022 "Wang R, Lu N, Liu C, Dixon RA, Wu Q, Mao Y, Yang Y, Zheng X, He L, Zhao B, Zhang F, Yang S, Chen H, Jun JH, Li Y, Liu C, Liu Y, Chen J. MtGSTF7, a TT19-like GST gene, is essential for accumulation of anthocyanins, but not proanthocyanins in Medicago truncatula. J Exp Bot. 2022 Jun 24;73(12):4129-4146. doi: 10.1093/jxb/erac112. PMID: 35294003; PMCID: PMC9232208." +10.1105/tpc.111.089128 22080596 PMC3246329 Peng, Yu et al., 2011 "" +10.1093/jxb/erw474 28073951 PMC6055581 Herrbach, Chirinos et al., 2017 "" +10.1104/pp.109.143024 19789288 PMC2773094 Kuppusamy, Ivashuta et al., 2009 "" +10.1371/journal.pone.0247170 33606812 PMC7894904 Hasan, Singh et al. 2021 "Hasan MS, Singh V, Islam S, Islam MS, Ahsan R, Kaundal A, Islam T, Ghosh A. Genome-wide identification and expression profiling of glutathione S-transferase family under multiple abiotic and biotic stresses in Medicago truncatula L. PLoS One. 2021 Feb 19;16(2):e0247170. doi: 10.1371/journal.pone.0247170. PMID: 33606812; PMCID: PMC7894904." +10.1111/j.1469-8137.2012.04147.x 22530598 null Cheng, Peng et al., 2012 "" diff --git a/Medicago/truncatula/gene_functions/medtr.references.txt b/Medicago/truncatula/gene_functions/medtr.references.txt deleted file mode 100644 index c63da27..0000000 --- a/Medicago/truncatula/gene_functions/medtr.references.txt +++ /dev/null @@ -1,3519 +0,0 @@ -##### PUB RECORD ##### -## 10.1105/tpc.105.035394 16199614 PMC1276019 Ivashuta, Liu, et al., 2005 "Ivashuta S, Liu J, Liu J, Lohar DP, Haridas S, Bucciarelli B, VandenBosch KA, Vance CP, Harrison MJ, Gantt JS. RNA interference identifies a calcium-dependent protein kinase involved in Medicago truncatula root development. Plant Cell. 2005 Nov;17(11):2911-21. doi: 10.1105/tpc.105.035394. Epub 2005 Sep 30. PMID: 16199614; PMCID: PMC1276019." ## - -PMID- 16199614 -OWN - NLM -STAT- MEDLINE -DCOM- 20060526 -LR - 20220408 -IS - 1040-4651 (Print) -IS - 1532-298X (Electronic) -IS - 1040-4651 (Linking) -VI - 17 -IP - 11 -DP - 2005 Nov -TI - RNA interference identifies a calcium-dependent protein kinase involved in - Medicago truncatula root development. -PG - 2911-21 -AB - Changes in cellular or subcellular Ca2+ concentrations play essential roles in - plant development and in the responses of plants to their environment. However, - the mechanisms through which Ca2+ acts, the downstream signaling components, as - well as the relationships among the various Ca2+-dependent processes remain - largely unknown. Using an RNA interference-based screen for gene function in - Medicago truncatula, we identified a gene that is involved in root development. - Silencing Ca2+-dependent protein kinase1 (CDPK1), which is predicted to encode a - Ca2+-dependent protein kinase, resulted in significantly reduced root hair and - root cell lengths. Inactivation of CDPK1 is also associated with significant - diminution of both rhizobial and mycorrhizal symbiotic colonization. - Additionally, microarray analysis revealed that silencing CDPK1 alters cell wall - and defense-related gene expression. We propose that M. truncatula CDPK1 is a key - component of one or more signaling pathways that directly or indirectly modulates - cell expansion or cell wall synthesis, possibly altering defense gene expression - and symbiotic interactions. -FAU - Ivashuta, Sergey -AU - Ivashuta S -AD - Department of Plant Biology, University of Minesota, St. Paul, Minesota 55108, - USA. -FAU - Liu, Jinyuan -AU - Liu J -FAU - Liu, Junqi -AU - Liu J -FAU - Lohar, Dasharath P -AU - Lohar DP -FAU - Haridas, Sajeet -AU - Haridas S -FAU - Bucciarelli, Bruna -AU - Bucciarelli B -FAU - VandenBosch, Kathryn A -AU - VandenBosch KA -FAU - Vance, Carroll P -AU - Vance CP -FAU - Harrison, Maria J -AU - Harrison MJ -FAU - Gantt, J Stephen -AU - Gantt JS -LA - eng -PT - Journal Article -PT - Research Support, Non-U.S. Gov't -PT - Research Support, U.S. Gov't, Non-P.H.S. -DEP - 20050930 -PL - England -TA - Plant Cell -JT - The Plant cell -JID - 9208688 -RN - 0 (ATCDPK1 protein, Arabidopsis) -RN - 0 (Arabidopsis Proteins) -RN - 0 (Calcium-Binding Proteins) -RN - EC 2.7.- (Protein Kinases) -RN - SY7Q814VUP (Calcium) -SB - IM -MH - Arabidopsis Proteins/genetics/metabolism -MH - Calcium/metabolism -MH - Calcium Signaling/physiology -MH - Calcium-Binding Proteins/genetics/isolation & purification/*metabolism -MH - Cell Wall/enzymology/genetics -MH - Gene Expression Regulation, Enzymologic/physiology -MH - Gene Expression Regulation, Plant/genetics -MH - Gene Silencing/physiology -MH - Immunity, Innate/genetics -MH - Medicago truncatula/*enzymology/genetics/*growth & development -MH - Plant Diseases/genetics -MH - Plant Roots/*enzymology/genetics/*growth & development -MH - Protein Kinases/genetics/isolation & purification/*metabolism -MH - RNA Interference/physiology -MH - Signal Transduction/genetics -MH - Symbiosis/genetics -PMC - PMC1276019 -EDAT- 2005/10/04 09:00 -MHDA- 2006/05/27 09:00 -CRDT- 2005/10/04 09:00 -PHST- 2005/10/04 09:00 [pubmed] -PHST- 2006/05/27 09:00 [medline] -PHST- 2005/10/04 09:00 [entrez] -AID - tpc.105.035394 [pii] -AID - 035394 [pii] -AID - 10.1105/tpc.105.035394 [doi] -PST - ppublish -SO - Plant Cell. 2005 Nov;17(11):2911-21. doi: 10.1105/tpc.105.035394. Epub 2005 Sep - 30. - - -##### PUB RECORD ##### -## 10.1111/j.1469-8137.2011.03718.x 21679315 PMC3206218 Godiard, Lepage, et al., 2011 "Godiard L, Lepage A, Moreau S, Laporte D, Verdenaud M, Timmers T, Gamas P. MtbHLH1, a bHLH transcription factor involved in Medicago truncatula nodule vascular patterning and nodule to plant metabolic exchanges. New Phytol. 2011 Jul;191(2):391-404. doi: 10.1111/j.1469-8137.2011.03718.x. Epub 2011 Jun 17. PMID: 21679315; PMCID: PMC3206218." ## - -PMID- 21679315 -OWN - NLM -STAT- MEDLINE -DCOM- 20130328 -LR - 20220310 -IS - 1469-8137 (Electronic) -IS - 0028-646X (Print) -IS - 0028-646X (Linking) -VI - 191 -IP - 2 -DP - 2011 Jul -TI - MtbHLH1, a bHLH transcription factor involved in Medicago truncatula nodule - vascular patterning and nodule to plant metabolic exchanges. -PG - 391-404 -LID - 10.1111/j.1469-8137.2011.03718.x [doi] -AB - This study aimed at defining the role of a basic helix-loop-helix (bHLH) - transcription factor gene from Medicago truncatula, MtbHLH1, whose expression is - upregulated during the development of root nodules produced upon infection by - rhizobia bacteria. We used MtbHLH1 promoter::GUS fusions and quantitative - reverse-transcription polymerase chain reaction analyses to finely characterize - the MtbHLH1 expression pattern. We altered MtbHLH1 function by expressing a - dominantly repressed construct (CRES-T approach) and looked for possible MtbHLH1 - target genes by transcriptomics. We found that MtbHLH1 is expressed in nodule - primordia cells derived from pericycle divisions, in nodule vascular bundles - (VBs) and in uninfected cells of the nitrogen (N) fixation zone. MtbHLH1 is also - expressed in root tips, lateral root primordia cells and root VBs, and induced - upon auxin treatment. Altering MtbHLH1 function led to an unusual phenotype, with - a modified patterning of nodule VB development and a reduced growth of aerial - parts of the plant, even though the nodules were able to fix atmospheric N. - Several putative MtbHLH1 regulated genes were identified, including an asparagine - synthase and a LOB (lateral organ boundary) transcription factor. Our results - suggest that the MtbHLH1 gene is involved in the control of nodule vasculature - patterning and nutrient exchanges between nodules and roots. -CI - (c) 2011 The Authors. New Phytologist (c) 2011 New Phytologist Trust. -FAU - Godiard, Laurence -AU - Godiard L -AD - Laboratoire des Interactions Plantes Microorganismes, Unite Mixte de Recherche, - Institut National de la Recherche Agronomique - Centre National de la Recherche - Scientifique 441/2594, F-31320 Castanet Tolosan, France. -FAU - Lepage, Agnes -AU - Lepage A -AD - Laboratoire des Interactions Plantes Microorganismes, Unite Mixte de Recherche, - Institut National de la Recherche Agronomique - Centre National de la Recherche - Scientifique 441/2594, F-31320 Castanet Tolosan, France. -FAU - Moreau, Sandra -AU - Moreau S -AD - Laboratoire des Interactions Plantes Microorganismes, Unite Mixte de Recherche, - Institut National de la Recherche Agronomique - Centre National de la Recherche - Scientifique 441/2594, F-31320 Castanet Tolosan, France. -FAU - Laporte, Damien -AU - Laporte D -AD - Jian-Qiu Wu's laboratory, Ohio State University, 612 Biosciences Building, 484 W - 12th Ave, Columbus, OH 43210, USA. -FAU - Verdenaud, Marion -AU - Verdenaud M -AD - Laboratoire des Interactions Plantes Microorganismes, Unite Mixte de Recherche, - Institut National de la Recherche Agronomique - Centre National de la Recherche - Scientifique 441/2594, F-31320 Castanet Tolosan, France. -FAU - Timmers, Ton -AU - Timmers T -AD - Laboratoire des Interactions Plantes Microorganismes, Unite Mixte de Recherche, - Institut National de la Recherche Agronomique - Centre National de la Recherche - Scientifique 441/2594, F-31320 Castanet Tolosan, France. -FAU - Gamas, Pascal -AU - Gamas P -AD - Laboratoire des Interactions Plantes Microorganismes, Unite Mixte de Recherche, - Institut National de la Recherche Agronomique - Centre National de la Recherche - Scientifique 441/2594, F-31320 Castanet Tolosan, France. -LA - eng -SI - GENBANK/FR697055 -PT - Journal Article -PT - Research Support, Non-U.S. Gov't -DEP - 20110617 -PL - England -TA - New Phytol -JT - The New phytologist -JID - 9882884 -RN - 0 (Basic Helix-Loop-Helix Transcription Factors) -RN - 0 (Indoleacetic Acids) -RN - 0 (Plant Growth Regulators) -RN - 0 (Plant Proteins) -SB - IM -MH - Basic Helix-Loop-Helix Transcription Factors/genetics/*metabolism -MH - Body Patterning -MH - Gene Expression Profiling -MH - Gene Expression Regulation, Plant/drug effects -MH - Indoleacetic Acids/pharmacology -MH - Medicago truncatula/genetics/*metabolism/microbiology/physiology -MH - Molecular Sequence Data -MH - Nitrogen Fixation/genetics -MH - Phenotype -MH - Plant Growth Regulators/pharmacology -MH - Plant Proteins/genetics/metabolism -MH - Plant Root Nodulation -MH - Plants, Genetically Modified -MH - Promoter Regions, Genetic -MH - Rhizobium/genetics/*physiology -MH - Root Nodules, Plant/genetics/growth & development/*metabolism -MH - Symbiosis/genetics -PMC - PMC3206218 -EDAT- 2011/06/18 06:00 -MHDA- 2013/03/30 06:00 -CRDT- 2011/06/18 06:00 -PHST- 2011/06/18 06:00 [entrez] -PHST- 2011/06/18 06:00 [pubmed] -PHST- 2013/03/30 06:00 [medline] -AID - 10.1111/j.1469-8137.2011.03718.x [doi] -PST - ppublish -SO - New Phytol. 2011 Jul;191(2):391-404. doi: 10.1111/j.1469-8137.2011.03718.x. Epub - 2011 Jun 17. - - -##### PUB RECORD ##### -## 10.1111/j.1365-313x.2009.04072.x 19912567 null Pumplin, Mondo, et al., 2009 "Pumplin N, Mondo SJ, Topp S, Starker CG, Gantt JS, Harrison MJ. Medicago truncatula Vapyrin is a novel protein required for arbuscular mycorrhizal symbiosis. Plant J. 2010 Feb 1;61(3):482-94. doi: 10.1111/j.1365-313X.2009.04072.x. Epub 2009 Nov 14. PMID: 19912567." ## - -PMID- 19912567 -OWN - NLM -STAT- MEDLINE -DCOM- 20100830 -LR - 20100422 -IS - 1365-313X (Electronic) -IS - 0960-7412 (Linking) -VI - 61 -IP - 3 -DP - 2010 Feb 1 -TI - Medicago truncatula Vapyrin is a novel protein required for arbuscular - mycorrhizal symbiosis. -PG - 482-94 -LID - 10.1111/j.1365-313X.2009.04072.x [doi] -AB - Arbuscular mycorrhizal (AM) symbiosis is a widespread mutualism formed between - vascular plants and fungi of the Glomeromycota. In this endosymbiosis, fungal - hyphae enter the roots, growing through epidermal cells to the cortex where they - establish differentiated hyphae called arbuscules in the cortical cells. - Reprogramming of the plant epidermal and cortical cells occurs to enable - intracellular growth of the fungal symbiont; however, the plant genes underlying - this process are largely unknown. Here, through the use of RNAi, we demonstrate - that the expression of a Medicago truncatula gene named Vapyrin is essential for - arbuscule formation, and also for efficient epidermal penetration by AM fungi. - Vapyrin is induced transiently in the epidermis coincident with hyphal - penetration, and then in the cortex during arbuscule formation. The Vapyrin - protein is cytoplasmic, and in cells containing AM fungal hyphae, the protein - accumulates in small puncta that move through the cytoplasm. Vapyrin is a novel - protein composed of two domains that mediate protein-protein interactions: an - N-terminal VAMP-associated protein (VAP)/major sperm protein (MSP) domain and a - C-terminal ankyrin-repeat domain. Putative Vapyrin orthologs exist widely in the - plant kingdom, but not in Arabidopsis, or in non-plant species. The data suggest - a role for Vapyrin in cellular remodeling to support the intracellular - development of fungal hyphae during AM symbiosis. -FAU - Pumplin, Nathan -AU - Pumplin N -AD - Boyce Thompson Institute for Plant Research, Tower Road, Ithaca, NY 14853, USA. -FAU - Mondo, Stephen J -AU - Mondo SJ -FAU - Topp, Stephanie -AU - Topp S -FAU - Starker, Colby G -AU - Starker CG -FAU - Gantt, J Stephen -AU - Gantt JS -FAU - Harrison, Maria J -AU - Harrison MJ -LA - eng -PT - Journal Article -PT - Research Support, U.S. Gov't, Non-P.H.S. -DEP - 20091114 -PL - England -TA - Plant J -JT - The Plant journal : for cell and molecular biology -JID - 9207397 -RN - 0 (Plant Proteins) -RN - 0 (Vesicular Transport Proteins) -SB - IM -MH - Amino Acid Sequence -MH - Animals -MH - Gene Expression Regulation, Plant -MH - Humans -MH - Medicago truncatula/chemistry/genetics/*metabolism -MH - Molecular Sequence Data -MH - Mycorrhizae/*metabolism -MH - Phylogeny -MH - Plant Proteins/chemistry/genetics/*metabolism -MH - RNA Interference -MH - *Symbiosis -MH - Vesicular Transport Proteins/chemistry/genetics/*metabolism -EDAT- 2009/11/17 06:00 -MHDA- 2010/08/31 06:00 -CRDT- 2009/11/17 06:00 -PHST- 2009/11/17 06:00 [entrez] -PHST- 2009/11/17 06:00 [pubmed] -PHST- 2010/08/31 06:00 [medline] -AID - TPJ4072 [pii] -AID - 10.1111/j.1365-313X.2009.04072.x [doi] -PST - ppublish -SO - Plant J. 2010 Feb 1;61(3):482-94. doi: 10.1111/j.1365-313X.2009.04072.x. Epub - 2009 Nov 14. - - -##### PUB RECORD ##### -## 10.1105/tpc.15.00476 26410301 PMC4682322 Jun, Liu, et al., 2015 "Jun JH, Liu C, Xiao X, Dixon RA. The Transcriptional Repressor MYB2 Regulates Both Spatial and Temporal Patterns of Proanthocyandin and Anthocyanin Pigmentation in Medicago truncatula. Plant Cell. 2015 Oct;27(10):2860-79. doi: 10.1105/tpc.15.00476. Epub 2015 Sep 26. PMID: 26410301; PMCID: PMC4682322." ## - -PMID- 26410301 -OWN - NLM -STAT- MEDLINE -DCOM- 20170905 -LR - 20220310 -IS - 1532-298X (Electronic) -IS - 1040-4651 (Print) -IS - 1040-4651 (Linking) -VI - 27 -IP - 10 -DP - 2015 Oct -TI - The Transcriptional Repressor MYB2 Regulates Both Spatial and Temporal Patterns - of Proanthocyandin and Anthocyanin Pigmentation in Medicago truncatula. -PG - 2860-79 -LID - 10.1105/tpc.15.00476 [doi] -AB - Accumulation of anthocyanins and proanthocyanidins (PAs) is limited to specific - cell types and developmental stages, but little is known about how - antagonistically acting transcriptional regulators work together to determine - temporal and spatial patterning of pigmentation at the cellular level, especially - for PAs. Here, we characterize MYB2, a transcriptional repressor regulating both - anthocyanin and PA biosynthesis in the model legume Medicago truncatula. MYB2 was - strongly upregulated by MYB5, a major regulator of PA biosynthesis in M. - truncatula and a component of MYB-basic helix loop helix-WD40 (MBW) activator - complexes. Overexpression of MYB2 abolished anthocyanin and PA accumulation in M. - truncatula hairy roots and Arabidopsis thaliana seeds, respectively. Anthocyanin - deposition was expanded in myb2 mutant seedlings and flowers accompanied by - increased anthocyanin content. PA mainly accumulated in the epidermal layer - derived from the outer integument in the M. truncatula seed coat, starting from - the hilum area. The area of PA accumulation and ANTHOCYANIDIN REDUCTASE - expression was expanded into the seed body at the early stage of seed development - in the myb2 mutant. Genetic, biochemical, and cell biological evidence suggests - that MYB2 functions as part of a multidimensional regulatory network to define - the temporal and spatial pattern of anthocyanin and PA accumulation linked to - developmental processes. -CI - (c) 2015 American Society of Plant Biologists. All rights reserved. -FAU - Jun, Ji Hyung -AU - Jun JH -AUID- ORCID: 0000-0002-2563-4144 -AD - Department of Biological Sciences, University of North Texas, Denton, Texas - 76203-5017. -FAU - Liu, Chenggang -AU - Liu C -AUID- ORCID: 0000-0002-0576-8567 -AD - Department of Biological Sciences, University of North Texas, Denton, Texas - 76203-5017. -FAU - Xiao, Xirong -AU - Xiao X -AUID- ORCID: 0000-0002-1785-6417 -AD - Department of Biological Sciences, University of North Texas, Denton, Texas - 76203-5017. -FAU - Dixon, Richard A -AU - Dixon RA -AUID- ORCID: 0000-0001-8393-9408 -AD - Department of Biological Sciences, University of North Texas, Denton, Texas - 76203-5017 richard.dixon@unt.edu. -LA - eng -PT - Journal Article -PT - Research Support, Non-U.S. Gov't -DEP - 20150926 -PL - England -TA - Plant Cell -JT - The Plant cell -JID - 9208688 -RN - 0 (Anthocyanins) -RN - 0 (Plant Proteins) -RN - 0 (Proanthocyanidins) -RN - 0 (Transcription Factors) -RN - EC 1.- (Oxidoreductases) -SB - IM -MH - Anthocyanins/*metabolism -MH - Arabidopsis/cytology/genetics/metabolism -MH - Flowers/cytology/genetics/metabolism -MH - Gene Expression -MH - *Gene Expression Regulation, Plant -MH - Medicago truncatula/cytology/*genetics/metabolism -MH - Mutation -MH - Oxidoreductases/genetics/metabolism -MH - Phylogeny -MH - Pigmentation -MH - Plant Proteins/genetics/metabolism -MH - Plant Roots/cytology/genetics/metabolism -MH - Plants, Genetically Modified -MH - Proanthocyanidins/*metabolism -MH - Seedlings/cytology/genetics/metabolism -MH - Seeds/cytology/genetics/metabolism -MH - Transcription Factors/genetics/*metabolism -PMC - PMC4682322 -EDAT- 2015/09/28 06:00 -MHDA- 2017/09/07 06:00 -CRDT- 2015/09/28 06:00 -PHST- 2015/05/29 00:00 [received] -PHST- 2015/09/10 00:00 [accepted] -PHST- 2015/09/28 06:00 [entrez] -PHST- 2015/09/28 06:00 [pubmed] -PHST- 2017/09/07 06:00 [medline] -AID - tpc.15.00476 [pii] -AID - TPC201500476RAR2 [pii] -AID - 10.1105/tpc.15.00476 [doi] -PST - ppublish -SO - Plant Cell. 2015 Oct;27(10):2860-79. doi: 10.1105/tpc.15.00476. Epub 2015 Sep 26. - - -##### PUB RECORD ##### -## 10.1104/pp.111.180182 21685176 PMC3149922 Laurie, Diwadkar, et al., 2011 "Laurie RE, Diwadkar P, Jaudal M, Zhang L, Hecht V, Wen J, Tadege M, Mysore KS, Putterill J, Weller JL, Macknight RC. The Medicago FLOWERING LOCUS T homolog, MtFTa1, is a key regulator of flowering time. Plant Physiol. 2011 Aug;156(4):2207-24. doi: 10.1104/pp.111.180182. Epub 2011 Jun 17. PMID: 21685176; PMCID: PMC3149922." ## - -PMID- 21685176 -OWN - NLM -STAT- MEDLINE -DCOM- 20111205 -LR - 20211020 -IS - 1532-2548 (Electronic) -IS - 0032-0889 (Print) -IS - 0032-0889 (Linking) -VI - 156 -IP - 4 -DP - 2011 Aug -TI - The Medicago FLOWERING LOCUS T homolog, MtFTa1, is a key regulator of flowering - time. -PG - 2207-24 -LID - 10.1104/pp.111.180182 [doi] -AB - FLOWERING LOCUS T (FT) genes encode proteins that function as the mobile floral - signal, florigen. In this study, we characterized five FT-like genes from the - model legume, Medicago (Medicago truncatula). The different FT genes showed - distinct patterns of expression and responses to environmental cues. Three of the - FT genes (MtFTa1, MtFTb1, and MtFTc) were able to complement the Arabidopsis - (Arabidopsis thaliana) ft-1 mutant, suggesting that they are capable of - functioning as florigen. MtFTa1 is the only one of the FT genes that is - up-regulated by both long days (LDs) and vernalization, conditions that promote - Medicago flowering, and transgenic Medicago plants overexpressing the MtFTa1 gene - flowered very rapidly. The key role MtFTa1 plays in regulating flowering was - demonstrated by the identification of fta1 mutants that flowered significantly - later in all conditions examined. fta1 mutants do not respond to vernalization - but are still responsive to LDs, indicating that the induction of flowering by - prolonged cold acts solely through MtFTa1, whereas photoperiodic induction of - flowering involves other genes, possibly MtFTb1, which is only expressed in - leaves under LD conditions and therefore might contribute to the photoperiodic - regulation of flowering. The role of the MtFTc gene is unclear, as the ftc - mutants did not have any obvious flowering-time or other phenotypes. Overall, - this work reveals the diversity of the regulation and function of the Medicago FT - family. -FAU - Laurie, Rebecca E -AU - Laurie RE -AD - Department of Biochemistry, University of Otago, Dunedin 9054, New Zealand. -FAU - Diwadkar, Payal -AU - Diwadkar P -FAU - Jaudal, Mauren -AU - Jaudal M -FAU - Zhang, Lulu -AU - Zhang L -FAU - Hecht, Valerie -AU - Hecht V -FAU - Wen, Jiangqi -AU - Wen J -FAU - Tadege, Million -AU - Tadege M -FAU - Mysore, Kirankumar S -AU - Mysore KS -FAU - Putterill, Joanna -AU - Putterill J -FAU - Weller, James L -AU - Weller JL -FAU - Macknight, Richard C -AU - Macknight RC -LA - eng -PT - Journal Article -PT - Research Support, Non-U.S. Gov't -DEP - 20110617 -PL - United States -TA - Plant Physiol -JT - Plant physiology -JID - 0401224 -RN - 0 (Plant Proteins) -SB - IM -MH - Amino Acid Sequence -MH - Arabidopsis/genetics -MH - Cold Temperature -MH - Flowers/genetics/growth & development/*physiology -MH - Gene Expression Regulation, Plant -MH - Genes, Plant/genetics -MH - Genetic Complementation Test -MH - Medicago/genetics/growth & development/*physiology -MH - Meristem/genetics -MH - Molecular Sequence Data -MH - Mutation/genetics -MH - Phenotype -MH - Photoperiod -MH - Plant Proteins/chemistry/genetics/*metabolism -MH - Plants, Genetically Modified -MH - *Sequence Homology, Amino Acid -MH - Time Factors -MH - Up-Regulation/genetics -PMC - PMC3149922 -EDAT- 2011/06/21 06:00 -MHDA- 2011/12/13 00:00 -CRDT- 2011/06/21 06:00 -PHST- 2011/06/21 06:00 [entrez] -PHST- 2011/06/21 06:00 [pubmed] -PHST- 2011/12/13 00:00 [medline] -AID - pp.111.180182 [pii] -AID - 180182 [pii] -AID - 10.1104/pp.111.180182 [doi] -PST - ppublish -SO - Plant Physiol. 2011 Aug;156(4):2207-24. doi: 10.1104/pp.111.180182. Epub 2011 Jun - 17. - - -##### PUB RECORD ##### -## 10.1094/mpmi-06-10-0144 20731530 null Miyahara, Richens, et al., 2010 "Miyahara A, Richens J, Starker C, Morieri G, Smith L, Long S, Downie JA, Oldroyd GE. Conservation in function of a SCAR/WAVE component during infection thread and root hair growth in Medicago truncatula. Mol Plant Microbe Interact. 2010 Dec;23(12):1553-62. doi: 10.1094/MPMI-06-10-0144. PMID: 20731530." ## - -PMID- 20731530 -OWN - NLM -STAT- MEDLINE -DCOM- 20110111 -LR - 20220310 -IS - 0894-0282 (Print) -IS - 0894-0282 (Linking) -VI - 23 -IP - 12 -DP - 2010 Dec -TI - Conservation in function of a SCAR/WAVE component during infection thread and - root hair growth in Medicago truncatula. -PG - 1553-62 -LID - 10.1094/MPMI-06-10-0144 [doi] -AB - Nitrogen-fixing symbioses of plants are often associated with bacterially - infected nodules where nitrogen fixation occurs. The plant host facilitates - bacterial infection with the formation of infection threads, unique structures - associated with these symbioses, which are invaginations of the host cell with - the capability of traversing cellular junctions. Here, we show that the infection - thread shares mechanistic similarities to polar-growing cells, because the - required for infection thread (RIT) locus of Medicago truncatula has roles in - root-hair, trichome, and infection-thread growth. We show that RIT encodes the M. - truncatula ortholog of NAP1, a component of the SCAR/WAVE (suppressor of cAMP - receptor/WASP-family verprolin homologous protein) complex that regulates actin - polymerization, through the activation of ARP2/3. NAP1 of Arabidopsis thaliana - functions equivalently to the M. truncatula gene, indicating that the mode of - action of NAP1 is functionally conserved across species and that legumes have not - evolved a unique functionality for NAP1 during rhizobial colonization. This work - highlights the surprising commonality between polar-growing cells and a - polar-growing cellular intrusion and reveals important insights into the - formation and maintenance of infection-thread development. -FAU - Miyahara, Akira -AU - Miyahara A -AD - Department of Disease and Stress Biology, John Innes Centre, Norwich Research - Park, Colney Lane, Norwich, NR4 7UH, UK. -FAU - Richens, Jennifer -AU - Richens J -FAU - Starker, Colby -AU - Starker C -FAU - Morieri, Giulia -AU - Morieri G -FAU - Smith, Lucinda -AU - Smith L -FAU - Long, Sharon -AU - Long S -FAU - Downie, J Allan -AU - Downie JA -FAU - Oldroyd, Giles E D -AU - Oldroyd GE -LA - eng -SI - GENBANK/HM590708 -GR - BBS/E/J/000CA336/BB_/Biotechnology and Biological Sciences Research - Council/United Kingdom -PT - Journal Article -PT - Research Support, Non-U.S. Gov't -PL - United States -TA - Mol Plant Microbe Interact -JT - Molecular plant-microbe interactions : MPMI -JID - 9107902 -RN - 0 (Plant Proteins) -SB - IM -MH - Gene Expression Regulation, Plant/*physiology -MH - Medicago truncatula/genetics/*metabolism -MH - Molecular Sequence Data -MH - Mutation -MH - Plant Proteins/genetics/*metabolism -MH - Plant Root Nodulation/*physiology -MH - Plant Roots/*growth & development/physiology -MH - Symbiosis -EDAT- 2010/08/25 06:00 -MHDA- 2011/01/12 06:00 -CRDT- 2010/08/25 06:00 -PHST- 2010/08/25 06:00 [entrez] -PHST- 2010/08/25 06:00 [pubmed] -PHST- 2011/01/12 06:00 [medline] -AID - 10.1094/MPMI-06-10-0144 [doi] -PST - ppublish -SO - Mol Plant Microbe Interact. 2010 Dec;23(12):1553-62. doi: - 10.1094/MPMI-06-10-0144. - - -##### PUB RECORD ##### -## 10.1111/j.1365-313x.2006.02910.x 17132148 null Gargantini, Gonzalez-Rizzo, et al., 2006 "Gargantini PR, Gonzalez-Rizzo S, Chinchilla D, Raices M, Giammaria V, Ulloa RM, Frugier F, Crespi MD. A CDPK isoform participates in the regulation of nodule number in Medicago truncatula. Plant J. 2006 Dec;48(6):843-56. doi: 10.1111/j.1365-313X.2006.02910.x. Epub 2006 Nov 21. PMID: 17132148." ## - -PMID- 17132148 -OWN - NLM -STAT- MEDLINE -DCOM- 20070417 -LR - 20220408 -IS - 0960-7412 (Print) -IS - 0960-7412 (Linking) -VI - 48 -IP - 6 -DP - 2006 Dec -TI - A CDPK isoform participates in the regulation of nodule number in Medicago - truncatula. -PG - 843-56 -AB - Medicago spp. are able to develop root nodules via symbiotic interaction with - Sinorhizobium meliloti. Calcium-dependent protein kinases (CDPKs) are involved in - various signalling pathways in plants, and we found that expression of MtCPK3, a - CDPK isoform present in roots of the model legume Medicago truncatula, is - regulated during the nodulation process. Early inductions were detected 15 min - and 3-4 days post-inoculation (dpi). The very early induction of CPK3 messengers - was also present in inoculated M. truncatula dmi mutants and in wild-type roots - subjected to salt stress, indicating that this rapid response is probably - stress-related. In contrast, the later response was concomitant with cortical - cell division and the formation of nodule primordia, and was not observed in - wild-type roots inoculated with nod (-) strains. This late induction correlated - with a change in the subcellular distribution of CDPK activities. Accordingly, an - anti-MtCPK3 antibody detected two bands in soluble root extracts and one in the - particulate fraction. CPK3::GFP fusions are targeted to the plasma membrane in - epidermal onion cells, a localization that depends on myristoylation and - palmitoylation sites of the protein, suggesting a dual subcellular localization. - MtCPK3 mRNA and protein were also up-regulated by cytokinin treatment, a hormone - linked to the regulation of cortical cell division and other nodulation-related - responses. An RNAi-CDPK construction was used to silence CPK3 in Agrobacterium - rhizogenes-transformed roots. Although no major phenotype was detected in these - roots, when infected with rhizobia, the total number of nodules was, on average, - twofold higher than in controls. This correlates with the lack of MtCPK3 - induction in the inoculated super-nodulator sunn mutant. Our results suggest that - CPK3 participates in the regulation of the symbiotic interaction. -FAU - Gargantini, Pablo R -AU - Gargantini PR -AD - Instituto de Investigaciones en Ingenieria Genetica y Biologia Molecular, Vuelta - de Obligado 2490, 2 piso, 1428 Buenos Aires, Argentina. -FAU - Gonzalez-Rizzo, Silvina -AU - Gonzalez-Rizzo S -FAU - Chinchilla, Delphine -AU - Chinchilla D -FAU - Raices, Marcela -AU - Raices M -FAU - Giammaria, Veronica -AU - Giammaria V -FAU - Ulloa, Rita M -AU - Ulloa RM -FAU - Frugier, Florian -AU - Frugier F -FAU - Crespi, Martin D -AU - Crespi MD -LA - eng -PT - Journal Article -PT - Research Support, Non-U.S. Gov't -DEP - 20061121 -PL - England -TA - Plant J -JT - The Plant journal : for cell and molecular biology -JID - 9207397 -RN - 0 (Cytokinins) -RN - 0 (Isoenzymes) -RN - 0 (Plant Proteins) -RN - 0 (RNA, Messenger) -RN - 0 (RNA, Plant) -RN - 147336-22-9 (Green Fluorescent Proteins) -RN - EC 2.7.11.17 (Calcium-Calmodulin-Dependent Protein Kinases) -SB - IM -MH - Calcium-Calmodulin-Dependent Protein Kinases/genetics/*metabolism -MH - Cytokinins/pharmacology -MH - Gene Expression Regulation, Enzymologic -MH - Gene Expression Regulation, Plant -MH - Genes, Plant -MH - Green Fluorescent Proteins/genetics -MH - Isoenzymes/genetics/metabolism -MH - Medicago sativa/enzymology -MH - Medicago truncatula/*enzymology/genetics/microbiology -MH - Onions/cytology -MH - Plant Proteins/genetics/*metabolism -MH - Plant Roots/*enzymology/microbiology -MH - RNA Interference -MH - RNA, Messenger -MH - RNA, Plant -MH - Rhizobium/enzymology -MH - Sinorhizobium meliloti/physiology -MH - Symbiosis/*physiology -MH - Up-Regulation -EDAT- 2006/11/30 09:00 -MHDA- 2007/04/18 09:00 -CRDT- 2006/11/30 09:00 -PHST- 2006/11/30 09:00 [pubmed] -PHST- 2007/04/18 09:00 [medline] -PHST- 2006/11/30 09:00 [entrez] -AID - TPJ2910 [pii] -AID - 10.1111/j.1365-313X.2006.02910.x [doi] -PST - ppublish -SO - Plant J. 2006 Dec;48(6):843-56. doi: 10.1111/j.1365-313X.2006.02910.x. Epub 2006 - Nov 21. - - -##### PUB RECORD ##### -## 10.1105/tpc.019406 15037734 PMC412876 Campalans, Kondorosi, et al., 2017 "Campalans A, Kondorosi A, Crespi M. Enod40, a short open reading frame-containing mRNA, induces cytoplasmic localization of a nuclear RNA binding protein in Medicago truncatula. Plant Cell. 2004 Apr;16(4):1047-59. doi: 10.1105/tpc.019406. Epub 2004 Mar 22. Erratum in: Plant Cell. 2017 Apr;29(4):912. PMID: 15037734; PMCID: PMC412876." ## - -PMID- 15037734 -OWN - NLM -STAT- MEDLINE -DCOM- 20040625 -LR - 20181113 -IS - 1040-4651 (Print) -IS - 1532-298X (Electronic) -IS - 1040-4651 (Linking) -VI - 16 -IP - 4 -DP - 2004 Apr -TI - Enod40, a short open reading frame-containing mRNA, induces cytoplasmic - localization of a nuclear RNA binding protein in Medicago truncatula. -PG - 1047-59 -AB - In eukaryotes, diverse mRNAs containing only short open reading frames - (sORF-mRNAs) are induced at specific stages of development. Their mechanisms of - action may involve the RNA itself and/or sORF-encoded oligopeptides. Enod40 genes - code for highly structured plant sORF-mRNAs involved in root nodule - organogenesis. A novel RNA binding protein interacting with the enod40 RNA, - MtRBP1 (for Medicago truncatula RNA Binding Protein 1), was identified using a - yeast three-hybrid screening. Immunolocalization studies and use of a - MtRBP1-DsRed2 fluorescent protein fusion showed that MtRBP1 localized to nuclear - speckles in plant cells but was exported into the cytoplasm during nodule - development in enod40-expressing cells. Direct involvement of the enod40 RNA in - MtRBP1 relocalization into cytoplasmic granules was shown using a transient - expression assay. Using a (green fluorescent protein)/MS2 bacteriophage system to - tag the enod40 RNA, we detected in vivo colocalization of the enod40 RNA and - MtRBP1 in these granules. This in vivo approach to monitor RNA-protein - interactions allowed us to demonstrate that cytoplasmic relocalization of nuclear - proteins is an RNA-mediated cellular function of a sORF-mRNA. -FAU - Campalans, Anna -AU - Campalans A -AD - Institut des Sciences du Vegetal, Centre National de la Recherche Scientifique, - 91198 Gif sur Yvette, France. -FAU - Kondorosi, Adam -AU - Kondorosi A -FAU - Crespi, Martin -AU - Crespi M -LA - eng -SI - GENBANK/AJ508392 -PT - Journal Article -PT - Research Support, Non-U.S. Gov't -DEP - 20040322 -PL - England -TA - Plant Cell -JT - The Plant cell -JID - 9208688 -RN - 0 (DNA, Plant) -RN - 0 (DNA-Binding Proteins) -RN - 0 (ENOD40 RNA) -RN - 0 (Nuclear Proteins) -RN - 0 (Plant Proteins) -RN - 0 (RNA, Long Noncoding) -RN - 0 (RNA, Messenger) -RN - 0 (RNA, Plant) -RN - 0 (RNA, Untranslated) -RN - 0 (Recombinant Fusion Proteins) -SB - IM -EIN - Plant Cell. 2017 Apr;29(4):912. PMID: 28351988 -MH - Amino Acid Sequence -MH - Base Sequence -MH - Cytoplasm/metabolism -MH - DNA, Plant/genetics -MH - DNA-Binding Proteins/genetics/metabolism -MH - Gene Expression -MH - Medicago/*genetics/*metabolism -MH - Molecular Sequence Data -MH - Nuclear Proteins/genetics/metabolism -MH - Onions/genetics/metabolism -MH - Plant Proteins/genetics/metabolism -MH - Plants, Genetically Modified -MH - RNA, Long Noncoding -MH - RNA, Messenger/*genetics -MH - RNA, Plant/*genetics -MH - RNA, Untranslated/*genetics -MH - Recombinant Fusion Proteins/genetics/metabolism -MH - Sequence Homology, Amino Acid -MH - Two-Hybrid System Techniques -PMC - PMC412876 -EDAT- 2004/03/24 05:00 -MHDA- 2004/06/26 05:00 -CRDT- 2004/03/24 05:00 -PHST- 2004/03/24 05:00 [pubmed] -PHST- 2004/06/26 05:00 [medline] -PHST- 2004/03/24 05:00 [entrez] -AID - tpc.019406 [pii] -AID - 019406 [pii] -AID - 10.1105/tpc.019406 [doi] -PST - ppublish -SO - Plant Cell. 2004 Apr;16(4):1047-59. doi: 10.1105/tpc.019406. Epub 2004 Mar 22. - - -##### PUB RECORD ##### -## 10.1073/pnas.0400595101 15070781 PMC384810 Mitra, Gleason, et al., 2004 "Mitra RM, Gleason CA, Edwards A, Hadfield J, Downie JA, Oldroyd GE, Long SR. A Ca2+/calmodulin-dependent protein kinase required for symbiotic nodule development: Gene identification by transcript-based cloning. Proc Natl Acad Sci U S A. 2004 Mar 30;101(13):4701-5. doi: 10.1073/pnas.0400595101. Epub 2004 Mar 1. PMID: 15070781; PMCID: PMC384810." ## - -PMID- 15070781 -OWN - NLM -STAT- MEDLINE -DCOM- 20040719 -LR - 20181113 -IS - 0027-8424 (Print) -IS - 1091-6490 (Electronic) -IS - 0027-8424 (Linking) -VI - 101 -IP - 13 -DP - 2004 Mar 30 -TI - A Ca2+/calmodulin-dependent protein kinase required for symbiotic nodule - development: Gene identification by transcript-based cloning. -PG - 4701-5 -AB - In the establishment of the legume-rhizobial symbiosis, bacterial - lipochitooligosaccharide signaling molecules termed Nod factors activate the - formation of a novel root organ, the nodule. Nod factors elicit several responses - in plant root hair cells, including oscillations in cytoplasmic calcium levels - (termed calcium spiking) and alterations in root hair growth. A number of plant - mutants with defects in the Nod factor signaling pathway have been identified. - One such Medicago truncatula mutant, dmi3, exhibits calcium spiking and root hair - swelling in response to Nod factor, but fails to initiate symbiotic gene - expression or cell divisions for nodule formation. On the basis of these data, it - is thought that the dmi3 mutant perceives Nod factor but fails to transduce the - signal downstream of calcium spiking. Additionally, the dmi3 mutant is defective - in the symbiosis with mycorrhizal fungi, indicating the importance of the encoded - protein in multiple symbioses. We report the identification of the DMI3 gene, - using a gene cloning method based on transcript abundance. We show that - transcript-based cloning is a valid approach for cloning genes in barley, - indicating the value of this technology in crop plants. DMI3 encodes a - calcium/calmodulin-dependent protein kinase. Mutants in pea sym9 have phenotypes - similar to dmi3 and have alterations in this gene. The DMI3 class of proteins is - well conserved among plants that interact with mycorrhizal fungi, but it is less - conserved in Arabidopsis thaliana, which does not participate in the mycorrhizal - symbiosis. -FAU - Mitra, Raka M -AU - Mitra RM -AD - Department of Biological Sciences, 371 Serra Mall, Stanford University, Stanford, - CA 94305-5020, USA. -FAU - Gleason, Cynthia A -AU - Gleason CA -FAU - Edwards, Anne -AU - Edwards A -FAU - Hadfield, James -AU - Hadfield J -FAU - Downie, J Allan -AU - Downie JA -FAU - Oldroyd, Giles E D -AU - Oldroyd GE -FAU - Long, Sharon R -AU - Long SR -LA - eng -SI - GENBANK/AJ621916 -SI - GENBANK/AY496049 -PT - Journal Article -PT - Research Support, Non-U.S. Gov't -PT - Research Support, U.S. Gov't, Non-P.H.S. -DEP - 20040301 -PL - United States -TA - Proc Natl Acad Sci U S A -JT - Proceedings of the National Academy of Sciences of the United States of America -JID - 7505876 -RN - 0 (DNA Primers) -RN - 0 (Recombinant Proteins) -RN - EC 2.7.11.17 (Calcium-Calmodulin-Dependent Protein Kinases) -SB - IM -CIN - Proc Natl Acad Sci U S A. 2004 Mar 30;101(13):4339-40. PMID: 15070718 -MH - Amino Acid Sequence -MH - Base Sequence -MH - Calcium-Calmodulin-Dependent Protein Kinases/*genetics/*metabolism -MH - Cloning, Molecular -MH - Conserved Sequence -MH - DNA Primers -MH - Hordeum/enzymology/physiology -MH - Medicago/*enzymology/*physiology -MH - Molecular Sequence Data -MH - Mycorrhizae/physiology -MH - Recombinant Proteins/metabolism -MH - Reverse Transcriptase Polymerase Chain Reaction -MH - Sequence Alignment -MH - Sequence Homology, Amino Acid -MH - Symbiosis -MH - Transcription, Genetic -PMC - PMC384810 -EDAT- 2004/04/09 05:00 -MHDA- 2004/07/20 05:00 -CRDT- 2004/04/09 05:00 -PHST- 2004/04/09 05:00 [pubmed] -PHST- 2004/07/20 05:00 [medline] -PHST- 2004/04/09 05:00 [entrez] -AID - 0400595101 [pii] -AID - 1014701 [pii] -AID - 10.1073/pnas.0400595101 [doi] -PST - ppublish -SO - Proc Natl Acad Sci U S A. 2004 Mar 30;101(13):4701-5. doi: - 10.1073/pnas.0400595101. Epub 2004 Mar 1. - - -##### PUB RECORD ##### -## 10.1104/pp.105.069054 16244141 PMC1283775 Isayenkov, Mrosk, et al., 2005 "Isayenkov S, Mrosk C, Stenzel I, Strack D, Hause B. Suppression of allene oxide cyclase in hairy roots of Medicago truncatula reduces jasmonate levels and the degree of mycorrhization with Glomus intraradices. Plant Physiol. 2005 Nov;139(3):1401-10. doi: 10.1104/pp.105.069054. Epub 2005 Oct 21. PMID: 16244141; PMCID: PMC1283775." ## - -PMID- 16244141 -OWN - NLM -STAT- MEDLINE -DCOM- 20060209 -LR - 20181113 -IS - 0032-0889 (Print) -IS - 1532-2548 (Electronic) -IS - 0032-0889 (Linking) -VI - 139 -IP - 3 -DP - 2005 Nov -TI - Suppression of allene oxide cyclase in hairy roots of Medicago truncatula reduces - jasmonate levels and the degree of mycorrhization with Glomus intraradices. -PG - 1401-10 -AB - During the symbiotic interaction between Medicago truncatula and the arbuscular - mycorrhizal (AM) fungus Glomus intraradices, an endogenous increase in jasmonic - acid (JA) occurs. Two full-length cDNAs coding for the JA-biosynthetic enzyme - allene oxide cyclase (AOC) from M. truncatula, designated as MtAOC1 and MtAOC2, - were cloned and characterized. The AOC protein was localized in plastids and - found to occur constitutively in all vascular tissues of M. truncatula. In leaves - and roots, MtAOCs are expressed upon JA application. Enhanced expression was also - observed during mycorrhization with G. intraradices. A partial suppression of - MtAOC expression was achieved in roots following transformation with - Agrobacterium rhizogenes harboring the MtAOC1 cDNA in the antisense direction - under control of the cauliflower mosaic virus 35S promoter. In comparison to - samples transformed with 35SuidA, roots with suppressed MtAOC1 expression - exhibited lower JA levels and a remarkable delay in the process of colonization - with G. intraradices. Both the mycorrhization rate, quantified by fungal rRNA, - and the arbuscule formation, analyzed by the expression level of the AM-specific - gene MtPT4, were affected. Staining of fungal material in roots with suppressed - MtAOC1 revealed a decreased number of arbuscules, but these did not exhibit an - altered structure. Our results indicate a crucial role for JA in the - establishment of AM symbiosis. -FAU - Isayenkov, Stanislav -AU - Isayenkov S -AD - Department of Secondary Metabolism , Leibniz Institute of Plant Biochemistry, - D-06120 Halle , Germany. -FAU - Mrosk, Cornelia -AU - Mrosk C -FAU - Stenzel, Irene -AU - Stenzel I -FAU - Strack, Dieter -AU - Strack D -FAU - Hause, Bettina -AU - Hause B -LA - eng -SI - GENBANK/AJ308489 -SI - GENBANK/AJ866733 -PT - Journal Article -PT - Research Support, Non-U.S. Gov't -DEP - 20051021 -PL - United States -TA - Plant Physiol -JT - Plant physiology -JID - 0401224 -RN - 0 (Cyclopentanes) -RN - 0 (DNA, Complementary) -RN - 0 (Oxylipins) -RN - 0 (RNA, Messenger) -RN - 6RI5N05OWW (jasmonic acid) -RN - EC 5.3.- (Intramolecular Oxidoreductases) -RN - EC 5.3.99.6 (hydroperoxide isomerase) -SB - IM -MH - Cyclopentanes/*metabolism/pharmacology -MH - DNA, Complementary/genetics -MH - Gene Expression Profiling -MH - Gene Expression Regulation, Developmental -MH - Intramolecular Oxidoreductases/*antagonists & inhibitors/genetics/metabolism -MH - Medicago truncatula/*enzymology/microbiology -MH - Molecular Sequence Data -MH - Mycorrhizae/cytology/drug effects/*metabolism -MH - Organ Specificity -MH - Oxylipins -MH - Plant Leaves/cytology/drug effects -MH - Plant Roots/cytology/drug effects/*enzymology -MH - Plants, Genetically Modified -MH - Protein Transport -MH - RNA, Messenger/genetics/metabolism -MH - Symbiosis -MH - Transformation, Genetic -PMC - PMC1283775 -EDAT- 2005/10/26 09:00 -MHDA- 2006/02/10 09:00 -CRDT- 2005/10/26 09:00 -PHST- 2005/10/26 09:00 [pubmed] -PHST- 2006/02/10 09:00 [medline] -PHST- 2005/10/26 09:00 [entrez] -AID - pp.105.069054 [pii] -AID - 069054 [pii] -AID - 10.1104/pp.105.069054 [doi] -PST - ppublish -SO - Plant Physiol. 2005 Nov;139(3):1401-10. doi: 10.1104/pp.105.069054. Epub 2005 Oct - 21. - - -##### PUB RECORD ##### -## 10.1093/jxb/erw474 28073951 PMC6055581 Herrbach, Chirinos, et al., 2017 "Herrbach V, Chirinos X, Rengel D, Agbevenou K, Vincent R, Pateyron S, Huguet S, Balzergue S, Pasha A, Provart N, Gough C, Bensmihen S. Nod factors potentiate auxin signaling for transcriptional regulation and lateral root formation in Medicago truncatula. J Exp Bot. 2017 Jan 1;68(3):569-583. doi: 10.1093/jxb/erw474. PMID: 28073951; PMCID: PMC6055581." ## - -PMID- 28073951 -OWN - NLM -STAT- MEDLINE -DCOM- 20171117 -LR - 20210109 -IS - 1460-2431 (Electronic) -IS - 0022-0957 (Print) -IS - 0022-0957 (Linking) -VI - 68 -IP - 3 -DP - 2017 Jan 1 -TI - Nod factors potentiate auxin signaling for transcriptional regulation and lateral - root formation in Medicago truncatula. -PG - 569-583 -LID - 10.1093/jxb/erw474 [doi] -AB - Nodulation (Nod) factors (NFs) are symbiotic molecules produced by rhizobia that - are essential for establishment of the rhizobium-legume endosymbiosis. Purified - NFs can stimulate lateral root formation (LRF) in Medicago truncatula, but little - is known about the molecular mechanisms involved. Using a combination of reporter - constructs, pharmacological and genetic approaches, we show that NFs act on early - steps of LRF in M. truncatula, independently of the ethylene signaling pathway - and of the cytokinin receptor MtCRE1, but in interaction with auxin. We conducted - a whole-genome transcriptomic study upon NF and/or auxin treatments, using a - lateral root inducible system adapted for M. truncatula. This revealed a large - overlap between NF and auxin signaling and, more interestingly, synergistic - interactions between these molecules. Three groups showing interaction effects - were defined: group 1 contained more than 1500 genes responding specifically to - the combinatorial treatment of NFs and auxin; group 2 comprised auxin-regulated - genes whose expression was enhanced or antagonized by NFs; and in group 3 the - expression of NF regulated genes was antagonized by auxin. Groups 1 and 2 were - enriched in signaling and metabolic functions, which highlights important - crosstalk between NF and auxin signaling for both developmental and symbiotic - processes. -CI - (c) The Author 2017. Published by Oxford University Press on behalf of the Society - for Experimental Biology. -FAU - Herrbach, Violaine -AU - Herrbach V -AD - LIPM, Universite de Toulouse, INRA, CNRS, Castanet-Tolosan, France. -FAU - Chirinos, Ximena -AU - Chirinos X -AD - LIPM, Universite de Toulouse, INRA, CNRS, Castanet-Tolosan, France. -FAU - Rengel, David -AU - Rengel D -AD - LIPM, Universite de Toulouse, INRA, CNRS, Castanet-Tolosan, France. -FAU - Agbevenou, Kokoevi -AU - Agbevenou K -AD - LIPM, Universite de Toulouse, INRA, CNRS, Castanet-Tolosan, France. -FAU - Vincent, Remy -AU - Vincent R -AD - LIPM, Universite de Toulouse, INRA, CNRS, Castanet-Tolosan, France. -FAU - Pateyron, Stephanie -AU - Pateyron S -AD - POPS (transcriptOmic Platform of IPS2) Platform, Institute of Plant Sciences - Paris Saclay (IPS2), CNRS, INRA, Universite Paris-Sud, Universite Evry, - Universite Paris-Saclay, Orsay, France. -AD - Institute of Plant Sciences Paris-Saclay IPS2, Paris Diderot, Sorbonne - Paris-Cite, Orsay, France. -FAU - Huguet, Stephanie -AU - Huguet S -AD - POPS (transcriptOmic Platform of IPS2) Platform, Institute of Plant Sciences - Paris Saclay (IPS2), CNRS, INRA, Universite Paris-Sud, Universite Evry, - Universite Paris-Saclay, Orsay, France. -AD - Institute of Plant Sciences Paris-Saclay IPS2, Paris Diderot, Sorbonne - Paris-Cite, Orsay, France. -FAU - Balzergue, Sandrine -AU - Balzergue S -AD - POPS (transcriptOmic Platform of IPS2) Platform, Institute of Plant Sciences - Paris Saclay (IPS2), CNRS, INRA, Universite Paris-Sud, Universite Evry, - Universite Paris-Saclay, Orsay, France. -AD - Institute of Plant Sciences Paris-Saclay IPS2, Paris Diderot, Sorbonne - Paris-Cite, Orsay, France. -FAU - Pasha, Asher -AU - Pasha A -AD - Department of Cell & Systems Biology/ Centre for the Analysis of Genome Evolution - and Function, University of Toronto, Toronto, Canada. -FAU - Provart, Nicholas -AU - Provart N -AD - Department of Cell & Systems Biology/ Centre for the Analysis of Genome Evolution - and Function, University of Toronto, Toronto, Canada. -FAU - Gough, Clare -AU - Gough C -AD - LIPM, Universite de Toulouse, INRA, CNRS, Castanet-Tolosan, France. -FAU - Bensmihen, Sandra -AU - Bensmihen S -AD - LIPM, Universite de Toulouse, INRA, CNRS, Castanet-Tolosan, France. -LA - eng -PT - Journal Article -PL - England -TA - J Exp Bot -JT - Journal of experimental botany -JID - 9882906 -RN - 0 (Indoleacetic Acids) -RN - 0 (Lipopolysaccharides) -RN - 0 (Plant Growth Regulators) -SB - IM -MH - *Gene Expression Regulation, Plant -MH - Indoleacetic Acids/*metabolism -MH - Lipopolysaccharides/*physiology -MH - Medicago truncatula/genetics/growth & development/microbiology/*physiology -MH - Plant Growth Regulators/*metabolism -MH - Plant Roots/genetics/growth & development/microbiology -MH - Sinorhizobium meliloti/*physiology -PMC - PMC6055581 -OTO - NOTNLM -OT - Auxin -OT - NimbleGen arrays -OT - Nod factors -OT - ethylene -OT - lateral root -OT - lateral root inducible system (LRIS) -OT - lipo-chitooligosaccharides (LCOs) -OT - symbiosis -OT - transcriptome -EDAT- 2017/01/12 06:00 -MHDA- 2017/11/29 06:00 -CRDT- 2017/01/12 06:00 -PHST- 2017/01/12 06:00 [pubmed] -PHST- 2017/11/29 06:00 [medline] -PHST- 2017/01/12 06:00 [entrez] -AID - erw474 [pii] -AID - 10.1093/jxb/erw474 [doi] -PST - ppublish -SO - J Exp Bot. 2017 Jan 1;68(3):569-583. doi: 10.1093/jxb/erw474. - - -##### PUB RECORD ##### -## 10.7554/elife.80741 36856086 PMC9991063 Lace, Su, et al., 2023 "Lace B, Su C, Invernot Perez D, Rodriguez-Franco M, Vernié T, Batzenschlager M, Egli S, Liu CW, Ott T. RPG acts as a central determinant for infectosome formation and cellular polarization during intracellular rhizobial infections. Elife. 2023 Mar 1;12:e80741. doi: 10.7554/eLife.80741. PMID: 36856086; PMCID: PMC9991063." ## - -PMID- 36856086 -OWN - NLM -STAT- MEDLINE -DCOM- 20230309 -LR - 20230321 -IS - 2050-084X (Electronic) -IS - 2050-084X (Linking) -VI - 12 -DP - 2023 Mar 1 -TI - RPG acts as a central determinant for infectosome formation and cellular - polarization during intracellular rhizobial infections. -LID - 10.7554/eLife.80741 [doi] -LID - e80741 -AB - Host-controlled intracellular accommodation of nitrogen-fixing bacteria is - essential for the establishment of a functional Root Nodule Symbiosis (RNS). In - many host plants, this occurs via transcellular tubular structures (infection - threads - ITs) that extend across cell layers via polar tip-growth. Comparative - phylogenomic studies have identified RPG (RHIZOBIUM-DIRECTED POLAR GROWTH) among - the critical genetic determinants for bacterial infection. In Medicago - truncatula, RPG is required for effective IT progression within root hairs but - the cellular and molecular function of the encoded protein remains elusive. Here, - we show that RPG resides in the protein complex formed by the core endosymbiotic - components VAPYRIN (VPY) and LUMPY INFECTION (LIN) required for IT polar growth, - co-localizes with both VPY and LIN in IT tip- and perinuclear-associated puncta - of M. truncatula root hairs undergoing infection and is necessary for VPY - recruitment into these structures. Fluorescence Lifetime Imaging Microscopy - (FLIM) of phosphoinositide species during bacterial infection revealed that - functional RPG is required to sustain strong membrane polarization at the - advancing tip of the IT. In addition, loss of RPG functionality alters the - cytoskeleton-mediated connectivity between the IT tip and the nucleus and affects - the polar secretion of the cell wall modifying enzyme NODULE PECTATE LYASE (NPL). - Our results integrate RPG into a core host machinery required to support symbiont - accommodation, suggesting that its occurrence in plant host genomes is essential - to co-opt a multimeric protein module committed to endosymbiosis to sustain - IT-mediated bacterial infection. -CI - (c) 2023, Lace et al. -FAU - Lace, Beatrice -AU - Lace B -AUID- ORCID: 0000-0002-4732-573X -AD - University of Freiburg, Faculty of Biology, Freiburg, Germany. -FAU - Su, Chao -AU - Su C -AD - University of Freiburg, Faculty of Biology, Freiburg, Germany. -FAU - Invernot Perez, Daniel -AU - Invernot Perez D -AD - University of Freiburg, Faculty of Biology, Freiburg, Germany. -FAU - Rodriguez-Franco, Marta -AU - Rodriguez-Franco M -AUID- ORCID: 0000-0003-1183-2075 -AD - University of Freiburg, Faculty of Biology, Freiburg, Germany. -FAU - Vernie, Tatiana -AU - Vernie T -AD - LRSV, Universite de Toulouse, CNRS, UPS, INP Toulouse, Castanet-Tolosan, France. -FAU - Batzenschlager, Morgane -AU - Batzenschlager M -AD - University of Freiburg, Faculty of Biology, Freiburg, Germany. -FAU - Egli, Sabrina -AU - Egli S -AD - University of Freiburg, Faculty of Biology, Freiburg, Germany. -FAU - Liu, Cheng-Wu -AU - Liu CW -AUID- ORCID: 0000-0002-6650-6245 -AD - School of Life Sciences, Division of Life Sciences and Medicine, MOE Key - Laboratory for Membraneless Organelles and Cellular Dynamics, University of - Science and Technology of China, Hefei, China. -FAU - Ott, Thomas -AU - Ott T -AUID- ORCID: 0000-0002-4494-9811 -AD - University of Freiburg, Faculty of Biology, Freiburg, Germany. -AD - CIBSS - Centre of Integrative Biological Signalling Studies, University of - Freiburg, Freiburg, Germany. -LA - eng -GR - OPP1172165/GATES/Bill & Melinda Gates Foundation/United States -PT - Journal Article -PT - Research Support, Non-U.S. Gov't -PT - Research Support, U.S. Gov't, Non-P.H.S. -DEP - 20230301 -PL - England -TA - Elife -JT - eLife -JID - 101579614 -SB - IM -UOF - doi: 10.1101/2022.06.03.494689 -MH - *Rhizobium -MH - Symbiosis -MH - *Nitrogen-Fixing Bacteria -MH - Cell Nucleus -MH - Cell Wall -PMC - PMC9991063 -OTO - NOTNLM -OT - infection thread -OT - legume -OT - nodulation -OT - plant biology -OT - polarity -OT - rhizobia -OT - symbiosis -COIS- BL, CS, DI, MR, TV, MB, SE, CL, TO No competing interests declared -EDAT- 2023/03/02 06:00 -MHDA- 2023/03/10 06:00 -CRDT- 2023/03/01 05:54 -PHST- 2022/06/01 00:00 [received] -PHST- 2023/02/21 00:00 [accepted] -PHST- 2023/03/02 06:00 [pubmed] -PHST- 2023/03/10 06:00 [medline] -PHST- 2023/03/01 05:54 [entrez] -AID - 80741 [pii] -AID - 10.7554/eLife.80741 [doi] -PST - epublish -SO - Elife. 2023 Mar 1;12:e80741. doi: 10.7554/eLife.80741. - - -##### PUB RECORD ##### -## 10.1104/pp.109.143024 19789288 PMC2773094 Kuppusamy, Ivashuta, et al., 2009 "Kuppusamy KT, Ivashuta S, Bucciarelli B, Vance CP, Gantt JS, Vandenbosch KA. Knockdown of CELL DIVISION CYCLE16 reveals an inverse relationship between lateral root and nodule numbers and a link to auxin in Medicago truncatula. Plant Physiol. 2009 Nov;151(3):1155-66. doi: 10.1104/pp.109.143024. Epub 2009 Sep 29. PMID: 19789288; PMCID: PMC2773094." ## - -PMID- 19789288 -OWN - NLM -STAT- MEDLINE -DCOM- 20100127 -LR - 20220318 -IS - 1532-2548 (Electronic) -IS - 0032-0889 (Print) -IS - 0032-0889 (Linking) -VI - 151 -IP - 3 -DP - 2009 Nov -TI - Knockdown of CELL DIVISION CYCLE16 reveals an inverse relationship between - lateral root and nodule numbers and a link to auxin in Medicago truncatula. -PG - 1155-66 -LID - 10.1104/pp.109.143024 [doi] -AB - The postembryonic development of lateral roots and nodules is a highly regulated - process. Recent studies suggest the existence of cross talk and interdependency - in the growth of these two organs. Although plant hormones, including auxin and - cytokinin, appear to be key players in coordinating this cross talk, very few - genes that cross-regulate root and nodule development have been uncovered so far. - This study reports that a homolog of CELL DIVISION CYCLE16 (CDC16), a core - component of the Anaphase Promoting Complex, is one of the key mediators in - controlling the overall number of lateral roots and nodules. A partial - suppression of this gene in Medicago truncatula leads to a decrease in number of - lateral roots and a 4-fold increase in number of nodules. The roots showing - lowered expression of MtCDC16 also show reduced sensitivity to phytohormone - auxin, thus providing a potential function of CDC16 in auxin signaling. -FAU - Kuppusamy, Kavitha T -AU - Kuppusamy KT -AD - Department of Plant Biology, University of Minnesota, St. Paul, Minnesota 55108, - USA. -FAU - Ivashuta, Sergey -AU - Ivashuta S -FAU - Bucciarelli, Bruna -AU - Bucciarelli B -FAU - Vance, Carroll P -AU - Vance CP -FAU - Gantt, J Stephen -AU - Gantt JS -FAU - Vandenbosch, Kathryn A -AU - Vandenbosch KA -LA - eng -SI - GENBANK/GU075685 -SI - GENBANK/GU075686 -PT - Journal Article -PT - Research Support, Non-U.S. Gov't -PT - Research Support, U.S. Gov't, Non-P.H.S. -DEP - 20090929 -PL - United States -TA - Plant Physiol -JT - Plant physiology -JID - 0401224 -RN - 0 (Cell Cycle Proteins) -RN - 0 (DNA, Plant) -RN - 0 (Indoleacetic Acids) -RN - 0 (Plant Growth Regulators) -RN - 0 (Plant Proteins) -SB - IM -MH - Amino Acid Sequence -MH - Cell Cycle Proteins/genetics/*metabolism -MH - DNA, Plant/genetics -MH - Gene Expression Regulation, Plant -MH - Gene Knockdown Techniques -MH - Indoleacetic Acids/*metabolism -MH - Medicago truncatula/cytology/*genetics/growth & development -MH - Molecular Sequence Data -MH - Oligonucleotide Array Sequence Analysis -MH - Plant Growth Regulators/metabolism -MH - Plant Proteins/genetics/*metabolism -MH - Plant Root Nodulation/*genetics -MH - Plants, Genetically Modified/cytology/genetics/growth & development -MH - RNA Interference -MH - Root Nodules, Plant/*growth & development -MH - Sequence Analysis, DNA -PMC - PMC2773094 -EDAT- 2009/10/01 06:00 -MHDA- 2010/01/28 06:00 -CRDT- 2009/10/01 06:00 -PHST- 2009/10/01 06:00 [entrez] -PHST- 2009/10/01 06:00 [pubmed] -PHST- 2010/01/28 06:00 [medline] -AID - pp.109.143024 [pii] -AID - 143024 [pii] -AID - 10.1104/pp.109.143024 [doi] -PST - ppublish -SO - Plant Physiol. 2009 Nov;151(3):1155-66. doi: 10.1104/pp.109.143024. Epub 2009 Sep - 29. - - -##### PUB RECORD ##### -## 10.1105/tpc.107.053975 18156218 PMC2217646 Kevei, Lougnon, et al., 2007 "Kevei Z, Lougnon G, Mergaert P, Horváth GV, Kereszt A, Jayaraman D, Zaman N, Marcel F, Regulski K, Kiss GB, Kondorosi A, Endre G, Kondorosi E, Ané JM. 3-hydroxy-3-methylglutaryl coenzyme a reductase 1 interacts with NORK and is crucial for nodulation in Medicago truncatula. Plant Cell. 2007 Dec;19(12):3974-89. doi: 10.1105/tpc.107.053975. Epub 2007 Dec 21. PMID: 18156218; PMCID: PMC2217646." ## - -PMID- 18156218 -OWN - NLM -STAT- MEDLINE -DCOM- 20080808 -LR - 20181113 -IS - 1040-4651 (Print) -IS - 1532-298X (Electronic) -IS - 1040-4651 (Linking) -VI - 19 -IP - 12 -DP - 2007 Dec -TI - 3-hydroxy-3-methylglutaryl coenzyme a reductase 1 interacts with NORK and is - crucial for nodulation in Medicago truncatula. -PG - 3974-89 -AB - NORK in legumes encodes a receptor-like kinase that is required for Nod factor - signaling and root nodule development. Using Medicago truncatula NORK as bait in - a yeast two-hybrid assay, we identified 3-hydroxy-3-methylglutaryl CoA reductase - 1 (Mt HMGR1) as a NORK interacting partner. HMGR1 belongs to a multigene family - in M. truncatula, and different HMGR isoforms are key enzymes in the mevalonate - biosynthetic pathway leading to the production of a diverse array of isoprenoid - compounds. Testing other HMGR members revealed a specific interaction between - NORK and HMGR1. Mutagenesis and deletion analysis showed that this interaction - requires the cytosolic active kinase domain of NORK and the cytosolic catalytic - domain of HMGR1. NORK homologs from Lotus japonicus and Sesbania rostrata also - interacted with Mt HMGR1, but homologous nonsymbiotic kinases of M. truncatula - did not. Pharmacological inhibition of HMGR activities decreased nodule number - and delayed nodulation, supporting the importance of the mevalonate pathway in - symbiotic development. Decreasing HMGR1 expression in M. truncatula transgenic - roots by RNA interference led to a dramatic decrease in nodulation, confirming - that HMGR1 is essential for nodule development. Recruitment of HMGR1 by NORK - could be required for production of specific isoprenoid compounds, such as - cytokinins, phytosteroids, or isoprenoid moieties involved in modification of - signaling proteins. -FAU - Kevei, Zoltan -AU - Kevei Z -AD - Institut des Sciences du Vegetal, Centre National de la Recherche Scientifique, - Unite Propre de Recherche 2355, 91198 Gif-sur-Yvette Cedex, France. -FAU - Lougnon, Geraldine -AU - Lougnon G -FAU - Mergaert, Peter -AU - Mergaert P -FAU - Horvath, Gabor V -AU - Horvath GV -FAU - Kereszt, Attila -AU - Kereszt A -FAU - Jayaraman, Dhileepkumar -AU - Jayaraman D -FAU - Zaman, Najia -AU - Zaman N -FAU - Marcel, Fabian -AU - Marcel F -FAU - Regulski, Krzysztof -AU - Regulski K -FAU - Kiss, Gyorgy B -AU - Kiss GB -FAU - Kondorosi, Adam -AU - Kondorosi A -FAU - Endre, Gabriella -AU - Endre G -FAU - Kondorosi, Eva -AU - Kondorosi E -FAU - Ane, Jean-Michel -AU - Ane JM -LA - eng -SI - GENBANK/AF492655 -SI - GENBANK/AJ418369 -SI - GENBANK/AY751547 -SI - GENBANK/EU302813 -SI - GENBANK/EU302814 -SI - GENBANK/EU302815 -SI - GENBANK/EU302816 -SI - GENBANK/EU302817 -PT - Journal Article -DEP - 20071221 -PL - England -TA - Plant Cell -JT - The Plant cell -JID - 9208688 -RN - 0 (Plant Proteins) -RN - 0 (Protein Isoforms) -RN - 9LHU78OQFD (Lovastatin) -RN - EC 1.1.1.- (Hydroxymethylglutaryl CoA Reductases) -SB - IM -MH - Amino Acid Sequence -MH - Enzyme Activation/drug effects -MH - Gene Expression Regulation, Plant/drug effects -MH - Hydroxymethylglutaryl CoA Reductases/genetics/*metabolism -MH - Immunoprecipitation -MH - In Situ Hybridization -MH - Lovastatin/pharmacology -MH - Medicago truncatula/genetics/*metabolism/microbiology -MH - Models, Genetic -MH - Molecular Sequence Data -MH - Mutation -MH - Plant Proteins/chemistry/genetics/*metabolism -MH - Protein Binding -MH - Protein Isoforms/chemistry/genetics/metabolism -MH - Protein Structure, Tertiary -MH - RNA Interference -MH - Reverse Transcriptase Polymerase Chain Reaction -MH - Root Nodules, Plant/genetics/*metabolism/microbiology -MH - Sequence Homology, Amino Acid -MH - Sinorhizobium meliloti/growth & development -MH - Symbiosis -MH - Two-Hybrid System Techniques -PMC - PMC2217646 -EDAT- 2007/12/25 09:00 -MHDA- 2008/08/09 09:00 -CRDT- 2007/12/25 09:00 -PHST- 2007/12/25 09:00 [pubmed] -PHST- 2008/08/09 09:00 [medline] -PHST- 2007/12/25 09:00 [entrez] -AID - tpc.107.053975 [pii] -AID - 053975 [pii] -AID - 10.1105/tpc.107.053975 [doi] -PST - ppublish -SO - Plant Cell. 2007 Dec;19(12):3974-89. doi: 10.1105/tpc.107.053975. Epub 2007 Dec - 21. - - -##### PUB RECORD ##### -## 10.1186/s13007-015-0053-y 25774204 PMC4359497 Oellrich, Walls et al., 2015 "Oellrich A, Walls RL, Cannon EK, Cannon SB, Cooper L, Gardiner J, Gkoutos GV, Harper L, He M, Hoehndorf R, Jaiswal P, Kalberer SR, Lloyd JP, Meinke D, Menda N, Moore L, Nelson RT, Pujar A, Lawrence CJ, Huala E. An ontology approach to comparative phenomics in plants. Plant Methods. 2015 Feb 25;11:10. doi: 10.1186/s13007-015-0053-y. PMID: 25774204; PMCID: PMC4359497." ## - -PMID- 25774204 -OWN - NLM -STAT- PubMed-not-MEDLINE -DCOM- 20150316 -LR - 20220310 -IS - 1746-4811 (Print) -IS - 1746-4811 (Electronic) -IS - 1746-4811 (Linking) -VI - 11 -DP - 2015 -TI - An ontology approach to comparative phenomics in plants. -PG - 10 -LID - 10.1186/s13007-015-0053-y [doi] -LID - 10 -AB - BACKGROUND: Plant phenotype datasets include many different types of data, - formats, and terms from specialized vocabularies. Because these datasets were - designed for different audiences, they frequently contain language and details - tailored to investigators with different research objectives and backgrounds. - Although phenotype comparisons across datasets have long been possible on a small - scale, comprehensive queries and analyses that span a broad set of reference - species, research disciplines, and knowledge domains continue to be severely - limited by the absence of a common semantic framework. RESULTS: We developed a - workflow to curate and standardize existing phenotype datasets for six plant - species, encompassing both model species and crop plants with established genetic - resources. Our effort focused on mutant phenotypes associated with genes of known - sequence in Arabidopsis thaliana (L.) Heynh. (Arabidopsis), Zea mays L. subsp. - mays (maize), Medicago truncatula Gaertn. (barrel medic or Medicago), Oryza - sativa L. (rice), Glycine max (L.) Merr. (soybean), and Solanum lycopersicum L. - (tomato). We applied the same ontologies, annotation standards, formats, and best - practices across all six species, thereby ensuring that the shared dataset could - be used for cross-species querying and semantic similarity analyses. Curated - phenotypes were first converted into a common format using taxonomically broad - ontologies such as the Plant Ontology, Gene Ontology, and Phenotype and Trait - Ontology. We then compared ontology-based phenotypic descriptions with an - existing classification system for plant phenotypes and evaluated our semantic - similarity dataset for its ability to enhance predictions of gene families, - protein functions, and shared metabolic pathways that underlie informative plant - phenotypes. CONCLUSIONS: The use of ontologies, annotation standards, shared - formats, and best practices for cross-taxon phenotype data analyses represents a - novel approach to plant phenomics that enhances the utility of model genetic - organisms and can be readily applied to species with fewer genetic resources and - less well-characterized genomes. In addition, these tools should enhance future - efforts to explore the relationships among phenotypic similarity, gene function, - and sequence similarity in plants, and to make genotype-to-phenotype predictions - relevant to plant biology, crop improvement, and potentially even human health. -FAU - Oellrich, Anika -AU - Oellrich A -AD - Wellcome Trust Sanger Institute, Wellcome Trust Genome Campus, Hinxton, CB10 1SA - UK. -FAU - Walls, Ramona L -AU - Walls RL -AD - iPlant Collaborative, University of Arizona, 1657 E. Helen St., Tucson, Arizona - 85721 USA. -FAU - Cannon, Ethalinda Ks -AU - Cannon EK -AD - Department of Electrical and Computer Engineering Iowa State University, 1018 - Crop Informatics Lab, Ames, Iowa 50011 USA. -FAU - Cannon, Steven B -AU - Cannon SB -AD - USDA-ARS Corn Insects and Crop Genetics Research Unit, Iowa State University, - Crop Genome Informatics Lab, Iowa State University, Ames, IA 50011 USA. -AD - Department of Agronomy, Agronomy Hall, Iowa State University, Ames, IA 50010 USA. -FAU - Cooper, Laurel -AU - Cooper L -AD - Department of Botany and Plant Pathology, 2082 Cordley Hall, Oregon State - University, Corvallis, OR 97331 USA. -FAU - Gardiner, Jack -AU - Gardiner J -AD - Department of Genetics, Development and Cell Biology, Roy J Carver Co-Laboratory, - Iowa State University, Ames, IA 50010 USA. -FAU - Gkoutos, Georgios V -AU - Gkoutos GV -AD - Department of Computer Science, Aberystwyth University, Llandinam Building, - Aberystwyth, SY23 3DB UK. -FAU - Harper, Lisa -AU - Harper L -AD - USDA-ARS Corn Insects and Crop Genetics Research Unit, Iowa State University, - Crop Genome Informatics Lab, Iowa State University, Ames, IA 50011 USA. -FAU - He, Mingze -AU - He M -AD - Department of Genetics, Development and Cell Biology, Roy J Carver Co-Laboratory, - Iowa State University, Ames, IA 50010 USA. -FAU - Hoehndorf, Robert -AU - Hoehndorf R -AD - Computer, Electrical and Mathematical Sciences & Engineering Division and - Computational Bioscience Research Center, King Abdullah University of Science and - Technology, 4700 King Abdullah University of Science and Technology, P.O. Box - 2882, Thuwal, 23955-6900 Kingdom of Saudi Arabia. -FAU - Jaiswal, Pankaj -AU - Jaiswal P -AD - Department of Botany and Plant Pathology, 2082 Cordley Hall, Oregon State - University, Corvallis, OR 97331 USA. -FAU - Kalberer, Scott R -AU - Kalberer SR -AD - USDA-ARS Corn Insects and Crop Genetics Research Unit, Iowa State University, - Crop Genome Informatics Lab, Iowa State University, Ames, IA 50011 USA. -FAU - Lloyd, John P -AU - Lloyd JP -AD - Department of Plant Biology, Michigan State University, 220 Trowbridge Rd, East - Lansing, MI 48824 USA. -FAU - Meinke, David -AU - Meinke D -AD - Department of Botany, Oklahoma State University, 301 Physical Sciences, - Stillwater, OK 74078 USA. -FAU - Menda, Naama -AU - Menda N -AD - Boyce Thompson Institute for Plant Research, 533 Tower Road, Ithaca, NY 14853 - USA. -FAU - Moore, Laura -AU - Moore L -AD - Department of Botany and Plant Pathology, 2082 Cordley Hall, Oregon State - University, Corvallis, OR 97331 USA. -FAU - Nelson, Rex T -AU - Nelson RT -AD - USDA-ARS Corn Insects and Crop Genetics Research Unit, Iowa State University, - Crop Genome Informatics Lab, Iowa State University, Ames, IA 50011 USA. -FAU - Pujar, Anuradha -AU - Pujar A -AD - Boyce Thompson Institute for Plant Research, 533 Tower Road, Ithaca, NY 14853 - USA. -FAU - Lawrence, Carolyn J -AU - Lawrence CJ -AD - Department of Agronomy, Agronomy Hall, Iowa State University, Ames, IA 50010 USA. -AD - Department of Genetics, Development and Cell Biology, Roy J Carver Co-Laboratory, - Iowa State University, Ames, IA 50010 USA. -FAU - Huala, Eva -AU - Huala E -AD - Phoenix Bioinformatics, 643 Bair Island Rd Suite 403, Redwood City, CA 94063 USA. -LA - eng -PT - Journal Article -DEP - 20150225 -PL - England -TA - Plant Methods -JT - Plant methods -JID - 101245798 -PMC - PMC4359497 -EDAT- 2015/03/17 06:00 -MHDA- 2015/03/17 06:01 -CRDT- 2015/03/17 06:00 -PHST- 2014/12/08 00:00 [received] -PHST- 2015/02/05 00:00 [accepted] -PHST- 2015/03/17 06:00 [entrez] -PHST- 2015/03/17 06:00 [pubmed] -PHST- 2015/03/17 06:01 [medline] -AID - 53 [pii] -AID - 10.1186/s13007-015-0053-y [doi] -PST - epublish -SO - Plant Methods. 2015 Feb 25;11:10. doi: 10.1186/s13007-015-0053-y. eCollection - 2015. - - -##### PUB RECORD ##### -## 10.1111/j.1469-8137.2012.04147.x 22530598 null Cheng, Peng, et al., 2012 "Cheng X, Peng J, Ma J, Tang Y, Chen R, Mysore KS, Wen J. NO APICAL MERISTEM (MtNAM) regulates floral organ identity and lateral organ separation in Medicago truncatula. New Phytol. 2012 Jul;195(1):71-84. doi: 10.1111/j.1469-8137.2012.04147.x. Epub 2012 Apr 24. PMID: 22530598." ## - -PMID- 22530598 -OWN - NLM -STAT- MEDLINE -DCOM- 20121009 -LR - 20220331 -IS - 1469-8137 (Electronic) -IS - 0028-646X (Linking) -VI - 195 -IP - 1 -DP - 2012 Jul -TI - NO APICAL MERISTEM (MtNAM) regulates floral organ identity and lateral organ - separation in Medicago truncatula. -PG - 71-84 -LID - 10.1111/j.1469-8137.2012.04147.x [doi] -AB - * The CUP-SHAPED COTYLEDON (CUC)/NO APICAL MERISTEM (NAM) family of genes control - boundary formation and lateral organ separation, which is critical for proper - leaf and flower patterning. However, most downstream targets of CUC/NAM genes - remain unclear. * In a forward screen of the tobacco retrotransposon1 (Tnt1) - insertion population in Medicago truncatula, we isolated a weak allele of the - no-apical-meristem mutant mtnam-2. Meanwhile, we regenerated a mature plant from - the null allele mtnam-1. These materials allowed us to extensively characterize - the function of MtNAM and its downstream genes. * MtNAM is highly expressed in - vegetative shoot buds and inflorescence apices, specifically at boundaries - between the shoot apical meristem and leaf/flower primordia. Mature plants of the - regenerated null allele and the weak allele display remarkable floral phenotypes: - floral whorls and organ numbers are reduced and the floral organ identity is - compromised. Microarray and quantitative RT-PCR analyses revealed that all - classes of floral homeotic genes are down-regulated in mtnam mutants. Mutations - in MtNAM also lead to fused cotyledons and leaflets of the compound leaf as well - as a defective shoot apical meristem. * Our results revealed that MtNAM shares - the role of CUC/NAM family genes in lateral organ separation and compound leaf - development, and is also required for floral organ identity and development. -CI - (c) 2012 The Authors. New Phytologist (c) 2012 New Phytologist Trust. -FAU - Cheng, Xiaofei -AU - Cheng X -AD - Plant Biology Division, Samuel Roberts Noble Foundation, Ardmore, OK 73401, USA. -FAU - Peng, Jianling -AU - Peng J -FAU - Ma, Junying -AU - Ma J -FAU - Tang, Yuhong -AU - Tang Y -FAU - Chen, Rujin -AU - Chen R -FAU - Mysore, Kirankumar S -AU - Mysore KS -FAU - Wen, Jiangqi -AU - Wen J -LA - eng -SI - GENBANK/JF929904 -PT - Journal Article -PT - Research Support, Non-U.S. Gov't -PT - Research Support, U.S. Gov't, Non-P.H.S. -DEP - 20120424 -PL - England -TA - New Phytol -JT - The New phytologist -JID - 9882884 -RN - 0 (Plant Proteins) -RN - 0 (Retroelements) -SB - IM -MH - Cotyledon/anatomy & histology/genetics -MH - Flowers/genetics/*physiology -MH - *Gene Expression Regulation, Plant -MH - Genetic Association Studies -MH - Inflorescence/anatomy & histology/genetics -MH - Medicago truncatula/genetics/*physiology -MH - Meristem/*genetics/physiology -MH - Molecular Sequence Data -MH - Mutation -MH - Plant Leaves/genetics/growth & development -MH - Plant Proteins/*genetics/*metabolism -MH - Retroelements -EDAT- 2012/04/26 06:00 -MHDA- 2012/10/10 06:00 -CRDT- 2012/04/26 06:00 -PHST- 2012/04/26 06:00 [entrez] -PHST- 2012/04/26 06:00 [pubmed] -PHST- 2012/10/10 06:00 [medline] -AID - 10.1111/j.1469-8137.2012.04147.x [doi] -PST - ppublish -SO - New Phytol. 2012 Jul;195(1):71-84. doi: 10.1111/j.1469-8137.2012.04147.x. Epub - 2012 Apr 24. - - -##### PUB RECORD ##### -## 10.3389/fpls.2015.00575 26284091 PMC4517396 Chen, Liu, et al., 2015 "Chen DS, Liu CW, Roy S, Cousins D, Stacey N, Murray JD. Identification of a core set of rhizobial infection genes using data from single cell-types. Front Plant Sci. 2015 Jul 28;6:575. doi: 10.3389/fpls.2015.00575. PMID: 26284091; PMCID: PMC4517396." ## - -PMID- 26284091 -OWN - NLM -STAT- PubMed-not-MEDLINE -DCOM- 20150818 -LR - 20220129 -IS - 1664-462X (Print) -IS - 1664-462X (Electronic) -IS - 1664-462X (Linking) -VI - 6 -DP - 2015 -TI - Identification of a core set of rhizobial infection genes using data from single - cell-types. -PG - 575 -LID - 10.3389/fpls.2015.00575 [doi] -LID - 575 -AB - Genome-wide expression studies on nodulation have varied in their scale from - entire root systems to dissected nodules or root sections containing nodule - primordia (NP). More recently efforts have focused on developing methods for - isolation of root hairs from infected plants and the application of laser-capture - microdissection technology to nodules. Here we analyze two published data sets to - identify a core set of infection genes that are expressed in the nodule and in - root hairs during infection. Among the genes identified were those encoding - phenylpropanoid biosynthesis enzymes including Chalcone-O-Methyltransferase which - is required for the production of the potent Nod gene inducer - 4',4-dihydroxy-2-methoxychalcone. A promoter-GUS analysis in transgenic hairy - roots for two genes encoding Chalcone-O-Methyltransferase isoforms revealed their - expression in rhizobially infected root hairs and the nodule infection zone but - not in the nitrogen fixation zone. We also describe a group of Rhizobially - Induced Peroxidases whose expression overlaps with the production of superoxide - in rhizobially infected root hairs and in nodules and roots. Finally, we identify - a cohort of co-regulated transcription factors as candidate regulators of these - processes. -FAU - Chen, Da-Song -AU - Chen DS -AD - State Key Laboratory of Agricultural Microbiology, College of Life Science and - Technology, Huazhong Agricultural University, Wuhan China. -FAU - Liu, Cheng-Wu -AU - Liu CW -AD - John Innes Centre, Department of Cell and Developmental Biology, Norfolk UK. -FAU - Roy, Sonali -AU - Roy S -AD - John Innes Centre, Department of Cell and Developmental Biology, Norfolk UK. -FAU - Cousins, Donna -AU - Cousins D -AD - John Innes Centre, Department of Cell and Developmental Biology, Norfolk UK. -FAU - Stacey, Nicola -AU - Stacey N -AD - John Innes Centre, Department of Cell and Developmental Biology, Norfolk UK. -FAU - Murray, Jeremy D -AU - Murray JD -AD - John Innes Centre, Department of Cell and Developmental Biology, Norfolk UK. -LA - eng -GR - BB/G023832/1/BB_/Biotechnology and Biological Sciences Research Council/United - Kingdom -PT - Journal Article -DEP - 20150728 -PL - Switzerland -TA - Front Plant Sci -JT - Frontiers in plant science -JID - 101568200 -PMC - PMC4517396 -OTO - NOTNLM -OT - CCAAT-box -OT - Nod factors -OT - infection threads -OT - infection zone -OT - medicarpin -OT - methoxychalcone -OT - nod genes -OT - nodulation -EDAT- 2015/08/19 06:00 -MHDA- 2015/08/19 06:01 -CRDT- 2015/08/19 06:00 -PHST- 2015/05/12 00:00 [received] -PHST- 2015/07/13 00:00 [accepted] -PHST- 2015/08/19 06:00 [entrez] -PHST- 2015/08/19 06:00 [pubmed] -PHST- 2015/08/19 06:01 [medline] -AID - 10.3389/fpls.2015.00575 [doi] -PST - epublish -SO - Front Plant Sci. 2015 Jul 28;6:575. doi: 10.3389/fpls.2015.00575. eCollection - 2015. - - -##### PUB RECORD ##### -## 10.1105/tpc.15.00461 26672071 PMC4707452 Verni, Kim, et al., 2015 "Vernié T, Kim J, Frances L, Ding Y, Sun J, Guan D, Niebel A, Gifford ML, de Carvalho-Niebel F, Oldroyd GE. The NIN Transcription Factor Coordinates Diverse Nodulation Programs in Different Tissues of the Medicago truncatula Root. Plant Cell. 2015 Dec;27(12):3410-24. doi: 10.1105/tpc.15.00461. Epub 2015 Dec 15. PMID: 26672071; PMCID: PMC4707452." ## - -PMID- 26672071 -OWN - NLM -STAT- MEDLINE -DCOM- 20170130 -LR - 20210304 -IS - 1532-298X (Electronic) -IS - 1040-4651 (Print) -IS - 1040-4651 (Linking) -VI - 27 -IP - 12 -DP - 2015 Dec -TI - The NIN Transcription Factor Coordinates Diverse Nodulation Programs in Different - Tissues of the Medicago truncatula Root. -PG - 3410-24 -LID - 10.1105/tpc.15.00461 [doi] -AB - Biological nitrogen fixation in legumes occurs in nodules that are initiated in - the root cortex following Nod factor recognition at the root surface, and this - requires coordination of diverse developmental programs in these different - tissues. We show that while early Nod factor signaling associated with calcium - oscillations is limited to the root surface, the resultant activation of Nodule - Inception (NIN) in the root epidermis is sufficient to promote cytokinin - signaling and nodule organogenesis in the inner root cortex. NIN or a product of - its action must be associated with the transmission of a signal between the root - surface and the cortical cells where nodule organogenesis is initiated. NIN - appears to have distinct functions in the root epidermis and the root cortex. In - the epidermis, NIN restricts the extent of Early Nodulin 11 (ENOD11) expression - and does so through competitive inhibition of ERF Required for Nodulation (ERN1). - In contrast, NIN is sufficient to promote the expression of the cytokinin - receptor Cytokinin Response 1 (CRE1), which is restricted to the root cortex. Our - work in Medicago truncatula highlights the complexity of NIN action and places - NIN as a central player in the coordination of the symbiotic developmental - programs occurring in differing tissues of the root that combined are necessary - for a nitrogen-fixing symbiosis. -CI - (c) 2015 American Society of Plant Biologists. All rights reserved. -FAU - Vernie, Tatiana -AU - Vernie T -AUID- ORCID: 0000-0003-1387-6370 -AD - Department of Cell and Developmental Biology, John Innes Centre, Norwich NR4 7UH, - United Kingdom. -FAU - Kim, Jiyoung -AU - Kim J -AD - Department of Cell and Developmental Biology, John Innes Centre, Norwich NR4 7UH, - United Kingdom. -FAU - Frances, Lisa -AU - Frances L -AD - Laboratoire des Interactions Plantes Microorganismes, CNRS-INRA 2594/441, F-31320 - Castanet Tolosan, France. -FAU - Ding, Yiliang -AU - Ding Y -AD - Department of Cell and Developmental Biology, John Innes Centre, Norwich NR4 7UH, - United Kingdom. -FAU - Sun, Jongho -AU - Sun J -AD - Department of Cell and Developmental Biology, John Innes Centre, Norwich NR4 7UH, - United Kingdom. -FAU - Guan, Dian -AU - Guan D -AD - Department of Cell and Developmental Biology, John Innes Centre, Norwich NR4 7UH, - United Kingdom. -FAU - Niebel, Andreas -AU - Niebel A -AUID- ORCID: 0000-0002-3402-8381 -AD - Laboratoire des Interactions Plantes Microorganismes, CNRS-INRA 2594/441, F-31320 - Castanet Tolosan, France. -FAU - Gifford, Miriam L -AU - Gifford ML -AUID- ORCID: 0000-0002-4005-2513 -AD - School of Life Sciences, University of Warwick, Coventry CV4 7AL, United Kingdom. -FAU - de Carvalho-Niebel, Fernanda -AU - de Carvalho-Niebel F -AD - Laboratoire des Interactions Plantes Microorganismes, CNRS-INRA 2594/441, F-31320 - Castanet Tolosan, France. -FAU - Oldroyd, Giles E D -AU - Oldroyd GE -AD - Department of Cell and Developmental Biology, John Innes Centre, Norwich NR4 7UH, - United Kingdom giles.oldroyd@jic.ac.uk. -LA - eng -GR - BB/H019502/1/BB_/Biotechnology and Biological Sciences Research Council/United - Kingdom -GR - BB/J001872/1/BB_/Biotechnology and Biological Sciences Research Council/United - Kingdom -PT - Journal Article -PT - Research Support, Non-U.S. Gov't -DEP - 20151215 -PL - England -TA - Plant Cell -JT - The Plant cell -JID - 9208688 -RN - 0 (Cytokinins) -RN - 0 (ENOD11 protein, Medicago truncatula) -RN - 0 (NIN protein, Lotus japonicus) -RN - 0 (Plant Growth Regulators) -RN - 0 (Plant Proteins) -RN - 0 (Transcription Factors) -RN - SY7Q814VUP (Calcium) -SB - IM -MH - Calcium/metabolism -MH - Cytokinins/metabolism -MH - Gene Expression Regulation, Plant -MH - Genes, Reporter -MH - Medicago truncatula/cytology/*genetics/physiology -MH - Nitrogen Fixation -MH - Plant Growth Regulators/metabolism -MH - Plant Proteins/genetics/*metabolism -MH - Plant Root Nodulation -MH - Plant Roots/cytology/genetics/metabolism/physiology -MH - Plants, Genetically Modified -MH - Root Nodules, Plant/cytology/genetics/physiology -MH - *Signal Transduction -MH - Sinorhizobium meliloti/*physiology -MH - *Symbiosis -MH - Tobacco/cytology/genetics/physiology -MH - Transcription Factors/genetics/*metabolism -PMC - PMC4707452 -EDAT- 2015/12/17 06:00 -MHDA- 2017/01/31 06:00 -CRDT- 2015/12/17 06:00 -PHST- 2015/05/21 00:00 [received] -PHST- 2015/11/20 00:00 [accepted] -PHST- 2015/12/17 06:00 [entrez] -PHST- 2015/12/17 06:00 [pubmed] -PHST- 2017/01/31 06:00 [medline] -AID - tpc.15.00461 [pii] -AID - TPC201500461RAR2 [pii] -AID - 10.1105/tpc.15.00461 [doi] -PST - ppublish -SO - Plant Cell. 2015 Dec;27(12):3410-24. doi: 10.1105/tpc.15.00461. Epub 2015 Dec 15. - - -##### PUB RECORD ##### -## 10.1094/mpmi.2000.13.7.763 10875337 null Salzer, Bonanomi, et al., 2000 "Salzer P, Bonanomi A, Beyer K, Vögeli-Lange R, Aeschbacher RA, Lange J, Wiemken A, Kim D, Cook DR, Boller T. Differential expression of eight chitinase genes in Medicago truncatula roots during mycorrhiza formation, nodulation, and pathogen infection. Mol Plant Microbe Interact. 2000 Jul;13(7):763-77. doi: 10.1094/MPMI.2000.13.7.763. PMID: 10875337." ## - -PMID- 10875337 -OWN - NLM -STAT- MEDLINE -DCOM- 20001026 -LR - 20161124 -IS - 0894-0282 (Print) -IS - 0894-0282 (Linking) -VI - 13 -IP - 7 -DP - 2000 Jul -TI - Differential expression of eight chitinase genes in Medicago truncatula roots - during mycorrhiza formation, nodulation, and pathogen infection. -PG - 763-77 -AB - Expression of eight different chitinase genes, representing members of five - chitinase classes, was studied in Medicago truncatula roots during formation of - arbuscular mycorrhiza with Glomus intraradices, nodulation with Rhizobium - meliloti, and pathogen attack by Phytophthora megasperma f. sp. medicaginis, - Fusarium solani f. sp. phaseoli (compatible interactions with root rot symptoms), - Ascochyta pisi (compatible, symptomless), and F. solani f. sp. pisi - (incompatible, nonhost interaction). In the compatible plant-pathogen - interactions, expression of class I, II, and IV chitinase genes was enhanced. The - same genes were induced during nodulation. Transcripts of class I and II - chitinase genes accumulated transiently during early stages of the interaction, - and transcripts of the class IV chitinase gene accumulated in mature nodules. The - pattern of chitinase gene expression in mycorrhizal roots was markedly different: - Expression of class I, II, and IV chitinase genes was not enhanced, whereas - expression of three class III chitinase genes, with almost no basal expression, - was strongly induced. Two of these three (Mtchitinase III-2 and Mtchitinase - III-3) were not induced at all in interactions with pathogens and rhizobia. Thus, - the expression of two mycorrhiza-specific class III chitinase genes can be - considered a hallmark for the establishment of arbuscular mycorrhiza in Medicago - truncatula. -FAU - Salzer, P -AU - Salzer P -AD - Botanisches Institut der Universitat Basel, Switzerland. Peter.Salzer@unibas.ch -FAU - Bonanomi, A -AU - Bonanomi A -FAU - Beyer, K -AU - Beyer K -FAU - Vogeli-Lange, R -AU - Vogeli-Lange R -FAU - Aeschbacher, R A -AU - Aeschbacher RA -FAU - Lange, J -AU - Lange J -FAU - Wiemken, A -AU - Wiemken A -FAU - Kim, D -AU - Kim D -FAU - Cook, D R -AU - Cook DR -FAU - Boller, T -AU - Boller T -LA - eng -SI - GENBANK/AF167322 -SI - GENBANK/AF167323 -SI - GENBANK/AF167324 -SI - GENBANK/AF167325 -SI - GENBANK/AF167326 -SI - GENBANK/AF167327 -SI - GENBANK/AF167328 -SI - GENBANK/AF167329 -SI - GENBANK/AJ238651 -SI - GENBANK/AJ245511 -SI - GENBANK/AJ245512 -PT - Journal Article -PT - Research Support, Non-U.S. Gov't -PL - United States -TA - Mol Plant Microbe Interact -JT - Molecular plant-microbe interactions : MPMI -JID - 9107902 -RN - 0 (DNA Primers) -RN - 0 (Isoenzymes) -RN - 0 (Ubiquitins) -RN - EC 3.2.1.14 (Chitinases) -SB - IM -MH - Amino Acid Sequence -MH - Base Sequence -MH - Chitinases/biosynthesis/chemistry/*genetics -MH - DNA Primers -MH - Enzyme Induction -MH - Fusarium/*pathogenicity -MH - Gene Expression Regulation, Enzymologic -MH - *Gene Expression Regulation, Plant -MH - Isoenzymes/biosynthesis/chemistry/genetics -MH - Medicago sativa/enzymology/*genetics/*microbiology -MH - Molecular Sequence Data -MH - Phytophthora/*pathogenicity -MH - Plant Diseases -MH - Plant Roots/enzymology/microbiology -MH - Polymerase Chain Reaction -MH - Sequence Alignment -MH - Sequence Homology, Nucleic Acid -MH - Ubiquitins/genetics -EDAT- 2000/06/30 11:00 -MHDA- 2001/02/28 10:01 -CRDT- 2000/06/30 11:00 -PHST- 2000/06/30 11:00 [pubmed] -PHST- 2001/02/28 10:01 [medline] -PHST- 2000/06/30 11:00 [entrez] -AID - 10.1094/MPMI.2000.13.7.763 [doi] -PST - ppublish -SO - Mol Plant Microbe Interact. 2000 Jul;13(7):763-77. doi: - 10.1094/MPMI.2000.13.7.763. - - -##### PUB RECORD ##### -## 10.1104/pp.108.125062 18790999 PMC2577242 Floss, Schliemann, et al., 2008 "Floss DS, Schliemann W, Schmidt J, Strack D, Walter MH. RNA interference-mediated repression of MtCCD1 in mycorrhizal roots of Medicago truncatula causes accumulation of C27 apocarotenoids, shedding light on the functional role of CCD1. Plant Physiol. 2008 Nov;148(3):1267-82. doi: 10.1104/pp.108.125062. Epub 2008 Sep 12. PMID: 18790999; PMCID: PMC2577242." ## - -PMID- 18790999 -OWN - NLM -STAT- MEDLINE -DCOM- 20090102 -LR - 20211020 -IS - 0032-0889 (Print) -IS - 1532-2548 (Electronic) -IS - 0032-0889 (Linking) -VI - 148 -IP - 3 -DP - 2008 Nov -TI - RNA interference-mediated repression of MtCCD1 in mycorrhizal roots of Medicago - truncatula causes accumulation of C27 apocarotenoids, shedding light on the - functional role of CCD1. -PG - 1267-82 -LID - 10.1104/pp.108.125062 [doi] -AB - Tailoring carotenoids by plant carotenoid cleavage dioxygenases (CCDs) generates - various bioactive apocarotenoids. Recombinant CCD1 has been shown to catalyze - symmetrical cleavage of C(40) carotenoid substrates at 9,10 and 9',10' positions. - The actual substrate(s) of the enzyme in planta, however, is still unknown. In - this study, we have carried out RNA interference (RNAi)-mediated repression of a - Medicago truncatula CCD1 gene in hairy roots colonized by the arbuscular - mycorrhizal (AM) fungus Glomus intraradices. As a consequence, the normal - AM-mediated accumulation of apocarotenoids (C(13) cyclohexenone and C(14) - mycorradicin derivatives) was differentially modified. Mycorradicin derivatives - were strongly reduced to 3% to 6% of the controls, while the cyclohexenone - derivatives were only reduced to 30% to 47%. Concomitantly, a yellow-orange color - appeared in RNAi roots. Based on ultraviolet light spectra and mass spectrometry - analyses, the new compounds are C(27) apocarotenoic acid derivatives. These - metabolic alterations did not lead to major changes in molecular markers of the - AM symbiosis, although a moderate shift to more degenerating arbuscules was - observed in RNAi roots. The unexpected outcome of the RNAi approach suggests - C(27) apocarotenoids as the major substrates of CCD1 in mycorrhizal root cells. - Moreover, literature data implicate C(27) apocarotenoid cleavage as the general - functional role of CCD1 in planta. A revised scheme of plant carotenoid cleavage - in two consecutive steps is proposed, in which CCD1 catalyzes only the second - step in the cytosol (C(27)-->C(14)+C(13)), while the first step - (C(40)-->C(27)+C(13)) may be catalyzed by CCD7 and/or CCD4 inside plastids. -FAU - Floss, Daniela S -AU - Floss DS -AD - Leibniz-Institut fur Pflanzenbiochemie, Abteilung Sekundarstoffwechsel , D-06120 - Halle, Germany. -FAU - Schliemann, Willibald -AU - Schliemann W -FAU - Schmidt, Jurgen -AU - Schmidt J -FAU - Strack, Dieter -AU - Strack D -FAU - Walter, Michael H -AU - Walter MH -LA - eng -SI - GENBANK/FM204879 -PT - Journal Article -PT - Research Support, Non-U.S. Gov't -DEP - 20080912 -PL - United States -TA - Plant Physiol -JT - Plant physiology -JID - 0401224 -RN - 0 (DNA Primers) -RN - 0 (DNA, Complementary) -RN - 0 (RNA, Messenger) -RN - 36-88-4 (Carotenoids) -RN - EC 1.13.11.- (Dioxygenases) -RN - EC 1.13.11.- (carotenoid cleavage dioxygenase 1) -SB - IM -MH - Base Sequence -MH - Carotenoids/*metabolism -MH - Chromatography, High Pressure Liquid -MH - Cloning, Molecular -MH - DNA Primers -MH - DNA, Complementary -MH - Dioxygenases/*genetics/metabolism -MH - *Genes, Plant -MH - Mass Spectrometry -MH - Medicago truncatula/genetics/*metabolism -MH - Molecular Sequence Data -MH - Plant Roots/*enzymology -MH - *RNA Interference -MH - RNA, Messenger/genetics -MH - Reverse Transcriptase Polymerase Chain Reaction -PMC - PMC2577242 -EDAT- 2008/09/16 09:00 -MHDA- 2009/01/03 09:00 -CRDT- 2008/09/16 09:00 -PHST- 2008/09/16 09:00 [pubmed] -PHST- 2009/01/03 09:00 [medline] -PHST- 2008/09/16 09:00 [entrez] -AID - pp.108.125062 [pii] -AID - 125062 [pii] -AID - 10.1104/pp.108.125062 [doi] -PST - ppublish -SO - Plant Physiol. 2008 Nov;148(3):1267-82. doi: 10.1104/pp.108.125062. Epub 2008 Sep - 12. - - -##### PUB RECORD ##### -## 10.1073/pnas.2205920119 35972963 PMC9407390 Liu, Lin, et al., 2022 "Liu H, Lin JS, Luo Z, Sun J, Huang X, Yang Y, Xu J, Wang YF, Zhang P, Oldroyd GED, Xie F. Constitutive activation of a nuclear-localized calcium channel complex in Medicago truncatula. Proc Natl Acad Sci U S A. 2022 Aug 23;119(34):e2205920119. doi: 10.1073/pnas.2205920119. Epub 2022 Aug 16. PMID: 35972963; PMCID: PMC9407390." ## - -PMID- 35972963 -OWN - NLM -STAT- MEDLINE -DCOM- 20220818 -LR - 20230217 -IS - 1091-6490 (Electronic) -IS - 0027-8424 (Print) -IS - 0027-8424 (Linking) -VI - 119 -IP - 34 -DP - 2022 Aug 23 -TI - Constitutive activation of a nuclear-localized calcium channel complex in - Medicago truncatula. -PG - e2205920119 -LID - 10.1073/pnas.2205920119 [doi] -LID - e2205920119 -AB - Nuclear Ca(2+) oscillations allow symbiosis signaling, facilitating plant - recognition of beneficial microsymbionts, nitrogen-fixing rhizobia, and - nutrient-capturing arbuscular mycorrhizal fungi. Two classes of channels, DMI1 - and CNGC15, in a complex on the nuclear membrane, coordinate symbiotic Ca(2+) - oscillations. However, the mechanism of Ca(2+) signature generation is unknown. - Here, we demonstrate spontaneous activation of this channel complex, through - gain-of-function mutations in DMI1, leading to spontaneous nuclear Ca(2+) - oscillations and spontaneous nodulation, in a CNGC15-dependent manner. The - mutations destabilize a hydrogen-bond or salt-bridge network between two RCK - domains, with the resultant structural changes, alongside DMI1 cation - permeability, activating the channel complex. This channel complex was - reconstituted in human HEK293T cell lines, with the resultant calcium influx - enhanced by autoactivated DMI1 and CNGC15s. Our results demonstrate the mode of - activation of this nuclear channel complex, show that DMI1 and CNGC15 are - sufficient to create oscillatory Ca(2+) signals, and provide insights into its - native mode of induction. -FAU - Liu, Haiyue -AU - Liu H -AUID- ORCID: 0000-0001-9009-2153 -AD - National Key Laboratory of Plant Molecular Genetics,Chinese Academy of Sciences - Center for Excellence in Molecular Plant Sciences, Shanghai Institute of Plant - Physiology and Ecology, Chinese Academy of Sciences, Shanghai, 200032, China. -AD - University of the Chinese Academy of Sciences, Beijing, 100049, China. -FAU - Lin, Jie-Shun -AU - Lin JS -AUID- ORCID: 0000-0002-3726-0303 -AD - National Key Laboratory of Plant Molecular Genetics,Chinese Academy of Sciences - Center for Excellence in Molecular Plant Sciences, Shanghai Institute of Plant - Physiology and Ecology, Chinese Academy of Sciences, Shanghai, 200032, China. -AD - University of the Chinese Academy of Sciences, Beijing, 100049, China. -FAU - Luo, Zhenpeng -AU - Luo Z -AUID- ORCID: 0000-0002-4512-8505 -AD - National Key Laboratory of Plant Molecular Genetics,Chinese Academy of Sciences - Center for Excellence in Molecular Plant Sciences, Shanghai Institute of Plant - Physiology and Ecology, Chinese Academy of Sciences, Shanghai, 200032, China. -AD - University of the Chinese Academy of Sciences, Beijing, 100049, China. -FAU - Sun, Jongho -AU - Sun J -AUID- ORCID: 0000-0002-3705-3072 -AD - Sainsbury Laboratory, University of Cambridge, 47 Bateman Street, Cambridge, CB2 - 1LR, United Kingdom. -FAU - Huang, Xiaowei -AU - Huang X -AUID- ORCID: 0000-0001-9964-687X -AD - National Key Laboratory of Plant Molecular Genetics,Chinese Academy of Sciences - Center for Excellence in Molecular Plant Sciences, Shanghai Institute of Plant - Physiology and Ecology, Chinese Academy of Sciences, Shanghai, 200032, China. -AD - University of the Chinese Academy of Sciences, Beijing, 100049, China. -FAU - Yang, Yang -AU - Yang Y -AD - National Key Laboratory of Plant Molecular Genetics,Chinese Academy of Sciences - Center for Excellence in Molecular Plant Sciences, Shanghai Institute of Plant - Physiology and Ecology, Chinese Academy of Sciences, Shanghai, 200032, China. -AD - University of the Chinese Academy of Sciences, Beijing, 100049, China. -FAU - Xu, Ji -AU - Xu J -AD - National Key Laboratory of Plant Molecular Genetics,Chinese Academy of Sciences - Center for Excellence in Molecular Plant Sciences, Shanghai Institute of Plant - Physiology and Ecology, Chinese Academy of Sciences, Shanghai, 200032, China. -FAU - Wang, Yong-Fei -AU - Wang YF -AUID- ORCID: 0000-0003-3139-7701 -AD - National Key Laboratory of Plant Molecular Genetics,Chinese Academy of Sciences - Center for Excellence in Molecular Plant Sciences, Shanghai Institute of Plant - Physiology and Ecology, Chinese Academy of Sciences, Shanghai, 200032, China. -FAU - Zhang, Peng -AU - Zhang P -AUID- ORCID: 0000-0003-0408-2923 -AD - National Key Laboratory of Plant Molecular Genetics,Chinese Academy of Sciences - Center for Excellence in Molecular Plant Sciences, Shanghai Institute of Plant - Physiology and Ecology, Chinese Academy of Sciences, Shanghai, 200032, China. -FAU - Oldroyd, Giles E D -AU - Oldroyd GED -AUID- ORCID: 0000-0002-5245-6355 -AD - Sainsbury Laboratory, University of Cambridge, 47 Bateman Street, Cambridge, CB2 - 1LR, United Kingdom. -FAU - Xie, Fang -AU - Xie F -AUID- ORCID: 0000-0002-0530-1430 -AD - National Key Laboratory of Plant Molecular Genetics,Chinese Academy of Sciences - Center for Excellence in Molecular Plant Sciences, Shanghai Institute of Plant - Physiology and Ecology, Chinese Academy of Sciences, Shanghai, 200032, China. -LA - eng -PT - Journal Article -PT - Research Support, Non-U.S. Gov't -DEP - 20220816 -PL - United States -TA - Proc Natl Acad Sci U S A -JT - Proceedings of the National Academy of Sciences of the United States of America -JID - 7505876 -RN - 0 (Calcium Channels) -RN - 0 (Plant Proteins) -RN - SY7Q814VUP (Calcium) -SB - IM -MH - Calcium/metabolism -MH - *Calcium Channels/genetics/metabolism -MH - *Calcium Signaling/physiology -MH - Cell Nucleus/metabolism -MH - Gain of Function Mutation -MH - Gene Expression Regulation, Plant -MH - HEK293 Cells -MH - Humans -MH - *Medicago truncatula/genetics/physiology -MH - *Plant Proteins/genetics/metabolism -MH - *Plant Root Nodulation/genetics/physiology -MH - *Plant Roots/genetics/physiology -MH - Symbiosis/physiology -PMC - PMC9407390 -OTO - NOTNLM -OT - CNGC15 -OT - DMI1 -OT - NF signaling -OT - calcium channel -OT - nuclear calcium spiking -COIS- The authors declare no competing interest. -EDAT- 2022/08/17 06:00 -MHDA- 2022/08/19 06:00 -CRDT- 2022/08/16 13:42 -PHST- 2022/08/16 13:42 [entrez] -PHST- 2022/08/17 06:00 [pubmed] -PHST- 2022/08/19 06:00 [medline] -AID - 202205920 [pii] -AID - 10.1073/pnas.2205920119 [doi] -PST - ppublish -SO - Proc Natl Acad Sci U S A. 2022 Aug 23;119(34):e2205920119. doi: - 10.1073/pnas.2205920119. Epub 2022 Aug 16. - - -##### PUB RECORD ##### -## 10.1111/nph.12198 23432463 null Rey, Nars, et al., 2013 "Rey T, Nars A, Bonhomme M, Bottin A, Huguet S, Balzergue S, Jardinaud MF, Bono JJ, Cullimore J, Dumas B, Gough C, Jacquet C. NFP, a LysM protein controlling Nod factor perception, also intervenes in Medicago truncatula resistance to pathogens. New Phytol. 2013 May;198(3):875-886. doi: 10.1111/nph.12198. Epub 2013 Feb 25. PMID: 23432463." ## - -PMID- 23432463 -OWN - NLM -STAT- MEDLINE -DCOM- 20131125 -LR - 20211203 -IS - 1469-8137 (Electronic) -IS - 0028-646X (Linking) -VI - 198 -IP - 3 -DP - 2013 May -TI - NFP, a LysM protein controlling Nod factor perception, also intervenes in - Medicago truncatula resistance to pathogens. -PG - 875-886 -LID - 10.1111/nph.12198 [doi] -AB - Plant LysM proteins control the perception of microbial-derived - N-acetylglucosamine compounds for the establishment of symbiosis or activation of - plant immunity. This raises questions about how plants, and notably legumes, can - differentiate friends and foes using similar molecular actors and whether any - receptors can intervene in both symbiosis and resistance. To study this question, - nfp and lyk3 LysM-receptor like kinase mutants of Medicago truncatula that are - affected in the early steps of nodulation, were analysed following inoculation - with Aphanomyces euteiches, a root oomycete. The role of NFP in this interaction - was further analysed by overexpression of NFP and by transcriptome analyses. nfp, - but not lyk3, mutants were significantly more susceptible than wildtype plants to - A. euteiches, whereas NFP overexpression increased resistance. Transcriptome - analyses on A. euteiches inoculation showed that mutation in the NFP gene led to - significant changes in the expression of c. 500 genes, notably involved in cell - dynamic processes previously associated with resistance to pathogen penetration. - nfp mutants also showed an increased susceptibility to the fungus Colletotrichum - trifolii. These results demonstrate that NFP intervenes in M. truncatula - immunity, suggesting an unsuspected role for NFP in the perception of pathogenic - signals. -CI - (c) 2013 The Authors. New Phytologist (c) 2013 New Phytologist Trust. -FAU - Rey, Thomas -AU - Rey T -AD - Universite de Toulouse, UPS, UMR 5546, Laboratoire de Recherche en Sciences - Vegetales, BP42617, Auzeville, F-31326, Castanet-Tolosan, France. -AD - CNRS, UMR 5546, Laboratoire de Recherche en Sciences Vegetales, BP42617, - Auzeville, F-31326, Castanet-Tolosan, France. -FAU - Nars, Amaury -AU - Nars A -AD - Universite de Toulouse, UPS, UMR 5546, Laboratoire de Recherche en Sciences - Vegetales, BP42617, Auzeville, F-31326, Castanet-Tolosan, France. -AD - CNRS, UMR 5546, Laboratoire de Recherche en Sciences Vegetales, BP42617, - Auzeville, F-31326, Castanet-Tolosan, France. -FAU - Bonhomme, Maxime -AU - Bonhomme M -AD - Universite de Toulouse, UPS, UMR 5546, Laboratoire de Recherche en Sciences - Vegetales, BP42617, Auzeville, F-31326, Castanet-Tolosan, France. -AD - CNRS, UMR 5546, Laboratoire de Recherche en Sciences Vegetales, BP42617, - Auzeville, F-31326, Castanet-Tolosan, France. -FAU - Bottin, Arnaud -AU - Bottin A -AD - Universite de Toulouse, UPS, UMR 5546, Laboratoire de Recherche en Sciences - Vegetales, BP42617, Auzeville, F-31326, Castanet-Tolosan, France. -AD - CNRS, UMR 5546, Laboratoire de Recherche en Sciences Vegetales, BP42617, - Auzeville, F-31326, Castanet-Tolosan, France. -FAU - Huguet, Stephanie -AU - Huguet S -AD - Unite de Recherche en Genomique Vegetale (URGV), UMR INRA 1165, Universite d'Evry - Val d'Essonne, ERL CNRS 8196, CP 5708, F-91057, Evry Cedex, France. -FAU - Balzergue, Sandrine -AU - Balzergue S -AD - Unite de Recherche en Genomique Vegetale (URGV), UMR INRA 1165, Universite d'Evry - Val d'Essonne, ERL CNRS 8196, CP 5708, F-91057, Evry Cedex, France. -FAU - Jardinaud, Marie-Francoise -AU - Jardinaud MF -AD - INRA, Laboratoire des Interactions Plantes-Microorganismes (LIPM), UMR441, - F-31326, Castanet-Tolosan, France. -FAU - Bono, Jean-Jacques -AU - Bono JJ -AD - INRA, Laboratoire des Interactions Plantes-Microorganismes (LIPM), UMR441, - F-31326, Castanet-Tolosan, France. -AD - CNRS, Laboratoire des Interactions Plantes-Microorganismes (LIPM), UMR2594, - F-31326, Castanet-Tolosan, France. -FAU - Cullimore, Julie -AU - Cullimore J -AD - INRA, Laboratoire des Interactions Plantes-Microorganismes (LIPM), UMR441, - F-31326, Castanet-Tolosan, France. -AD - CNRS, Laboratoire des Interactions Plantes-Microorganismes (LIPM), UMR2594, - F-31326, Castanet-Tolosan, France. -FAU - Dumas, Bernard -AU - Dumas B -AD - Universite de Toulouse, UPS, UMR 5546, Laboratoire de Recherche en Sciences - Vegetales, BP42617, Auzeville, F-31326, Castanet-Tolosan, France. -AD - CNRS, UMR 5546, Laboratoire de Recherche en Sciences Vegetales, BP42617, - Auzeville, F-31326, Castanet-Tolosan, France. -FAU - Gough, Clare -AU - Gough C -AD - INRA, Laboratoire des Interactions Plantes-Microorganismes (LIPM), UMR441, - F-31326, Castanet-Tolosan, France. -AD - CNRS, Laboratoire des Interactions Plantes-Microorganismes (LIPM), UMR2594, - F-31326, Castanet-Tolosan, France. -FAU - Jacquet, Christophe -AU - Jacquet C -AD - Universite de Toulouse, UPS, UMR 5546, Laboratoire de Recherche en Sciences - Vegetales, BP42617, Auzeville, F-31326, Castanet-Tolosan, France. -AD - CNRS, UMR 5546, Laboratoire de Recherche en Sciences Vegetales, BP42617, - Auzeville, F-31326, Castanet-Tolosan, France. -LA - eng -PT - Journal Article -PT - Research Support, Non-U.S. Gov't -DEP - 20130225 -PL - England -TA - New Phytol -JT - The New phytologist -JID - 9882884 -RN - 0 (Plant Proteins) -RN - EC 2.7.11.1 (Protein Serine-Threonine Kinases) -SB - IM -MH - Aphanomyces/pathogenicity/physiology -MH - Colletotrichum/*pathogenicity -MH - Disease Resistance/genetics -MH - Gene Expression Profiling -MH - Gene Expression Regulation, Plant -MH - *Host-Pathogen Interactions -MH - Medicago truncatula/genetics/*metabolism/*microbiology -MH - Mutation -MH - Plant Diseases/genetics/microbiology -MH - Plant Proteins/genetics/*metabolism -MH - Plant Roots/metabolism/microbiology -MH - Plants, Genetically Modified -MH - Protein Serine-Threonine Kinases/genetics/metabolism -MH - Symbiosis/physiology -EDAT- 2013/02/26 06:00 -MHDA- 2013/12/16 06:00 -CRDT- 2013/02/26 06:00 -PHST- 2012/11/21 00:00 [received] -PHST- 2013/01/17 00:00 [accepted] -PHST- 2013/02/26 06:00 [entrez] -PHST- 2013/02/26 06:00 [pubmed] -PHST- 2013/12/16 06:00 [medline] -AID - 10.1111/nph.12198 [doi] -PST - ppublish -SO - New Phytol. 2013 May;198(3):875-886. doi: 10.1111/nph.12198. Epub 2013 Feb 25. - - -##### PUB RECORD ##### -## 10.1104/pp.18.01588 30782966 PMC6501087 Laffont, Huault, et al., 2019 "Laffont C, Huault E, Gautrat P, Endre G, Kalo P, Bourion V, Duc G, Frugier F. Independent Regulation of Symbiotic Nodulation by the SUNN Negative and CRA2 Positive Systemic Pathways. Plant Physiol. 2019 May;180(1):559-570. doi: 10.1104/pp.18.01588. Epub 2019 Feb 19. PMID: 30782966; PMCID: PMC6501087." ## - -PMID- 30782966 -OWN - NLM -STAT- MEDLINE -DCOM- 20200226 -LR - 20200501 -IS - 1532-2548 (Electronic) -IS - 0032-0889 (Print) -IS - 0032-0889 (Linking) -VI - 180 -IP - 1 -DP - 2019 May -TI - Independent Regulation of Symbiotic Nodulation by the SUNN Negative and CRA2 - Positive Systemic Pathways. -PG - 559-570 -LID - 10.1104/pp.18.01588 [doi] -AB - Plant systemic signaling pathways allow the integration and coordination of shoot - and root organ metabolism and development at the whole-plant level depending on - nutrient availability. In legumes, two systemic pathways have been reported in - the Medicago truncatula model to regulate root nitrogen-fixing symbiotic - nodulation. Both pathways involve leucine-rich repeat receptor-like kinases - acting in shoots and proposed to perceive signaling peptides produced in roots - depending on soil nutrient availability. In this study, we characterized in the - M. truncatula Jemalong A17 genotype a mutant allelic series affecting the Compact - Root Architecture2 (CRA2) receptor. These analyses revealed that this pathway - acts systemically from shoots to positively regulate nodulation and is required - for the activity of carboxyl-terminally encoded peptides (CEPs). In addition, we - generated a double mutant to test genetic interactions of the CRA2 systemic - pathway with the CLAVATA3/EMBRYO SURROUNDING REGION peptide (CLE)/Super Numeric - Nodule (SUNN) receptor systemic pathway negatively regulating nodule number from - shoots, which revealed an intermediate nodule number phenotype close to the wild - type. Finally, we showed that the nitrate inhibition of nodule numbers was - observed in cra2 mutants but not in sunn and cra2 sunn mutants. Overall, these - results suggest that CEP/CRA2 and CLE/SUNN systemic pathways act independently - from shoots to regulate nodule numbers. -CI - (c) 2019 American Society of Plant Biologists. All Rights Reserved. -FAU - Laffont, Carole -AU - Laffont C -AUID- ORCID: 0000-0002-8447-1736 -AD - Institute of Plant Sciences Paris-Saclay, Centre National de la Recherche - Scientifique, Universite Paris Sud, Universite Paris Diderot, Institut National - de la Recherche Agronomique, Universite d'Evry, Universite Paris-Saclay, 91190 - Gif-sur-Yvette, France. -FAU - Huault, Emeline -AU - Huault E -AD - Institute of Plant Sciences Paris-Saclay, Centre National de la Recherche - Scientifique, Universite Paris Sud, Universite Paris Diderot, Institut National - de la Recherche Agronomique, Universite d'Evry, Universite Paris-Saclay, 91190 - Gif-sur-Yvette, France. -FAU - Gautrat, Pierre -AU - Gautrat P -AD - Institute of Plant Sciences Paris-Saclay, Centre National de la Recherche - Scientifique, Universite Paris Sud, Universite Paris Diderot, Institut National - de la Recherche Agronomique, Universite d'Evry, Universite Paris-Saclay, 91190 - Gif-sur-Yvette, France. -FAU - Endre, Gabriella -AU - Endre G -AD - Institute of Plant Biology, Biological Research Centre, 6726 Szeged, Hungary. -FAU - Kalo, Peter -AU - Kalo P -AUID- ORCID: 0000-0002-0404-8904 -AD - National Agricultural and Innovation Center, Agricultural Biotechnology - Institute, 2100 Godollo, Hungary. -FAU - Bourion, Virginie -AU - Bourion V -AD - Agroecologie, Institut National de la Recherche Agronomique, AgroSup Dijon, - Universite Bourgogne Franche-Comte, 21065 Dijon, France. -FAU - Duc, Gerard -AU - Duc G -AUID- ORCID: 0000-0002-2921-3152 -AD - Agroecologie, Institut National de la Recherche Agronomique, AgroSup Dijon, - Universite Bourgogne Franche-Comte, 21065 Dijon, France. -FAU - Frugier, Florian -AU - Frugier F -AUID- ORCID: 0000-0002-9783-7418 -AD - Institute of Plant Sciences Paris-Saclay, Centre National de la Recherche - Scientifique, Universite Paris Sud, Universite Paris Diderot, Institut National - de la Recherche Agronomique, Universite d'Evry, Universite Paris-Saclay, 91190 - Gif-sur-Yvette, France florian.frugier@cnrs.fr. -LA - eng -PT - Journal Article -PT - Research Support, Non-U.S. Gov't -DEP - 20190219 -PL - United States -TA - Plant Physiol -JT - Plant physiology -JID - 0401224 -RN - 0 (Plant Proteins) -SB - IM -MH - Medicago truncatula/*physiology -MH - Metabolic Networks and Pathways -MH - Mutation -MH - Plant Proteins/genetics/*metabolism -MH - Plant Root Nodulation/*physiology -MH - Plant Roots/physiology -MH - Symbiosis -PMC - PMC6501087 -EDAT- 2019/02/21 06:00 -MHDA- 2020/02/27 06:00 -CRDT- 2019/02/21 06:00 -PHST- 2019/01/03 00:00 [received] -PHST- 2019/02/06 00:00 [accepted] -PHST- 2019/02/21 06:00 [pubmed] -PHST- 2020/02/27 06:00 [medline] -PHST- 2019/02/21 06:00 [entrez] -AID - pp.18.01588 [pii] -AID - 201801588DR1 [pii] -AID - 10.1104/pp.18.01588 [doi] -PST - ppublish -SO - Plant Physiol. 2019 May;180(1):559-570. doi: 10.1104/pp.18.01588. Epub 2019 Feb - 19. - - -##### PUB RECORD ##### -## 10.3389/fpls.2016.00034 26858743 PMC4732000 Qiao, Pingault, et al., 2016 "Qiao Z, Pingault L, Nourbakhsh-Rey M, Libault M. Comprehensive Comparative Genomic and Transcriptomic Analyses of the Legume Genes Controlling the Nodulation Process. Front Plant Sci. 2016 Jan 29;7:34. doi: 10.3389/fpls.2016.00034. PMID: 26858743; PMCID: PMC4732000." ## - -PMID- 26858743 -OWN - NLM -STAT- PubMed-not-MEDLINE -DCOM- 20160209 -LR - 20200930 -IS - 1664-462X (Print) -IS - 1664-462X (Electronic) -IS - 1664-462X (Linking) -VI - 7 -DP - 2016 -TI - Comprehensive Comparative Genomic and Transcriptomic Analyses of the Legume Genes - Controlling the Nodulation Process. -PG - 34 -LID - 10.3389/fpls.2016.00034 [doi] -LID - 34 -AB - Nitrogen is one of the most essential plant nutrients and one of the major - factors limiting crop productivity. Having the goal to perform a more sustainable - agriculture, there is a need to maximize biological nitrogen fixation, a feature - of legumes. To enhance our understanding of the molecular mechanisms controlling - the interaction between legumes and rhizobia, the symbiotic partner fixing and - assimilating the atmospheric nitrogen for the plant, researchers took advantage - of genetic and genomic resources developed across different legume models (e.g., - Medicago truncatula, Lotus japonicus, Glycine max, and Phaseolus vulgaris) to - identify key regulatory protein coding genes of the nodulation process. In this - study, we are presenting the results of a comprehensive comparative genomic - analysis to highlight orthologous and paralogous relationships between the legume - genes controlling nodulation. Mining large transcriptomic datasets, we also - identified several orthologous and paralogous genes characterized by the - induction of their expression during nodulation across legume plant species. This - comprehensive study prompts new insights into the evolution of the nodulation - process in legume plant and will benefit the scientific community interested in - the transfer of functional genomic information between species. -FAU - Qiao, Zhenzhen -AU - Qiao Z -AD - Department of Microbiology and Plant Biology, University of Oklahoma Norman, OK, - USA. -FAU - Pingault, Lise -AU - Pingault L -AD - Department of Microbiology and Plant Biology, University of Oklahoma Norman, OK, - USA. -FAU - Nourbakhsh-Rey, Mehrnoush -AU - Nourbakhsh-Rey M -AD - Department of Microbiology and Plant Biology, University of Oklahoma Norman, OK, - USA. -FAU - Libault, Marc -AU - Libault M -AD - Department of Microbiology and Plant Biology, University of Oklahoma Norman, OK, - USA. -LA - eng -PT - Journal Article -DEP - 20160129 -PL - Switzerland -TA - Front Plant Sci -JT - Frontiers in plant science -JID - 101568200 -PMC - PMC4732000 -OTO - NOTNLM -OT - comparative genomic -OT - comparative transcriptomic -OT - legume -OT - neo-/sub-functionalization -OT - nodulation -OT - orthologs -OT - paralogs -OT - root hair cell -EDAT- 2016/02/10 06:00 -MHDA- 2016/02/10 06:01 -CRDT- 2016/02/10 06:00 -PHST- 2015/10/28 00:00 [received] -PHST- 2016/01/10 00:00 [accepted] -PHST- 2016/02/10 06:00 [entrez] -PHST- 2016/02/10 06:00 [pubmed] -PHST- 2016/02/10 06:01 [medline] -AID - 10.3389/fpls.2016.00034 [doi] -PST - epublish -SO - Front Plant Sci. 2016 Jan 29;7:34. doi: 10.3389/fpls.2016.00034. eCollection - 2016. - - -##### PUB RECORD ##### -## 10.1186/s12870-020-02619-6 32867687 null Jiao, Wang, et al., 2020 "Jiao Z, Wang L, Du H, Wang Y, Wang W, Liu J, Huang J, Huang W, Ge L. Genome-wide study of C2H2 zinc finger gene family in Medicago truncatula. BMC Plant Biol. 2020 Aug 31;20(1):401. doi: 10.1186/s12870-020-02619-6. PMID: 32867687; PMCID: PMC7460785." ## - -PMID- 32867687 -OWN - NLM -STAT- MEDLINE -DCOM- 20210218 -LR - 20210218 -IS - 1471-2229 (Electronic) -IS - 1471-2229 (Linking) -VI - 20 -IP - 1 -DP - 2020 Aug 31 -TI - Genome-wide study of C2H2 zinc finger gene family in Medicago truncatula. -PG - 401 -LID - 10.1186/s12870-020-02619-6 [doi] -LID - 401 -AB - BACKGROUND: C2H2 zinc finger proteins (C2H2 ZFPs) play vital roles in shaping - many aspects of plant growth and adaptation to the environment. Plant genomes - harbor hundreds of C2H2 ZFPs, which compose one of the most important and largest - transcription factor families in higher plants. Although the C2H2 ZFP gene family - has been reported in several plant species, it has not been described in the - model leguminous species Medicago truncatula. RESULTS: In this study, we - identified 218 C2H2 type ZFPs with 337 individual C2H2 motifs in M. truncatula. - We showed that the high rate of local gene duplication has significantly - contributed to the expansion of the C2H2 gene family in M. truncatula. The - identified ZFPs exhibit high variation in motif arrangement and expression - pattern, suggesting that the short C2H2 zinc finger motif has been adopted as a - scaffold by numerous transcription factors with different functions to recognize - cis-elements. By analyzing the public expression datasets and quantitative RT-PCR - (qRT-PCR), we identified several C2H2 ZFPs that are specifically expressed in - certain tissues, such as the nodule, seed, and flower. CONCLUSION: Our - genome-wide work revealed an expanded C2H2 ZFP gene family in an important legume - M. truncatula, and provides new insights into the diversification and expansion - of C2H2 ZFPs in higher plants. -FAU - Jiao, Zhicheng -AU - Jiao Z -AD - Department of Grassland Science, College of Forestry and Landscape Architecture, - South China Agricultural University, Guangzhou, 510642, Guangdong, China. -AD - Guangdong Engineering Research Center for Grassland Science, Tianhe, 483 Wushan - Road, Guangzhou, 510642, Guangdong, China. -AD - Guangdong Key Laboratory for Innovative Development and Utilization of Forest - Plant Germplasm, South China Agricultural University, Guangzhou, 510642, - Guangdong, China. -FAU - Wang, Liping -AU - Wang L -AD - State Key Laboratory for Conservation and Utilization of Subtropical - Agro-Bioresources, South China Agricultural University, Guangzhou, 510642, - Guangdong, China. -AD - College of Life Sciences, South China Agricultural University, Guangzhou, 510642, - Guangdong, China. -FAU - Du, Huan -AU - Du H -AD - Department of Grassland Science, College of Forestry and Landscape Architecture, - South China Agricultural University, Guangzhou, 510642, Guangdong, China. -AD - Guangdong Engineering Research Center for Grassland Science, Tianhe, 483 Wushan - Road, Guangzhou, 510642, Guangdong, China. -AD - Guangdong Key Laboratory for Innovative Development and Utilization of Forest - Plant Germplasm, South China Agricultural University, Guangzhou, 510642, - Guangdong, China. -FAU - Wang, Ying -AU - Wang Y -AD - Department of Grassland Science, College of Forestry and Landscape Architecture, - South China Agricultural University, Guangzhou, 510642, Guangdong, China. -AD - Guangdong Engineering Research Center for Grassland Science, Tianhe, 483 Wushan - Road, Guangzhou, 510642, Guangdong, China. -AD - Guangdong Key Laboratory for Innovative Development and Utilization of Forest - Plant Germplasm, South China Agricultural University, Guangzhou, 510642, - Guangdong, China. -FAU - Wang, Weixu -AU - Wang W -AD - Department of Grassland Science, College of Forestry and Landscape Architecture, - South China Agricultural University, Guangzhou, 510642, Guangdong, China. -AD - Guangdong Engineering Research Center for Grassland Science, Tianhe, 483 Wushan - Road, Guangzhou, 510642, Guangdong, China. -FAU - Liu, Junjie -AU - Liu J -AD - Department of Grassland Science, College of Forestry and Landscape Architecture, - South China Agricultural University, Guangzhou, 510642, Guangdong, China. -AD - Guangdong Engineering Research Center for Grassland Science, Tianhe, 483 Wushan - Road, Guangzhou, 510642, Guangdong, China. -FAU - Huang, Jinhang -AU - Huang J -AD - Department of Grassland Science, College of Forestry and Landscape Architecture, - South China Agricultural University, Guangzhou, 510642, Guangdong, China. -AD - Guangdong Engineering Research Center for Grassland Science, Tianhe, 483 Wushan - Road, Guangzhou, 510642, Guangdong, China. -FAU - Huang, Wei -AU - Huang W -AD - State Key Laboratory for Conservation and Utilization of Subtropical - Agro-Bioresources, South China Agricultural University, Guangzhou, 510642, - Guangdong, China. -AD - College of Life Sciences, South China Agricultural University, Guangzhou, 510642, - Guangdong, China. -FAU - Ge, Liangfa -AU - Ge L -AUID- ORCID: 0000-0002-4831-4637 -AD - Department of Grassland Science, College of Forestry and Landscape Architecture, - South China Agricultural University, Guangzhou, 510642, Guangdong, China. - lge@scau.edu.cn. -AD - Guangdong Engineering Research Center for Grassland Science, Tianhe, 483 Wushan - Road, Guangzhou, 510642, Guangdong, China. lge@scau.edu.cn. -AD - Guangdong Key Laboratory for Innovative Development and Utilization of Forest - Plant Germplasm, South China Agricultural University, Guangzhou, 510642, - Guangdong, China. lge@scau.edu.cn. -LA - eng -PT - Journal Article -DEP - 20200831 -PL - England -TA - BMC Plant Biol -JT - BMC plant biology -JID - 100967807 -SB - IM -MH - CYS2-HIS2 Zinc Fingers/*genetics -MH - *Gene Duplication -MH - Genes, Plant/*genetics -MH - *Genome-Wide Association Study -MH - Medicago truncatula/*genetics -MH - *Multigene Family -PMC - PMC7460785 -OTO - NOTNLM -OT - C2H2 -OT - EAR motif -OT - Expression -OT - Gene family -OT - Local gene duplication -OT - Zinc finger -COIS- The authors declare that they have no competing interests. -EDAT- 2020/09/02 06:00 -MHDA- 2021/02/20 06:00 -CRDT- 2020/09/02 06:00 -PHST- 2019/07/24 00:00 [received] -PHST- 2020/08/25 00:00 [accepted] -PHST- 2020/09/02 06:00 [entrez] -PHST- 2020/09/02 06:00 [pubmed] -PHST- 2021/02/20 06:00 [medline] -AID - 10.1186/s12870-020-02619-6 [pii] -AID - 2619 [pii] -AID - 10.1186/s12870-020-02619-6 [doi] -PST - epublish -SO - BMC Plant Biol. 2020 Aug 31;20(1):401. doi: 10.1186/s12870-020-02619-6. - - -##### PUB RECORD ##### -## 10.1038/s41477-018-0286-7 30397259 null Pecrix, Staton, et al., 2018 "Pecrix Y, Staton SE, Sallet E, Lelandais-Brière C, Moreau S, Carrère S, Blein T, Jardinaud MF, Latrasse D, Zouine M, Zahm M, Kreplak J, Mayjonade B, Satgé C, Perez M, Cauet S, Marande W, Chantry-Darmon C, Lopez-Roques C, Bouchez O, Bérard A, Debellé F, Muños S, Bendahmane A, Bergès H, Niebel A, Buitink J, Frugier F, Benhamed M, Crespi M, Gouzy J, Gamas P. Whole-genome landscape of Medicago truncatula symbiotic genes. Nat Plants. 2018 Dec;4(12):1017-1025. doi: 10.1038/s41477-018-0286-7. Epub 2018 Nov 5. PMID: 30397259." ## - -PMID- 30397259 -OWN - NLM -STAT- MEDLINE -DCOM- 20190701 -LR - 20191029 -IS - 2055-0278 (Electronic) -IS - 2055-0278 (Linking) -VI - 4 -IP - 12 -DP - 2018 Dec -TI - Whole-genome landscape of Medicago truncatula symbiotic genes. -PG - 1017-1025 -LID - 10.1038/s41477-018-0286-7 [doi] -AB - Advances in deciphering the functional architecture of eukaryotic genomes have - been facilitated by recent breakthroughs in sequencing technologies, enabling a - more comprehensive representation of genes and repeat elements in genome sequence - assemblies, as well as more sensitive and tissue-specific analyses of gene - expression. Here we show that PacBio sequencing has led to a substantially - improved genome assembly of Medicago truncatula A17, a legume model species - notable for endosymbiosis studies(1), and has enabled the identification of - genome rearrangements between genotypes at a near-base-pair resolution. - Annotation of the new M. truncatula genome sequence has allowed for a thorough - analysis of transposable elements and their dynamics, as well as the - identification of new players involved in symbiotic nodule development, in - particular 1,037 upregulated long non-coding RNAs (lncRNAs). We have also - discovered that a substantial proportion (~35% and 38%, respectively) of the - genes upregulated in nodules or expressed in the nodule differentiation zone - colocalize in genomic clusters (270 and 211, respectively), here termed symbiotic - islands. These islands contain numerous expressed lncRNA genes and display - differentially both DNA methylation and histone marks. Epigenetic regulations and - lncRNAs are therefore attractive candidate elements for the orchestration of - symbiotic gene expression in the M. truncatula genome. -FAU - Pecrix, Yann -AU - Pecrix Y -AUID- ORCID: 0000-0002-6537-3145 -AD - LIPM, Universite de Toulouse, INRA, CNRS, Castanet-Tolosan, France. -FAU - Staton, S Evan -AU - Staton SE -AUID- ORCID: 0000-0002-5681-6047 -AD - University of British Columbia, Vancouver, Canada. -FAU - Sallet, Erika -AU - Sallet E -AUID- ORCID: 0000-0003-4637-473X -AD - LIPM, Universite de Toulouse, INRA, CNRS, Castanet-Tolosan, France. -FAU - Lelandais-Briere, Christine -AU - Lelandais-Briere C -AD - IPS2, CNRS, INRA, Universities of Paris Diderot and Sorbonne Paris Cite, Gif sur - Yvette, France. -AD - IPS2, CNRS, INRA, Universities of Paris Diderot, Paris Sud, Evry and - Paris-Saclay, Gif sur Yvette, France. -FAU - Moreau, Sandra -AU - Moreau S -AD - LIPM, Universite de Toulouse, INRA, CNRS, Castanet-Tolosan, France. -FAU - Carrere, Sebastien -AU - Carrere S -AUID- ORCID: 0000-0002-2348-0778 -AD - LIPM, Universite de Toulouse, INRA, CNRS, Castanet-Tolosan, France. -FAU - Blein, Thomas -AU - Blein T -AD - IPS2, CNRS, INRA, Universities of Paris Diderot and Sorbonne Paris Cite, Gif sur - Yvette, France. -AD - IPS2, CNRS, INRA, Universities of Paris Diderot, Paris Sud, Evry and - Paris-Saclay, Gif sur Yvette, France. -FAU - Jardinaud, Marie-Francoise -AU - Jardinaud MF -AD - LIPM, Universite de Toulouse, INPT, ENSAT, Castanet-Tolosan, France. -FAU - Latrasse, David -AU - Latrasse D -AD - IPS2, CNRS, INRA, Universities of Paris Diderot and Sorbonne Paris Cite, Gif sur - Yvette, France. -AD - IPS2, CNRS, INRA, Universities of Paris Diderot, Paris Sud, Evry and - Paris-Saclay, Gif sur Yvette, France. -FAU - Zouine, Mohamed -AU - Zouine M -AD - GBF, Universite de Toulouse, INPT, ENSAT, Castanet-Tolosan, France. -FAU - Zahm, Margot -AU - Zahm M -AD - GBF, Universite de Toulouse, INPT, ENSAT, Castanet-Tolosan, France. -FAU - Kreplak, Jonathan -AU - Kreplak J -AD - AGROECOLOGIE, INRA, Dijon, France. -FAU - Mayjonade, Baptiste -AU - Mayjonade B -AD - LIPM, Universite de Toulouse, INRA, CNRS, Castanet-Tolosan, France. -FAU - Satge, Carine -AU - Satge C -AD - LIPM, Universite de Toulouse, INRA, CNRS, Castanet-Tolosan, France. -AD - CNRGV, INRA, Castanet-Tolosan, France. -FAU - Perez, Magali -AU - Perez M -AD - IPS2, CNRS, INRA, Universities of Paris Diderot and Sorbonne Paris Cite, Gif sur - Yvette, France. -AD - IPS2, CNRS, INRA, Universities of Paris Diderot, Paris Sud, Evry and - Paris-Saclay, Gif sur Yvette, France. -FAU - Cauet, Stephane -AU - Cauet S -AD - CNRGV, INRA, Castanet-Tolosan, France. -FAU - Marande, William -AU - Marande W -AD - CNRGV, INRA, Castanet-Tolosan, France. -FAU - Chantry-Darmon, Celine -AU - Chantry-Darmon C -AD - CNRGV, INRA, Castanet-Tolosan, France. -FAU - Lopez-Roques, Celine -AU - Lopez-Roques C -AD - INRA, US1426, GeT-PlaGe, Genotoul, Castanet-Tolosan, France. -FAU - Bouchez, Olivier -AU - Bouchez O -AD - INRA, US1426, GeT-PlaGe, Genotoul, Castanet-Tolosan, France. -FAU - Berard, Aurelie -AU - Berard A -AD - INRA, US 1279 EPGV, Universite Paris-Saclay, Evry, France. -FAU - Debelle, Frederic -AU - Debelle F -AD - LIPM, Universite de Toulouse, INRA, CNRS, Castanet-Tolosan, France. -FAU - Munos, Stephane -AU - Munos S -AD - LIPM, Universite de Toulouse, INRA, CNRS, Castanet-Tolosan, France. -FAU - Bendahmane, Abdelhafid -AU - Bendahmane A -AD - IPS2, CNRS, INRA, Universities of Paris Diderot and Sorbonne Paris Cite, Gif sur - Yvette, France. -AD - IPS2, CNRS, INRA, Universities of Paris Diderot, Paris Sud, Evry and - Paris-Saclay, Gif sur Yvette, France. -FAU - Berges, Helene -AU - Berges H -AD - CNRGV, INRA, Castanet-Tolosan, France. -FAU - Niebel, Andreas -AU - Niebel A -AD - LIPM, Universite de Toulouse, INRA, CNRS, Castanet-Tolosan, France. -FAU - Buitink, Julia -AU - Buitink J -AUID- ORCID: 0000-0002-1457-764X -AD - IRHS, Agrocampus-Ouest, INRA, Universite d'Angers, Beaucouze, France. -FAU - Frugier, Florian -AU - Frugier F -AD - IPS2, CNRS, INRA, Universities of Paris Diderot and Sorbonne Paris Cite, Gif sur - Yvette, France. -AD - IPS2, CNRS, INRA, Universities of Paris Diderot, Paris Sud, Evry and - Paris-Saclay, Gif sur Yvette, France. -FAU - Benhamed, Moussa -AU - Benhamed M -AD - IPS2, CNRS, INRA, Universities of Paris Diderot and Sorbonne Paris Cite, Gif sur - Yvette, France. -AD - IPS2, CNRS, INRA, Universities of Paris Diderot, Paris Sud, Evry and - Paris-Saclay, Gif sur Yvette, France. -FAU - Crespi, Martin -AU - Crespi M -AD - IPS2, CNRS, INRA, Universities of Paris Diderot and Sorbonne Paris Cite, Gif sur - Yvette, France. -AD - IPS2, CNRS, INRA, Universities of Paris Diderot, Paris Sud, Evry and - Paris-Saclay, Gif sur Yvette, France. -FAU - Gouzy, Jerome -AU - Gouzy J -AUID- ORCID: 0000-0001-5695-4557 -AD - LIPM, Universite de Toulouse, INRA, CNRS, Castanet-Tolosan, France. - Jerome.Gouzy@inra.fr. -FAU - Gamas, Pascal -AU - Gamas P -AUID- ORCID: 0000-0002-6253-4249 -AD - LIPM, Universite de Toulouse, INRA, CNRS, Castanet-Tolosan, France. - Pascal.Gamas@inra.fr. -LA - eng -PT - Journal Article -PT - Research Support, Non-U.S. Gov't -DEP - 20181105 -PL - England -TA - Nat Plants -JT - Nature plants -JID - 101651677 -RN - 0 (Plant Proteins) -RN - 0 (RNA, Plant) -RN - 0 (RNA, Untranslated) -SB - IM -MH - DNA Methylation -MH - *Epigenesis, Genetic -MH - Gene Expression Regulation, Plant -MH - Genome, Plant/*genetics -MH - Genomics -MH - Medicago truncatula/*genetics -MH - Multigene Family -MH - Plant Proteins/genetics -MH - RNA, Plant/genetics -MH - RNA, Untranslated/*genetics -MH - Root Nodules, Plant/genetics -MH - Symbiosis/*genetics -EDAT- 2018/11/07 06:00 -MHDA- 2019/07/02 06:00 -CRDT- 2018/11/07 06:00 -PHST- 2018/03/07 00:00 [received] -PHST- 2018/09/21 00:00 [accepted] -PHST- 2018/11/07 06:00 [pubmed] -PHST- 2019/07/02 06:00 [medline] -PHST- 2018/11/07 06:00 [entrez] -AID - 10.1038/s41477-018-0286-7 [pii] -AID - 10.1038/s41477-018-0286-7 [doi] -PST - ppublish -SO - Nat Plants. 2018 Dec;4(12):1017-1025. doi: 10.1038/s41477-018-0286-7. Epub 2018 - Nov 5. - - -##### PUB RECORD ##### -## 10.1093/plphys/kiaa005 33631796 PMC8133602 Cheng, Li, et al., 2021 "Cheng X, Li G, Krom N, Tang Y, Wen J. Genetic regulation of flowering time and inflorescence architecture by MtFDa and MtFTa1 in Medicago truncatula. Plant Physiol. 2021 Feb 25;185(1):161-178. doi: 10.1093/plphys/kiaa005. PMID: 33631796; PMCID: PMC8133602." ## - -PMID- 33631796 -OWN - NLM -STAT- MEDLINE -DCOM- 20210705 -LR - 20211120 -IS - 1532-2548 (Electronic) -IS - 0032-0889 (Print) -IS - 0032-0889 (Linking) -VI - 185 -IP - 1 -DP - 2021 Feb 25 -TI - Genetic regulation of flowering time and inflorescence architecture by MtFDa and - MtFTa1 in Medicago truncatula. -PG - 161-178 -LID - 10.1093/plphys/kiaa005 [doi] -AB - Regulation of floral transition and inflorescence development is crucial for - plant reproductive success. FLOWERING LOCUS T (FT) is one of the central players - in the flowering genetic regulatory network, whereas FLOWERING LOCUS D (FD), an - interactor of FT and TERMINAL FLOWER 1 (TFL1), plays significant roles in both - floral transition and inflorescence development. Here we show the genetic - regulatory networks of floral transition and inflorescence development in - Medicago truncatula by characterizing MtFTa1 and MtFDa and their genetic - interactions with key inflorescence meristem (IM) regulators. Both MtFTa1 and - MtFDa promote flowering; the double mutant mtfda mtfta1 does not proceed to - floral transition. RNAseq analysis reveals that a broad range of genes involved - in flowering regulation and flower development are up- or downregulated by MtFTa1 - and/or MtFDa mutations. Furthermore, mutation of MtFDa also affects the - inflorescence architecture. Genetic analyses of MtFDa, MtFTa1, MtTFL1, and MtFULc - show that MtFDa is epistatic to MtFULc and MtTFL1 in controlling IM identity. Our - results demonstrate that MtFTa1 and MtFDa are major flowering regulators in M. - truncatula, and MtFDa is essential both in floral transition and secondary - inflorescence development. The study will advance our understanding of the - genetic regulation of flowering time and inflorescence development in legumes. -CI - (c) The Author(s) 2020. Published by Oxford University Press on behalf of American - Society of Plant Biologists. -FAU - Cheng, Xiaofei -AU - Cheng X -AD - Noble Research Institute, Ardmore, Oklahoma 73401, USA. -FAU - Li, Guifen -AU - Li G -AD - Noble Research Institute, Ardmore, Oklahoma 73401, USA. -FAU - Krom, Nick -AU - Krom N -AD - Noble Research Institute, Ardmore, Oklahoma 73401, USA. -FAU - Tang, Yuhong -AU - Tang Y -AD - Noble Research Institute, Ardmore, Oklahoma 73401, USA. -FAU - Wen, Jiangqi -AU - Wen J -AD - Noble Research Institute, Ardmore, Oklahoma 73401, USA. -LA - eng -PT - Comparative Study -PT - Journal Article -PT - Research Support, Non-U.S. Gov't -PL - United States -TA - Plant Physiol -JT - Plant physiology -JID - 0401224 -SB - IM -MH - Gene Expression Regulation, Developmental -MH - Gene Expression Regulation, Plant -MH - Gene Regulatory Networks -MH - Genes, Plant -MH - Genetic Variation -MH - Genotype -MH - Inflorescence/*anatomy & histology/*genetics/*growth & development -MH - Magnoliopsida/*genetics/*growth & development -MH - Medicago truncatula/*genetics/*growth & development -MH - Mutation -MH - Phenotype -MH - Plants, Genetically Modified -PMC - PMC8133602 -EDAT- 2021/02/26 06:00 -MHDA- 2021/07/06 06:00 -CRDT- 2021/02/25 20:19 -PHST- 2020/08/03 00:00 [received] -PHST- 2020/10/11 00:00 [accepted] -PHST- 2021/02/25 20:19 [entrez] -PHST- 2021/02/26 06:00 [pubmed] -PHST- 2021/07/06 06:00 [medline] -AID - 5985539 [pii] -AID - kiaa005 [pii] -AID - 10.1093/plphys/kiaa005 [doi] -PST - ppublish -SO - Plant Physiol. 2021 Feb 25;185(1):161-178. doi: 10.1093/plphys/kiaa005. - - -##### PUB RECORD ##### -## 10.1105/tpc.111.089128 22080596 PMC3246329 Peng, Yu, et al., 2011 "Peng J, Yu J, Wang H, Guo Y, Li G, Bai G, Chen R. Regulation of compound leaf development in Medicago truncatula by fused compound leaf1, a class M KNOX gene. Plant Cell. 2011 Nov;23(11):3929-43. doi: 10.1105/tpc.111.089128. Epub 2011 Nov 11. PMID: 22080596; PMCID: PMC3246329." ## - -PMID- 22080596 -OWN - NLM -STAT- MEDLINE -DCOM- 20120821 -LR - 20220408 -IS - 1532-298X (Electronic) -IS - 1040-4651 (Print) -IS - 1040-4651 (Linking) -VI - 23 -IP - 11 -DP - 2011 Nov -TI - Regulation of compound leaf development in Medicago truncatula by fused compound - leaf1, a class M KNOX gene. -PG - 3929-43 -LID - 10.1105/tpc.111.089128 [doi] -AB - Medicago truncatula is a legume species belonging to the inverted repeat lacking - clade (IRLC) with trifoliolate compound leaves. However, the regulatory - mechanisms underlying development of trifoliolate leaves in legumes remain - largely unknown. Here, we report isolation and characterization of fused compound - leaf1 (fcl1) mutants of M. truncatula. Phenotypic analysis suggests that FCL1 - plays a positive role in boundary separation and proximal-distal axis development - of compound leaves. Map-based cloning indicates that FCL1 encodes a class M KNOX - protein that harbors the MEINOX domain but lacks the homeodomain. Yeast - two-hybrid assays show that FCL1 interacts with a subset of Arabidopsis thaliana - BEL1-like proteins with slightly different substrate specificities from the - Arabidopsis homolog KNATM-B. Double mutant analyses with M. truncatula single - leaflet1 (sgl1) and palmate-like pentafoliata1 (palm1) leaf mutants show that - fcl1 is epistatic to palm1 and sgl1 is epistatic to fcl1 in terms of leaf - complexity and that SGL1 and FCL1 act additively and are required for petiole - development. Previous studies have shown that the canonical KNOX proteins are not - involved in compound leaf development in IRLC legumes. The identification of FCL1 - supports the role of a truncated KNOX protein in compound leaf development in M. - truncatula. -FAU - Peng, Jianling -AU - Peng J -AD - Plant Biology Division, The Samuel Roberts Noble Foundation, Ardmore, Oklahoma - 73401, USA. -FAU - Yu, Jianbin -AU - Yu J -FAU - Wang, Hongliang -AU - Wang H -FAU - Guo, Yingqing -AU - Guo Y -FAU - Li, Guangming -AU - Li G -FAU - Bai, Guihua -AU - Bai G -FAU - Chen, Rujin -AU - Chen R -LA - eng -PT - Journal Article -PT - Research Support, Non-U.S. Gov't -PT - Research Support, U.S. Gov't, Non-P.H.S. -DEP - 20111111 -PL - England -TA - Plant Cell -JT - The Plant cell -JID - 9208688 -RN - 0 (Arabidopsis Proteins) -RN - 0 (BEL1 protein, Arabidopsis) -RN - 0 (Homeodomain Proteins) -RN - 0 (Plant Proteins) -RN - 0 (Transcription Factors) -SB - IM -MH - Arabidopsis Proteins/genetics -MH - Cloning, Molecular -MH - Epistasis, Genetic -MH - Gene Expression Regulation, Plant -MH - Genes, Plant -MH - Homeodomain Proteins/genetics -MH - Medicago truncatula/*genetics/*growth & development -MH - Mutation -MH - Plant Leaves/genetics/*growth & development -MH - Plant Proteins/*genetics/*metabolism -MH - Sequence Homology, Nucleic Acid -MH - Transcription Factors/genetics -MH - Two-Hybrid System Techniques -PMC - PMC3246329 -EDAT- 2011/11/15 06:00 -MHDA- 2012/08/22 06:00 -CRDT- 2011/11/15 06:00 -PHST- 2011/11/15 06:00 [entrez] -PHST- 2011/11/15 06:00 [pubmed] -PHST- 2012/08/22 06:00 [medline] -AID - tpc.111.089128 [pii] -AID - 089128 [pii] -AID - 10.1105/tpc.111.089128 [doi] -PST - ppublish -SO - Plant Cell. 2011 Nov;23(11):3929-43. doi: 10.1105/tpc.111.089128. Epub 2011 Nov - 11. - - -##### PUB RECORD ##### -## 10.1104/pp.15.00164 25792252 null Weller, Foo, et al., 2015 "Weller JL, Foo EM, Hecht V, Ridge S, Vander Schoor JK, Reid JB. Ethylene Signaling Influences Light-Regulated Development in Pea. Plant Physiol. 2015 Sep;169(1):115-24. doi: 10.1104/pp.15.00164. Epub 2015 Mar 19. PMID: 25792252; PMCID: PMC4577373." ## - -PMID- 25792252 -OWN - NLM -STAT- MEDLINE -DCOM- 20160707 -LR - 20220310 -IS - 1532-2548 (Electronic) -IS - 0032-0889 (Print) -IS - 0032-0889 (Linking) -VI - 169 -IP - 1 -DP - 2015 Sep -TI - Ethylene Signaling Influences Light-Regulated Development in Pea. -PG - 115-24 -LID - 10.1104/pp.15.00164 [doi] -AB - Plant responses to light involve a complex network of interactions among multiple - plant hormones. In a screen for mutants showing altered photomorphogenesis under - red light, we identified a mutant with dramatically enhanced leaf expansion and - delayed petal senescence. We show that this mutant exhibits reduced sensitivity - to ethylene and carries a nonsense mutation in the single pea (Pisum sativum) - ortholog of the ethylene signaling gene ETHYLENE INSENSITIVE2 (EIN2). Consistent - with this observation, the ein2 mutation rescues the previously described effects - of ethylene overproduction in mature phytochrome-deficient plants. In seedlings, - ein2 confers a marked increase in leaf expansion under monochromatic red, - far-red, or blue light, and interaction with phytochromeA, phytochromeB, and - long1 mutants confirms that ein2 enhances both phytochrome- and - cryptochrome-dependent responses in a LONG1-dependent manner. In contrast, - minimal effects of ein2 on seedling development in darkness or high-irradiance - white light show that ethylene is not limiting for development under these - conditions. These results indicate that ethylene signaling constrains leaf - expansion during deetiolation in pea and provide further evidence that - down-regulation of ethylene production may be an important component mechanism in - the broader control of photomorphogenic development by phytochrome and - cryptochrome. -CI - (c) 2015 American Society of Plant Biologists. All Rights Reserved. -FAU - Weller, James L -AU - Weller JL -AUID- ORCID: 0000-0003-2423-8286 -AD - School of Biological Sciences, University of Tasmania, Hobart, Tasmania 7001, - Australia jim.weller@utas.edu.au. -FAU - Foo, Eloise M -AU - Foo EM -AUID- ORCID: 0000-0002-9751-8433 -AD - School of Biological Sciences, University of Tasmania, Hobart, Tasmania 7001, - Australia. -FAU - Hecht, Valerie -AU - Hecht V -AUID- ORCID: 0000-0002-3539-3356 -AD - School of Biological Sciences, University of Tasmania, Hobart, Tasmania 7001, - Australia. -FAU - Ridge, Stephen -AU - Ridge S -AD - School of Biological Sciences, University of Tasmania, Hobart, Tasmania 7001, - Australia. -FAU - Vander Schoor, Jacqueline K -AU - Vander Schoor JK -AD - School of Biological Sciences, University of Tasmania, Hobart, Tasmania 7001, - Australia. -FAU - Reid, James B -AU - Reid JB -AD - School of Biological Sciences, University of Tasmania, Hobart, Tasmania 7001, - Australia. -LA - eng -SI - GENBANK/KP202149 -PT - Journal Article -PT - Research Support, Non-U.S. Gov't -DEP - 20150319 -PL - United States -TA - Plant Physiol -JT - Plant physiology -JID - 0401224 -RN - 0 (Cryptochromes) -RN - 0 (Ethylenes) -RN - 0 (Plant Growth Regulators) -RN - 0 (Plant Proteins) -RN - 11121-56-5 (Phytochrome) -RN - 91GW059KN7 (ethylene) -SB - IM -MH - Cryptochromes/metabolism -MH - Darkness -MH - Down-Regulation -MH - Ethylenes/*metabolism -MH - Gene Expression Regulation, Developmental -MH - Gene Expression Regulation, Plant -MH - Light -MH - Molecular Sequence Data -MH - Mutation -MH - Peas/genetics/growth & development/*physiology/radiation effects -MH - Phytochrome/*metabolism -MH - Plant Growth Regulators/*metabolism -MH - Plant Leaves/genetics/growth & development/physiology/radiation effects -MH - Plant Proteins/genetics/*metabolism -MH - Seedlings/genetics/growth & development/physiology/radiation effects -MH - Signal Transduction -PMC - PMC4577373 -EDAT- 2015/03/21 06:00 -MHDA- 2016/07/09 06:00 -CRDT- 2015/03/21 06:00 -PHST- 2015/02/02 00:00 [received] -PHST- 2015/03/17 00:00 [accepted] -PHST- 2015/03/21 06:00 [entrez] -PHST- 2015/03/21 06:00 [pubmed] -PHST- 2016/07/09 06:00 [medline] -AID - pp.15.00164 [pii] -AID - PP201500164 [pii] -AID - 10.1104/pp.15.00164 [doi] -PST - ppublish -SO - Plant Physiol. 2015 Sep;169(1):115-24. doi: 10.1104/pp.15.00164. Epub 2015 Mar - 19. - - -##### PUB RECORD ##### -## 10.1105/tpc.19.00609 32303662 PMC7268793 Ribeiro, Lacchini, et al., 2020 "Ribeiro B, Lacchini E, Bicalho KU, Mertens J, Arendt P, Vanden Bossche R, Calegario G, Gryffroy L, Ceulemans E, Buitink J, Goossens A, Pollier J. A Seed-Specific Regulator of Triterpene Saponin Biosynthesis in Medicago truncatula. Plant Cell. 2020 Jun;32(6):2020-2042. doi: 10.1105/tpc.19.00609. Epub 2020 Apr 17. PMID: 32303662; PMCID: PMC7268793." ## - -PMID- 32303662 -OWN - NLM -STAT- MEDLINE -DCOM- 20210204 -LR - 20210602 -IS - 1532-298X (Electronic) -IS - 1040-4651 (Print) -IS - 1040-4651 (Linking) -VI - 32 -IP - 6 -DP - 2020 Jun -TI - A Seed-Specific Regulator of Triterpene Saponin Biosynthesis in Medicago - truncatula. -PG - 2020-2042 -LID - 10.1105/tpc.19.00609 [doi] -AB - Plants produce a vast array of defense compounds to protect themselves from - pathogen attack or herbivore predation. Saponins are a specific class of defense - compounds comprising bioactive glycosides with a steroidal or triterpenoid - aglycone backbone. The model legume Medicago truncatula synthesizes two types of - saponins, hemolytic saponins and nonhemolytic soyasaponins, which accumulate as - specific blends in different plant organs. Here, we report the identification of - the seed-specific transcription factor TRITERPENE SAPONIN ACTIVATION REGULATOR3 - (TSAR3), which controls hemolytic saponin biosynthesis in developing M. - truncatula seeds. Analysis of genes that are coexpressed with TSAR3 in - transcriptome data sets from developing M. truncatula seeds led to the - identification of CYP88A13, a cytochrome P450 that catalyzes the C-16alpha - hydroxylation of medicagenic acid toward zanhic acid, the final oxidation step of - the hemolytic saponin biosynthesis branch in M. truncatula In addition, two - uridine diphosphate glycosyltransferases, UGT73F18 and UGT73F19, which - glucosylate hemolytic sapogenins at the C-3 position, were identified. The genes - encoding the identified biosynthetic enzymes are present in clusters of - duplicated genes in the M. truncatula genome. This appears to be a common theme - among saponin biosynthesis genes, especially glycosyltransferases, and may be the - driving force of the metabolic evolution of saponins. -CI - (c) 2020 American Society of Plant Biologists. All rights reserved. -FAU - Ribeiro, Bianca -AU - Ribeiro B -AUID- ORCID: 0000-0002-1843-0258 -AD - Ghent University, Department of Plant Biotechnology and Bioinformatics, 9052 - Ghent, Belgium. -AD - VIB Center for Plant Systems Biology, 9052 Ghent, Belgium. -FAU - Lacchini, Elia -AU - Lacchini E -AUID- ORCID: 0000-0002-1598-8950 -AD - Ghent University, Department of Plant Biotechnology and Bioinformatics, 9052 - Ghent, Belgium. -AD - VIB Center for Plant Systems Biology, 9052 Ghent, Belgium. -FAU - Bicalho, Keylla U -AU - Bicalho KU -AUID- ORCID: 0000-0002-5165-9070 -AD - Ghent University, Department of Plant Biotechnology and Bioinformatics, 9052 - Ghent, Belgium. -AD - VIB Center for Plant Systems Biology, 9052 Ghent, Belgium. -AD - Department of Organic Chemistry, Institute of Chemistry, Sao Paulo State - University (UNESP), Araraquara, Sao Paulo 14800-900, Brazil. -FAU - Mertens, Jan -AU - Mertens J -AUID- ORCID: 0000-0002-8095-0748 -AD - Ghent University, Department of Plant Biotechnology and Bioinformatics, 9052 - Ghent, Belgium. -AD - VIB Center for Plant Systems Biology, 9052 Ghent, Belgium. -FAU - Arendt, Philipp -AU - Arendt P -AUID- ORCID: 0000-0001-7429-0803 -AD - Ghent University, Department of Plant Biotechnology and Bioinformatics, 9052 - Ghent, Belgium. -AD - VIB Center for Plant Systems Biology, 9052 Ghent, Belgium. -FAU - Vanden Bossche, Robin -AU - Vanden Bossche R -AUID- ORCID: 0000-0001-6407-8139 -AD - Ghent University, Department of Plant Biotechnology and Bioinformatics, 9052 - Ghent, Belgium. -AD - VIB Center for Plant Systems Biology, 9052 Ghent, Belgium. -FAU - Calegario, Gabriela -AU - Calegario G -AUID- ORCID: 0000-0002-3772-8447 -AD - Ghent University, Department of Plant Biotechnology and Bioinformatics, 9052 - Ghent, Belgium. -AD - VIB Center for Plant Systems Biology, 9052 Ghent, Belgium. -FAU - Gryffroy, Lore -AU - Gryffroy L -AUID- ORCID: 0000-0001-9202-2992 -AD - Ghent University, Department of Plant Biotechnology and Bioinformatics, 9052 - Ghent, Belgium. -AD - VIB Center for Plant Systems Biology, 9052 Ghent, Belgium. -FAU - Ceulemans, Evi -AU - Ceulemans E -AUID- ORCID: 0000-0002-3083-5768 -AD - Ghent University, Department of Plant Biotechnology and Bioinformatics, 9052 - Ghent, Belgium. -AD - VIB Center for Plant Systems Biology, 9052 Ghent, Belgium. -FAU - Buitink, Julia -AU - Buitink J -AUID- ORCID: 0000-0002-1457-764X -AD - Institut de Recherche en Horticulture et Semences-Unites Mixtes de Recherche, - Universite d'Angers, INRAE, Institut Agro, SFR 4207 QuaSaV, 49071 Beaucouze, - France. -FAU - Goossens, Alain -AU - Goossens A -AUID- ORCID: 0000-0002-1599-551X -AD - Ghent University, Department of Plant Biotechnology and Bioinformatics, 9052 - Ghent, Belgium alain.goossens@psb-vib.ugent.be jacob.pollier@psb-vib.ugent.be. -AD - VIB Center for Plant Systems Biology, 9052 Ghent, Belgium. -FAU - Pollier, Jacob -AU - Pollier J -AUID- ORCID: 0000-0002-1134-9238 -AD - Ghent University, Department of Plant Biotechnology and Bioinformatics, 9052 - Ghent, Belgium alain.goossens@psb-vib.ugent.be jacob.pollier@psb-vib.ugent.be. -AD - VIB Center for Plant Systems Biology, 9052 Ghent, Belgium. -AD - VIB Metabolomics Core, 9052 Ghent, Belgium. -LA - eng -PT - Journal Article -PT - Research Support, Non-U.S. Gov't -DEP - 20200417 -PL - England -TA - Plant Cell -JT - The Plant cell -JID - 9208688 -RN - 0 (Plant Proteins) -RN - 0 (Triterpenes) -SB - IM -MH - Gene Expression Regulation, Plant -MH - Medicago truncatula/genetics/*metabolism -MH - Plant Proteins/genetics/*metabolism -MH - Seeds/*metabolism -MH - Triterpenes/*metabolism -PMC - PMC7268793 -EDAT- 2020/04/19 06:00 -MHDA- 2021/02/05 06:00 -CRDT- 2020/04/19 06:00 -PHST- 2019/08/07 00:00 [received] -PHST- 2020/03/27 00:00 [revised] -PHST- 2020/04/10 00:00 [accepted] -PHST- 2020/04/19 06:00 [pubmed] -PHST- 2021/02/05 06:00 [medline] -PHST- 2020/04/19 06:00 [entrez] -AID - tpc.19.00609 [pii] -AID - 201900609R2 [pii] -AID - 10.1105/tpc.19.00609 [doi] -PST - ppublish -SO - Plant Cell. 2020 Jun;32(6):2020-2042. doi: 10.1105/tpc.19.00609. Epub 2020 Apr - 17. - - -##### PUB RECORD ##### -## 10.1111/nph.13162 25406544 null Carelli, Biazzi, et al., 2014 "Carelli M, Biazzi E, Tava A, Losini I, Abbruscato P, Depedro C, Scotti C. Sapogenin content variation in Medicago inter-specific hybrid derivatives highlights some aspects of saponin synthesis and control. New Phytol. 2015 Apr;206(1):303-314. doi: 10.1111/nph.13162. Epub 2014 Nov 18. PMID: 25406544." ## - -PMID- 25406544 -OWN - NLM -STAT- MEDLINE -DCOM- 20160211 -LR - 20201109 -IS - 1469-8137 (Electronic) -IS - 0028-646X (Linking) -VI - 206 -IP - 1 -DP - 2015 Apr -TI - Sapogenin content variation in Medicago inter-specific hybrid derivatives - highlights some aspects of saponin synthesis and control. -PG - 303-314 -LID - 10.1111/nph.13162 [doi] -AB - In the Medicago genus, saponins are a complex mixture of triterpene glycosides - showing a broad spectrum of biological properties. Here we analyzed the variation - in the sapogenin content and composition of inter-specific hybrid Medicago - sativa x Medicago arborea derivatives to highlight the pattern of this variation - in plant organs (leaves/roots) and the possible mechanisms underlying it. In - Sativa Arborea Cross (SAC) leaves and roots, saponins and sapogenins were - evaluated using chromatographic methods. Phenotypic correlations between - sapogenin content and bio-agronomic traits were examined. Expression studies on - beta-amyrin synthase and four cytochromes P450 (CYPs) involved in sapogenin - biosynthesis and sequence analysis of the key gene of the hemolytic sapogenin - pathway (CYP716A12) were performed. Chromatographic analyses revealed a different - pattern of among-family variation for hemolytic and nonhemolytic sapogenins and - saponins and for the two organs/tissues. Different correlation patterns of gene - expression in roots and leaves were found. Diachronic analysis revealed a - relationship between sapogenin content and gene transcriptional levels in the - early stages of the productive cycle. The results suggest that there are - different control mechanisms acting on sapogenin biosynthesis for leaves and - roots, which are discussed. A key role for medicagenic acid in the control of - sapogenin content in both the tissues is proposed and discussed. -CI - (c) 2014 The Authors. New Phytologist (c) 2014 New Phytologist Trust. -FAU - Carelli, Maria -AU - Carelli M -AD - Consiglio per la Ricerca e la Sperimentazione in Agricoltura, Centro di Ricerca - per le Produzioni Foraggere e Lattiero-Casearie, viale Piacenza 29, 26900, Lodi, - Italy. -FAU - Biazzi, Elisa -AU - Biazzi E -AD - Consiglio per la Ricerca e la Sperimentazione in Agricoltura, Centro di Ricerca - per le Produzioni Foraggere e Lattiero-Casearie, viale Piacenza 29, 26900, Lodi, - Italy. -FAU - Tava, Aldo -AU - Tava A -AD - Consiglio per la Ricerca e la Sperimentazione in Agricoltura, Centro di Ricerca - per le Produzioni Foraggere e Lattiero-Casearie, viale Piacenza 29, 26900, Lodi, - Italy. -FAU - Losini, Ilaria -AU - Losini I -AD - Parco Tecnologico Padano, via Einsten- Loc. Cascina Codazza, 26900, Lodi, Italy. -FAU - Abbruscato, Pamela -AU - Abbruscato P -AD - Parco Tecnologico Padano, via Einsten- Loc. Cascina Codazza, 26900, Lodi, Italy. -FAU - Depedro, Claudia -AU - Depedro C -AD - Consiglio per la Ricerca e la Sperimentazione in Agricoltura, Centro di Ricerca - per le Produzioni Foraggere e Lattiero-Casearie, viale Piacenza 29, 26900, Lodi, - Italy. -FAU - Scotti, Carla -AU - Scotti C -AD - Consiglio per la Ricerca e la Sperimentazione in Agricoltura, Centro di Ricerca - per le Produzioni Foraggere e Lattiero-Casearie, viale Piacenza 29, 26900, Lodi, - Italy. -LA - eng -SI - GENBANK/KM978958 -PT - Journal Article -PT - Research Support, Non-U.S. Gov't -DEP - 20141118 -PL - England -TA - New Phytol -JT - The New phytologist -JID - 9882884 -RN - 0 (Plant Proteins) -RN - 0 (Sapogenins) -RN - 0 (Saponins) -RN - 0 (Triterpenes) -RN - 7X05537I17 (medicagenic acid) -RN - 9035-51-2 (Cytochrome P-450 Enzyme System) -RN - EC 5.4.- (Intramolecular Transferases) -RN - EC 5.4.99.- (2,3-oxidosqualene-beta-amyrin-cyclase) -SB - IM -MH - Base Sequence -MH - Cytochrome P-450 Enzyme System/*genetics/metabolism -MH - Gene Expression Regulation, Plant -MH - Intramolecular Transferases/*genetics/metabolism -MH - Medicago/genetics/*metabolism -MH - Medicago sativa/genetics/metabolism -MH - Medicago truncatula/genetics/metabolism -MH - Molecular Sequence Data -MH - Organ Specificity -MH - Plant Leaves/genetics/metabolism -MH - Plant Proteins/genetics/metabolism -MH - Plant Roots/genetics/metabolism -MH - Sapogenins/*metabolism -MH - Saponins/*metabolism -MH - Sequence Analysis, DNA -MH - Triterpenes/metabolism -OTO - NOTNLM -OT - Medicago arborea -OT - Medicago sativa (alfalfa) -OT - cytochrome P450 expression -OT - inter-specific cross -OT - sapogenin synthesis -OT - triterpene saponin -EDAT- 2014/11/20 06:00 -MHDA- 2016/02/13 06:00 -CRDT- 2014/11/20 06:00 -PHST- 2014/08/08 00:00 [received] -PHST- 2014/10/09 00:00 [accepted] -PHST- 2014/11/20 06:00 [entrez] -PHST- 2014/11/20 06:00 [pubmed] -PHST- 2016/02/13 06:00 [medline] -AID - 10.1111/nph.13162 [doi] -PST - ppublish -SO - New Phytol. 2015 Apr;206(1):303-314. doi: 10.1111/nph.13162. Epub 2014 Nov 18. - - diff --git a/Medicago/truncatula/gene_functions/medtr.traits.yml b/Medicago/truncatula/gene_functions/medtr.traits.yml index 5d83f00..d3078f0 100644 --- a/Medicago/truncatula/gene_functions/medtr.traits.yml +++ b/Medicago/truncatula/gene_functions/medtr.traits.yml @@ -1,25 +1,21 @@ ## DOCUMENT 1 ## --- gene_symbols: - - ANS -gene_symbol_long: Anthocyanidin synthase -gene_model_pub_name: Medtr5g011250 -gene_model_full_id: medtr.A17_HM341.gnm4.ann2.Medtr5g011250 + - ENOD40 +gene_symbol_long: Abnormal tissue development +gene_model_pub_name: CAD48198.1 +gene_model_full_id: medtr.A17_HM341.gnm4.ann2.Medtr6g034835 confidence: 5 curators: - Steven Cannon -phenotype_synopsis: MtANS (anthocyanidin synthase) gene expression was down-regulated in M. truncatula genotype R108 using an antisense construct. Anthocyanin levels were strongly reduced in leaf tissues of antisense lines. The presence of a red anthocyanin-rich circle at the base of the axial side of the leaflet and small red dots on the adaxial side results from anthocyanin deposition. Six independent transgenic antisense MtANS lines lacked the red circle and spots and another 10 such lines had reduced levels of pigmentation. There was a strong reduction in the levels of both soluble and insoluble PAs (Oligomeric proanthocyanidins) in seeds, consistent with involvement of ANS in PA biosynthesis. +phenotype_synopsis: Use of antisense constructs of Mtenod40 arrested callus growth of Medicago explants, while overexpressing Mtenod40 embryos developed into teratomas. Enod40 genes might have a role in plant development, acting as 'riboregulators'. traits: - - entity_name: anthocyanin content - entity: TO:0000071 - - entity_name: leaf - entity: PO:0025034 - - entity_name: seed - entity: PO:0009010 + - entity_name: plant tissue development trait + entity: TO:0006015 references: - - citation: Jun, Liu et al., 2015 - doi: 10.1105/tpc.15.00476 - pmid: 26410301 + - citation: Campalans, Kondorosi et al., 2017 + doi: 10.1105/tpc.019406 + pmid: 15037734 - citation: Oellrich, Walls et al., 2015 doi: 10.1186/s13007-015-0053-y pmid: 25774204 @@ -28,239 +24,211 @@ references: ## DOCUMENT 2 ## --- gene_symbols: - - bHLH1 -gene_symbol_long: basic helix loop helix 1 -gene_model_pub_name: Medtr3g099620 -gene_model_full_id: medtr.A17_HM341.gnm4.ann2.Medtr3g099620 -confidence: 5 -curators: - - Steven Cannon -phenotype_synopsis: Repressing MtbHLH1 (using Chimeric REpressor Silencing Technology) caused an assymetrical pattern of nodule vascular bundle development with variable angles of growth in inoculated roots. The growth and vigor of aerial parts of the plant was impaired; the nodules were still able to fix atmospheric Nitrogen but the aboveground tissues could not benefit for whatever reason. Nodules on repressed plants appeared later than in control plants and were smaller in size. -traits: - - entity_name: vascular bundle development trait - entity: TO:0020109 - - entity_name: plant organ growth and development trait - entity: TO:0000927 - - entity_name: shoot system - entity: PO:0009006 - - entity_name: vascular bundle - entity: PO:0005020 - - entity_name: root nodule - entity: PO:0003023 -references: - - citation: Godiard, Lepage et al., 2011 - doi: 10.1111/j.1469-8137.2011.03718.x - pmid: 21679315 - - citation: Oellrich, Walls et al., 2015 - doi: 10.1186/s13007-015-0053-y - pmid: 25774204 - - -## DOCUMENT 3 ## ---- -gene_symbols: - - CBF4 -gene_symbol_long: C-repeat binding factor 4 -gene_model_pub_name: Medtr1g101600 -gene_model_full_id: medtr.A17_HM341.gnm4.ann2.Medtr1g101600 + - cyp716A12 +gene_symbol_long: cytochrome P450 monoxygenase +gene_model_pub_name: Medtr3g021350 +gene_model_full_id: medtr.A17_HM341.gnm4.ann2.Medtr3g021350 confidence: 5 curators: - Steven Cannon -phenotype_synopsis: Expression of MtCBF4 (transcription factor) in M. truncatula was induced by most of the abiotic stresses, including salt, drought, cold, and abscisic acid, suggesting crosstalk between these abiotic stresses. Upon exposure to a salt medium the primary root growth in the MtCBF4-overexpressing lines was greater than that of the control plants. MtCAS31 belongs to the CBF regulon and is associated with salt tolerance; under salt treatment, expression of MtCAS31 increased more in d35S:MtCBF4 transgenic plants than in controls. To summarize, over-expression of MtCBF4 enhanced tolerance to salt stress. +phenotype_synopsis: A cytochrome P450 gene (CYP716A12) is involved in an early step in saponin biosynthesis and is found in most tissues. CYP716A12 loss-of-function mutants do not produce hemolytic saponins and only synthetize soyasaponins, and were thus named lacking hemolytic activity (lha). CYP716A12 catalyzes the oxidation of _-amyrin and erythrodiol at the C-28 position, yielding oleanolic acid. Transcriptome changes in the lha mutant showed a modulation in the main steps of the triterpenic saponin biosynthetic pathway, which includes squalene cyclization, _-amyrin oxidation, and glycosylation. Growth of homozygous lha/lha plants was stunted. traits: - - entity_name: salt tolerance - entity: TO:0006001 - - entity_name: root length - entity: TO:0000227 - - entity_name: primary root - entity: PO:0020127 + - entity_name: plant structure growth and development trait + entity: TO:0000928 - entity_name: whole plant entity: PO:0000003 references: - - citation: Pecrix, Staton et al., 2018 - doi: 10.1038/s41477-018-0286-7 - pmid: 30397259 - - citation: Oellrich, Walls et al., 2015 - doi: 10.1186/s13007-015-0053-y - pmid: 25774204 - - -## DOCUMENT 4 ## ---- -gene_symbols: - - CDC16 -gene_symbol_long: cell division cycle 16 -gene_model_pub_name: Medtr8g058380 -gene_model_full_id: medtr.A17_HM341.gnm4.ann2.Medtr8g058380 -confidence: 5 -curators: - - Steven Cannon -phenotype_synopsis: Partial suppression of the CDC16 gene homolog in Medicago truncatula leads to a decreased number of lateral roots, an increased number of nodules, and reduced auxin sensitivity. -traits: - - entity_name: root nodule morphology trait - entity: TO:0000898 - - entity_name: auxin sensitivity - entity: TO:0000163 - - entity_name: root system - entity: PO:0025025 - - entity_name: lateral root - entity: PO:0020121 - - entity_name: root - entity: PO:0009005 - - entity_name: root nodule - entity: PO:0003023 -references: - - citation: Kuppusamy, Ivashuta et al., 2009 - doi: 10.1104/pp.109.143024 - pmid: 19789288 + - citation: Carelli, Biazzi et al., 2014 + doi: 10.1111/nph.13162 + pmid: 25406544 - citation: Oellrich, Walls et al., 2015 doi: 10.1186/s13007-015-0053-y pmid: 25774204 -## DOCUMENT 5 ## +## DOCUMENT 3 ## --- gene_symbols: - - CDPK1 -gene_symbol_long: calcium-dependent protein kinase 1 -gene_model_pub_name: Medtr5g022030 -gene_model_full_id: medtr.A17_HM341.gnm4.ann2.Medtr5g022030 + - HAP2.1 +gene_model_pub_name: Medtr1g056530 +gene_model_full_id: medtr.A17_HM341.gnm4.ann2.Medtr1g056530 confidence: 5 curators: - Steven Cannon -phenotype_synopsis: Reduced root hair and root cell lengths; diminution of rhizobial and mycorrhizal symbiotic colonization +phenotype_synopsis: Small and nonfunctional nodules arrested in growth when both normally spliced and alternatively spliced variants repressed. When only the alternative spliced form repressed the nodules are small but still fix nitrogen successfully. traits: - - entity_name: root cortical cell length - entity: TO:0020108 - - entity_name: root hair length - entity: TO:0002665 - entity_name: root nodule morphology trait entity: TO:0000898 - - entity_name: root system - entity: PO:0025025 - entity_name: root nodule entity: PO:0003023 - - entity_name: root hair cell - entity: PO:0000256 references: - - citation: Ivashuta, Liu et al., 2005 - doi: 10.1105/tpc.105.035394 - pmid: 16199614 + - citation: Chen, Liu et al., 2015 + doi: 10.3389/fpls.2015.00575 + pmid: 26284091 - citation: Oellrich, Walls et al., 2015 doi: 10.1186/s13007-015-0053-y pmid: 25774204 -## DOCUMENT 6 ## +## DOCUMENT 4 ## --- gene_symbols: - - chitIII-3 -gene_symbol_long: class III chitinase -gene_model_pub_name: Medtr8g055940 -gene_model_full_id: medtr.A17_HM341.gnm4.ann2.Medtr8g055940 + - SGL1 +gene_symbol_long: single leaflet1 +gene_model_pub_name: Medtr3g098560 +gene_model_full_id: medtr.A17_HM341.gnm4.ann2.Medtr3g098560 confidence: 5 curators: - Steven Cannon -phenotype_synopsis: Mtchit 3-3 expression (class III chitinase gene) is specifically induced by arbuscular mycorrhizal (AM) fungi in roots of the model legume Medicago truncatula. Mtchit 3-3 expression was artificially induced with a CaMV 35S promoter in root cells; this stimulated spore germination of Glomus intraradices and Glomus constrictum, and in the case of G. intraradices resulted in a higher probability of root colonization and spore formation. There was no measurable effect on the abundance of arbuscules within colonized roots. +phenotype_synopsis: Mutant displays simple, unifoliate (not compound) leaves. Petiole length is decreased. Defective, fused flowers traits: - - entity_name: root system - entity: PO:0025025 + - entity_name: petiole length + entity: TO:0000766 + - entity_name: flower morphology trait + entity: TO:0000499 + - entity_name: leaf shape + entity: TO:0000492 + - entity_name: petiole + entity: PO:0020038 + - entity_name: flower + entity: PO:0009046 references: - - citation: Salzer, Bonanomi et al., 2000 - doi: 10.1094/mpmi.2000.13.7.763 - pmid: 10875337 + - citation: Cheng, Li et al., 2021 + doi: 10.1093/plphys/kiaa005 + pmid: 33631796 - citation: Oellrich, Walls et al., 2015 doi: 10.1186/s13007-015-0053-y pmid: 25774204 -## DOCUMENT 7 ## +## DOCUMENT 5 ## --- gene_symbols: - - CPK3 -gene_symbol_long: calcium dependent protein kinase 3 -gene_model_pub_name: ABE72958.1 -gene_model_full_id: medtr.A17_HM341.gnm4.ann2.Medtr3g051770 + - NAM + - NAM-2 +gene_symbol_long: No Apical Meristem (weak allele) +gene_model_pub_name: AFI56799.1 +gene_model_full_id: medtr.A17_HM341.gnm4.ann2.Medtr2g078700 confidence: 5 curators: - Steven Cannon -phenotype_synopsis: Expression of MtCPK3 in Medicago truncatula is regulated during nodulation. RNAi silenced CPK3 in transformed roots but no major phenotype was detected. When infected with rhizobia the nodule number was twice as high as the controls. +phenotype_synopsis: null traits: - - entity_name: root nodule number - entity: TO:0000900 - - entity_name: root system - entity: PO:0025025 - - entity_name: root nodule - entity: PO:0003023 + - entity_name: shoot apical meristem development + entity: TO:0006020 + - entity_name: carpel morphology trait + entity: TO:0006012 + - entity_name: trichome morphology trait + entity: TO:0000911 + - entity_name: cotyledon morphology trait + entity: TO:0000749 + - entity_name: male sterility + entity: TO:0000437 + - entity_name: vascular leaf morphology trait + entity: TO:0000419 + - entity_name: female sterility + entity: TO:0000358 + - entity_name: stamen morphology trait + entity: TO:0000215 + - entity_name: embryo shape + entity: TO:0000193 + - entity_name: carpel trichome + entity: PO:0025208 + - entity_name: reproductive shoot system + entity: PO:0025082 + - entity_name: leaflet + entity: PO:0020049 + - entity_name: cotyledon + entity: PO:0020030 + - entity_name: plant ovule + entity: PO:0020003 + - entity_name: flower + entity: PO:0009046 + - entity_name: carpel + entity: PO:0009030 + - entity_name: stamen + entity: PO:0009029 + - entity_name: plant embryo + entity: PO:0009009 + - entity_name: fruit + entity: PO:0009001 + - entity_name: juvenile vascular leaf + entity: PO:0006339 references: - - citation: Gargantini, Gonzalez-Rizzo et al., 2006 - doi: 10.1111/j.1365-313x.2006.02910.x - pmid: 17132148 + - citation: Cheng, Peng et al., 2012 + doi: 10.1111/j.1469-8137.2012.04147.x + pmid: 22530598 - citation: Oellrich, Walls et al., 2015 doi: 10.1186/s13007-015-0053-y pmid: 25774204 -## DOCUMENT 8 ## +## DOCUMENT 6 ## --- +scientific_name: Medicago truncatula gene_symbols: - - CYCLOPS -gene_model_pub_name: Medtr5g026850 -gene_model_full_id: medtr.A17_HM341.gnm4.ann2.Medtr5g026850 + - MtDMI2 +gene_symbol_long: Doesnt Make Infections +gene_model_pub_name: Medtr5g030920 +gene_model_full_id: medtr.A17_HM341.gnm4.ann2.Medtr5g030920 confidence: 5 curators: - - Steven Cannon -phenotype_synopsis: Symbiotic infection of roots by rhizobia bacteria and arbuscular mycorrhiza fungi was inhibited or blocked, i.e. infection threads were not observed despite colonization of root hairs by rhizobia and AM fungal hyphae formed abnormal hyphal swellings with no arbuscles observed. Nodule organogenesis was initiated but arrested prematurely at the level of primordia as an indirect consequence of the aborted infection. + - Marlene Dorneich-Hayes +comments: + - SYMRK is activated in root hairs by phosphorylation in response to the perception of NOD factors + - SYMRK-EGFP (enhanced green fluorescence protein) is endocytosed from the plasma membrane to intracellular puncta and affects the SYMRK signaling pathway + - SYMRK-suppressed mutants can't form infection threads and therefore can't form functional nodules, though they do form pseudo-nodules lacking symbiotic bacteria and fungi + - SYMRK overexpressing mutants form non-functional nodules without rhizobia +phenotype_synopsis: SYMRK is necessary for nodule organogenesis. traits: - - entity_name: root nodule morphology trait - entity: TO:0000898 - - entity_name: root system - entity: PO:0025025 + - entity_name: bioloical process involved in symbiotic interaction + entity: GO:0044403 + - entity_name: kinase activity + entity: GO:0016301 + - entity_name: positive regulation of receptor-mediated endocytosis + entity: GO:0048260 references: - - citation: Liu, Breakspear et al., 2019 - doi: 10.1104/pp.18.01572 - pmid: null - - citation: Oellrich, Walls et al., 2015 - doi: 10.1186/s13007-015-0053-y - pmid: 25774204 + - citation: Dvila-Delgado, Flores-Canl, et al., 2023 + doi: 10.1007/s00425-023-04116-0 + pmid: 36928335 -## DOCUMENT 9 ## +## DOCUMENT 7 ## --- gene_symbols: - - cyp716A12 -gene_symbol_long: cytochrome P450 monoxygenase -gene_model_pub_name: Medtr3g021350 -gene_model_full_id: medtr.A17_HM341.gnm4.ann2.Medtr3g021350 + - MtCCD1 +gene_symbol_long: carotenoid cleavage dioxygenase 1 +gene_model_pub_name: CAR57918.1 +gene_model_full_id: medtr.A17_HM341.gnm4.ann2.Medtr6g034835 confidence: 5 curators: - Steven Cannon -phenotype_synopsis: A cytochrome P450 gene (CYP716A12) is involved in an early step in saponin biosynthesis and is found in most tissues. CYP716A12 loss-of-function mutants do not produce hemolytic saponins and only synthetize soyasaponins, and were thus named lacking hemolytic activity (lha). CYP716A12 catalyzes the oxidation of _-amyrin and erythrodiol at the C-28 position, yielding oleanolic acid. Transcriptome changes in the lha mutant showed a modulation in the main steps of the triterpenic saponin biosynthetic pathway, which includes squalene cyclization, _-amyrin oxidation, and glycosylation. Growth of homozygous lha/lha plants was stunted. +phenotype_synopsis: RNA interference (RNAi) was used to repress a M. truncatula CCD1 gene in hairy roots colonized by the arbuscular mycorrhizal (AM) fungus Glomus intraradices. The normal AM-mediated accumulation of apocarotenoids (C13 cyclohexenone and C14 mycorradicin derivatives) was reduced in repressed plants; mycorradicin derivatives were reduced to 3% to 6% of the controls and the cyclohexenone derivatives were reduced to 30% to 47%. The RNAi roots turned a yellow-orange color because of C27 apocarotenoid accumulation (the probable substrate of the CCD1 enzyme). More degenerating arbuscules was observed in RNAi roots. traits: - - entity_name: plant structure growth and development trait - entity: TO:0000928 - - entity_name: whole plant - entity: PO:0000003 + - entity_name: carotene content + entity: TO:0000289 + - entity_name: root + entity: PO:0009005 references: - - citation: Carelli, Biazzi et al., 2014 - doi: 10.1111/nph.13162 - pmid: 25406544 + - citation: Floss, Schliemann et al., 2008 + doi: 10.1104/pp.108.125062 + pmid: 18790999 - citation: Oellrich, Walls et al., 2015 doi: 10.1186/s13007-015-0053-y pmid: 25774204 -## DOCUMENT 10 ## +## DOCUMENT 8 ## --- gene_symbols: - - DMI1 -gene_symbol_long: doesn't make infections 1 -gene_model_pub_name: Medtr2g005870 -gene_model_full_id: medtr.A17_HM341.gnm4.ann2.Medtr2g005870 + - CPK3 +gene_symbol_long: calcium dependent protein kinase 3 +gene_model_pub_name: ABE72958.1 +gene_model_full_id: medtr.A17_HM341.gnm4.ann2.Medtr3g051770 confidence: 5 curators: - Steven Cannon -phenotype_synopsis: Doesn't make nodules; infection thread aborts +phenotype_synopsis: Expression of MtCPK3 in Medicago truncatula is regulated during nodulation. RNAi silenced CPK3 in transformed roots but no major phenotype was detected. When infected with rhizobia the nodule number was twice as high as the controls. traits: - entity_name: root nodule number entity: TO:0000900 @@ -269,291 +237,276 @@ traits: - entity_name: root nodule entity: PO:0003023 references: - - citation: Liu, Lin et al., 2022 - doi: 10.1073/pnas.2205920119 - pmid: 35972963 + - citation: Gargantini, Gonzalez-Rizzo et al., 2006 + doi: 10.1111/j.1365-313x.2006.02910.x + pmid: 17132148 - citation: Oellrich, Walls et al., 2015 doi: 10.1186/s13007-015-0053-y pmid: 25774204 -## DOCUMENT 11 ## +## DOCUMENT 9 ## --- gene_symbols: - - DMI3 -gene_symbol_long: doesn't make infections 3 -gene_model_pub_name: Medtr8g043970 -gene_model_full_id: medtr.A17_HM341.gnm4.ann2.Medtr8g043970 + - bHLH1 +gene_symbol_long: basic helix loop helix 1 +gene_model_pub_name: Medtr3g099620 +gene_model_full_id: medtr.A17_HM341.gnm4.ann2.Medtr3g099620 confidence: 5 curators: - Steven Cannon -phenotype_synopsis: Doesn't make nodules or mycorrhizae +phenotype_synopsis: Repressing MtbHLH1 (using Chimeric REpressor Silencing Technology) caused an assymetrical pattern of nodule vascular bundle development with variable angles of growth in inoculated roots. The growth and vigor of aerial parts of the plant was impaired; the nodules were still able to fix atmospheric Nitrogen but the aboveground tissues could not benefit for whatever reason. Nodules on repressed plants appeared later than in control plants and were smaller in size. traits: - - entity_name: root nodule number - entity: TO:0000900 - - entity_name: root system - entity: PO:0025025 + - entity_name: vascular bundle development trait + entity: TO:0020109 + - entity_name: plant organ growth and development trait + entity: TO:0000927 + - entity_name: shoot system + entity: PO:0009006 + - entity_name: vascular bundle + entity: PO:0005020 - entity_name: root nodule entity: PO:0003023 references: - - citation: Mitra, Gleason et al., 2004 - doi: 10.1073/pnas.0400595101 - pmid: 15070781 - - citation: Oellrich, Walls et al., 2015 - doi: 10.1186/s13007-015-0053-y - pmid: 25774204 - - -## DOCUMENT 12 ## ---- -gene_symbols: - - ENOD40 -gene_symbol_long: Abnormal tissue development -gene_model_pub_name: CAD48198.1 -gene_model_full_id: medtr.A17_HM341.gnm4.ann2.Medtr6g034835 -confidence: 5 -curators: - - Steven Cannon -phenotype_synopsis: Use of antisense constructs of Mtenod40 arrested callus growth of Medicago explants, while overexpressing Mtenod40 embryos developed into teratomas. Enod40 genes might have a role in plant development, acting as 'riboregulators'. -traits: - - entity_name: plant tissue development trait - entity: TO:0006015 -references: - - citation: Campalans, Kondorosi et al., 2017 - doi: 10.1105/tpc.019406 - pmid: 15037734 + - citation: Godiard, Lepage et al., 2011 + doi: 10.1111/j.1469-8137.2011.03718.x + pmid: 21679315 - citation: Oellrich, Walls et al., 2015 doi: 10.1186/s13007-015-0053-y pmid: 25774204 -## DOCUMENT 13 ## ---- -gene_symbols: - - FCL1 -gene_symbol_long: fused compound leaf 1 -gene_model_pub_name: Medtr6g071190 -gene_model_full_id: medtr.A17_HM341.gnm4.ann2.Medtr6g071190 +## DOCUMENT 10 ## +--- +gene_symbols: + - LYK3 +gene_symbol_long: LYSIN MOTIF RECEPTOR-LIKE KINASE 3 +gene_model_pub_name: Medtr5g086130 +gene_model_full_id: medtr.A17_HM341.gnm4.ann2.Medtr5g086130 confidence: 5 curators: - Steven Cannon -phenotype_synopsis: Leaflets fused or partially fused, rachis between leaflets is absent, petiole is foreshortened. +phenotype_synopsis: Doesn't make nodules; infection thread aborts traits: - - entity_name: petiole length - entity: TO:0000766 - - entity_name: vascular leaf morphology trait - entity: TO:0000419 - - entity_name: leaf rachis - entity: PO:0020055 - - entity_name: leaflet - entity: PO:0020049 - - entity_name: petiole - entity: PO:0020038 + - entity_name: root nodule number + entity: TO:0000900 + - entity_name: root system + entity: PO:0025025 + - entity_name: root nodule + entity: PO:0003023 references: - - citation: Peng, Yu et al., 2011 - doi: 10.1105/tpc.111.089128 - pmid: 22080596 + - citation: Herrbach, Chirinos et al., 2017 + doi: 10.1093/jxb/erw474 + pmid: 28073951 - citation: Oellrich, Walls et al., 2015 doi: 10.1186/s13007-015-0053-y pmid: 25774204 -## DOCUMENT 14 ## +## DOCUMENT 11 ## --- gene_symbols: - - FLOT2 -gene_symbol_long: Flotillin-like protein 2 -gene_model_pub_name: Medtr3g106420 -gene_model_full_id: medtr.A17_HM341.gnm4.ann2.Medtr3g106420 + - LYK4 +gene_symbol_long: LYSIN MOTIF RECEPTOR-LIKE KINASE 4 +gene_model_pub_name: Medtr5g086120 +gene_model_full_id: medtr.A17_HM341.gnm4.ann2.Medtr5g086120 confidence: 5 curators: - Steven Cannon -phenotype_synopsis: Fewer nodules per plant, an increase in no-nodule plants, and a decrease in plants that form pink nodules. A decrease in primary root length and long primary lateral roots, reduced reduction of acetylene, and reduced number of infection events. +phenotype_synopsis: Doesn't make nodules; infection thread aborts traits: - - entity_name: lateral root length - entity: TO:0001012 - entity_name: root nodule number entity: TO:0000900 - - entity_name: seminal root length - entity: TO:0000586 - entity_name: root system entity: PO:0025025 - - entity_name: primary root - entity: PO:0020127 - - entity_name: lateral root - entity: PO:0020121 - entity_name: root nodule entity: PO:0003023 references: - - citation: Qiao, Pingault et al., 2016 - doi: 10.3389/fpls.2016.00034 - pmid: 26858743 + - citation: Herrbach, Chirinos et al., 2017 + doi: 10.1093/jxb/erw474 + pmid: 28073951 - citation: Oellrich, Walls et al., 2015 doi: 10.1186/s13007-015-0053-y pmid: 25774204 -## DOCUMENT 15 ## +## DOCUMENT 12 ## --- gene_symbols: - - FLOT3 -gene_symbol_long: Flotillin-like protein 3 -gene_model_pub_name: Medtr3g106480 -gene_model_full_id: medtr.A17_HM341.gnm4.ann2.Medtr3g106480 + - MtAOC +gene_symbol_long: Allene-oxide cyclase +gene_model_pub_name: CAI29046.1 +gene_model_full_id: medtr.A17_HM341.gnm4.ann2.Medtr7g417750 confidence: 5 curators: - Steven Cannon -phenotype_synopsis: Shorter roots and reduced root weight. +phenotype_synopsis: MtAOC (allene oxide cyclase) gene expression was partially suppressed in roots following transformation with cDNA in the antisense direction. These roots exhibited lower jasmonic acid levels and delayed colonization by Glomus intraradices. The number of arbuscles decreased and their development was delayed, yet their physical structure was unaltered. traits: - - entity_name: root weight - entity: TO:0000279 - - entity_name: root length - entity: TO:0000227 + - entity_name: root system + entity: PO:0025025 - entity_name: root entity: PO:0009005 references: - - citation: Qiao, Pingault et al., 2016 - doi: 10.3389/fpls.2016.00034 - pmid: 26858743 + - citation: Isayenkov, Mrosk et al., 2005 + doi: 10.1104/pp.105.069054 + pmid: 16244141 - citation: Oellrich, Walls et al., 2015 doi: 10.1186/s13007-015-0053-y pmid: 25774204 -## DOCUMENT 16 ## +## DOCUMENT 13 ## --- gene_symbols: - - FLOT4 -gene_symbol_long: Flotillin-like protein 4 -gene_model_pub_name: Medtr3g106430 -gene_model_full_id: medtr.A17_HM341.gnm4.ann2.Medtr3g106430 + - CDPK1 +gene_symbol_long: calcium-dependent protein kinase 1 +gene_model_pub_name: Medtr5g022030 +gene_model_full_id: medtr.A17_HM341.gnm4.ann2.Medtr5g022030 confidence: 5 curators: - Steven Cannon -phenotype_synopsis: Decrease in plants that form pink nodules and an increase in numbers of secondary lateral roots, reduced reduction of acetylene. Weak association with reduction in nodule numbers. Both decreased number of infection events and defective infection thread elongation. +phenotype_synopsis: Reduced root hair and root cell lengths; diminution of rhizobial and mycorrhizal symbiotic colonization traits: - - entity_name: root nodule number - entity: TO:0000900 - - entity_name: root number - entity: TO:0000084 + - entity_name: root cortical cell length + entity: TO:0020108 + - entity_name: root hair length + entity: TO:0002665 + - entity_name: root nodule morphology trait + entity: TO:0000898 - entity_name: root system entity: PO:0025025 - entity_name: root nodule entity: PO:0003023 + - entity_name: root hair cell + entity: PO:0000256 references: - - citation: Qiao, Pingault et al., 2016 - doi: 10.3389/fpls.2016.00034 - pmid: 26858743 + - citation: Ivashuta, Liu et al., 2005 + doi: 10.1105/tpc.105.035394 + pmid: 16199614 - citation: Oellrich, Walls et al., 2015 doi: 10.1186/s13007-015-0053-y pmid: 25774204 -## DOCUMENT 17 ## +## DOCUMENT 14 ## --- gene_symbols: - - FTa1 -gene_symbol_long: Delayed flowering -gene_model_pub_name: Medtr7g084970 -gene_model_full_id: medtr.A17_HM341.gnm4.ann2.Medtr7g084970 + - PALM1 +gene_symbol_long: PALMATE-LIKE PENTAFOLIATA1 +gene_model_pub_name: Medtr5g014400 +gene_model_full_id: medtr.A17_HM341.gnm4.ann2.Medtr5g014400 confidence: 5 curators: - Steven Cannon -phenotype_synopsis: Delayed flowering +phenotype_synopsis: Forms dissected leaves with five leaflets clustered at the tip (palmate-like pentafoliate in contrast to the trifoliate WT leaves). The distal lateral leaflets developed in a manner morphologically/anatomically similar to terminal leaflets. The length of the petiole increased and that of the rachis decreased. traits: - - entity_name: flowering time trait - entity: TO:0002616 + - entity_name: petiole length + entity: TO:0000766 + - entity_name: leaf morphology trait + entity: TO:0000748 + - entity_name: leaf + entity: PO:0025034 + - entity_name: leaf rachis + entity: PO:0020055 + - entity_name: petiole + entity: PO:0020038 references: - - citation: Laurie, Diwadkar et al., 2011 - doi: 10.1104/pp.111.180182 - pmid: 21685176 + - citation: Jiao, Wang et al., 2020 + doi: 10.1186/s12870-020-02619-6 + pmid: 32867687 - citation: Oellrich, Walls et al., 2015 doi: 10.1186/s13007-015-0053-y pmid: 25774204 -## DOCUMENT 18 ## +## DOCUMENT 15 ## --- gene_symbols: - - FTc -gene_symbol_long: Flower development normal under long days -gene_model_pub_name: Medtr7g085040 -gene_model_full_id: medtr.A17_HM341.gnm4.ann2.Medtr7g085040 + - ANS +gene_symbol_long: Anthocyanidin synthase +gene_model_pub_name: Medtr5g011250 +gene_model_full_id: medtr.A17_HM341.gnm4.ann2.Medtr5g011250 confidence: 5 curators: - Steven Cannon -phenotype_synopsis: null +phenotype_synopsis: MtANS (anthocyanidin synthase) gene expression was down-regulated in M. truncatula genotype R108 using an antisense construct. Anthocyanin levels were strongly reduced in leaf tissues of antisense lines. The presence of a red anthocyanin-rich circle at the base of the axial side of the leaflet and small red dots on the adaxial side results from anthocyanin deposition. Six independent transgenic antisense MtANS lines lacked the red circle and spots and another 10 such lines had reduced levels of pigmentation. There was a strong reduction in the levels of both soluble and insoluble PAs (Oligomeric proanthocyanidins) in seeds, consistent with involvement of ANS in PA biosynthesis. traits: - - entity_name: flower development trait - entity: TO:0000622 + - entity_name: anthocyanin content + entity: TO:0000071 + - entity_name: leaf + entity: PO:0025034 + - entity_name: seed + entity: PO:0009010 references: - - citation: Laurie, Diwadkar et al., 2011 - doi: 10.1104/pp.111.180182 - pmid: 21685176 + - citation: Jun, Liu et al., 2015 + doi: 10.1105/tpc.15.00476 + pmid: 26410301 - citation: Oellrich, Walls et al., 2015 doi: 10.1186/s13007-015-0053-y pmid: 25774204 -## DOCUMENT 19 ## +## DOCUMENT 16 ## --- gene_symbols: - - GT3 - - UGT73F3 -gene_symbol_long: Glycosyltransferase 3 -gene_model_pub_name: Medtr2g035020 -gene_model_full_id: medtr.A17_HM341.gnm4.ann2.Medtr2g035020 + - nork +gene_symbol_long: nodulation receptor kinase +gene_model_pub_name: Medtr5g030920 +gene_model_full_id: medtr.A17_HM341.gnm4.ann2.Medtr5g030920 confidence: 5 curators: - Steven Cannon -phenotype_synopsis: The uridine diphosphate glycosyltransferase (GT3, UGT73F3) showed specificity for multiple sapogenins and functions in saponin biosynthesis. Homozygous plants were retarded in growth relative to normal plants, whereas heterozygous plants did not show dwarfism. Homozygous plants could flower and produce a few pods. The seeds did not show visible morphological changes but took an unusually long time to germinate (at least 3 weeks). Roots in homozygous lines were very short and less branched compared with the wild type. Leaf saponin levels did not differ between controls and mutants. Levels of 5 different saponins were lower in mutant lines (approx. 3-fold) compared with controls, while only one saponin was higher in the mutants. The large (10-fold) increase of 3-Glc-28-Ara-Rha-Xyl-medicagenic acid in UGT73F3 knockout lines suggests that the UDP-glucose pool is being diverted toward increased formation of non-C-28-glucosylated sapogenins. Levels of the isoflavone formononetin and its conjugates were also increased in UGT73F3 knockouts. +phenotype_synopsis: Lacks symbiotic root responses in the presence of compatible Sinorhizobium meliloti or Nod factor, and resists mycorrhizal colonization traits: - - entity_name: plant structure growth and development trait - entity: TO:0000928 - - entity_name: germination rate - entity: TO:0000430 - - entity_name: root branching - entity: TO:0000257 - - entity_name: root length - entity: TO:0000227 - - entity_name: root - entity: PO:0009005 - - entity_name: whole plant - entity: PO:0000003 + - entity_name: root nodule number + entity: TO:0000900 + - entity_name: root system + entity: PO:0025025 + - entity_name: root nodule + entity: PO:0003023 references: - - citation: Ribeiro, Lacchini et al., 2020 - doi: 10.1105/tpc.19.00609 - pmid: 32303662 + - citation: Kevei, Lougnon et al., 2007 + doi: 10.1105/tpc.107.053975 + pmid: 18156218 - citation: Oellrich, Walls et al., 2015 doi: 10.1186/s13007-015-0053-y pmid: 25774204 -## DOCUMENT 20 ## +## DOCUMENT 17 ## --- gene_symbols: - - HAP2.1 -gene_model_pub_name: Medtr1g056530 -gene_model_full_id: medtr.A17_HM341.gnm4.ann2.Medtr1g056530 + - CDC16 +gene_symbol_long: cell division cycle 16 +gene_model_pub_name: Medtr8g058380 +gene_model_full_id: medtr.A17_HM341.gnm4.ann2.Medtr8g058380 confidence: 5 curators: - Steven Cannon -phenotype_synopsis: Small and nonfunctional nodules arrested in growth when both normally spliced and alternatively spliced variants repressed. When only the alternative spliced form repressed the nodules are small but still fix nitrogen successfully. +phenotype_synopsis: Partial suppression of the CDC16 gene homolog in Medicago truncatula leads to a decreased number of lateral roots, an increased number of nodules, and reduced auxin sensitivity. traits: - entity_name: root nodule morphology trait entity: TO:0000898 + - entity_name: auxin sensitivity + entity: TO:0000163 + - entity_name: root system + entity: PO:0025025 + - entity_name: lateral root + entity: PO:0020121 + - entity_name: root + entity: PO:0009005 - entity_name: root nodule entity: PO:0003023 references: - - citation: Chen, Liu et al., 2015 - doi: 10.3389/fpls.2015.00575 - pmid: 26284091 + - citation: Kuppusamy, Ivashuta et al., 2009 + doi: 10.1104/pp.109.143024 + pmid: 19789288 - citation: Oellrich, Walls et al., 2015 doi: 10.1186/s13007-015-0053-y pmid: 25774204 -## DOCUMENT 21 ## +## DOCUMENT 18 ## --- gene_symbols: - LIN @@ -568,152 +521,170 @@ traits: - entity_name: root nodule entity: PO:0003023 references: - - citation: Lace, Su et al., 2023 - doi: 10.7554/elife.80741 - pmid: 36856086 + - citation: Lace, Su et al., 2023 + doi: 10.7554/elife.80741 + pmid: 36856086 + - citation: Oellrich, Walls et al., 2015 + doi: 10.1186/s13007-015-0053-y + pmid: 25774204 + + +## DOCUMENT 19 ## +--- +gene_symbols: + - SUNN +gene_symbol_long: super numeric nodules +gene_model_pub_name: Medtr4g070970 +gene_model_full_id: medtr.A17_HM341.gnm4.ann2.Medtr4g070970 +confidence: 5 +curators: + - Steven Cannon +phenotype_synopsis: Shortened roots even in the absence of rhizobia. A dramatic increase in the number of root nodules. Nodulation occurred even under a high nitrogen regime. Unlike wild type, both infection by rhizobia and nodulation occur randomly throughout the circumference of the developing root. Nodulation is normally sensitive to ethylene, similar to wild type. +traits: + - entity_name: root nodule number + entity: TO:0000900 + - entity_name: root length + entity: TO:0000227 + - entity_name: root system + entity: PO:0025025 + - entity_name: root + entity: PO:0009005 + - entity_name: root nodule + entity: PO:0003023 +references: + - citation: Laffont, Huault et al., 2019 + doi: 10.1104/pp.18.01588 + pmid: 30782966 - citation: Oellrich, Walls et al., 2015 doi: 10.1186/s13007-015-0053-y pmid: 25774204 -## DOCUMENT 22 ## +## DOCUMENT 20 ## --- gene_symbols: - - LYK3 -gene_symbol_long: LYSIN MOTIF RECEPTOR-LIKE KINASE 3 -gene_model_pub_name: Medtr5g086130 -gene_model_full_id: medtr.A17_HM341.gnm4.ann2.Medtr5g086130 + - FTa1 +gene_symbol_long: Delayed flowering +gene_model_pub_name: Medtr7g084970 +gene_model_full_id: medtr.A17_HM341.gnm4.ann2.Medtr7g084970 confidence: 5 curators: - Steven Cannon -phenotype_synopsis: Doesn't make nodules; infection thread aborts +phenotype_synopsis: Delayed flowering traits: - - entity_name: root nodule number - entity: TO:0000900 - - entity_name: root system - entity: PO:0025025 - - entity_name: root nodule - entity: PO:0003023 + - entity_name: flowering time trait + entity: TO:0002616 references: - - citation: Herrbach, Chirinos et al., 2017 - doi: 10.1093/jxb/erw474 - pmid: 28073951 + - citation: Laurie, Diwadkar et al., 2011 + doi: 10.1104/pp.111.180182 + pmid: 21685176 - citation: Oellrich, Walls et al., 2015 doi: 10.1186/s13007-015-0053-y pmid: 25774204 -## DOCUMENT 23 ## +## DOCUMENT 21 ## --- gene_symbols: - - LYK4 -gene_symbol_long: LYSIN MOTIF RECEPTOR-LIKE KINASE 4 -gene_model_pub_name: Medtr5g086120 -gene_model_full_id: medtr.A17_HM341.gnm4.ann2.Medtr5g086120 + - FTc +gene_symbol_long: Flower development normal under long days +gene_model_pub_name: Medtr7g085040 +gene_model_full_id: medtr.A17_HM341.gnm4.ann2.Medtr7g085040 confidence: 5 curators: - Steven Cannon -phenotype_synopsis: Doesn't make nodules; infection thread aborts +phenotype_synopsis: Normal flower development traits: - - entity_name: root nodule number - entity: TO:0000900 - - entity_name: root system - entity: PO:0025025 - - entity_name: root nodule - entity: PO:0003023 + - entity_name: flower development trait + entity: TO:0000622 references: - - citation: Herrbach, Chirinos et al., 2017 - doi: 10.1093/jxb/erw474 - pmid: 28073951 + - citation: Laurie, Diwadkar et al., 2011 + doi: 10.1104/pp.111.180182 + pmid: 21685176 - citation: Oellrich, Walls et al., 2015 doi: 10.1186/s13007-015-0053-y pmid: 25774204 -## DOCUMENT 24 ## +## DOCUMENT 22 ## --- gene_symbols: - - MtAOC -gene_symbol_long: Allene-oxide cyclase -gene_model_pub_name: CAI29046.1 -gene_model_full_id: medtr.A17_HM341.gnm4.ann2.Medtr7g417750 + - CYCLOPS +gene_model_pub_name: Medtr5g026850 +gene_model_full_id: medtr.A17_HM341.gnm4.ann2.Medtr5g026850 confidence: 5 curators: - Steven Cannon -phenotype_synopsis: MtAOC (allene oxide cyclase) gene expression was partially suppressed in roots following transformation with cDNA in the antisense direction. These roots exhibited lower jasmonic acid levels and delayed colonization by Glomus intraradices. The number of arbuscles decreased and their development was delayed, yet their physical structure was unaltered. +phenotype_synopsis: Symbiotic infection of roots by rhizobia bacteria and arbuscular mycorrhiza fungi was inhibited or blocked, i.e. infection threads were not observed despite colonization of root hairs by rhizobia and AM fungal hyphae formed abnormal hyphal swellings with no arbuscles observed. Nodule organogenesis was initiated but arrested prematurely at the level of primordia as an indirect consequence of the aborted infection. traits: + - entity_name: root nodule morphology trait + entity: TO:0000898 - entity_name: root system entity: PO:0025025 - - entity_name: root - entity: PO:0009005 references: - - citation: Isayenkov, Mrosk et al., 2005 - doi: 10.1104/pp.105.069054 - pmid: 16244141 + - citation: Liu, Breakspear et al., 2019 + doi: 10.1104/pp.18.01572 + pmid: null - citation: Oellrich, Walls et al., 2015 doi: 10.1186/s13007-015-0053-y pmid: 25774204 -## DOCUMENT 25 ## +## DOCUMENT 23 ## --- gene_symbols: - - MtCCD1 -gene_symbol_long: carotenoid cleavage dioxygenase 1 -gene_model_pub_name: CAR57918.1 -gene_model_full_id: medtr.A17_HM341.gnm4.ann2.Medtr6g034835 + - DMI1 +gene_symbol_long: doesn't make infections 1 +gene_model_pub_name: Medtr2g005870 +gene_model_full_id: medtr.A17_HM341.gnm4.ann2.Medtr2g005870 confidence: 5 curators: - Steven Cannon -phenotype_synopsis: RNA interference (RNAi) was used to repress a M. truncatula CCD1 gene in hairy roots colonized by the arbuscular mycorrhizal (AM) fungus Glomus intraradices. The normal AM-mediated accumulation of apocarotenoids (C13 cyclohexenone and C14 mycorradicin derivatives) was reduced in repressed plants; mycorradicin derivatives were reduced to 3% to 6% of the controls and the cyclohexenone derivatives were reduced to 30% to 47%. The RNAi roots turned a yellow-orange color because of C27 apocarotenoid accumulation (the probable substrate of the CCD1 enzyme). More degenerating arbuscules was observed in RNAi roots. +phenotype_synopsis: Doesn't make nodules; infection thread aborts traits: - - entity_name: carotene content - entity: TO:0000289 - - entity_name: root - entity: PO:0009005 + - entity_name: root nodule number + entity: TO:0000900 + - entity_name: root system + entity: PO:0025025 + - entity_name: root nodule + entity: PO:0003023 references: - - citation: Floss, Schliemann et al., 2008 - doi: 10.1104/pp.108.125062 - pmid: 18790999 + - citation: Liu, Lin et al., 2022 + doi: 10.1073/pnas.2205920119 + pmid: 35972963 - citation: Oellrich, Walls et al., 2015 doi: 10.1186/s13007-015-0053-y pmid: 25774204 -## DOCUMENT 26 ## +## DOCUMENT 24 ## --- gene_symbols: - - MtCre1 -gene_symbol_long: Cytokinin Response1 -gene_model_pub_name: Medtr8g106150 -gene_model_full_id: medtr.A17_HM341.gnm4.ann2.Medtr8g106150 + - DMI3 +gene_symbol_long: doesn't make infections 3 +gene_model_pub_name: Medtr8g043970 +gene_model_full_id: medtr.A17_HM341.gnm4.ann2.Medtr8g043970 confidence: 5 curators: - Steven Cannon -phenotype_synopsis: Roots growth was not inhibited by exogenous cytokinin application. Expression of the primary cytokinin response gene, Mt RR4, was not induced by cytokinins. Plants had an increased number of lateral roots (higher lateral root density) and a strong reduction in numbers of root nodules. The development of infection threads was inhibited and early nodule primordia development was also impaired. Expression of early nodulation genes was reduced in plants in which expression of MtCre1 was interfered with by RNAi. +phenotype_synopsis: Doesn't make nodules or mycorrhizae traits: - entity_name: root nodule number entity: TO:0000900 - - entity_name: cytokinin sensitivity - entity: TO:0000167 - - entity_name: root number - entity: TO:0000084 - entity_name: root system entity: PO:0025025 - - entity_name: lateral root - entity: PO:0020121 - entity_name: root nodule entity: PO:0003023 references: - - citation: Vernie, Kim et al., 2015 - doi: 10.1105/tpc.15.00461 - pmid: 26672071 + - citation: Mitra, Gleason et al., 2004 + doi: 10.1073/pnas.0400595101 + pmid: 15070781 - citation: Oellrich, Walls et al., 2015 doi: 10.1186/s13007-015-0053-y pmid: 25774204 -## DOCUMENT 27 ## +## DOCUMENT 25 ## --- gene_symbols: - MtNAP1 @@ -746,63 +717,88 @@ references: pmid: 25774204 -## DOCUMENT 28 ## +## DOCUMENT 26 ## --- gene_symbols: - - NAM - - NAM-2 -gene_symbol_long: No Apical Meristem (weak allele) -gene_model_pub_name: AFI56799.1 -gene_model_full_id: medtr.A17_HM341.gnm4.ann2.Medtr2g078700 + - CBF4 +gene_symbol_long: C-repeat binding factor 4 +gene_model_pub_name: Medtr1g101600 +gene_model_full_id: medtr.A17_HM341.gnm4.ann2.Medtr1g101600 confidence: 5 curators: - Steven Cannon -phenotype_synopsis: null +phenotype_synopsis: Expression of MtCBF4 (transcription factor) in M. truncatula was induced by most of the abiotic stresses, including salt, drought, cold, and abscisic acid, suggesting crosstalk between these abiotic stresses. Upon exposure to a salt medium the primary root growth in the MtCBF4-overexpressing lines was greater than that of the control plants. MtCAS31 belongs to the CBF regulon and is associated with salt tolerance; under salt treatment, expression of MtCAS31 increased more in d35S:MtCBF4 transgenic plants than in controls. To summarize, over-expression of MtCBF4 enhanced tolerance to salt stress. traits: - - entity_name: shoot apical meristem development - entity: TO:0006020 - - entity_name: carpel morphology trait - entity: TO:0006012 - - entity_name: trichome morphology trait - entity: TO:0000911 - - entity_name: cotyledon morphology trait - entity: TO:0000749 - - entity_name: male sterility - entity: TO:0000437 + - entity_name: salt tolerance + entity: TO:0006001 + - entity_name: root length + entity: TO:0000227 + - entity_name: primary root + entity: PO:0020127 + - entity_name: whole plant + entity: PO:0000003 +references: + - citation: Pecrix, Staton et al., 2018 + doi: 10.1038/s41477-018-0286-7 + pmid: 30397259 + - citation: Oellrich, Walls et al., 2015 + doi: 10.1186/s13007-015-0053-y + pmid: 25774204 + + +## DOCUMENT 27 ## +--- +gene_symbols: + - FCL1 +gene_symbol_long: fused compound leaf 1 +gene_model_pub_name: Medtr6g071190 +gene_model_full_id: medtr.A17_HM341.gnm4.ann2.Medtr6g071190 +confidence: 5 +curators: + - Steven Cannon +phenotype_synopsis: Leaflets fused or partially fused, rachis between leaflets is absent, petiole is foreshortened. +traits: + - entity_name: petiole length + entity: TO:0000766 - entity_name: vascular leaf morphology trait entity: TO:0000419 - - entity_name: female sterility - entity: TO:0000358 - - entity_name: stamen morphology trait - entity: TO:0000215 - - entity_name: embryo shape - entity: TO:0000193 - - entity_name: carpel trichome - entity: PO:0025208 - - entity_name: reproductive shoot system - entity: PO:0025082 + - entity_name: leaf rachis + entity: PO:0020055 - entity_name: leaflet entity: PO:0020049 - - entity_name: cotyledon - entity: PO:0020030 - - entity_name: plant ovule - entity: PO:0020003 - - entity_name: flower - entity: PO:0009046 - - entity_name: carpel - entity: PO:0009030 - - entity_name: stamen - entity: PO:0009029 - - entity_name: plant embryo - entity: PO:0009009 - - entity_name: fruit - entity: PO:0009001 - - entity_name: juvenile vascular leaf - entity: PO:0006339 + - entity_name: petiole + entity: PO:0020038 references: - - citation: Cheng, Peng et al., 2012 - doi: 10.1111/j.1469-8137.2012.04147.x - pmid: 22530598 + - citation: Peng, Yu et al., 2011 + doi: 10.1105/tpc.111.089128 + pmid: 22080596 + - citation: Oellrich, Walls et al., 2015 + doi: 10.1186/s13007-015-0053-y + pmid: 25774204 + + +## DOCUMENT 28 ## +--- +gene_symbols: + - VPY +gene_symbol_long: Vapyrin +gene_model_pub_name: ADC33495.1 +gene_model_full_id: medtr.A17_HM341.gnm4.ann2.Medtr6g027840 +confidence: 5 +curators: + - Steven Cannon +phenotype_synopsis: In Medicago truncatula, the Vapyrin (VPY) gene is essential for the establishment of the arbuscular mycorrhizal symbiosis. Analyses of mutants shows that the same VPYgene is also required for rhizobial colonization and nodulation. Plants mutated in this gene have abnormal rhizobial infection threads and fewer nodules, and in the case of interactions with AM fungi, epidermal penetration defects and aborted arbuscule formation. +traits: + - entity_name: root nodule number + entity: TO:0000900 + - entity_name: root system + entity: PO:0025025 + - entity_name: root nodule + entity: PO:0003023 +references: + - citation: Pumplin, Mondo et al., 2009 + doi: 10.1111/j.1365-313x.2009.04072.x + pmid: 19912567 - citation: Oellrich, Walls et al., 2015 doi: 10.1186/s13007-015-0053-y pmid: 25774204 @@ -811,21 +807,33 @@ references: ## DOCUMENT 29 ## --- gene_symbols: - - NFP -gene_symbol_long: Nod Factor Perception -gene_model_pub_name: Medtr5g019040 -gene_model_full_id: medtr.A17_HM341.gnm4.ann2.Medtr5g019040 + - FLOT2 +gene_symbol_long: Flotillin-like protein 2 +gene_model_pub_name: Medtr3g106420 +gene_model_full_id: medtr.A17_HM341.gnm4.ann2.Medtr3g106420 confidence: 5 curators: - Steven Cannon -phenotype_synopsis: Root nodules did not form and infection threads aborted during development. +phenotype_synopsis: Fewer nodules per plant, an increase in no-nodule plants, and a decrease in plants that form pink nodules. A decrease in primary root length and long primary lateral roots, reduced reduction of acetylene, and reduced number of infection events. traits: + - entity_name: lateral root length + entity: TO:0001012 + - entity_name: root nodule number + entity: TO:0000900 + - entity_name: seminal root length + entity: TO:0000586 + - entity_name: root system + entity: PO:0025025 + - entity_name: primary root + entity: PO:0020127 + - entity_name: lateral root + entity: PO:0020121 - entity_name: root nodule entity: PO:0003023 references: - - citation: Rey, Nars et al., 2013 - doi: 10.1111/nph.12198 - pmid: 23432463 + - citation: Qiao, Pingault et al., 2016 + doi: 10.3389/fpls.2016.00034 + pmid: 26858743 - citation: Oellrich, Walls et al., 2015 doi: 10.1186/s13007-015-0053-y pmid: 25774204 @@ -834,25 +842,25 @@ references: ## DOCUMENT 30 ## --- gene_symbols: - - nork -gene_symbol_long: nodulation receptor kinase -gene_model_pub_name: Medtr5g030920 -gene_model_full_id: medtr.A17_HM341.gnm4.ann2.Medtr5g030920 + - FLOT3 +gene_symbol_long: Flotillin-like protein 3 +gene_model_pub_name: Medtr3g106480 +gene_model_full_id: medtr.A17_HM341.gnm4.ann2.Medtr3g106480 confidence: 5 curators: - Steven Cannon -phenotype_synopsis: Lacks symbiotic root responses in the presence of compatible Sinorhizobium meliloti or Nod factor, and resists mycorrhizal colonization +phenotype_synopsis: Shorter roots and reduced root weight. traits: - - entity_name: root nodule number - entity: TO:0000900 - - entity_name: root system - entity: PO:0025025 - - entity_name: root nodule - entity: PO:0003023 + - entity_name: root weight + entity: TO:0000279 + - entity_name: root length + entity: TO:0000227 + - entity_name: root + entity: PO:0009005 references: - - citation: Kevei, Lougnon et al., 2007 - doi: 10.1105/tpc.107.053975 - pmid: 18156218 + - citation: Qiao, Pingault et al., 2016 + doi: 10.3389/fpls.2016.00034 + pmid: 26858743 - citation: Oellrich, Walls et al., 2015 doi: 10.1186/s13007-015-0053-y pmid: 25774204 @@ -861,29 +869,27 @@ references: ## DOCUMENT 31 ## --- gene_symbols: - - PALM1 -gene_symbol_long: PALMATE-LIKE PENTAFOLIATA1 -gene_model_pub_name: Medtr5g014400 -gene_model_full_id: medtr.A17_HM341.gnm4.ann2.Medtr5g014400 + - FLOT4 +gene_symbol_long: Flotillin-like protein 4 +gene_model_pub_name: Medtr3g106430 +gene_model_full_id: medtr.A17_HM341.gnm4.ann2.Medtr3g106430 confidence: 5 curators: - Steven Cannon -phenotype_synopsis: Forms dissected leaves with five leaflets clustered at the tip (palmate-like pentafoliate in contrast to the trifoliate WT leaves). The distal lateral leaflets developed in a manner morphologically/anatomically similar to terminal leaflets. The length of the petiole increased and that of the rachis decreased. +phenotype_synopsis: Decrease in plants that form pink nodules and an increase in numbers of secondary lateral roots, reduced reduction of acetylene. Weak association with reduction in nodule numbers. Both decreased number of infection events and defective infection thread elongation. traits: - - entity_name: petiole length - entity: TO:0000766 - - entity_name: TO:0000748 - entity: TO:0000748 - - entity_name: leaf - entity: PO:0025034 - - entity_name: leaf rachis - entity: PO:0020055 - - entity_name: petiole - entity: PO:0020038 + - entity_name: root nodule number + entity: TO:0000900 + - entity_name: root number + entity: TO:0000084 + - entity_name: root system + entity: PO:0025025 + - entity_name: root nodule + entity: PO:0003023 references: - - citation: Jiao, Wang et al., 2020 - doi: 10.1186/s12870-020-02619-6 - pmid: 32867687 + - citation: Qiao, Pingault et al., 2016 + doi: 10.3389/fpls.2016.00034 + pmid: 26858743 - citation: Oellrich, Walls et al., 2015 doi: 10.1186/s13007-015-0053-y pmid: 25774204 @@ -892,29 +898,21 @@ references: ## DOCUMENT 32 ## --- gene_symbols: - - SGL1 -gene_symbol_long: single leaflet1 -gene_model_pub_name: Medtr3g098560 -gene_model_full_id: medtr.A17_HM341.gnm4.ann2.Medtr3g098560 + - NFP +gene_symbol_long: Nod Factor Perception +gene_model_pub_name: Medtr5g019040 +gene_model_full_id: medtr.A17_HM341.gnm4.ann2.Medtr5g019040 confidence: 5 curators: - Steven Cannon -phenotype_synopsis: Mutant displays simple, unifoliate (not compound) leaves. Petiole length is decreased. Defective, fused flowers +phenotype_synopsis: Root nodules did not form and infection threads aborted during development. traits: - - entity_name: petiole length - entity: TO:0000766 - - entity_name: flower morphology trait - entity: TO:0000499 - - entity_name: leaf shape - entity: TO:0000492 - - entity_name: petiole - entity: PO:0020038 - - entity_name: flower - entity: PO:0009046 + - entity_name: root nodule + entity: PO:0003023 references: - - citation: Cheng, Li et al., 2021 - doi: 10.1093/plphys/kiaa005 - pmid: 33631796 + - citation: Rey, Nars et al., 2013 + doi: 10.1111/nph.12198 + pmid: 23432463 - citation: Oellrich, Walls et al., 2015 doi: 10.1186/s13007-015-0053-y pmid: 25774204 @@ -923,44 +921,32 @@ references: ## DOCUMENT 33 ## --- gene_symbols: - - EIN2 - - Skl1 -gene_symbol_long: Ethylene Insensitive2 -gene_model_pub_name: Medtr7g101410 -gene_model_full_id: medtr.A17.gnm5.ann1_6.MtrunA17Chr7g0264231 + - GT3 + - UGT73F3 +gene_symbol_long: Glycosyltransferase 3 +gene_model_pub_name: Medtr2g035020 +gene_model_full_id: medtr.A17_HM341.gnm4.ann2.Medtr2g035020 confidence: 5 curators: - Steven Cannon -phenotype_synopsis: Absence of discrete nodules, increased persistant rhizobila infection, radial swelling of primary infection zone, larger cotyledons, reduced apical hook angle, reduced develoment of ectopic root hairs, no loss of geotropism,and a lack of inhibition of both hypocotyl and root growth. Reduced inhibition of root growth in response to application of exogenous cytokinin benzyl adenine. Increased primary mycorrhizal infections by Glomus versiforme and Glomus intraradices. Increased susceptability to damage caused by infection with R. solani necrotrophic fungus and P. medicaginis necrotrophic oomycete as well as larger numbers of P. medicaginis reproductive structures. Reduced biphasic ethylene production after inoculation with P. medicaginis, reduced gene expression for one isoform of ACC oxidase transcripts, and reduced responsiveness of ethylene levels to exogenous ACC (all indicators of impaired autocatalytic ethylene production). +phenotype_synopsis: The uridine diphosphate glycosyltransferase (GT3, UGT73F3) showed specificity for multiple sapogenins and functions in saponin biosynthesis. Homozygous plants were retarded in growth relative to normal plants, whereas heterozygous plants did not show dwarfism. Homozygous plants could flower and produce a few pods. The seeds did not show visible morphological changes but took an unusually long time to germinate (at least 3 weeks). Roots in homozygous lines were very short and less branched compared with the wild type. Leaf saponin levels did not differ between controls and mutants. Levels of 5 different saponins were lower in mutant lines (approx. 3-fold) compared with controls, while only one saponin was higher in the mutants. The large (10-fold) increase of 3-Glc-28-Ara-Rha-Xyl-medicagenic acid in UGT73F3 knockout lines suggests that the UDP-glucose pool is being diverted toward increased formation of non-C-28-glucosylated sapogenins. Levels of the isoflavone formononetin and its conjugates were also increased in UGT73F3 knockouts. traits: - - entity_name: gravity response trait - entity: TO:0002693 - - entity_name: root hair length - entity: TO:0002665 - - entity_name: root nodule number - entity: TO:0000900 - - entity_name: TO:0000757 - entity: TO:0000757 - - entity_name: seedling cotyledon size - entity: TO:0000752 - - entity_name: root development trait - entity: TO:0000656 - - entity_name: root system - entity: PO:0025025 - - entity_name: hypocotyl - entity: PO:0020100 - - entity_name: cotyledon - entity: PO:0020030 + - entity_name: plant structure growth and development trait + entity: TO:0000928 + - entity_name: germination rate + entity: TO:0000430 + - entity_name: root branching + entity: TO:0000257 + - entity_name: root length + entity: TO:0000227 - entity_name: root entity: PO:0009005 - - entity_name: non-hair root epidermal cell - entity: PO:0000263 - - entity_name: apical hook - entity: PO:0000012 + - entity_name: whole plant + entity: PO:0000003 references: - - citation: Weller, Foo et al., 2015 - doi: 10.1104/pp.15.00164 - pmid: 25792252 + - citation: Ribeiro, Lacchini et al., 2020 + doi: 10.1105/tpc.19.00609 + pmid: 32303662 - citation: Oellrich, Walls et al., 2015 doi: 10.1186/s13007-015-0053-y pmid: 25774204 @@ -969,29 +955,21 @@ references: ## DOCUMENT 34 ## --- gene_symbols: - - SUNN -gene_symbol_long: super numeric nodules -gene_model_pub_name: Medtr4g070970 -gene_model_full_id: medtr.A17_HM341.gnm4.ann2.Medtr4g070970 + - chitIII-3 +gene_symbol_long: class III chitinase +gene_model_pub_name: Medtr8g055940 +gene_model_full_id: medtr.A17_HM341.gnm4.ann2.Medtr8g055940 confidence: 5 curators: - Steven Cannon -phenotype_synopsis: Shortened roots even in the absence of rhizobia. A dramatic increase in the number of root nodules. Nodulation occurred even under a high nitrogen regime. Unlike wild type, both infection by rhizobia and nodulation occur randomly throughout the circumference of the developing root. Nodulation is normally sensitive to ethylene, similar to wild type. +phenotype_synopsis: Mtchit 3-3 expression (class III chitinase gene) is specifically induced by arbuscular mycorrhizal (AM) fungi in roots of the model legume Medicago truncatula. Mtchit 3-3 expression was artificially induced with a CaMV 35S promoter in root cells; this stimulated spore germination of Glomus intraradices and Glomus constrictum, and in the case of G. intraradices resulted in a higher probability of root colonization and spore formation. There was no measurable effect on the abundance of arbuscules within colonized roots. traits: - - entity_name: root nodule number - entity: TO:0000900 - - entity_name: root length - entity: TO:0000227 - entity_name: root system entity: PO:0025025 - - entity_name: root - entity: PO:0009005 - - entity_name: root nodule - entity: PO:0003023 references: - - citation: Laffont, Huault et al., 2019 - doi: 10.1104/pp.18.01588 - pmid: 30782966 + - citation: Salzer, Bonanomi et al., 2000 + doi: 10.1094/mpmi.2000.13.7.763 + pmid: 10875337 - citation: Oellrich, Walls et al., 2015 doi: 10.1186/s13007-015-0053-y pmid: 25774204 @@ -1000,25 +978,31 @@ references: ## DOCUMENT 35 ## --- gene_symbols: - - VPY -gene_symbol_long: Vapyrin -gene_model_pub_name: ADC33495.1 -gene_model_full_id: medtr.A17_HM341.gnm4.ann2.Medtr6g027840 + - MtCre1 +gene_symbol_long: Cytokinin Response 1 +gene_model_pub_name: Medtr8g106150 +gene_model_full_id: medtr.A17_HM341.gnm4.ann2.Medtr8g106150 confidence: 5 curators: - Steven Cannon -phenotype_synopsis: In Medicago truncatula, the Vapyrin (VPY) gene is essential for the establishment of the arbuscular mycorrhizal symbiosis. Analyses of mutants shows that the same VPYgene is also required for rhizobial colonization and nodulation. Plants mutated in this gene have abnormal rhizobial infection threads and fewer nodules, and in the case of interactions with AM fungi, epidermal penetration defects and aborted arbuscule formation. +phenotype_synopsis: Roots growth was not inhibited by exogenous cytokinin application. Expression of the primary cytokinin response gene, MtRR4, was not induced by cytokinins. Plants had an increased number of lateral roots (higher lateral root density) and a strong reduction in numbers of root nodules. The development of infection threads was inhibited and early nodule primordia development was also impaired. Expression of early nodulation genes was reduced in plants in which expression of MtCre1 was interfered with by RNAi. traits: - entity_name: root nodule number entity: TO:0000900 + - entity_name: cytokinin sensitivity + entity: TO:0000167 + - entity_name: root number + entity: TO:0000084 - entity_name: root system entity: PO:0025025 + - entity_name: lateral root + entity: PO:0020121 - entity_name: root nodule entity: PO:0003023 references: - - citation: Pumplin, Mondo et al., 2009 - doi: 10.1111/j.1365-313x.2009.04072.x - pmid: 19912567 + - citation: Vernie, Kim et al., 2015 + doi: 10.1105/tpc.15.00461 + pmid: 26672071 - citation: Oellrich, Walls et al., 2015 doi: 10.1186/s13007-015-0053-y pmid: 25774204 @@ -1028,7 +1012,7 @@ references: --- gene_symbols: - ERN1 -gene_symbol_long: Ethylene Response Factor Required for Nodulation1 +gene_symbol_long: Ethylene Response Factor Required for Nodulation 1 gene_model_pub_name: EU038802 gene_model_full_id: medtr.A17_HM341.gnm4.ann2.Medtr7g085810 confidence: 5 @@ -1051,7 +1035,7 @@ references: --- gene_symbols: - ERN2 -gene_symbol_long: Ethylene Response Factor Required for Nodulation2 +gene_symbol_long: Ethylene Response Factor Required for Nodulation 2 gene_model_pub_name: EU038803 gene_model_full_id: medtr.A17_HM341.gnm4.ann2.Medtr6g029180 confidence: 5 @@ -1182,3 +1166,73 @@ references: pmid: 26672071 +## DOCUMENT 43 ## +--- +scientific_name: Medicago truncatula +gene_symbols: + - MtGSTF7 +gene_symbol_long: Glutathione S-transferase family protein +gene_model_pub_name: Medtr3g064700 +gene_model_full_id: medtr.A17_HM341.gnm4.ann2.Medtr3g064700 +confidence: 5 +curators: + - Wei Huang +phenotype_synopsis: MtGSTF7, a homolog of AtTT19, is essential for anthocyanin accumulation but not required for PA accumulation in Medicago truncatula. MtGSTF7 was induced by the anthocyanin regulator LEGUME ANTHOCYANIN PRODUCTION 1 (LAP1), and its tissue expression pattern correlated with anthocyanin deposition in M. truncatula. +traits: + - entity_name: anthocyanin accumulation + entity: NCIT:C16641 +references: + - citation: Wang, Lu et al., 2022 + doi: 10.1093/jxb/erac112 + pmid: 35294003 + - citation: Hasan, Singh et al. 2021 + doi: 10.1371/journal.pone.0247170 + pmid: 33606812 + + +## DOCUMENT 44 ## +--- +gene_symbols: + - EIN2 + - Skl1 +gene_symbol_long: Ethylene Insensitive 2 +gene_model_pub_name: Medtr7g101410 +gene_model_full_id: medtr.A17.gnm5.ann1_6.MtrunA17Chr7g0264231 +confidence: 5 +curators: + - Steven Cannon +phenotype_synopsis: Absence of discrete nodules, increased persistant rhizobila infection, radial swelling of primary infection zone, larger cotyledons, reduced apical hook angle, reduced develoment of ectopic root hairs, no loss of geotropism,and a lack of inhibition of both hypocotyl and root growth. Reduced inhibition of root growth in response to application of exogenous cytokinin benzyl adenine. Increased primary mycorrhizal infections by Glomus versiforme and Glomus intraradices. Increased susceptability to damage caused by infection with R. solani necrotrophic fungus and P. medicaginis necrotrophic oomycete as well as larger numbers of P. medicaginis reproductive structures. Reduced biphasic ethylene production after inoculation with P. medicaginis, reduced gene expression for one isoform of ACC oxidase transcripts, and reduced responsiveness of ethylene levels to exogenous ACC (all indicators of impaired autocatalytic ethylene production). +traits: + - entity_name: gravity response trait + entity: TO:0002693 + - entity_name: root hair length + entity: TO:0002665 + - entity_name: root nodule number + entity: TO:0000900 + - entity_name: hypocotyl morphology trait + entity: TO:0000757 + - entity_name: seedling cotyledon size + entity: TO:0000752 + - entity_name: root development trait + entity: TO:0000656 + - entity_name: root system + entity: PO:0025025 + - entity_name: hypocotyl + entity: PO:0020100 + - entity_name: cotyledon + entity: PO:0020030 + - entity_name: root + entity: PO:0009005 + - entity_name: non-hair root epidermal cell + entity: PO:0000263 + - entity_name: apical hook + entity: PO:0000012 +references: + - citation: Weller, Foo et al., 2015 + doi: 10.1104/pp.15.00164 + pmid: 25792252 + - citation: Oellrich, Walls et al., 2015 + doi: 10.1186/s13007-015-0053-y + pmid: 25774204 + + diff --git a/Phaseolus/vulgaris/gene_functions/phavu.citations.txt b/Phaseolus/vulgaris/gene_functions/phavu.citations.txt new file mode 100644 index 0000000..eed965f --- /dev/null +++ b/Phaseolus/vulgaris/gene_functions/phavu.citations.txt @@ -0,0 +1,3 @@ +10.1007/s00425-023-04116-0 36928335 PMC10020325 Dvila-Delgado, Flores-Canl et al., 2023 "Dávila-Delgado R, Flores-Canúl K, Juárez-Verdayes MA, Sánchez-López R. Rhizobia induce SYMRK endocytosis in Phaseolus vulgaris root hair cells. Planta. 2023 Mar 16;257(4):83. doi: 10.1007/s00425-023-04116-0. PMID: 36928335; PMCID: PMC10020325." +10.1111/nph.15259 29897103 null McClean, Bett et al., 2018 "McClean PE, Bett KE, Stonehouse R, Lee R, Pflieger S, Moghaddam SM, Geffroy V, Miklas P, Mamidi S. White seed color in common bean (Phaseolus vulgaris) results from convergent evolution in the P (pigment) gene. New Phytol. 2018 Aug;219(3):1112-1123. doi: 10.1111/nph.15259. Epub 2018 Jun 13. PMID: 29897103." +10.1002/ppp3.10132 34268482 PMC8262261 Islam, Bett et al., 2020 "Islam NS, Bett KE, Pauls KP, Marsolais F, Dhaubhadel S. Postharvest seed coat darkening in pinto bean (Phaseolus vulgaris) is regulated by Psd , an allele of the basic helix-loop-helix transcription factor P. Plants People Planet. 2020 Nov;2(6):663-677. doi: 10.1002/ppp3.10132. Epub 2020 Aug 19. PMID: 34268482; PMCID: PMC8262261." diff --git a/Phaseolus/vulgaris/gene_functions/phavu.traits.yml b/Phaseolus/vulgaris/gene_functions/phavu.traits.yml new file mode 100644 index 0000000..7b7004b --- /dev/null +++ b/Phaseolus/vulgaris/gene_functions/phavu.traits.yml @@ -0,0 +1,71 @@ +## DOCUMENT 1 ## +--- +scientific_name: Phaseolus vulgaris +gene_symbols: + - PvSYMRK +gene_symbol_long: Symbiosis Receptor-like Kinase +gene_model_pub_name: Phvul.002G143400 +gene_model_full_id: phavu.G19833.gnm2.ann1.Phvul.002G143400 +confidence: 5 +curators: + - Marlene Dorneich-Hayes + - Scott Kalberer +comments: + - PvSYMRK is activated in root hairs by phosphorylation of the T589 residue in response to the perception of NOD factors produced by rhizobia. + - SYMRK labeled with EGFP (enhanced green fluorescence protein) is endocytosed from the plasma membrane to intracellular puncta in response to Rhizobium etli inoculation. The consequent redistribution affects the SYMRK signaling pathway. + - Deletion of the SYMRK endocytic sorting motif YKTL and application of endocytosis inhibitors reduced the prevalence of SYMRK-EGFP intracellular puncta. Endocytosis was also negatively impacted in phosphorylation-deficient (T589A) and kinase-inactivated (K618E) mutants of SYMRK. +phenotype_synopsis: The PvSYMRK protein undergoes rhizobia-induced endocytosis and regulates a dependent kinase signal transduction cascade leading to rhizobial infection and nodule organogenesis. +traits: + - entity_name: biological process involved in symbiotic interaction + entity: GO:0044403 + - entity_name: kinase activity + entity: GO:0016301 + - entity_name: positive regulation of receptor-mediated endocytosis + entity: GO:0048260 + - entity_name: nodulation + entity: GO:0009877 +references: + - citation: Dvila-Delgado, Flores-Canl et al., 2023 + doi: 10.1007/s00425-023-04116-0 + pmid: 36928335 + + +## DOCUMENT 2 ## +--- +scientific_name: Phaseolus vulgaris +classical_locus: Sd +gene_symbols: + - PvP +gene_symbol_long: Pigment +gene_model_pub_name: Phvul.007G171333 +gene_model_full_id: phavu.G19833.gnm2.ann1.Phvul.007G171333 +confidence: 5 +curators: + - Scott Kalberer +comments: + - Postharvest seed coat darkening results in decreased consumer preference and lower economic value for the Common bean market class of Pintos. Rapid and saturated darkening after harvest of dry beans results from heavy accumulation of proanthocyanidins (PAs) and PA monomers (epicatechin and catechin) in developing seed coat tissues. + - Psd is a recessive allele of the Pigment (P) candidate gene responsible for the slow darkening seed coat in Pinto beans (Phaseolus vulgaris). Evidence provided in Islam, Bett et al. (2020) that shows Pigment (allele Psd) is the SLOW DARKENING (Sd) gene included genetic complementation, transcript abundance, metabolite analysis, and an inheritance study. + - The P gene encodes a basic helix-loop-helix transcription factor. One of its two transcript variants (P-1) is involved in proanthocyanidin (PA) biosynthesis and the other truncated variant (P-2) has either no or unknown function. Two mutations in the Psd allele- supplemental glutamate residue in the activation domain; arginine to histidine substitution in the bHLH domain- are likely responsible for reduced protein activity and PA accumulation in the slow-darkening (SD) cultivar. Flavonoid biosynthesis leading to PAs is regulated by an MBW complex consisting of members of the myeloblastosis (MYB), bHLH transcription factor, and WD40 repeat protein (WDR) families. + - The P gene is a functional ortholog of the bHLH transcription factor AtTT8 that regulates testa pigment biosynthesis in Arabidopsis thaliana. In genetic complementation tests, ectopic expression among Arabidopsis tt8 mutants of the P-1 allele from regular darkening (RD) bean cultivar CDC Pintium completely restored both the activity of Dihydroflavonol 4-Reductase (AtDFR) and Anthocyanidin Reductase (AtANR) as well as the wild-type testa phenotype with expected PA levels. Transgenic expression of the Psd-1 allele from SD cultivar 1533-15 only partially redeemed the mutant phenotype, whereas transformation with constructs containing P-2 (CDC Pintium) failed to recover the wild-type phenotype. Loss-of-function alleles of the P gene were shown to cause white seed coat color in common bean (McClean, Bett et al., 2018). + - The gene model Phvul.007G171333 corresponds to the P gene and was previously annotated as a transcription factor known as TRANSPARENT TESTA 8 (TT8). Evidence that P is Sd includes its gene expression being highest in seed coat tissue among the six candidate genes on chromosome 7 near markers Pvsd-1158 and Pvsd-1157 in both cultivars CDC Pintium and 1533-15. +phenotype_synopsis: Pinto bean cultivars carrying the Psd allele of the Pigment gene have seed coats that darken more slowly following harvest. +traits: + - entity_name: seed coat color + entity: TO:0000190 + - quality_name: brown + quality: PATO:0000952 + - relation_name: positively regulates + relation: RO:0002213 + - entity_name: regulation of proanthocyanidin biosynthetic process + entity: GO:2000029 + - entity_name: bHLH transcription factor binding + entity: GO:0043425 +references: + - citation: Islam, Bett et al., 2020 + doi: 10.1002/ppp3.10132 + pmid: 34268482 + - citation: McClean, Bett et al., 2018 + doi: 10.1111/nph.15259 + pmid: 29897103 + + diff --git a/Pisum/sativum/gene_functions/pissa.citations.txt b/Pisum/sativum/gene_functions/pissa.citations.txt new file mode 100644 index 0000000..984a3fb --- /dev/null +++ b/Pisum/sativum/gene_functions/pissa.citations.txt @@ -0,0 +1,4 @@ +10.1007/s11103-008-9314-8 18301989 null Aubry, Mani et al., 2008 "Aubry S, Mani J, Hörtensteiner S. Stay-green protein, defective in Mendel's green cotyledon mutant, acts independent and upstream of pheophorbide a oxygenase in the chlorophyll catabolic pathway. Plant Mol Biol. 2008 Jun;67(3):243-56. doi: 10.1007/s11103-008-9314-8. PMID: 18301989." +10.1126/science.1132912 17204643 null Armstead, Donnison et al., 2007 "Armstead I, Donnison I, Aubry S, Harper J, Hörtensteiner S, James C, Mani J, Moffet M, Ougham H, Roberts L, Thomas A, Weeden N, Thomas H, King I. Cross-species identification of Mendel's I locus. Science. 2007 Jan 5;315(5808):73. doi: 10.1126/science.1132912. PMID: 17204643." +10.1016/j.tplants.2009.01.002 19237309 null Hrtensteiner, 2009 "Hörtensteiner S. Stay-green regulates chlorophyll and chlorophyll-binding protein degradation during senescence. Trends Plant Sci. 2009 Mar;14(3):155-62. doi: 10.1016/j.tplants.2009.01.002. Epub 2009 Feb 23. PMID: 19237309." +10.1073/pnas.0705521104 17709752 PMC1955798 Sato, Morita et al., 2007 "" diff --git a/Pisum/sativum/gene_functions/pissa.traits.yml b/Pisum/sativum/gene_functions/pissa.traits.yml new file mode 100644 index 0000000..2abf748 --- /dev/null +++ b/Pisum/sativum/gene_functions/pissa.traits.yml @@ -0,0 +1,40 @@ +## DOCUMENT 1 ## +--- +scientific_name: Pisum sativum +classical_locus: I +gene_symbols: + - PsSGR +gene_symbol_long: Staygreen +gene_model_pub_name: AB303332 +gene_model_full_id: pissa.Cameor.gnm1.ann1.Psat2g181040 +confidence: 5 +curators: + - Marlene Dorneich-Hayes + - Scott Kalberer +comments: + - Complementation test confirms that PsSGR is the Mendelian I locus. SGR is a positive regulator of pathways involved in breakdown of chlorophyll via translational or post-translational regulation of chlorophyll degrading enzymes. The products of SGR are required to separate chlorophyll from the photosynthetic complex, allowing chlorophyll degrading enzymes access to their substrate. The sgr loss-of-function mutation is due to lower expression of the SGR gene and a small insertion that disrupts SGR protein fuction. +phenotype_synopsis: The recessive phenotype sgr retains a high chlorophyll content during senescence, causing cotyledons to stay green as they mature and leaves to stay green as they die. PsSGR is a cosmetic stay-green mutant and does not retain the ability to photosynthesize. +traits: + - entity_name: chlorophyll catabolic process + entity: GO:0015996 + - entity_name: positive regulation of chlorophyll catabolic process + entity: GO:1903648 + - entity_name: plant embryo cotyledon color + entity: TO:0000980 + - entity_name: leaf senescence trait + entity: TO:0000249 +references: + - citation: Sato, Morita et al., 2007 + doi: 10.1073/pnas.0705521104 + pmid: 17709752 + - citation: Armstead, Donnison et al., 2007 + doi: 10.1126/science.1132912 + pmid: 17204643 + - citation: Aubry, Mani et al., 2008 + doi: 10.1007/s11103-008-9314-8 + pmid: 18301989 + - citation: Hrtensteiner, 2009 + doi: 10.1016/j.tplants.2009.01.002 + pmid: 19237309 + + diff --git a/Vicia/faba/gene_functions/vicfa.references.txt b/Vicia/faba/gene_functions/vicfa.references.txt deleted file mode 100644 index 4890d54..0000000 --- a/Vicia/faba/gene_functions/vicfa.references.txt +++ /dev/null @@ -1,342 +0,0 @@ -##### PUB RECORD ##### -## 10.1038/s41586-023-05791-5 36890232 PMC10033403 Jayakodi, Golicz et al., 2023 "Jayakodi M, Golicz AA, Kreplak J, Fechete LI, Angra D, Bednář P, Bornhofen E, Zhang H, Boussageon R, Kaur S, Cheung K, Čížková J, Gundlach H, Hallab A, Imbert B, Keeble-Gagnère G, Koblížková A, Kobrlová L, Krejčí P, Mouritzen TW, Neumann P, Nadzieja M, Nielsen LK, Novák P, Orabi J, Padmarasu S, Robertson-Shersby-Harvie T, Robledillo LÁ, Schiemann A, Tanskanen J, Törönen P, Warsame AO, Wittenberg AHJ, Himmelbach A, Aubert G, Courty PE, Doležel J, Holm LU, Janss LL, Khazaei H, Macas J, Mascher M, Smýkal P, Snowdon RJ, Stein N, Stoddard FL, Stougaard J, Tayeh N, Torres AM, Usadel B, Schubert I, O'Sullivan DM, Schulman AH, Andersen SU. The giant diploid faba genome unlocks variation in a global protein crop. Nature. 2023 Mar;615(7953):652-659. doi: 10.1038/s41586-023-05791-5. Epub 2023 Mar 8. PMID: 36890232; PMCID: PMC10033403." ## - -PMID- 36890232 -OWN - NLM -STAT- MEDLINE -DCOM- 20230331 -LR - 20230403 -IS - 1476-4687 (Electronic) -IS - 0028-0836 (Print) -IS - 0028-0836 (Linking) -VI - 615 -IP - 7953 -DP - 2023 Mar -TI - The giant diploid faba genome unlocks variation in a global protein crop. -PG - 652-659 -LID - 10.1038/s41586-023-05791-5 [doi] -AB - Increasing the proportion of locally produced plant protein in currently - meat-rich diets could substantially reduce greenhouse gas emissions and loss of - biodiversity(1). However, plant protein production is hampered by the lack of a - cool-season legume equivalent to soybean in agronomic value(2). Faba bean (Vicia - faba L.) has a high yield potential and is well suited for cultivation in - temperate regions, but genomic resources are scarce. Here, we report a - high-quality chromosome-scale assembly of the faba bean genome and show that it - has expanded to a massive 13 Gb in size through an imbalance between the rates of - amplification and elimination of retrotransposons and satellite repeats. Genes - and recombination events are evenly dispersed across chromosomes and the gene - space is remarkably compact considering the genome size, although with - substantial copy number variation driven by tandem duplication. Demonstrating - practical application of the genome sequence, we develop a targeted genotyping - assay and use high-resolution genome-wide association analysis to dissect the - genetic basis of seed size and hilum colour. The resources presented constitute a - genomics-based breeding platform for faba bean, enabling breeders and geneticists - to accelerate the improvement of sustainable protein production across - the Mediterranean, subtropical and northern temperate agroecological zones. -CI - (c) 2023. The Author(s). -FAU - Jayakodi, Murukarthick -AU - Jayakodi M -AUID- ORCID: 0000-0003-2951-0541 -AD - Leibniz Institute of Plant Genetics and Crop Plant Research (IPK) Gatersleben, - Seeland, Germany. -FAU - Golicz, Agnieszka A -AU - Golicz AA -AUID- ORCID: 0000-0002-9711-4826 -AD - Department of Plant Breeding, Justus Liebig University Giessen, Giessen, Germany. -FAU - Kreplak, Jonathan -AU - Kreplak J -AD - Agroecologie, INRAE, Institut Agro, University Bourgogne, University Bourgogne - Franche-Comte, Dijon, France. -FAU - Fechete, Lavinia I -AU - Fechete LI -AUID- ORCID: 0000-0002-8502-9210 -AD - Department of Molecular Biology and Genetics, Aarhus University, Aarhus C, - Denmark. -FAU - Angra, Deepti -AU - Angra D -AD - School of Agriculture, Policy and Development, University of Reading, Reading, - UK. -FAU - Bednar, Petr -AU - Bednar P -AUID- ORCID: 0000-0001-7070-6015 -AD - Department of Analytical Chemistry, Faculty of Science, Palacky University, - Olomouc, Czech Republic. -FAU - Bornhofen, Elesandro -AU - Bornhofen E -AUID- ORCID: 0000-0002-7447-6226 -AD - Center for Quantitative Genetics and Genomics, Aarhus University, Aarhus C, - Denmark. -FAU - Zhang, Hailin -AU - Zhang H -AUID- ORCID: 0000-0001-8757-9905 -AD - Leibniz Institute of Plant Genetics and Crop Plant Research (IPK) Gatersleben, - Seeland, Germany. -FAU - Boussageon, Raphael -AU - Boussageon R -AUID- ORCID: 0000-0002-5858-8105 -AD - Agroecologie, INRAE, Institut Agro, University Bourgogne, University Bourgogne - Franche-Comte, Dijon, France. -FAU - Kaur, Sukhjiwan -AU - Kaur S -AUID- ORCID: 0000-0003-3972-7058 -AD - Agriculture Victoria, AgriBio, Centre for AgriBioscience, Bundoora, Victoria, - Australia. -FAU - Cheung, Kwok -AU - Cheung K -AUID- ORCID: 0000-0002-3418-3840 -AD - School of Agriculture, Policy and Development, University of Reading, Reading, - UK. -FAU - Cizkova, Jana -AU - Cizkova J -AUID- ORCID: 0000-0001-7787-1849 -AD - Institute of Experimental Botany of the Czech Academy of Sciences, Centre of the - Region Hana for Biotechnological and Agricultural Research, Olomouc, Czech - Republic. -FAU - Gundlach, Heidrun -AU - Gundlach H -AUID- ORCID: 0000-0002-6757-0943 -AD - Plant Genome and Systems Biology (PGSB), Helmholtz Center Munich, German Research - Center for Environmental Health, Neuherberg, Germany. -FAU - Hallab, Asis -AU - Hallab A -AD - IBG-4 Bioinformatics Forschungszentrum Julich, Julich, Germany. -AD - Bingen Technical University of Applied Sciences, Bingen, Germany. -FAU - Imbert, Baptiste -AU - Imbert B -AUID- ORCID: 0000-0002-8229-8693 -AD - Agroecologie, INRAE, Institut Agro, University Bourgogne, University Bourgogne - Franche-Comte, Dijon, France. -FAU - Keeble-Gagnere, Gabriel -AU - Keeble-Gagnere G -AD - Agriculture Victoria, AgriBio, Centre for AgriBioscience, Bundoora, Victoria, - Australia. -FAU - Koblizkova, Andrea -AU - Koblizkova A -AD - Biology Centre, Czech Academy of Sciences, Institute of Plant Molecular Biology, - Ceske Budejovice, Czech Republic. -FAU - Kobrlova, Lucie -AU - Kobrlova L -AUID- ORCID: 0000-0001-9024-7717 -AD - Department of Botany, Faculty of Science, Palacky University, Olomouc, Czech - Republic. -FAU - Krejci, Petra -AU - Krejci P -AUID- ORCID: 0000-0002-4653-1195 -AD - Department of Analytical Chemistry, Faculty of Science, Palacky University, - Olomouc, Czech Republic. -FAU - Mouritzen, Troels W -AU - Mouritzen TW -AUID- ORCID: 0000-0003-0558-1425 -AD - Department of Molecular Biology and Genetics, Aarhus University, Aarhus C, - Denmark. -FAU - Neumann, Pavel -AU - Neumann P -AUID- ORCID: 0000-0001-6711-6639 -AD - Biology Centre, Czech Academy of Sciences, Institute of Plant Molecular Biology, - Ceske Budejovice, Czech Republic. -FAU - Nadzieja, Marcin -AU - Nadzieja M -AUID- ORCID: 0000-0002-6643-8019 -AD - Department of Molecular Biology and Genetics, Aarhus University, Aarhus C, - Denmark. -FAU - Nielsen, Linda Kaergaard -AU - Nielsen LK -AUID- ORCID: 0000-0003-3215-9481 -AD - Sejet Planteforaedling, Horsens, Denmark. -FAU - Novak, Petr -AU - Novak P -AUID- ORCID: 0000-0002-5068-9681 -AD - Biology Centre, Czech Academy of Sciences, Institute of Plant Molecular Biology, - Ceske Budejovice, Czech Republic. -FAU - Orabi, Jihad -AU - Orabi J -AD - Nordic Seed, Odder, Denmark. -FAU - Padmarasu, Sudharsan -AU - Padmarasu S -AUID- ORCID: 0000-0003-3125-3695 -AD - Leibniz Institute of Plant Genetics and Crop Plant Research (IPK) Gatersleben, - Seeland, Germany. -FAU - Robertson-Shersby-Harvie, Tom -AU - Robertson-Shersby-Harvie T -AD - School of Agriculture, Policy and Development, University of Reading, Reading, - UK. -FAU - Robledillo, Laura Avila -AU - Robledillo LA -AD - Biology Centre, Czech Academy of Sciences, Institute of Plant Molecular Biology, - Ceske Budejovice, Czech Republic. -FAU - Schiemann, Andrea -AU - Schiemann A -AD - Nordic Seed, Odder, Denmark. -FAU - Tanskanen, Jaakko -AU - Tanskanen J -AD - Natural Resources Institute Finland (Luke), Helsinki, Finland. -FAU - Toronen, Petri -AU - Toronen P -AD - Institute of Biotechnology, University of Helsinki, Helsinki, Finland. -FAU - Warsame, Ahmed O -AU - Warsame AO -AUID- ORCID: 0000-0002-9281-0443 -AD - School of Agriculture, Policy and Development, University of Reading, Reading, - UK. -FAU - Wittenberg, Alexander H J -AU - Wittenberg AHJ -AUID- ORCID: 0000-0002-0482-2592 -AD - KeyGene, Wageningen, The Netherlands. -FAU - Himmelbach, Axel -AU - Himmelbach A -AD - Leibniz Institute of Plant Genetics and Crop Plant Research (IPK) Gatersleben, - Seeland, Germany. -FAU - Aubert, Gregoire -AU - Aubert G -AUID- ORCID: 0000-0002-1867-5730 -AD - Agroecologie, INRAE, Institut Agro, University Bourgogne, University Bourgogne - Franche-Comte, Dijon, France. -FAU - Courty, Pierre-Emmanuel -AU - Courty PE -AD - Agroecologie, INRAE, Institut Agro, University Bourgogne, University Bourgogne - Franche-Comte, Dijon, France. -FAU - Dolezel, Jaroslav -AU - Dolezel J -AUID- ORCID: 0000-0002-6263-0492 -AD - Institute of Experimental Botany of the Czech Academy of Sciences, Centre of the - Region Hana for Biotechnological and Agricultural Research, Olomouc, Czech - Republic. -FAU - Holm, Liisa U -AU - Holm LU -AUID- ORCID: 0000-0002-7807-2966 -AD - Institute of Biotechnology, University of Helsinki, Helsinki, Finland. -FAU - Janss, Luc L -AU - Janss LL -AUID- ORCID: 0000-0001-9804-1529 -AD - Center for Quantitative Genetics and Genomics, Aarhus University, Aarhus C, - Denmark. -FAU - Khazaei, Hamid -AU - Khazaei H -AUID- ORCID: 0000-0002-5202-8764 -AD - Natural Resources Institute Finland (Luke), Helsinki, Finland. -FAU - Macas, Jiri -AU - Macas J -AUID- ORCID: 0000-0003-0829-1570 -AD - Biology Centre, Czech Academy of Sciences, Institute of Plant Molecular Biology, - Ceske Budejovice, Czech Republic. -FAU - Mascher, Martin -AU - Mascher M -AUID- ORCID: 0000-0001-6373-6013 -AD - Leibniz Institute of Plant Genetics and Crop Plant Research (IPK) Gatersleben, - Seeland, Germany. -AD - German Centre for Integrative Biodiversity Research (iDiv) Halle-Jena-Leipzig, - Leipzig, Germany. -FAU - Smykal, Petr -AU - Smykal P -AUID- ORCID: 0000-0002-6117-8510 -AD - Department of Botany, Faculty of Science, Palacky University, Olomouc, Czech - Republic. -FAU - Snowdon, Rod J -AU - Snowdon RJ -AUID- ORCID: 0000-0001-5577-7616 -AD - Department of Plant Breeding, Justus Liebig University Giessen, Giessen, Germany. -FAU - Stein, Nils -AU - Stein N -AUID- ORCID: 0000-0003-3011-8731 -AD - Leibniz Institute of Plant Genetics and Crop Plant Research (IPK) Gatersleben, - Seeland, Germany. -AD - Center of Integrated Breeding Research (CiBreed), Georg-August-University, - Gottingen, Germany. -FAU - Stoddard, Frederick L -AU - Stoddard FL -AUID- ORCID: 0000-0002-8097-5750 -AD - Department of Agricultural Sciences, University of Helsinki, Helsinki, Finland. -AD - Viikki Plant Science Centre, University of Helsinki, Helsinki, Finland, Cordoba, - Spain. -FAU - Stougaard, Jens -AU - Stougaard J -AD - Department of Molecular Biology and Genetics, Aarhus University, Aarhus C, - Denmark. -FAU - Tayeh, Nadim -AU - Tayeh N -AD - Agroecologie, INRAE, Institut Agro, University Bourgogne, University Bourgogne - Franche-Comte, Dijon, France. -FAU - Torres, Ana M -AU - Torres AM -AUID- ORCID: 0000-0002-2907-4287 -AD - Instituto Andaluz de Investigacion y Formacion Agraria, Pesquera, Alimentaria y - de la Produccion Ecologica (IFAPA), Area de Mejora y Biotecnologia, Centro - Alameda del Obispo, Cordoba, Spain. -FAU - Usadel, Bjorn -AU - Usadel B -AUID- ORCID: 0000-0003-0921-8041 -AD - IBG-4 Bioinformatics Forschungszentrum Julich, Julich, Germany. -AD - Institute for Biological Data Science, CEPLAS, Heinrich Heine University - Dusseldorf, Dusseldorf, Germany. -FAU - Schubert, Ingo -AU - Schubert I -AD - Leibniz Institute of Plant Genetics and Crop Plant Research (IPK) Gatersleben, - Seeland, Germany. -FAU - O'Sullivan, Donal Martin -AU - O'Sullivan DM -AUID- ORCID: 0000-0003-4889-056X -AD - School of Agriculture, Policy and Development, University of Reading, Reading, - UK. d.m.osullivan@reading.ac.uk. -FAU - Schulman, Alan H -AU - Schulman AH -AUID- ORCID: 0000-0002-4126-6177 -AD - Natural Resources Institute Finland (Luke), Helsinki, Finland. - alan.schulman@helsinki.fi. -AD - Institute of Biotechnology, University of Helsinki, Helsinki, Finland. - alan.schulman@helsinki.fi. -AD - Viikki Plant Science Centre, University of Helsinki, Helsinki, Finland, Cordoba, - Spain. alan.schulman@helsinki.fi. -FAU - Andersen, Stig Uggerhoj -AU - Andersen SU -AUID- ORCID: 0000-0002-1096-1468 -AD - Department of Molecular Biology and Genetics, Aarhus University, Aarhus C, - Denmark. sua@mbg.au.dk. -LA - eng -GR - BB/P023509/1/BB_/Biotechnology and Biological Sciences Research Council/United - Kingdom -PT - Journal Article -DEP - 20230308 -PL - England -TA - Nature -JT - Nature -JID - 0410462 -RN - 0 (DNA, Satellite) -RN - 0 (Plant Proteins) -RN - 0 (Retroelements) -SB - IM -MH - Chromosomes, Plant/genetics -MH - *Crops, Agricultural/genetics/metabolism -MH - *Diploidy -MH - DNA Copy Number Variations/genetics -MH - DNA, Satellite/genetics -MH - Gene Amplification/genetics -MH - Genes, Plant/genetics -MH - *Genetic Variation/genetics -MH - *Genome, Plant/genetics -MH - Genome-Wide Association Study -MH - *Genomics -MH - Geography -MH - *Plant Breeding/methods -MH - *Plant Proteins/genetics/metabolism -MH - Recombination, Genetic -MH - Retroelements/genetics -MH - Seeds/anatomy & histology/genetics -MH - *Vicia faba/anatomy & histology/genetics/metabolism -PMC - PMC10033403 -COIS- The authors declare no competing interests. -EDAT- 2023/03/09 06:00 -MHDA- 2023/03/25 06:00 -CRDT- 2023/03/08 23:18 -PHST- 2022/09/23 00:00 [received] -PHST- 2023/02/03 00:00 [accepted] -PHST- 2023/03/09 06:00 [pubmed] -PHST- 2023/03/25 06:00 [medline] -PHST- 2023/03/08 23:18 [entrez] -AID - 10.1038/s41586-023-05791-5 [pii] -AID - 5791 [pii] -AID - 10.1038/s41586-023-05791-5 [doi] -PST - ppublish -SO - Nature. 2023 Mar;615(7953):652-659. doi: 10.1038/s41586-023-05791-5. Epub 2023 - Mar 8. - - diff --git a/Vicia/faba/gene_functions/vicfa.traits.yml b/Vicia/faba/gene_functions/vicfa.traits.yml index aa9ebc1..ba9b831 100644 --- a/Vicia/faba/gene_functions/vicfa.traits.yml +++ b/Vicia/faba/gene_functions/vicfa.traits.yml @@ -1,9 +1,13 @@ ## DOCUMENT 1 ## --- +scientific_name: Vicia faba gene_symbols: + - VfCYP78A gene_model_pub_name: Vfaba.Hedin2.R1.4g051440.1 gene_model_full_id: vicfa.Hedin2.gnm1.ann1.4g051440.1 confidence: 4 +curators: + - Steven Cannon comments: - Evidence based on GWAS, allele analysis, and homology to an Arabidopsis gene (CYP78A) involved in seed size regulation phenotype_synopsis: Seed size regulation @@ -18,15 +22,18 @@ references: ## DOCUMENT 2 ## --- +scientific_name: Vicia faba gene_symbols: - VfPPO-2 gene_symbol_long: polyphenol oxidase 2 gene_model_pub_name: Vfaba.Tiffany.R1.1g391400.1 gene_model_full_id: vicfa.Tiffany.gnm1.ann1.1g391400.1 confidence: 4 +curators: + - Steven Cannon comments: - Evidence based on association and allelic variant analysis, and homology to an orthologous locus in pea (gene Psat1g2063360) that controls hilum color. - - \[Evidence suggests that the] regulation of expression of VfPPO-2 controls hilum colour variation in faba bean.\ + - Evidence suggests that the] regulation of expression of VfPPO-2 controls hilum colour variation in faba bean. phenotype_synopsis: Control of hilum color traits: - entity_name: hilum color diff --git a/Vigna/radiata/gene_functions/vigra.citations.txt b/Vigna/radiata/gene_functions/vigra.citations.txt new file mode 100644 index 0000000..d47d3e1 --- /dev/null +++ b/Vigna/radiata/gene_functions/vigra.citations.txt @@ -0,0 +1 @@ +10.1186/s12864-022-08620-7 35581536 PMC9115955 Liu, Zhang, et. al., 2022 "Liu C, Zhang Q, Dong J, Cai C, Zhu H, Li S. Genome-wide identification and characterization of mungbean CIRCADIAN CLOCK ASSOCIATED 1 like genes reveals an important role of VrCCA1L26 in flowering time regulation. BMC Genomics. 2022 May 17;23(1):374. doi: 10.1186/s12864-022-08620-7. PMID: 35581536; PMCID: PMC9115955." diff --git a/Vigna/radiata/gene_functions/vigra.traits.yml b/Vigna/radiata/gene_functions/vigra.traits.yml new file mode 100644 index 0000000..cefd238 --- /dev/null +++ b/Vigna/radiata/gene_functions/vigra.traits.yml @@ -0,0 +1,28 @@ +## DOCUMENT 1 ## +--- +scientific_name: Vigna radiata +gene_symbols: + - VrCCA1L26 +gene_symbol_long: Circadian Clock Assoicated 1 Like 26 +gene_model_pub_name: Vradi05g00310 +gene_model_full_id: vigra.VC1973A.gnm6.ann1.Vradi05g00310 +confidence: 3 +curators: + - Marlene Dorneich-Hayes +comments: + - VrCCA1L26 shares homology with AtCCA1, AtLHY, and GmLCL genes. + - In transgenic Arabidopsis, VrCCA1L26 delays flowering time by supressing Constans (CO), Flowering locus T (FT), Supressor of Overexpression of Constans 1 (SOC1), and Timing of Cab Expression 1 (TOC1). + - VrCCA1L26 expression is affected by photoperiod and is supressed by expression of TOC1. + - VrCCA1L26 may play a role in isoflavonoid synthesis, stress response, hypocotyl growth, seed germination, and leaf senescence. This has not been experimentally validated. +phenotype_synopsis: VrCCA1L26 delays flowering time in transgenic Arabidopsis thaliana, but its function in Vigna radiata has not been experimentally validated. +traits: + - entity_name: transcription factor binding + entity: GO:0008134 + - entity_name: photoperiod-sensitive flowering time trait + entity: TO:0000934 +references: + - citation: Liu, Zhang, et. al., 2022 + doi: 10.1186/s12864-022-08620-7 + pmid: 35581536 + + From 5c6191d69299974cc3aeceea8ca51cc74bbbcd40 Mon Sep 17 00:00:00 2001 From: StevenCannon-USDA Date: Thu, 12 Sep 2024 14:57:26 -0500 Subject: [PATCH 15/18] Attempt to fix utf-8 error seen in yamllint check --- Vicia/faba/gene_functions/vicfa.traits.yml | 2 +- Vicia/faba/studies/vicfa.Jayakodi_Golicz_2023.yml | 2 +- 2 files changed, 2 insertions(+), 2 deletions(-) diff --git a/Vicia/faba/gene_functions/vicfa.traits.yml b/Vicia/faba/gene_functions/vicfa.traits.yml index aa9ebc1..d6f40f2 100644 --- a/Vicia/faba/gene_functions/vicfa.traits.yml +++ b/Vicia/faba/gene_functions/vicfa.traits.yml @@ -26,7 +26,7 @@ gene_model_full_id: vicfa.Tiffany.gnm1.ann1.1g391400.1 confidence: 4 comments: - Evidence based on association and allelic variant analysis, and homology to an orthologous locus in pea (gene Psat1g2063360) that controls hilum color. - - \[Evidence suggests that the] regulation of expression of VfPPO-2 controls hilum colour variation in faba bean.\ + - Evidence suggests that the regulation of expression of VfPPO-2 controls hilum colour variation in faba bean. phenotype_synopsis: Control of hilum color traits: - entity_name: hilum color diff --git a/Vicia/faba/studies/vicfa.Jayakodi_Golicz_2023.yml b/Vicia/faba/studies/vicfa.Jayakodi_Golicz_2023.yml index 3230db2..c53c1bd 100644 --- a/Vicia/faba/studies/vicfa.Jayakodi_Golicz_2023.yml +++ b/Vicia/faba/studies/vicfa.Jayakodi_Golicz_2023.yml @@ -28,7 +28,7 @@ curators: - Steven Cannon comments: - Evidence based on association and allelic variant analysis, and homology to an orthologous locus in pea (gene Psat1g2063360) that controls hilum color. - - \[Evidence suggests that the] regulation of expression of VfPPO-2 controls hilum colour variation in faba bean.\ + - Evidence suggests that the regulation of expression of VfPPO-2 controls hilum colour variation in faba bean. phenotype_synopsis: Control of hilum color traits: - entity_name: hilum color From eae98742fe7b63abaaa2df3881881bc49756d2f3 Mon Sep 17 00:00:00 2001 From: StevenCannon-USDA Date: Thu, 12 Sep 2024 15:07:04 -0500 Subject: [PATCH 16/18] More tweaks for yaml compliance --- Vicia/faba/studies/vicfa.Jayakodi_Golicz_2023.yml | 10 +++++----- 1 file changed, 5 insertions(+), 5 deletions(-) diff --git a/Vicia/faba/studies/vicfa.Jayakodi_Golicz_2023.yml b/Vicia/faba/studies/vicfa.Jayakodi_Golicz_2023.yml index 1adf853..1f08dc7 100644 --- a/Vicia/faba/studies/vicfa.Jayakodi_Golicz_2023.yml +++ b/Vicia/faba/studies/vicfa.Jayakodi_Golicz_2023.yml @@ -1,9 +1,9 @@ --- scientific_name: Vicia faba -gene_symbols: +gene_symbols: - VfCYP78A -gene_model_pub_name: Vfaba.Hedin2.R1.4g051440.1 -gene_model_full_id: vicfa.Hedin2.gnm1.ann1.4g051440.1 +gene_model_pub_name: Vfaba.Hedin2.R1.4g051440 +gene_model_full_id: vicfa.Hedin2.gnm1.ann1.4g051440 confidence: 4 curators: - Steven Cannon @@ -22,8 +22,8 @@ scientific_name: Vicia faba gene_symbols: - VfPPO-2 gene_symbol_long: polyphenol oxidase 2 -gene_model_pub_name: Vfaba.Tiffany.R1.1g391400.1 -gene_model_full_id: vicfa.Tiffany.gnm1.ann1.1g391400.1 +gene_model_pub_name: Vfaba.Tiffany.R1.1g391400 +gene_model_full_id: vicfa.Tiffany.gnm1.ann1.1g391400 confidence: 4 curators: - Steven Cannon From d25f6fb52784bc70e0bb6e9f34ef512faa57a12f Mon Sep 17 00:00:00 2001 From: StevenCannon-USDA Date: Fri, 13 Sep 2024 09:51:04 -0500 Subject: [PATCH 17/18] Tweaks for yaml compliance --- Glycine/max/studies/glyma.Lu_Zhao_2017.yml | 2 +- Vicia/faba/studies/vicfa.Jayakodi_Golicz_2023.yml | 2 -- 2 files changed, 1 insertion(+), 3 deletions(-) diff --git a/Glycine/max/studies/glyma.Lu_Zhao_2017.yml b/Glycine/max/studies/glyma.Lu_Zhao_2017.yml index ef68823..1289610 100644 --- a/Glycine/max/studies/glyma.Lu_Zhao_2017.yml +++ b/Glycine/max/studies/glyma.Lu_Zhao_2017.yml @@ -93,7 +93,7 @@ confidence: 5 curators: - Steven Cannon phenotype_synopsis: Photoperiodic flowering time regulation -comments: +comments: - Encodes a MYB transciption factor that affects plant height through mediating the GA pathway in soybean traits: - entity_name: flowering time diff --git a/Vicia/faba/studies/vicfa.Jayakodi_Golicz_2023.yml b/Vicia/faba/studies/vicfa.Jayakodi_Golicz_2023.yml index 1f08dc7..6a7c65d 100644 --- a/Vicia/faba/studies/vicfa.Jayakodi_Golicz_2023.yml +++ b/Vicia/faba/studies/vicfa.Jayakodi_Golicz_2023.yml @@ -38,5 +38,3 @@ references: - citation: Jayakodi, Golicz et al., 2023 doi: 10.1038/s41586-023-05791-5 pmid: 36890232 - - From 607a464dcfafb3b83ddfbc44872fdab5ee77041c Mon Sep 17 00:00:00 2001 From: Steven Cannon Date: Fri, 13 Sep 2024 09:56:01 -0500 Subject: [PATCH 18/18] yml tweaks --- Glycine/max/gene_functions/glyma.traits.yml | 1 - Glycine/max/studies/glyma.Wang_Li_2021.yml | 1 - 2 files changed, 2 deletions(-) diff --git a/Glycine/max/gene_functions/glyma.traits.yml b/Glycine/max/gene_functions/glyma.traits.yml index 8481250..29d43a1 100644 --- a/Glycine/max/gene_functions/glyma.traits.yml +++ b/Glycine/max/gene_functions/glyma.traits.yml @@ -2874,7 +2874,6 @@ comments: - ncbi says the locus for gibberellin 2-beta-dioxygenase 8 [Glycine max] -> "LOCUS NP_001242439" - Cannot find plant trait ontology for trailing growth and shoot length -> "shoot height (related)" is for plant height - glyma.Wm82.gnm2.ann1.Glyma.13G287600.1 also works - - phenotype_synopsis: Negatively correlated with shoot length and trailing growth traits: - entity_name: plant height diff --git a/Glycine/max/studies/glyma.Wang_Li_2021.yml b/Glycine/max/studies/glyma.Wang_Li_2021.yml index 45adac1..13d8f0c 100644 --- a/Glycine/max/studies/glyma.Wang_Li_2021.yml +++ b/Glycine/max/studies/glyma.Wang_Li_2021.yml @@ -13,7 +13,6 @@ comments: "LOCUS NP_001242439" - Cannot find plant trait ontology for trailing growth and shoot length -> "shoot height (related)" is for plant height - glyma.Wm82.gnm2.ann1.Glyma.13G287600.1 also works - - phenotype_synopsis: Negatively correlated with shoot length and trailing growth traits: - entity_name: plant height