From f957f0a77c9ec9e1152571982b8bb04f79027f62 Mon Sep 17 00:00:00 2001 From: StevenCannon-USDA Date: Thu, 4 Jan 2024 15:19:30 -0600 Subject: [PATCH] Wholesale rearrangement. Removed all wip_name directories and moved yaml files into new studies/ directories. --- .gitignore | 1 + .../done => studies}/Bai_Jing_2021.yml | 0 .../Cai_Wang_2017.yml | 0 .../done => studies}/Campbell_Mani_2014.yml | 0 .../Chen_Cai_2020.yml | 0 .../done => studies}/Chen_Fang_2019.yml | 0 .../Chen_Wang_2016.yml | 0 .../Cheng_Dong_2019.yml | 0 .../Chiasson_Loughlin_2014_GmbHLHm1.yml | 0 .../done => studies}/Dobbels_Michno_2017.yml | 0 .../done => studies}/Du_Zhao_2018.yml | 0 .../done => studies}/Fang_Li_2014.yml | 0 .../{wip_marlene => studies}/Ge_Yu_2016.yml | 0 .../Head_Galos_2012_traits.yml | 0 .../done => studies}/Hu_Jin_2014.yml | 0 .../Indrasumunar_Searle_2011.yml | 0 .../done => studies}/Khatri_Pant_2022.yml | 0 .../done => studies}/Li_Liu_2019.yml | 0 .../Liang_Chen_2022.yml} | 21 - .../done => studies}/Liu_Liao_2020.yml | 0 Glycine/max/studies/Liu_Watanabe_2010.yml | 21 + .../Lu_Cheng_2020.yml | 0 .../done => studies}/Lu_Wei_2021.yml | 0 .../done => studies}/Manan_Ahmad_2017.yml | 0 .../done => studies}/Noman_Jameel_2019.yml | 0 .../done => studies}/Pan_Yu_2021.yml | 0 .../Pant_Matsye_2014.yml | 0 .../Pham_Lee_2010.yml | 0 .../{wip_greg/done => studies}/Qi_Li_2014.yml | 0 .../done => studies}/Redekar_Glover_2020.yml | 0 .../done => studies}/Reid_Ferguson_2011.yml | 0 .../RojasRodas_Rodriguez_2013.yml | 0 .../Searle_Men_2003.yml | 0 .../done => studies}/Shi_Zhang_2020.yml | 0 .../{wip_marlene => studies}/Song_Li_2013.yml | 0 .../Song_Montez-Luz_2022.yml | 0 .../Soyano_Hirakawa_2014_lotja.yml | 0 .../Sugawara_Umehara_2019.yml | 0 .../{wip_marlene => studies}/Tang_Su_2017.yml | 0 .../done => studies}/Tian_Liu_2019.yml | 0 .../Vadivel_McDowell_2021.yml} | 0 .../Wang_Guo_2021.yml | 0 .../done => studies}/Wang_Li_2021.yml | 0 .../done => studies}/Wang_Shine_2014.yml | 0 .../Wang_Wang_2014.yml | 0 .../done => studies}/Wang_Wang_2015.yml | 0 .../Wang_Yang_2020.yml | 0 .../Wang_Yuan_2019.yml | 0 .../done => studies}/Wu_Price_2014.yml | 0 .../Yan_Wang_2018.yml | 0 .../done => studies}/Yang_Zhang_2021.yml | 0 .../done => studies}/Yu_Chang_2019.yml | 0 .../{wip_marlene => studies}/Yu_Jin_2019.yml | 0 .../supplemental => studies}/Yue_Li_2021.yml | 0 .../Zhang_Burton_2008.yml | 0 .../Zhang_Cheng_2021.yml | 0 .../done => studies}/Zhang_Goettel_2020.yml | 0 .../done => studies}/Zhang_Luo_2013.yml | 0 .../Zhang_Sun_2017.yml | 0 .../Zhang_Wang_2021.yml | 0 .../{wip_will => studies}/Zhao_Bi_2019.yml | 0 .../done => studies}/Zhao_Li_2018.yml | 0 .../done => studies}/Zhou_He_2014.yml | 0 .../Zhou_Lakhssassi_2021.yml | 0 .../Zhuang_Xue_2021.yml | 0 .../wip_brandon/done/glyma_work.citations.txt | 2 - .../To_delete_Campbell_Mani_2014.yml | 42 - .../Oellrich_Walls_2015_glyma.citations.txt | 23 - .../Oellrich_Walls_2015_glyma.references.txt | 2492 ----------------- .../Oellrich_Walls_2015_glyma.traits.yml | 651 ----- .../max/wip_wei/Head_Galos_2012_traits.yml | 33 - Glycine/max/wip_will/README.md | 15 - .../max/wip_will/gene_model_full_id_finder.py | 60 - .../{wip_greg => studies}/Jin_Sun_2021.yml | 0 .../soja/{wip_greg => studies}/Qi_Li_2014.yml | 0 .../Soyano_Hirakawa_2014.yml | 0 .../Oellrich_Walls_2015.traits.yml | 0 .../Wang_Lu_2022.MtGSTF7.yml | 0 .../done/Oellrich_Walls_2015.citations.txt | 31 - .../Davila-Delgado_Flores-Canul_2023.yml} | 0 .../Sato_Morita_2007.yml | 0 README.md | 84 - Vicia/faba/studies/Jayakodi_Golicz_2023.yml | 35 + .../Liu_Zhang_2022.yml} | 0 84 files changed, 57 insertions(+), 3454 deletions(-) create mode 100644 .gitignore rename Glycine/max/{wip_greg/done => studies}/Bai_Jing_2021.yml (100%) rename Glycine/max/{wip_marlene => studies}/Cai_Wang_2017.yml (100%) rename Glycine/max/{wip_marlene/done => studies}/Campbell_Mani_2014.yml (100%) rename Glycine/max/{wip_greg/done/supplemental => studies}/Chen_Cai_2020.yml (100%) rename Glycine/max/{wip_greg/done => studies}/Chen_Fang_2019.yml (100%) rename Glycine/max/{wip_marlene => studies}/Chen_Wang_2016.yml (100%) rename Glycine/max/{wip_greg/done/supplemental => studies}/Cheng_Dong_2019.yml (100%) rename Glycine/max/{wip_steven => studies}/Chiasson_Loughlin_2014_GmbHLHm1.yml (100%) rename Glycine/max/{wip_greg/done => studies}/Dobbels_Michno_2017.yml (100%) rename Glycine/max/{wip_will/done => studies}/Du_Zhao_2018.yml (100%) rename Glycine/max/{wip_will/done => studies}/Fang_Li_2014.yml (100%) rename Glycine/max/{wip_marlene => studies}/Ge_Yu_2016.yml (100%) rename Glycine/max/{wip_wei/done => studies}/Head_Galos_2012_traits.yml (100%) rename Glycine/max/{wip_will/done => studies}/Hu_Jin_2014.yml (100%) rename Glycine/max/{wip_marlene => studies}/Indrasumunar_Searle_2011.yml (100%) rename Glycine/max/{wip_marlene/done => studies}/Khatri_Pant_2022.yml (100%) rename Glycine/max/{wip_will/done => studies}/Li_Liu_2019.yml (100%) rename Glycine/max/{wip_brandon/done/traits_determinacy.yml => studies/Liang_Chen_2022.yml} (61%) rename Glycine/max/{wip_will/done => studies}/Liu_Liao_2020.yml (100%) create mode 100644 Glycine/max/studies/Liu_Watanabe_2010.yml rename Glycine/max/{wip_marlene => studies}/Lu_Cheng_2020.yml (100%) rename Glycine/max/{wip_marlene/done => studies}/Lu_Wei_2021.yml (100%) rename Glycine/max/{wip_greg/done => studies}/Manan_Ahmad_2017.yml (100%) rename Glycine/max/{wip_marlene/done => studies}/Noman_Jameel_2019.yml (100%) rename Glycine/max/{wip_marlene/done => studies}/Pan_Yu_2021.yml (100%) rename Glycine/max/{wip_greg => studies}/Pant_Matsye_2014.yml (100%) rename Glycine/max/{wip_marlene => studies}/Pham_Lee_2010.yml (100%) rename Glycine/max/{wip_greg/done => studies}/Qi_Li_2014.yml (100%) rename Glycine/max/{wip_marlene/done => studies}/Redekar_Glover_2020.yml (100%) rename Glycine/max/{wip_marlene/done => studies}/Reid_Ferguson_2011.yml (100%) rename Glycine/max/{wip_greg/done => studies}/RojasRodas_Rodriguez_2013.yml (100%) rename Glycine/max/{wip_marlene => studies}/Searle_Men_2003.yml (100%) rename Glycine/max/{wip_marlene/done => studies}/Shi_Zhang_2020.yml (100%) rename Glycine/max/{wip_marlene => studies}/Song_Li_2013.yml (100%) rename Glycine/max/{wip_marlene => studies}/Song_Montez-Luz_2022.yml (100%) rename Glycine/max/{wip_marlene => studies}/Soyano_Hirakawa_2014_lotja.yml (100%) rename Glycine/max/{wip_greg/done => studies}/Sugawara_Umehara_2019.yml (100%) rename Glycine/max/{wip_marlene => studies}/Tang_Su_2017.yml (100%) rename Glycine/max/{wip_marlene/done => studies}/Tian_Liu_2019.yml (100%) rename Glycine/max/{wip_wei/done/Vadivel_McDowell_2021_traits.yml => studies/Vadivel_McDowell_2021.yml} (100%) rename Glycine/max/{wip_marlene => studies}/Wang_Guo_2021.yml (100%) rename Glycine/max/{wip_will/done => studies}/Wang_Li_2021.yml (100%) rename Glycine/max/{wip_marlene/done => studies}/Wang_Shine_2014.yml (100%) rename Glycine/max/{wip_marlene => studies}/Wang_Wang_2014.yml (100%) rename Glycine/max/{wip_will/done => studies}/Wang_Wang_2015.yml (100%) rename Glycine/max/{wip_marlene => studies}/Wang_Yang_2020.yml (100%) rename Glycine/max/{wip_marlene => studies}/Wang_Yuan_2019.yml (100%) rename Glycine/max/{wip_will/done => studies}/Wu_Price_2014.yml (100%) rename Glycine/max/{wip_marlene => studies}/Yan_Wang_2018.yml (100%) rename Glycine/max/{wip_marlene/done => studies}/Yang_Zhang_2021.yml (100%) rename Glycine/max/{wip_will/done => studies}/Yu_Chang_2019.yml (100%) rename Glycine/max/{wip_marlene => studies}/Yu_Jin_2019.yml (100%) rename Glycine/max/{wip_greg/done/supplemental => studies}/Yue_Li_2021.yml (100%) rename Glycine/max/{wip_marlene => studies}/Zhang_Burton_2008.yml (100%) rename Glycine/max/{wip_marlene => studies}/Zhang_Cheng_2021.yml (100%) rename Glycine/max/{wip_marlene/done => studies}/Zhang_Goettel_2020.yml (100%) rename Glycine/max/{wip_greg/done => studies}/Zhang_Luo_2013.yml (100%) rename Glycine/max/{wip_marlene => studies}/Zhang_Sun_2017.yml (100%) rename Glycine/max/{wip_marlene => studies}/Zhang_Wang_2021.yml (100%) rename Glycine/max/{wip_will => studies}/Zhao_Bi_2019.yml (100%) rename Glycine/max/{wip_will/done => studies}/Zhao_Li_2018.yml (100%) rename Glycine/max/{wip_marlene/done => studies}/Zhou_He_2014.yml (100%) rename Glycine/max/{wip_marlene => studies}/Zhou_Lakhssassi_2021.yml (100%) rename Glycine/max/{wip_marlene => studies}/Zhuang_Xue_2021.yml (100%) delete mode 100644 Glycine/max/wip_brandon/done/glyma_work.citations.txt delete mode 100644 Glycine/max/wip_jackie/To_delete_Campbell_Mani_2014.yml delete mode 100644 Glycine/max/wip_steven/Oellrich_Walls_2015_glyma.citations.txt delete mode 100644 Glycine/max/wip_steven/Oellrich_Walls_2015_glyma.references.txt delete mode 100644 Glycine/max/wip_steven/Oellrich_Walls_2015_glyma.traits.yml delete mode 100644 Glycine/max/wip_wei/Head_Galos_2012_traits.yml delete mode 100644 Glycine/max/wip_will/README.md delete mode 100644 Glycine/max/wip_will/gene_model_full_id_finder.py rename Glycine/soja/{wip_greg => studies}/Jin_Sun_2021.yml (100%) rename Glycine/soja/{wip_greg => studies}/Qi_Li_2014.yml (100%) rename Lotus/japonicus/{wip_marlene => studies}/Soyano_Hirakawa_2014.yml (100%) rename Medicago/truncatula/{wip_steven/done => studies}/Oellrich_Walls_2015.traits.yml (100%) rename Medicago/truncatula/{wip_wei => studies}/Wang_Lu_2022.MtGSTF7.yml (100%) delete mode 100644 Medicago/truncatula/wip_steven/done/Oellrich_Walls_2015.citations.txt rename Phaseolus/vulgaris/{wip_marlene/phavu_Davila-Delgado_Flores-Canul_2023.yml => studies/Davila-Delgado_Flores-Canul_2023.yml} (100%) rename Pisum/sativum/{wip_marlene => studies}/Sato_Morita_2007.yml (100%) delete mode 100644 README.md create mode 100644 Vicia/faba/studies/Jayakodi_Golicz_2023.yml rename Vigna/radiata/{wip_marlene/vigra_Liu_Zhang_2022.yml => studies/Liu_Zhang_2022.yml} (100%) diff --git a/.gitignore b/.gitignore new file mode 100644 index 0000000..e43b0f9 --- /dev/null +++ b/.gitignore @@ -0,0 +1 @@ +.DS_Store diff --git a/Glycine/max/wip_greg/done/Bai_Jing_2021.yml b/Glycine/max/studies/Bai_Jing_2021.yml similarity index 100% rename from Glycine/max/wip_greg/done/Bai_Jing_2021.yml rename to Glycine/max/studies/Bai_Jing_2021.yml diff --git a/Glycine/max/wip_marlene/Cai_Wang_2017.yml b/Glycine/max/studies/Cai_Wang_2017.yml similarity index 100% rename from Glycine/max/wip_marlene/Cai_Wang_2017.yml rename to Glycine/max/studies/Cai_Wang_2017.yml diff --git a/Glycine/max/wip_marlene/done/Campbell_Mani_2014.yml b/Glycine/max/studies/Campbell_Mani_2014.yml similarity index 100% rename from Glycine/max/wip_marlene/done/Campbell_Mani_2014.yml rename to Glycine/max/studies/Campbell_Mani_2014.yml diff --git a/Glycine/max/wip_greg/done/supplemental/Chen_Cai_2020.yml b/Glycine/max/studies/Chen_Cai_2020.yml similarity index 100% rename from Glycine/max/wip_greg/done/supplemental/Chen_Cai_2020.yml rename to Glycine/max/studies/Chen_Cai_2020.yml diff --git a/Glycine/max/wip_greg/done/Chen_Fang_2019.yml b/Glycine/max/studies/Chen_Fang_2019.yml similarity index 100% rename from Glycine/max/wip_greg/done/Chen_Fang_2019.yml rename to Glycine/max/studies/Chen_Fang_2019.yml diff --git a/Glycine/max/wip_marlene/Chen_Wang_2016.yml b/Glycine/max/studies/Chen_Wang_2016.yml similarity index 100% rename from Glycine/max/wip_marlene/Chen_Wang_2016.yml rename to Glycine/max/studies/Chen_Wang_2016.yml diff --git a/Glycine/max/wip_greg/done/supplemental/Cheng_Dong_2019.yml b/Glycine/max/studies/Cheng_Dong_2019.yml similarity index 100% rename from Glycine/max/wip_greg/done/supplemental/Cheng_Dong_2019.yml rename to Glycine/max/studies/Cheng_Dong_2019.yml diff --git a/Glycine/max/wip_steven/Chiasson_Loughlin_2014_GmbHLHm1.yml b/Glycine/max/studies/Chiasson_Loughlin_2014_GmbHLHm1.yml similarity index 100% rename from Glycine/max/wip_steven/Chiasson_Loughlin_2014_GmbHLHm1.yml rename to Glycine/max/studies/Chiasson_Loughlin_2014_GmbHLHm1.yml diff --git a/Glycine/max/wip_greg/done/Dobbels_Michno_2017.yml b/Glycine/max/studies/Dobbels_Michno_2017.yml similarity index 100% rename from Glycine/max/wip_greg/done/Dobbels_Michno_2017.yml rename to Glycine/max/studies/Dobbels_Michno_2017.yml diff --git a/Glycine/max/wip_will/done/Du_Zhao_2018.yml b/Glycine/max/studies/Du_Zhao_2018.yml similarity index 100% rename from Glycine/max/wip_will/done/Du_Zhao_2018.yml rename to Glycine/max/studies/Du_Zhao_2018.yml diff --git a/Glycine/max/wip_will/done/Fang_Li_2014.yml b/Glycine/max/studies/Fang_Li_2014.yml similarity index 100% rename from Glycine/max/wip_will/done/Fang_Li_2014.yml rename to Glycine/max/studies/Fang_Li_2014.yml diff --git a/Glycine/max/wip_marlene/Ge_Yu_2016.yml b/Glycine/max/studies/Ge_Yu_2016.yml similarity index 100% rename from Glycine/max/wip_marlene/Ge_Yu_2016.yml rename to Glycine/max/studies/Ge_Yu_2016.yml diff --git a/Glycine/max/wip_wei/done/Head_Galos_2012_traits.yml b/Glycine/max/studies/Head_Galos_2012_traits.yml similarity index 100% rename from Glycine/max/wip_wei/done/Head_Galos_2012_traits.yml rename to Glycine/max/studies/Head_Galos_2012_traits.yml diff --git a/Glycine/max/wip_will/done/Hu_Jin_2014.yml b/Glycine/max/studies/Hu_Jin_2014.yml similarity index 100% rename from Glycine/max/wip_will/done/Hu_Jin_2014.yml rename to Glycine/max/studies/Hu_Jin_2014.yml diff --git a/Glycine/max/wip_marlene/Indrasumunar_Searle_2011.yml b/Glycine/max/studies/Indrasumunar_Searle_2011.yml similarity index 100% rename from Glycine/max/wip_marlene/Indrasumunar_Searle_2011.yml rename to Glycine/max/studies/Indrasumunar_Searle_2011.yml diff --git a/Glycine/max/wip_marlene/done/Khatri_Pant_2022.yml b/Glycine/max/studies/Khatri_Pant_2022.yml similarity index 100% rename from Glycine/max/wip_marlene/done/Khatri_Pant_2022.yml rename to Glycine/max/studies/Khatri_Pant_2022.yml diff --git a/Glycine/max/wip_will/done/Li_Liu_2019.yml b/Glycine/max/studies/Li_Liu_2019.yml similarity index 100% rename from Glycine/max/wip_will/done/Li_Liu_2019.yml rename to Glycine/max/studies/Li_Liu_2019.yml diff --git a/Glycine/max/wip_brandon/done/traits_determinacy.yml b/Glycine/max/studies/Liang_Chen_2022.yml similarity index 61% rename from Glycine/max/wip_brandon/done/traits_determinacy.yml rename to Glycine/max/studies/Liang_Chen_2022.yml index 6bc95c0..2dcb1e2 100644 --- a/Glycine/max/wip_brandon/done/traits_determinacy.yml +++ b/Glycine/max/studies/Liang_Chen_2022.yml @@ -25,24 +25,3 @@ references: pmid: 25005919 ---- -classical_locus: -gene_symbols: - - GmDT1 -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 -phenotype_synopsis: determinate stem growth habit -traits: - - entity_name: meristem identity - entity: TO:0006017 - relation_name: terminal - relation: PATO:0002476 -references: - - citation: Liu, Watanabe et al., 2010 - doi: doi.org/10.1104/pp.109.150607 - pmid: 20219831 - diff --git a/Glycine/max/wip_will/done/Liu_Liao_2020.yml b/Glycine/max/studies/Liu_Liao_2020.yml similarity index 100% rename from Glycine/max/wip_will/done/Liu_Liao_2020.yml rename to Glycine/max/studies/Liu_Liao_2020.yml diff --git a/Glycine/max/studies/Liu_Watanabe_2010.yml b/Glycine/max/studies/Liu_Watanabe_2010.yml new file mode 100644 index 0000000..f6de409 --- /dev/null +++ b/Glycine/max/studies/Liu_Watanabe_2010.yml @@ -0,0 +1,21 @@ +--- +classical_locus: +gene_symbols: + - GmDT1 +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 +phenotype_synopsis: determinate stem growth habit +traits: + - entity_name: meristem identity + entity: TO:0006017 + relation_name: terminal + relation: PATO:0002476 +references: + - citation: Liu, Watanabe et al., 2010 + doi: doi.org/10.1104/pp.109.150607 + pmid: 20219831 + diff --git a/Glycine/max/wip_marlene/Lu_Cheng_2020.yml b/Glycine/max/studies/Lu_Cheng_2020.yml similarity index 100% rename from Glycine/max/wip_marlene/Lu_Cheng_2020.yml rename to Glycine/max/studies/Lu_Cheng_2020.yml diff --git a/Glycine/max/wip_marlene/done/Lu_Wei_2021.yml b/Glycine/max/studies/Lu_Wei_2021.yml similarity index 100% rename from Glycine/max/wip_marlene/done/Lu_Wei_2021.yml rename to Glycine/max/studies/Lu_Wei_2021.yml diff --git a/Glycine/max/wip_greg/done/Manan_Ahmad_2017.yml b/Glycine/max/studies/Manan_Ahmad_2017.yml similarity index 100% rename from Glycine/max/wip_greg/done/Manan_Ahmad_2017.yml rename to Glycine/max/studies/Manan_Ahmad_2017.yml diff --git a/Glycine/max/wip_marlene/done/Noman_Jameel_2019.yml b/Glycine/max/studies/Noman_Jameel_2019.yml similarity index 100% rename from Glycine/max/wip_marlene/done/Noman_Jameel_2019.yml rename to Glycine/max/studies/Noman_Jameel_2019.yml diff --git a/Glycine/max/wip_marlene/done/Pan_Yu_2021.yml b/Glycine/max/studies/Pan_Yu_2021.yml similarity index 100% rename from Glycine/max/wip_marlene/done/Pan_Yu_2021.yml rename to Glycine/max/studies/Pan_Yu_2021.yml diff --git a/Glycine/max/wip_greg/Pant_Matsye_2014.yml b/Glycine/max/studies/Pant_Matsye_2014.yml similarity index 100% rename from Glycine/max/wip_greg/Pant_Matsye_2014.yml rename to Glycine/max/studies/Pant_Matsye_2014.yml diff --git a/Glycine/max/wip_marlene/Pham_Lee_2010.yml b/Glycine/max/studies/Pham_Lee_2010.yml similarity index 100% rename from Glycine/max/wip_marlene/Pham_Lee_2010.yml rename to Glycine/max/studies/Pham_Lee_2010.yml diff --git a/Glycine/max/wip_greg/done/Qi_Li_2014.yml b/Glycine/max/studies/Qi_Li_2014.yml similarity index 100% rename from Glycine/max/wip_greg/done/Qi_Li_2014.yml rename to Glycine/max/studies/Qi_Li_2014.yml diff --git a/Glycine/max/wip_marlene/done/Redekar_Glover_2020.yml b/Glycine/max/studies/Redekar_Glover_2020.yml similarity index 100% rename from Glycine/max/wip_marlene/done/Redekar_Glover_2020.yml rename to Glycine/max/studies/Redekar_Glover_2020.yml diff --git a/Glycine/max/wip_marlene/done/Reid_Ferguson_2011.yml b/Glycine/max/studies/Reid_Ferguson_2011.yml similarity index 100% rename from Glycine/max/wip_marlene/done/Reid_Ferguson_2011.yml rename to Glycine/max/studies/Reid_Ferguson_2011.yml diff --git a/Glycine/max/wip_greg/done/RojasRodas_Rodriguez_2013.yml b/Glycine/max/studies/RojasRodas_Rodriguez_2013.yml similarity index 100% rename from Glycine/max/wip_greg/done/RojasRodas_Rodriguez_2013.yml rename to Glycine/max/studies/RojasRodas_Rodriguez_2013.yml diff --git a/Glycine/max/wip_marlene/Searle_Men_2003.yml b/Glycine/max/studies/Searle_Men_2003.yml similarity index 100% rename from Glycine/max/wip_marlene/Searle_Men_2003.yml rename to Glycine/max/studies/Searle_Men_2003.yml diff --git a/Glycine/max/wip_marlene/done/Shi_Zhang_2020.yml b/Glycine/max/studies/Shi_Zhang_2020.yml similarity index 100% rename from Glycine/max/wip_marlene/done/Shi_Zhang_2020.yml rename to Glycine/max/studies/Shi_Zhang_2020.yml diff --git a/Glycine/max/wip_marlene/Song_Li_2013.yml b/Glycine/max/studies/Song_Li_2013.yml similarity index 100% rename from Glycine/max/wip_marlene/Song_Li_2013.yml rename to Glycine/max/studies/Song_Li_2013.yml diff --git a/Glycine/max/wip_marlene/Song_Montez-Luz_2022.yml b/Glycine/max/studies/Song_Montez-Luz_2022.yml similarity index 100% rename from Glycine/max/wip_marlene/Song_Montez-Luz_2022.yml rename to Glycine/max/studies/Song_Montez-Luz_2022.yml diff --git a/Glycine/max/wip_marlene/Soyano_Hirakawa_2014_lotja.yml b/Glycine/max/studies/Soyano_Hirakawa_2014_lotja.yml similarity index 100% rename from Glycine/max/wip_marlene/Soyano_Hirakawa_2014_lotja.yml rename to Glycine/max/studies/Soyano_Hirakawa_2014_lotja.yml diff --git a/Glycine/max/wip_greg/done/Sugawara_Umehara_2019.yml b/Glycine/max/studies/Sugawara_Umehara_2019.yml similarity index 100% rename from Glycine/max/wip_greg/done/Sugawara_Umehara_2019.yml rename to Glycine/max/studies/Sugawara_Umehara_2019.yml diff --git a/Glycine/max/wip_marlene/Tang_Su_2017.yml b/Glycine/max/studies/Tang_Su_2017.yml similarity index 100% rename from Glycine/max/wip_marlene/Tang_Su_2017.yml rename to Glycine/max/studies/Tang_Su_2017.yml diff --git a/Glycine/max/wip_marlene/done/Tian_Liu_2019.yml b/Glycine/max/studies/Tian_Liu_2019.yml similarity index 100% rename from Glycine/max/wip_marlene/done/Tian_Liu_2019.yml rename to Glycine/max/studies/Tian_Liu_2019.yml diff --git a/Glycine/max/wip_wei/done/Vadivel_McDowell_2021_traits.yml b/Glycine/max/studies/Vadivel_McDowell_2021.yml similarity index 100% rename from Glycine/max/wip_wei/done/Vadivel_McDowell_2021_traits.yml rename to Glycine/max/studies/Vadivel_McDowell_2021.yml diff --git a/Glycine/max/wip_marlene/Wang_Guo_2021.yml b/Glycine/max/studies/Wang_Guo_2021.yml similarity index 100% rename from Glycine/max/wip_marlene/Wang_Guo_2021.yml rename to Glycine/max/studies/Wang_Guo_2021.yml diff --git a/Glycine/max/wip_will/done/Wang_Li_2021.yml 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diff --git a/Glycine/max/wip_marlene/Zhuang_Xue_2021.yml b/Glycine/max/studies/Zhuang_Xue_2021.yml similarity index 100% rename from Glycine/max/wip_marlene/Zhuang_Xue_2021.yml rename to Glycine/max/studies/Zhuang_Xue_2021.yml diff --git a/Glycine/max/wip_brandon/done/glyma_work.citations.txt b/Glycine/max/wip_brandon/done/glyma_work.citations.txt deleted file mode 100644 index 863b274..0000000 --- a/Glycine/max/wip_brandon/done/glyma_work.citations.txt +++ /dev/null @@ -1,2 +0,0 @@ -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.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." diff --git a/Glycine/max/wip_jackie/To_delete_Campbell_Mani_2014.yml b/Glycine/max/wip_jackie/To_delete_Campbell_Mani_2014.yml deleted file mode 100644 index e80d85a..0000000 --- a/Glycine/max/wip_jackie/To_delete_Campbell_Mani_2014.yml +++ /dev/null @@ -1,42 +0,0 @@ ---- -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 -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: leaf - entity: PO:0025034 - - entity_name: magnesium chelatase activity - entity: GO:0016851 - - entity_name: leaf chlorophyll content - entity: TO:0012002 -references: - - citation: Campbell, Mani et al., 2014 - doi: 10.1534/g3.114.015255 - pmid: 25452420 ---- -gene_symbols: - - ChlI1b -gene_symbol_long: -gene_model_pub_name: Glyma.15g08680 -gene_model_full_id: glyma.Wm82.gnm2.ann1.Glyma.15G086800 -confidence: 4 -comments: - - The CD-5 phenotype cosegregates with ChlI1b. -phenotype_synopsis: defective Mg-chetelase is responsible for chlorophyll deficient CD-5 phenotype -traits: - - entity_name: leaf - entity: PO:0025034 - - entity_name: magnesium chelatase activity - entity: GO:0016851 - - entity_name: leaf chlorophyll content - entity: TO:0012002 -references: - - citation: Campbell, Mani et al., 2014 - doi: 10.1534/g3.114.015255 - pmid: 25452420 diff --git a/Glycine/max/wip_steven/Oellrich_Walls_2015_glyma.citations.txt b/Glycine/max/wip_steven/Oellrich_Walls_2015_glyma.citations.txt deleted file mode 100644 index 29b9b37..0000000 --- a/Glycine/max/wip_steven/Oellrich_Walls_2015_glyma.citations.txt +++ /dev/null @@ -1,23 +0,0 @@ -10.1270/jsbbs.16201 29085246 PMC5654458 Sayama, Tanabata, et al., 2017 "Sayama T, Tanabata T, Saruta M, Yamada T, Anai T, Kaga A, Ishimoto M. Confirmation of the pleiotropic control of leaflet shape and number of seeds per pod by the Ln gene in induced soybean mutants. Breed Sci. 2017 Sep;67(4):363-369. doi: 10.1270/jsbbs.16201. Epub 2017 Jul 28. PMID: 29085246; PMCID: PMC5654458." -10.1186/1471-2164-15-702 25149281 PMC4161901 Lauter, Peiffer, et al., 2014 "Moran Lauter AN, Peiffer GA, Yin T, Whitham SA, Cook D, Shoemaker RC, Graham MA. Identification of candidate genes involved in early iron deficiency chlorosis signaling in soybean (Glycine max) roots and leaves. BMC Genomics. 2014 Aug 22;15:702. doi: 10.1186/1471-2164-15-702. PMID: 25149281; PMCID: PMC4161901." -10.1371/journal.pone.0111959 25369033 PMC4219821 Zabala, Vodkin, et al., 2014 "Zabala G, Vodkin LO. Methylation affects transposition and splicing of a large CACTA transposon from a MYB transcription factor regulating anthocyanin synthase genes in soybean seed coats. PLoS One. 2014 Nov 4;9(11):e111959. doi: 10.1371/journal.pone.0111959. PMID: 25369033; PMCID: PMC4219821." -10.1007/s00122-007-0621-2 17701395 null Yuan, Zhao, et al., 2007 "Yuan FJ, Zhao HJ, Ren XL, Zhu SL, Fu XJ, Shu QY. Generation and characterization of two novel low phytate mutations in soybean (Glycine max L. Merr.). Theor Appl Genet. 2007 Nov;115(7):945-57. doi: 10.1007/s00122-007-0621-2. Epub 2007 Aug 16. PMID: 17701395." -10.1007/s00122-015-2575-0 26179337 PMC4624830 Qiu, Vuong, et al., 2015 "Qiu D, Vuong T, Valliyodan B, Shi H, Guo B, Shannon JG, Nguyen HT. Identification and characterization of a stachyose synthase gene controlling reduced stachyose content in soybean. Theor Appl Genet. 2015 Nov;128(11):2167-76. doi: 10.1007/s00122-015-2575-0. Epub 2015 Jul 16. PMID: 26179337; PMCID: PMC4624830." -10.3390/ijms23084116 35456933 PMC9030070 Qian, Jin, et al., 2022 "Qian L, Jin H, Yang Q, Zhu L, Yu X, Fu X, Zhao M, Yuan F. A Sequence Variation in GmBADH2 Enhances Soybean Aroma and Is a Functional Marker for Improving Soybean Flavor. 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PMID: 21406680; PMCID: PMC3122305." diff --git a/Glycine/max/wip_steven/Oellrich_Walls_2015_glyma.references.txt b/Glycine/max/wip_steven/Oellrich_Walls_2015_glyma.references.txt deleted file mode 100644 index c8a0f80..0000000 --- a/Glycine/max/wip_steven/Oellrich_Walls_2015_glyma.references.txt +++ /dev/null @@ -1,2492 +0,0 @@ -##### PUB RECORD ##### -## 10.1270/jsbbs.16201 29085246 PMC5654458 Sayama, Tanabata, et al., 2017 "Sayama T, Tanabata T, Saruta M, Yamada T, Anai T, Kaga A, Ishimoto M. Confirmation of the pleiotropic control of leaflet shape and number of seeds per pod by the Ln gene in induced soybean mutants. Breed Sci. 2017 Sep;67(4):363-369. doi: 10.1270/jsbbs.16201. Epub 2017 Jul 28. PMID: 29085246; PMCID: PMC5654458." ## - -PMID- 29085246 -OWN - NLM -STAT- PubMed-not-MEDLINE -LR - 20200930 -IS - 1344-7610 (Print) -IS - 1347-3735 (Electronic) -IS - 1344-7610 (Linking) -VI - 67 -IP - 4 -DP - 2017 Sep -TI - Confirmation of the pleiotropic control of leaflet shape and number of seeds per - pod by the Ln gene in induced soybean mutants. -PG - 363-369 -LID - 10.1270/jsbbs.16201 [doi] -AB - Most soybean cultivars possess broad leaflets; however, a recessive allele on the - Ln locus is known to cause the alteration of broad to narrow leaflets. The - recessive allele ln has also been considered to increase the number of seeds per - pod (NSP) and has the potential to improve yield. Recently, Gm-JAG1 - (Glyma20g25000), a gene controlling Ln, has been shown to complement leaf shape - and silique length in Arabidopsis mutants. However, whether Gm-JAG1 is - responsible for those traits in soybean is not yet known. In this study, we - investigated the pleiotropic effect of soybean Ln gene on leaflet shape and NSP - by using two independent soybean Gm-jag1 mutants and four ln near isogenic lines - (NILs). The leaflet shape was evaluated using a leaf image analysis software, - SmartLeaf, which was customized from SmartGrain. The leaflets of both the Gm-jag1 - mutants were longer and narrower than those of the wild-type plants. - Interestingly, the image analysis results clarified that the perimeter of the - mutant leaflets did not change, although their leaflet area decreased. - Furthermore, one mutant line with narrow leaflets showed significantly higher NSP - than that in the wild (or Ln) genotype, indicating that soybean Ln gene - pleiotropically controls leaflet shape and NSP. -FAU - Sayama, Takashi -AU - Sayama T -AD - Institute of Crop Science, National Agriculture and Food Research Organization - (NARO), 2-1-2 Kannondai, Tsukuba, Ibaraki 305-8518, Japan. -AD - Western Region Agricultural Research Center, NARO, 1-3-1 Senyu, Zentsuji, Kagawa - 765-8508, Japan. -FAU - Tanabata, Takanari -AU - Tanabata T -AD - Kazusa DNA Research Institute, 2-6-7 Kazusa-kamatari, Kisarazu, Chiba 292-0818, - Japan. -FAU - Saruta, Masayasu -AU - Saruta M -AD - Western Region Agricultural Research Center, NARO, 1-3-1 Senyu, Zentsuji, Kagawa - 765-8508, Japan. -AD - Present address: Agriculture, Forestry and Fisheries Research Council, Ministry - of Agriculture, Forestry and Fisheries, 1-2-1 Kasumigaseki, Chiyoda, Tokyo - 100-8950, Japan. -FAU - Yamada, Testsuya -AU - Yamada T -AD - Institute of Crop Science, National Agriculture and Food Research Organization - (NARO), 2-1-2 Kannondai, Tsukuba, Ibaraki 305-8518, Japan. -FAU - Anai, Toyoaki -AU - Anai T -AD - Laboratory of Plant Genetics and Breeding, Faculty of Agriculture, Saga - University, Honjyo-machi 1, Saga 840-8502, Japan. -FAU - Kaga, Akito -AU - Kaga A -AD - Institute of Crop Science, National Agriculture and Food Research Organization - (NARO), 2-1-2 Kannondai, Tsukuba, Ibaraki 305-8518, Japan. -FAU - Ishimoto, Masao -AU - Ishimoto M -AD - Institute of Crop Science, National Agriculture and Food Research Organization - (NARO), 2-1-2 Kannondai, Tsukuba, Ibaraki 305-8518, Japan. -LA - eng -PT - Journal Article -DEP - 20170728 -PL - Japan -TA - Breed Sci -JT - Breeding science -JID - 9888571 -PMC - PMC5654458 -OTO - NOTNLM -OT - Glycine max (L.) Merrill -OT - Ln gene -OT - leaflet shape -OT - pleiotropic effect -OT - seed number per pod -EDAT- 2017/11/01 06:00 -MHDA- 2017/11/01 06:01 -CRDT- 2017/11/01 06:00 -PHST- 2016/12/26 00:00 [received] -PHST- 2017/05/15 00:00 [accepted] -PHST- 2017/11/01 06:00 [entrez] -PHST- 2017/11/01 06:00 [pubmed] -PHST- 2017/11/01 06:01 [medline] -AID - 67_16201 [pii] -AID - 10.1270/jsbbs.16201 [doi] -PST - ppublish -SO - Breed Sci. 2017 Sep;67(4):363-369. doi: 10.1270/jsbbs.16201. Epub 2017 Jul 28. - - -##### PUB RECORD ##### -## 10.1186/1471-2164-15-702 25149281 PMC4161901 Lauter, Peiffer, et al., 2014 "Moran Lauter AN, Peiffer GA, Yin T, Whitham SA, Cook D, Shoemaker RC, Graham MA. Identification of candidate genes involved in early iron deficiency chlorosis signaling in soybean (Glycine max) roots and leaves. BMC Genomics. 2014 Aug 22;15:702. doi: 10.1186/1471-2164-15-702. PMID: 25149281; PMCID: PMC4161901." ## - -PMID- 25149281 -OWN - NLM -STAT- MEDLINE -DCOM- 20150528 -LR - 20211203 -IS - 1471-2164 (Electronic) -IS - 1471-2164 (Linking) -VI - 15 -DP - 2014 Aug 22 -TI - Identification of candidate genes involved in early iron deficiency chlorosis - signaling in soybean (Glycine max) roots and leaves. -PG - 702 -LID - 10.1186/1471-2164-15-702 [doi] -LID - 702 -AB - BACKGROUND: Iron is an essential micronutrient for all living things, required in - plants for photosynthesis, respiration and metabolism. A lack of bioavailable - iron in soil leads to iron deficiency chlorosis (IDC), causing a reduction in - photosynthesis and interveinal yellowing of leaves. Soybeans (Glycine max (L.) - Merr.) grown in high pH soils often suffer from IDC, resulting in substantial - yield losses. Iron efficient soybean cultivars maintain photosynthesis and have - higher yields under IDC-promoting conditions than inefficient cultivars. RESULTS: - To capture signaling between roots and leaves and identify genes acting early in - the iron efficient cultivar Clark, we conducted a RNA-Seq study at one and six - hours after replacing iron sufficient hydroponic media (100 muM iron(III) nitrate - nonahydrate) with iron deficient media (50 muM iron(III) nitrate nonahydrate). At - one hour of iron stress, few genes were differentially expressed in leaves but - many were already changing expression in roots. By six hours, more genes were - differentially expressed in the leaves, and a massive shift was observed in the - direction of gene expression in both roots and leaves. Further, there was little - overlap in differentially expressed genes identified in each tissue and time - point. CONCLUSIONS: Genes involved in hormone signaling, regulation of DNA - replication and iron uptake utilization are key aspects of the early - iron-efficiency response. We observed dynamic gene expression differences between - roots and leaves, suggesting the involvement of many transcription factors in - eliciting rapid changes in gene expression. In roots, genes involved iron uptake - and development of Casparian strips were induced one hour after iron stress. In - leaves, genes involved in DNA replication and sugar signaling responded to iron - deficiency. The differentially expressed genes (DEGs) and signaling components - identified here represent new targets for soybean improvement. -FAU - Moran Lauter, Adrienne N -AU - Moran Lauter AN -FAU - Peiffer, Gregory A -AU - Peiffer GA -FAU - Yin, Tengfei -AU - Yin T -FAU - Whitham, Steven A -AU - Whitham SA -FAU - Cook, Dianne -AU - Cook D -FAU - Shoemaker, Randy C -AU - Shoemaker RC -FAU - Graham, Michelle A -AU - Graham MA -AD - USDA-Agricultural Research Service, Corn Insects and Crop Genetics Research Unit, - 1565 Agronomy Hall, Ames, IA 50011, USA. michelle.graham@ars.usda.gov. -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 - 20140822 -PL - England -TA - BMC Genomics -JT - BMC genomics -JID - 100965258 -RN - 0 (Transcription Factors) -SB - IM -MH - Binding Sites -MH - Gene Expression Profiling -MH - Gene Expression Regulation, Plant -MH - Homeostasis -MH - *Iron Deficiencies -MH - Multigene Family -MH - Plant Diseases/*genetics -MH - Plant Leaves/*genetics/metabolism -MH - Plant Roots/*genetics/metabolism -MH - Protein Binding -MH - *Signal Transduction -MH - Soybeans/*genetics/*metabolism -MH - Stress, Physiological -MH - Time Factors -MH - Transcription Factors/genetics/metabolism -PMC - PMC4161901 -EDAT- 2014/08/26 06:00 -MHDA- 2015/05/29 06:00 -CRDT- 2014/08/24 06:00 -PHST- 2014/05/14 00:00 [received] -PHST- 2014/08/12 00:00 [accepted] -PHST- 2014/08/24 06:00 [entrez] -PHST- 2014/08/26 06:00 [pubmed] -PHST- 2015/05/29 06:00 [medline] -AID - 1471-2164-15-702 [pii] -AID - 6420 [pii] -AID - 10.1186/1471-2164-15-702 [doi] -PST - epublish -SO - BMC Genomics. 2014 Aug 22;15:702. doi: 10.1186/1471-2164-15-702. - - -##### PUB RECORD ##### -## 10.1371/journal.pone.0111959 25369033 PMC4219821 Zabala, Vodkin, et al., 2014 "Zabala G, Vodkin LO. Methylation affects transposition and splicing of a large CACTA transposon from a MYB transcription factor regulating anthocyanin synthase genes in soybean seed coats. PLoS One. 2014 Nov 4;9(11):e111959. doi: 10.1371/journal.pone.0111959. PMID: 25369033; PMCID: PMC4219821." ## - -PMID- 25369033 -OWN - NLM -STAT- MEDLINE -DCOM- 20151224 -LR - 20181113 -IS - 1932-6203 (Electronic) -IS - 1932-6203 (Linking) -VI - 9 -IP - 11 -DP - 2014 -TI - Methylation affects transposition and splicing of a large CACTA transposon from a - MYB transcription factor regulating anthocyanin synthase genes in soybean seed - coats. -PG - e111959 -LID - 10.1371/journal.pone.0111959 [doi] -LID - e111959 -AB - We determined the molecular basis of three soybean lines that vary in seed coat - color at the R locus which is thought to encode a MYB transcription factor. - RM55-r(m) is homozygous for a mutable allele (r(m)) that specifies black and - brown striped seeds; RM30-R* is a stable black revertant isoline derived from the - mutable line; and RM38-r has brown seed coats due to a recessive r allele shown - to translate a truncated MYB protein. Using long range PCR, 454 sequencing of - amplicons, and whole genome re-sequencing, we determined that the variegated - RM55-r(m) line had a 13 kb CACTA subfamily transposon insertion (designated - TgmR*) at a position 110 bp from the beginning of Intron2 of the R locus, - Glyma09g36983. Although the MYB encoded by R was expressed at only very low - levels in older seed coats of the black revertant RM30-R* line, it upregulated - expression of anthocyanidin synthase genes (ANS2, ANS3) to promote the synthesis - of anthocyanins. Surprisingly, the RM30-R* revertant also carried the 13 kb TgmR* - insertion in Intron2. Using RNA-Seq, we showed that intron splicing was accurate, - albeit at lower levels, despite the presence of the 13 kb TgmR* element. As - determined by whole genome methylation sequencing, we demonstrate that the TgmR* - sequence was relatively more methylated in RM30-R* than in the mutable RM55-r(m) - progenitor line. The stabilized and more methylated RM30-R* revertant line - apparently lacks effective binding of a transposae to its subterminal repeats, - thus allowing intron splicing to proceed resulting in sufficient MYB protein to - stimulate anthocyanin production and thus black seed coats. In this regard, the - TgmR* element in soybean resembles McClintock's Spm-suppressible and - change-of-state alleles of maize. This comparison explains the opposite effects - of the TgmR* element on intron splicing of the MYB gene in which it resides - depending on the methylation state of the element. -FAU - Zabala, Gracia -AU - Zabala G -AD - Department of Crop Sciences, University of Illinois, Urbana, Illinois, United - States of America. -FAU - Vodkin, Lila O -AU - Vodkin LO -AD - Department of Crop Sciences, University of Illinois, Urbana, Illinois, United - States of America. -LA - eng -SI - GENBANK/KM077446 -SI - GEO/GSE60593 -SI - GEO/GSE61116 -PT - Journal Article -PT - Research Support, Non-U.S. Gov't -PT - Research Support, U.S. Gov't, Non-P.H.S. -DEP - 20141104 -PL - United States -TA - PLoS One -JT - PloS one -JID - 101285081 -RN - 0 (DNA Transposable Elements) -RN - 0 (Oncogene Proteins v-myb) -RN - 0 (Plant Proteins) -RN - EC 1.13.- (Oxygenases) -RN - EC 1.14.99.- (anthocyanidin synthase) -SB - IM -MH - Alternative Splicing -MH - Amino Acid Sequence -MH - Base Sequence -MH - DNA Methylation -MH - *DNA Transposable Elements -MH - Gene Expression -MH - Genetic Loci -MH - Metabolic Networks and Pathways -MH - Molecular Sequence Data -MH - Oncogene Proteins v-myb/*physiology -MH - Oxygenases/*genetics/metabolism -MH - Plant Proteins/*genetics/metabolism -MH - Seeds/enzymology/*genetics -MH - Sequence Analysis, DNA -MH - Soybeans/enzymology/*genetics -MH - Translocation, Genetic -PMC - PMC4219821 -COIS- Competing Interests: United Soybean Board and the Illinois Soybean Association - provided funding towards this study. There are no patents, products in - development or marketed products to declare. This does not alter the authors' - adherence to all the PLOS ONE policies on sharing data and materials. -EDAT- 2014/11/05 06:00 -MHDA- 2015/12/25 06:00 -CRDT- 2014/11/05 06:00 -PHST- 2014/08/01 00:00 [received] -PHST- 2014/10/07 00:00 [accepted] -PHST- 2014/11/05 06:00 [entrez] -PHST- 2014/11/05 06:00 [pubmed] -PHST- 2015/12/25 06:00 [medline] -AID - PONE-D-14-34662 [pii] -AID - 10.1371/journal.pone.0111959 [doi] -PST - epublish -SO - PLoS One. 2014 Nov 4;9(11):e111959. doi: 10.1371/journal.pone.0111959. - eCollection 2014. - - -##### PUB RECORD ##### -## 10.1007/s00122-007-0621-2 17701395 null Yuan, Zhao, et al., 2007 "Yuan FJ, Zhao HJ, Ren XL, Zhu SL, Fu XJ, Shu QY. Generation and characterization of two novel low phytate mutations in soybean (Glycine max L. Merr.). Theor Appl Genet. 2007 Nov;115(7):945-57. doi: 10.1007/s00122-007-0621-2. Epub 2007 Aug 16. PMID: 17701395." ## - -PMID- 17701395 -OWN - NLM -STAT- MEDLINE -DCOM- 20080116 -LR - 20220716 -IS - 0040-5752 (Print) -IS - 0040-5752 (Linking) -VI - 115 -IP - 7 -DP - 2007 Nov -TI - Generation and characterization of two novel low phytate mutations in soybean - (Glycine max L. Merr.). -PG - 945-57 -AB - Phytic acid (PA, myo-inositol 1, 2, 3, 4, 5, 6 hexakisphosphate) is important to - the nutritional quality of soybean meal. Organic phosphorus (P) in PA is - indigestible in humans and non-ruminant animals, which affects nutrition and - causes P pollution of ground water from animal wastes. Two novel soybean - [(Glycine max L. (Merr.)] low phytic acid (lpa) mutations were isolated and - characterized. Gm-lpa-TW-1 had a phytic acid P (PA-P) reduction of 66.6% and a - sixfold increase in inorganic P (Pi), and Gm-lpa-ZC-2 had a PA-P reduction of - 46.3% and a 1.4-fold increase in Pi, compared with their respective non-mutant - progenitor lines. The reduction of PA-P and increase of Pi in Gm-lpa-TW-1 were - molar equivalent; the decrease of PA-P in Gm-lpa-ZC-2, however, was accompanied - by the increase of both Pi and lower inositol phosphates. In both mutant lines, - the total P content remained similar to their wild type parents. The two lpa - mutations were both inherited in a single recessive gene model but were - non-allelic. Sequence data and progeny analysis indicate that Gm-lpa-TW-1 lpa - mutation resulted from a 2 bp deletion in the soybean D: -myo-inositol - 3-phosphate synthase (MIPS1 EC 5.5.1.4) gene 1 (MIPS1). The lpa mutation in - Gm-lpa-ZC-2 was mapped on LG B2, closely linked with microsatellite loci Satt416 - and Satt168, at genetic distances of approximately 4.63 and approximately 9.25 - cM, respectively. Thus this mutation probably represents a novel soybean lpa - locus. The seed emergence rate of Gm-lpa-ZC-2 was similar to its progenitor line - and was not affected by seed source and its lpa mutation. However, Gm-lpa-TW-1 - had a significantly reduced field emergence when seeds were produced in a - subtropic environment. Field tests of the mutants and their progenies further - demonstrated that the lpa mutation in Gm-lpa-ZC-2 does not negatively affect - plant yield traits. These results will advance understanding of the genetic, - biochemical and molecular control of PA synthesis in soybean. The novel lpa - mutation in Gm-lpa-ZC-2, together with linked simple sequence repeat (SSR) - markers, will be of value for breeding productive lpa soybeans, with meal high in - digestible Pi eventually to improve animal nutrition and lessen environmental - pollution. -FAU - Yuan, Feng-Jie -AU - Yuan FJ -AD - IAEA-Zhejiang University Collaborating Center, Institute of Nuclear Agricultural - Sciences, Zhejiang University, Hangzhou, 310029, China. -FAU - Zhao, Hai-Jun -AU - Zhao HJ -FAU - Ren, Xue-Liang -AU - Ren XL -FAU - Zhu, Shen-Long -AU - Zhu SL -FAU - Fu, Xu-Jun -AU - Fu XJ -FAU - Shu, Qing-Yao -AU - Shu QY -LA - eng -PT - Journal Article -DEP - 20070816 -PL - Germany -TA - Theor Appl Genet -JT - TAG. Theoretical and applied genetics. Theoretische und angewandte Genetik -JID - 0145600 -RN - 7IGF0S7R8I (Phytic Acid) -SB - IM -MH - *Mutation -MH - Phytic Acid/chemistry/*metabolism -MH - Seeds/chemistry/genetics/metabolism -MH - Soybeans/chemistry/*genetics/metabolism -EDAT- 2007/08/19 09:00 -MHDA- 2008/01/17 09:00 -CRDT- 2007/08/19 09:00 -PHST- 2006/12/06 00:00 [received] -PHST- 2007/07/20 00:00 [accepted] -PHST- 2007/08/19 09:00 [pubmed] -PHST- 2008/01/17 09:00 [medline] -PHST- 2007/08/19 09:00 [entrez] -AID - 10.1007/s00122-007-0621-2 [doi] -PST - ppublish -SO - Theor Appl Genet. 2007 Nov;115(7):945-57. doi: 10.1007/s00122-007-0621-2. Epub - 2007 Aug 16. - - -##### PUB RECORD ##### -## 10.1007/s00122-015-2575-0 26179337 PMC4624830 Qiu, Vuong, et al., 2015 "Qiu D, Vuong T, Valliyodan B, Shi H, Guo B, Shannon JG, Nguyen HT. Identification and characterization of a stachyose synthase gene controlling reduced stachyose content in soybean. Theor Appl Genet. 2015 Nov;128(11):2167-76. doi: 10.1007/s00122-015-2575-0. Epub 2015 Jul 16. PMID: 26179337; PMCID: PMC4624830." ## - -PMID- 26179337 -OWN - NLM -STAT- MEDLINE -DCOM- 20160224 -LR - 20181113 -IS - 1432-2242 (Electronic) -IS - 0040-5752 (Print) -IS - 0040-5752 (Linking) -VI - 128 -IP - 11 -DP - 2015 Nov -TI - Identification and characterization of a stachyose synthase gene controlling - reduced stachyose content in soybean. -PG - 2167-76 -LID - 10.1007/s00122-015-2575-0 [doi] -AB - We identified and characterized a mutant of soybean stachyose synthase gene - controlling reduced stachyose content which benefit the soybean seed composition - breeding program in the future. It has been shown that in soybean, increased - sucrose and reduced raffinose family oligosaccharides would have a positive - impact on the world's feed industry by improving digestibility and feed - efficiency. We searched for new sources of modified oligosaccharide content in a - subset of the USDA Soybean Germplasm Collection and then identified plant - introduction (PI) 603176A as having ultra-low stachyose content (0.5%). We - identified a 33-bp deletion mutant in the putative stachyose synthase gene (STS - gene, Glyma19g40550) of PI 603176A. A co-dominate indel marker was successfully - developed from this 33-bp deletion area and was genetically mapped into two F 2:3 - populations and a F 4:5 population, which associated with low stachyose content - in the progeny lines. These observations provided strong evidence that the STS - gene is responsible for stachyose biosynthesis in the soybean plant. Expression - of the sts gene remained at the normal level, suggesting the loss of function in - the gene is due to defective protein function. This gene-based perfect genetic - marker for low stachyose content can be useful for marker-assisted selection in - soybean molecular breeding programs. -FAU - Qiu, Dan -AU - Qiu D -AD - Division of Plant Sciences, National Center for Soybean Biotechnology (NCSB), - University of Missouri, Columbia, MO, 65211, USA. -FAU - Vuong, Tri -AU - Vuong T -AD - Division of Plant Sciences, National Center for Soybean Biotechnology (NCSB), - University of Missouri, Columbia, MO, 65211, USA. -FAU - Valliyodan, Babu -AU - Valliyodan B -AD - Division of Plant Sciences, National Center for Soybean Biotechnology (NCSB), - University of Missouri, Columbia, MO, 65211, USA. -FAU - Shi, Haiying -AU - Shi H -AD - Division of Plant Sciences, National Center for Soybean Biotechnology (NCSB), - University of Missouri, Columbia, MO, 65211, USA. -FAU - Guo, Binhui -AU - Guo B -AD - Division of Plant Sciences, National Center for Soybean Biotechnology (NCSB), - University of Missouri, Columbia, MO, 65211, USA. -FAU - Shannon, J Grover -AU - Shannon JG -AD - Division of Plant Sciences and NCSB, University of Missouri, Portageville, MO, - 63873, USA. -FAU - Nguyen, Henry T -AU - Nguyen HT -AD - Division of Plant Sciences, National Center for Soybean Biotechnology (NCSB), - University of Missouri, Columbia, MO, 65211, USA. nguyenhenry@missouri.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 - 20150716 -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 (Oligosaccharides) -RN - 0 (Plant Proteins) -RN - 25VX64653N (stachyose) -RN - EC 2.4.1.- (Galactosyltransferases) -RN - EC 2.4.1.67 (galactinol -raffinose galactosyltransferase) -RN - N5O3QU595M (Raffinose) -SB - IM -MH - Chromosome Mapping -MH - DNA, Plant/genetics -MH - Galactosyltransferases/*genetics -MH - Genetic Markers -MH - INDEL Mutation -MH - Oligosaccharides/*chemistry -MH - Plant Breeding -MH - Plant Proteins/*genetics -MH - Raffinose/chemistry -MH - Seeds/chemistry -MH - Sequence Analysis, DNA -MH - Sequence Deletion -MH - Soybeans/enzymology/*genetics -PMC - PMC4624830 -EDAT- 2015/07/17 06:00 -MHDA- 2016/02/26 06:00 -CRDT- 2015/07/17 06:00 -PHST- 2015/01/26 00:00 [received] -PHST- 2015/06/27 00:00 [accepted] -PHST- 2015/07/17 06:00 [entrez] -PHST- 2015/07/17 06:00 [pubmed] -PHST- 2016/02/26 06:00 [medline] -AID - 10.1007/s00122-015-2575-0 [pii] -AID - 2575 [pii] -AID - 10.1007/s00122-015-2575-0 [doi] -PST - ppublish -SO - Theor Appl Genet. 2015 Nov;128(11):2167-76. doi: 10.1007/s00122-015-2575-0. Epub - 2015 Jul 16. - - -##### PUB RECORD ##### -## 10.3390/ijms23084116 35456933 PMC9030070 Qian, Jin, et al., 2022 "Qian L, Jin H, Yang Q, Zhu L, Yu X, Fu X, Zhao M, Yuan F. A Sequence Variation in GmBADH2 Enhances Soybean Aroma and Is a Functional Marker for Improving Soybean Flavor. Int J Mol Sci. 2022 Apr 8;23(8):4116. doi: 10.3390/ijms23084116. PMID: 35456933; PMCID: PMC9030070." ## - -PMID- 35456933 -OWN - NLM -STAT- MEDLINE -DCOM- 20220426 -LR - 20220716 -IS - 1422-0067 (Electronic) -IS - 1422-0067 (Linking) -VI - 23 -IP - 8 -DP - 2022 Apr 8 -TI - A Sequence Variation in GmBADH2 Enhances Soybean Aroma and Is a Functional Marker - for Improving Soybean Flavor. -LID - 10.3390/ijms23084116 [doi] -LID - 4116 -AB - The vegetable soybean (Glycine max L. Merr.) plant is commonly consumed in - Southeast Asian countries because of its nutritional value and desirable taste. A - "pandan-like" aroma is an important value-added quality trait that is rarely - found in commercial vegetable soybean varieties. In this study, three novel - aromatic soybean cultivars with a fragrant volatile compound were isolated. We - confirmed that the aroma of these cultivars is due to the potent volatile - compound 2-acetyl-1-pyrroline (2AP) that was previously identified in soybean. A - sequence comparison of GmBADH1/2 (encoding an aminoaldehyde dehydrogenase) - between aromatic and non-aromatic soybean varieties revealed a mutation with 10 - SNPs and an 11-nucleotide deletion in exon 1 of GmBADH2 in Quxian No. 1 and - Xiangdou. Additionally, a 2-bp deletion was detected in exon 10 of GmBADH2 in - ZK1754. The mutations resulted in a frame shift and the introduction of premature - stop codons. Moreover, genetic analyses indicated that the aromatic trait in - these three varieties was inherited according to a single recessive gene model. - These results suggested that a mutated GmBADH2 may be responsible for the aroma - of these three aromatic soybean cultivars. The expression and function of GmBADH2 - in aromatic soybean seeds were confirmed by qRT-PCR and CRISPR/Cas9. A functional - marker developed on the basis of the mutated GmBADH2 sequence in Quxian No. 1 and - Xiangdou was validated in an F(2) population. A perfect association between the - marker genotypes and aroma phenotypes implied that GmBADH2 is a major - aroma-conferring gene. The results of this study are potentially useful for an - in-depth analysis of the molecular basis of 2-AP formation in soybean and the - marker-assisted breeding of aromatic vegetable soybean cultivars. -FAU - Qian, Linlin -AU - Qian L -AD - Hangzhou Sub-Center of National Soybean Improvement, Institute of Crop and - Nuclear Technology Utilization, Zhejiang Academy of Agricultural Sciences, - Hangzhou 310021, China. -AD - Key Laboratory of Information Traceability for Agricultural Products, Ministry of - Agriculture and Rural Affairs of China, Hangzhou 310021, China. -AD - The National and Local Joint Engineering Research Center for Bio-Manufacturing of - Chiral Chemicals, College of Biotechnology and Bioengineering, Zhejiang - University of Technology, Hangzhou 310014, China. -FAU - Jin, Hangxia -AU - Jin H -AD - Hangzhou Sub-Center of National Soybean Improvement, Institute of Crop and - Nuclear Technology Utilization, Zhejiang Academy of Agricultural Sciences, - Hangzhou 310021, China. -AD - Zhejiang Key Laboratory of Digital Dry Land Crops, Zhejiang Academy of - Agricultural Sciences, Hangzhou 310021, China. -FAU - Yang, Qinghua -AU - Yang Q -AD - Hangzhou Sub-Center of National Soybean Improvement, Institute of Crop and - Nuclear Technology Utilization, Zhejiang Academy of Agricultural Sciences, - Hangzhou 310021, China. -AD - Key Laboratory of Information Traceability for Agricultural Products, Ministry of - Agriculture and Rural Affairs of China, Hangzhou 310021, China. -AD - Zhejiang Key Laboratory of Digital Dry Land Crops, Zhejiang Academy of - Agricultural Sciences, Hangzhou 310021, China. -FAU - Zhu, Longming -AU - Zhu L -AD - Hangzhou Sub-Center of National Soybean Improvement, Institute of Crop and - Nuclear Technology Utilization, Zhejiang Academy of Agricultural Sciences, - Hangzhou 310021, China. -AD - Zhejiang Key Laboratory of Digital Dry Land Crops, Zhejiang Academy of - Agricultural Sciences, Hangzhou 310021, China. -FAU - Yu, Xiaomin -AU - Yu X -AUID- ORCID: 0000-0003-2530-2809 -AD - Hangzhou Sub-Center of National Soybean Improvement, Institute of Crop and - Nuclear Technology Utilization, Zhejiang Academy of Agricultural Sciences, - Hangzhou 310021, China. -AD - Zhejiang Key Laboratory of Digital Dry Land Crops, Zhejiang Academy of - Agricultural Sciences, Hangzhou 310021, China. -FAU - Fu, Xujun -AU - Fu X -AD - Hangzhou Sub-Center of National Soybean Improvement, Institute of Crop and - Nuclear Technology Utilization, Zhejiang Academy of Agricultural Sciences, - Hangzhou 310021, China. -AD - Zhejiang Key Laboratory of Digital Dry Land Crops, Zhejiang Academy of - Agricultural Sciences, Hangzhou 310021, China. -FAU - Zhao, Man -AU - Zhao M -AUID- ORCID: 0000-0003-2631-1977 -AD - The National and Local Joint Engineering Research Center for Bio-Manufacturing of - Chiral Chemicals, College of Biotechnology and Bioengineering, Zhejiang - University of Technology, Hangzhou 310014, China. -FAU - Yuan, Fengjie -AU - Yuan F -AD - Hangzhou Sub-Center of National Soybean Improvement, Institute of Crop and - Nuclear Technology Utilization, Zhejiang Academy of Agricultural Sciences, - Hangzhou 310021, China. -AD - Zhejiang Key Laboratory of Digital Dry Land Crops, Zhejiang Academy of - Agricultural Sciences, Hangzhou 310021, China. -LA - eng -GR - 2021C02064-5/Major Science and Technology Special Program for Crop Breeding in - Zhejiang of China/ -PT - Journal Article -DEP - 20220408 -PL - Switzerland -TA - Int J Mol Sci -JT - International journal of molecular sciences -JID - 101092791 -SB - IM -MH - Genotype -MH - *Odorants/analysis -MH - Phenotype -MH - Plant Breeding -MH - *Soybeans/genetics/metabolism -PMC - PMC9030070 -OTO - NOTNLM -OT - CRISPR/Cas9 gene editing -OT - HRM molecular marker -OT - aromatic vegetable soybean -OT - gene sequence comparison -OT - soybean breeding -COIS- The authors have no relevant financial or non-financial interest to disclose. -EDAT- 2022/04/24 06:00 -MHDA- 2022/04/27 06:00 -CRDT- 2022/04/23 01:10 -PHST- 2022/01/07 00:00 [received] -PHST- 2022/03/25 00:00 [revised] -PHST- 2022/04/03 00:00 [accepted] -PHST- 2022/04/23 01:10 [entrez] -PHST- 2022/04/24 06:00 [pubmed] -PHST- 2022/04/27 06:00 [medline] -AID - ijms23084116 [pii] -AID - ijms-23-04116 [pii] -AID - 10.3390/ijms23084116 [doi] -PST - epublish -SO - Int J Mol Sci. 2022 Apr 8;23(8):4116. doi: 10.3390/ijms23084116. - - -##### PUB RECORD ##### -## 10.1371/journal.pone.0097891 24846334 PMC4028252 Carrero-Colón, 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." ## - -PMID- 24846334 -OWN - NLM -STAT- MEDLINE -DCOM- 20150115 -LR - 20211021 -IS - 1932-6203 (Electronic) -IS - 1932-6203 (Linking) -VI - 9 -IP - 5 -DP - 2014 -TI - Mutations in SACPD-C result in a range of elevated stearic acid concentration in - soybean seed. -PG - e97891 -LID - 10.1371/journal.pone.0097891 [doi] -LID - e97891 -AB - Soybean oil has a wide variety of uses, and stearic acid, which is a relatively - minor component of soybean oil is increasingly desired for both industrial and - food applications. New soybean mutants containing high levels of the saturated - fatty acid stearate in seeds were recently identified from a chemically - mutagenized population. Six mutants ranged in stearate content from 6-14% stearic - acid, which is 1.5 to 3 times the levels contained in wild-type seed of the - Williams 82 cultivar. Candidate gene sequencing revealed that all of these lines - carried amino acid substitutions in the gene encoding the - delta-9-stearoyl-acyl-carrier protein desaturase enzyme (SACPD-C) required for - the conversion of stearic acid to oleic acid. Five of these missense mutations - were in highly conserved residues clustered around the predicted di-iron center - of the SACPD-C enzyme. Co-segregation analysis demonstrated a positive - association of the elevated stearate trait with the SACPD-C mutation for three - populations. These missense mutations may provide additional alleles that may be - used in the development of new soybean cultivars with increased levels of stearic - acid. -FAU - Carrero-Colon, Militza -AU - Carrero-Colon M -AD - Crop Production and Pest Control Research Unit, Agricultural Research Service - (ARS), United States Department of Agriculture (USDA), West Lafayette, Indiana, - United States of America. -FAU - Abshire, Nathan -AU - Abshire N -AD - Department of Agronomy, Purdue University, West Lafayette, Indiana, United States - of America. -FAU - Sweeney, Daniel -AU - Sweeney D -AD - Department of Agronomy, Purdue University, West Lafayette, Indiana, United States - of America. -FAU - Gaskin, Erik -AU - Gaskin E -AD - Department of Agronomy, Purdue University, West Lafayette, Indiana, United States - of America. -FAU - Hudson, Karen -AU - Hudson K -AD - Crop Production and Pest Control Research Unit, Agricultural Research Service - (ARS), United States Department of Agriculture (USDA), West Lafayette, Indiana, - United States of America. -LA - eng -SI - GENBANK/KJ522450 -SI - GENBANK/KJ522451 -SI - GENBANK/KJ522452 -SI - GENBANK/KJ522453 -SI - GENBANK/KJ522454 -SI - GENBANK/KJ522455 -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 (Fatty Acids) -RN - 0 (Stearic Acids) -RN - 4ELV7Z65AP (stearic acid) -RN - EC 1.- (Mixed Function Oxygenases) -RN - EC 1.14.19.2 (acyl-(acyl-carrier-protein)desaturase) -SB - IM -MH - Amino Acid Sequence -MH - Fatty Acids/metabolism -MH - Genotype -MH - Mixed Function Oxygenases/chemistry/*genetics -MH - Molecular Sequence Data -MH - *Mutation -MH - Phenotype -MH - Seeds/*genetics/*metabolism -MH - Sequence Alignment -MH - Soybeans/*genetics/*metabolism -MH - Stearic Acids/*metabolism -PMC - PMC4028252 -COIS- Competing Interests: The authors have declared that no competing interests exist. -EDAT- 2014/05/23 06:00 -MHDA- 2015/01/16 06:00 -CRDT- 2014/05/22 06:00 -PHST- 2013/11/07 00:00 [received] -PHST- 2014/04/24 00:00 [accepted] -PHST- 2014/05/22 06:00 [entrez] -PHST- 2014/05/23 06:00 [pubmed] -PHST- 2015/01/16 06:00 [medline] -AID - PONE-D-13-46353 [pii] -AID - 10.1371/journal.pone.0097891 [doi] -PST - epublish -SO - PLoS One. 2014 May 20;9(5):e97891. doi: 10.1371/journal.pone.0097891. eCollection - 2014. - - -##### PUB RECORD ##### -## 10.1073/pnas.1708508116 31676549 PMC6876155 Li, Cao, et al., 2019 "" ## - -PMID- 31676549 -OWN - NLM -STAT- MEDLINE -DCOM- 20200402 -LR - 20200402 -IS - 1091-6490 (Electronic) -IS - 0027-8424 (Print) -IS - 0027-8424 (Linking) -VI - 116 -IP - 47 -DP - 2019 Nov 19 -TI - Comprehensive mapping of abiotic stress inputs into the soybean circadian clock. -PG - 23840-23849 -LID - 10.1073/pnas.1708508116 [doi] -AB - The plant circadian clock evolved to increase fitness by synchronizing - physiological processes with environmental oscillations. Crop fitness was - artificially selected through domestication and breeding, and the circadian clock - was identified by both natural and artificial selections as a key to improved - fitness. Despite progress in Arabidopsis, our understanding of the crop circadian - clock is still limited, impeding its rational improvement for enhanced fitness. - To unveil the interactions between the crop circadian clock and various - environmental cues, we comprehensively mapped abiotic stress inputs to the - soybean circadian clock using a 2-module discovery pipeline. Using the "molecular - timetable" method, we computationally surveyed publicly available abiotic - stress-related soybean transcriptomes to identify stresses that have strong - impacts on the global rhythm. These findings were then experimentally confirmed - using a multiplexed RNA sequencing technology. Specific clock components - modulated by each stress were further identified. This comprehensive mapping - uncovered inputs to the plant circadian clock such as alkaline stress. Moreover, - short-term iron deficiency targeted different clock components in soybean and - Arabidopsis and thus had opposite effects on the clocks of these 2 species. - Comparing soybean varieties with different iron uptake efficiencies suggests that - phase modulation might be a mechanism to alleviate iron deficiency symptoms in - soybean. These unique responses in soybean demonstrate the need to directly study - crop circadian clocks. Our discovery pipeline may serve as a broadly applicable - tool to facilitate these explorations. -CI - Copyright (c) 2019 the Author(s). Published by PNAS. -FAU - Li, Meina -AU - Li M -AD - School of Life Sciences, Guangzhou University, 510006 Guangzhou, China. -AD - Department of Plant Pathology and Microbiology, Iowa State University, Ames, IA - 50011. -FAU - Cao, Lijun -AU - Cao L -AD - Department of Plant Pathology and Microbiology, Iowa State University, Ames, IA - 50011. -FAU - Mwimba, Musoki -AU - Mwimba M -AD - Howard Hughes Medical Institute and Gordon and Betty Moore Foundation, Duke - University, Durham, NC 27708. -AD - Department of Biology, Duke University, Durham, NC 27708. -FAU - Zhou, Yan -AU - Zhou Y -AD - Department of Agronomy, Iowa State University, Ames, IA 50011. -FAU - Li, Ling -AU - Li L -AUID- ORCID: 0000-0003-2371-6215 -AD - Department of Biological Sciences, Mississippi State University, Starkville, MS - 39762. -FAU - Zhou, Mian -AU - Zhou M -AD - Department of Plant Pathology and Microbiology, Iowa State University, Ames, IA - 50011. -AD - College of Life Sciences, Capital Normal University, 100048 Beijing, China. -FAU - Schnable, Patrick S -AU - Schnable PS -AUID- ORCID: 0000-0001-9169-5204 -AD - Department of Agronomy, Iowa State University, Ames, IA 50011. -FAU - O'Rourke, Jamie A -AU - O'Rourke JA -AUID- ORCID: 0000-0003-2403-8946 -AD - Department of Agronomy, Iowa State University, Ames, IA 50011. -AD - Corn Insects and Crop Genetics Research Unit, Agricultural Research Service, US - Department of Agriculture, Ames, IA 50011. -FAU - Dong, Xinnian -AU - Dong X -AUID- ORCID: 0000-0002-1120-0951 -AD - Howard Hughes Medical Institute and Gordon and Betty Moore Foundation, Duke - University, Durham, NC 27708; xdong@duke.edu oneway1985@pku.edu.cn. -AD - Department of Biology, Duke University, Durham, NC 27708. -FAU - Wang, Wei -AU - Wang W -AD - Department of Plant Pathology and Microbiology, Iowa State University, Ames, IA - 50011; xdong@duke.edu oneway1985@pku.edu.cn. -AD - State Key Laboratory for Protein and Plant Gene Research, School of Life - Sciences, Peking University, 100871 Beijing, China. -AD - Peking-Tsinghua Center for Life Sciences, 100871 Beijing, China. -LA - eng -GR - R35 GM118036/GM/NIGMS NIH HHS/United States -GR - HHMI/Howard Hughes Medical Institute/United States -PT - Journal Article -PT - Research Support, N.I.H., Extramural -PT - Research Support, Non-U.S. Gov't -PT - Research Support, U.S. Gov't, Non-P.H.S. -DEP - 20191101 -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 -SB - IM -MH - Arabidopsis/genetics/physiology -MH - *Circadian Clocks/genetics -MH - Genes, Plant -MH - Plant Leaves/physiology -MH - Soybeans/genetics/*physiology -MH - *Stress, Physiological -PMC - PMC6876155 -OTO - NOTNLM -OT - RASL-seq -OT - abiotic stress -OT - comprehensive map -OT - molecular timetable -OT - soybean circadian clock -COIS- The authors declare no competing interest. -EDAT- 2019/11/05 06:00 -MHDA- 2020/04/03 06:00 -CRDT- 2019/11/03 06:00 -PHST- 2019/11/05 06:00 [pubmed] -PHST- 2020/04/03 06:00 [medline] -PHST- 2019/11/03 06:00 [entrez] -AID - 1708508116 [pii] -AID - 201708508 [pii] -AID - 10.1073/pnas.1708508116 [doi] -PST - ppublish -SO - Proc Natl Acad Sci U S A. 2019 Nov 19;116(47):23840-23849. doi: - 10.1073/pnas.1708508116. Epub 2019 Nov 1. - - -##### PUB RECORD ##### -## 10.1371/journal.pone.0054154 23342093 PMC3546919 Cheng, Wang, et al., 2013 "" ## - -PMID- 23342093 -OWN - NLM -STAT- MEDLINE -DCOM- 20130802 -LR - 20220331 -IS - 1932-6203 (Electronic) -IS - 1932-6203 (Linking) -VI - 8 -IP - 1 -DP - 2013 -TI - Diversifying selection on flavanone 3-hydroxylase and isoflavone synthase genes - in cultivated soybean and its wild progenitors. -PG - e54154 -LID - 10.1371/journal.pone.0054154 [doi] -LID - e54154 -AB - Soybean isoflavone synthase (IFS) and flavanone 3-hydroxylase (F3H) are two key - enzymes catalyzing the biosynthesis of isoflavonoids and flavonoids, both of - which play diverse roles in stress responses. However, little is known about the - evolutionary pattern of these genes in cultivated soybean and its wild - progenitors. Herein, we investigated the nucleotide polymorphisms in Isoflavone - synthase (IFS1, IFS2) and Flavanone 3-hydroxylase (F3H2) genes from 33 soybean - accessions, including 17 cultivars (Glycine max) and 16 their wild progenitors - (Glycine soja). Our data showed that the target genes shared the levels of - nucleotide polymorphism with three reference genes involved in plant-microbe - interactions, but possessed a much higher nucleotide polymorphism than other - reference genes. Moreover, no significant genetic differentiation was found - between cultivated soybean and its wild relatives in three target genes, despite - of considering bottleneck and founder effect during domestication. These results - indicate that IFS and F3H genes could have experienced gene introgressions or - diversifying selection events during domestication process. Especially, F3H2 gene - appears to evolve under positive selection and enjoy a faster evolutionary rate - than IFS1 and IFS2 genes. -FAU - Cheng, Hao -AU - Cheng H -AD - National Center for Soybean Improvement, National Key Laboratory of Crop Genetics - and Germplasm Enhancement, Nanjing Agricultural University, Nanjing, China. -FAU - Wang, Jiao -AU - Wang J -FAU - Chu, Shanshan -AU - Chu S -FAU - Yan, Hong-Lang -AU - Yan HL -FAU - Yu, Deyue -AU - Yu D -LA - eng -PT - Journal Article -PT - Research Support, Non-U.S. Gov't -DEP - 20130116 -PL - United States -TA - PLoS One -JT - PloS one -JID - 101285081 -RN - 0 (Plant Proteins) -RN - EC 1.- (Mixed Function Oxygenases) -RN - EC 1.13.- (Oxygenases) -RN - EC 1.14.11.9 (flavanone 3-dioxygenase) -RN - EC 1.14.13.- (isoflavone synthase) -SB - IM -MH - Mixed Function Oxygenases/classification/*genetics -MH - Oxygenases/classification/*genetics -MH - Phylogeny -MH - Plant Proteins/classification/*genetics -MH - Polymorphism, Genetic/genetics -MH - Soybeans/*enzymology/genetics -PMC - PMC3546919 -COIS- Competing Interests: The authors have declared that no competing interests exist. -EDAT- 2013/01/24 06:00 -MHDA- 2013/08/03 06:00 -CRDT- 2013/01/24 06:00 -PHST- 2012/07/09 00:00 [received] -PHST- 2012/12/07 00:00 [accepted] -PHST- 2013/01/24 06:00 [entrez] -PHST- 2013/01/24 06:00 [pubmed] -PHST- 2013/08/03 06:00 [medline] -AID - PONE-D-12-19957 [pii] -AID - 10.1371/journal.pone.0054154 [doi] -PST - ppublish -SO - PLoS One. 2013;8(1):e54154. doi: 10.1371/journal.pone.0054154. Epub 2013 Jan 16. - - -##### PUB RECORD ##### -## 10.1073/pnas.1117982109 22619331 PMC3420212 Xia, Watanabe, et al., 2012 "" ## - -PMID- 22619331 -OWN - NLM -STAT- MEDLINE -DCOM- 20121015 -LR - 20220408 -IS - 1091-6490 (Electronic) -IS - 0027-8424 (Print) -IS - 0027-8424 (Linking) -VI - 109 -IP - 32 -DP - 2012 Aug 7 -TI - Positional cloning and characterization reveal the molecular basis for soybean - maturity locus E1 that regulates photoperiodic flowering. -PG - E2155-64 -LID - 10.1073/pnas.1117982109 [doi] -AB - The complex and coordinated regulation of flowering has high ecological and - agricultural significance. The maturity locus E1 has a large impact on flowering - time in soybean, but the molecular basis for the E1 locus is largely unknown. - Through positional cloning, we delimited the E1 locus to a 17.4-kb region - containing an intron-free gene (E1). The E1 protein contains a putative bipartite - nuclear localization signal and a region distantly related to B3 domain. In the - recessive allele, a nonsynonymous substitution occurred in the putative nuclear - localization signal, leading to the loss of localization specificity of the E1 - protein and earlier flowering. The early-flowering phenotype was consistently - observed in three ethylmethanesulfonate-induced mutants and two natural mutations - that harbored a premature stop codon or a deletion of the entire E1 gene. E1 - expression was significantly suppressed under short-day conditions and showed a - bimodal diurnal pattern under long-day conditions, suggesting its response to - photoperiod and its dominant effect induced by long day length. When a functional - E1 gene was transformed into the early-flowering cultivar Kariyutaka with low E1 - expression, transgenic plants carrying exogenous E1 displayed late flowering. - Furthermore, the transcript abundance of E1 was negatively correlated with that - of GmFT2a and GmFT5a, homologues of FLOWERING LOCUS T that promote flowering. - These findings demonstrated the key role of E1 in repressing flowering and - delaying maturity in soybean. The molecular identification of the maturity locus - E1 will contribute to our understanding of the molecular mechanisms by which a - short-day plant regulates flowering time and maturity. -FAU - Xia, Zhengjun -AU - Xia Z -AD - Northeast Institute of Geography and Agroecology, Chinese Academy of Sciences, - Harbin 150081, China. xiazhj@neigaehrb.ac.cn -FAU - Watanabe, Satoshi -AU - Watanabe S -FAU - Yamada, Tetsuya -AU - Yamada T -FAU - Tsubokura, Yasutaka -AU - Tsubokura Y -FAU - Nakashima, Hiroko -AU - Nakashima H -FAU - Zhai, Hong -AU - Zhai H -FAU - Anai, Toyoaki -AU - Anai T -FAU - Sato, Shusei -AU - Sato S -FAU - Yamazaki, Toshimasa -AU - Yamazaki T -FAU - Lu, Shixiang -AU - Lu S -FAU - Wu, Hongyan -AU - Wu H -FAU - Tabata, Satoshi -AU - Tabata S -FAU - Harada, Kyuya -AU - Harada K -LA - eng -SI - GENBANK/AB552962 -SI - GENBANK/AB552963 -SI - GENBANK/AB552971 -SI - GENBANK/AP011812 -SI - GENBANK/AP011814 -SI - GENBANK/AP011815 -SI - GENBANK/AP011816 -SI - GENBANK/AP011817 -SI - GENBANK/AP011818 -SI - GENBANK/AP011819 -SI - GENBANK/AP011820 -SI - GENBANK/AP011823 -PT - Journal Article -PT - Research Support, Non-U.S. Gov't -DEP - 20120522 -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 - 9H154DI0UP (Ethyl Methanesulfonate) -SB - IM -MH - Base Sequence -MH - Blotting, Southern -MH - Chromosome Mapping -MH - Chromosomes, Artificial, Bacterial/genetics -MH - Cloning, Molecular -MH - Cluster Analysis -MH - DNA Primers/genetics -MH - Ethyl Methanesulfonate -MH - Flowers/genetics/*physiology -MH - Gene Expression Regulation, Plant/*genetics -MH - Genes, Plant/*genetics -MH - Genetic Loci/*genetics -MH - Genetic Variation -MH - Models, Genetic -MH - Molecular Sequence Data -MH - Mutagenesis -MH - *Photoperiod -MH - Phylogeny -MH - Real-Time Polymerase Chain Reaction -MH - Reverse Transcriptase Polymerase Chain Reaction -MH - Sequence Analysis, DNA -MH - Soybeans/*genetics/*growth & development -PMC - PMC3420212 -COIS- The authors declare no conflict of interest. -EDAT- 2012/05/24 06:00 -MHDA- 2012/10/16 06:00 -CRDT- 2012/05/24 06:00 -PHST- 2012/05/24 06:00 [entrez] -PHST- 2012/05/24 06:00 [pubmed] -PHST- 2012/10/16 06:00 [medline] -AID - 1117982109 [pii] -AID - 201117982 [pii] -AID - 10.1073/pnas.1117982109 [doi] -PST - ppublish -SO - Proc Natl Acad Sci U S A. 2012 Aug 7;109(32):E2155-64. doi: - 10.1073/pnas.1117982109. Epub 2012 May 22. - - -##### PUB RECORD ##### -## 10.1093/jxb/err054 21430294 PMC3130180 Polacco, Hyten, et al., 2011 "" ## - -PMID- 21430294 -OWN - NLM -STAT- MEDLINE -DCOM- 20111027 -LR - 20211020 -IS - 1460-2431 (Electronic) -IS - 0022-0957 (Print) -IS - 0022-0957 (Linking) -VI - 62 -IP - 10 -DP - 2011 Jun -TI - Mutational analysis of the major soybean UreF paralogue involved in urease - activation. -PG - 3599-608 -LID - 10.1093/jxb/err054 [doi] -AB - The soybean genome duplicated approximately 14 and 45 million years ago and has many - paralogous genes, including those in urease activation (emplacement of Ni and - CO(2) in the active site). Activation requires the UreD and UreF proteins, each - encoded by two paralogues. UreG, a third essential activation protein, is encoded - by the single-copy Eu3, and eu3 mutants lack activity of both urease isozymes. - eu2 has the same urease-negative phenotype, consistent with Eu2 being a - single-copy gene, possibly encoding a Ni carrier. Unexpectedly, two eu2 alleles - co-segregated with missense mutations in the chromosome 2 UreF paralogue - (Ch02UreF), suggesting lack of expression/function of Ch14UreF. However, Ch02UreF - and Ch14UreF transcripts accumulate at the same level. Further, it had been shown - that expression of the Ch14UreF ORF complemented a fungal ureF mutant. A third, - nonsense (Q2*) allelic mutant, eu2-c, exhibited 5- to 10-fold more residual - urease activity than missense eu2-a or eu2-b, though eu2-c should lack all - Ch02UreF protein. It is hypothesized that low-level activation by Ch14UreF is - 'spoiled' by the altered missense Ch02UreF proteins ('epistatic - dominant-negative'). In agreement with active 'spoiling' by eu2-b-encoded - Ch02UreF (G31D), eu2-b/eu2-c heterozygotes had less than half the urease activity - of eu2-c/eu2-c siblings. Ch02UreF (G31D) could spoil activation by Chr14UreF - because of higher affinity for the activation complex, or because Ch02UreF (G31D) - is more abundant than Ch14UreF. Here, the latter is favoured, consistent with a - reported in-frame AUG in the 5' leader of Chr14UreF transcript. Translational - inhibition could represent a form of 'functional divergence' of duplicated genes. -FAU - Polacco, Joe C -AU - Polacco JC -AD - Biochemistry Department, 117 Schweitzer Hall, University of Missouri, Columbia, - MO 65211, USA. polaccoj@missouri.edu -FAU - Hyten, David L -AU - Hyten DL -FAU - Medeiros-Silva, Monica -AU - Medeiros-Silva M -FAU - Sleper, David A -AU - Sleper DA -FAU - Bilyeu, Kristin D -AU - Bilyeu KD -LA - eng -PT - Journal Article -PT - Research Support, Non-U.S. Gov't -DEP - 20110323 -PL - England -TA - J Exp Bot -JT - Journal of experimental botany -JID - 9882906 -RN - 0 (Plant Proteins) -RN - 7OV03QG267 (Nickel) -RN - EC 3.5.1.5 (Urease) -SB - IM -MH - DNA Mutational Analysis/*methods -MH - Nickel/metabolism -MH - Phenotype -MH - Plant Leaves/enzymology/genetics/metabolism -MH - Plant Proteins/genetics/metabolism -MH - Polymorphism, Single Nucleotide/genetics -MH - Reverse Transcriptase Polymerase Chain Reaction -MH - Seeds/enzymology/genetics/metabolism -MH - Soybeans/*enzymology/*genetics/metabolism -MH - Urease/genetics/*metabolism -PMC - PMC3130180 -EDAT- 2011/03/25 06:00 -MHDA- 2011/10/28 06:00 -CRDT- 2011/03/25 06:00 -PHST- 2011/03/25 06:00 [entrez] -PHST- 2011/03/25 06:00 [pubmed] -PHST- 2011/10/28 06:00 [medline] -AID - err054 [pii] -AID - 10.1093/jxb/err054 [doi] -PST - ppublish -SO - J Exp Bot. 2011 Jun;62(10):3599-608. doi: 10.1093/jxb/err054. Epub 2011 Mar 23. - - -##### PUB RECORD ##### -## 10.1104/pp.103.2.467 8029334 PMC159005 Yadav, Wierzbicki, et al., 1993 "" ## - -PMID- 8029334 -OWN - NLM -STAT- MEDLINE -DCOM- 19940808 -LR - 20220310 -IS - 0032-0889 (Print) -IS - 1532-2548 (Electronic) -IS - 0032-0889 (Linking) -VI - 103 -IP - 2 -DP - 1993 Oct -TI - Cloning of higher plant omega-3 fatty acid desaturases. -PG - 467-76 -AB - Arabidopsis thaliana T-DNA transformants were screened for mutations affecting - seed fatty acid composition. A mutant line was found with reduced levels of - linolenic acid (18:3) due to a T-DNA insertion. Genomic DNA flanking the T-DNA - insertion was used to obtain an Arabidopsis cDNA that encodes a polypeptide - identified as a microsomal omega-3 fatty acid desaturase by its complementation - of the mutation. Analysis of lipid content in transgenic tissues demonstrated - that this enzyme is limiting for 18:3 production in Arabidopsis seeds and carrot - hairy roots. This cDNA was used to isolate a related Arabidopsis cDNA, whose mRNA - is accumulated to a much higher level in leaf tissue relative to root tissue. - This related cDNA encodes a protein that is a homolog of the microsomal - desaturase but has an N-terminal extension deduced to be a transit peptide, and - its gene maps to a position consistent with that of the Arabidopsis fad D locus, - which controls plastid omega-3 desaturation. These Arabidopsis cDNAs were used as - hybridization probes to isolate cDNAs encoding homologous proteins from - developing seeds of soybean and rapeseed. The high degree of sequence similarity - between these sequences suggests that the omega-3 desaturases use a common enzyme - mechanism. -FAU - Yadav, N S -AU - Yadav NS -AD - Agricultural Products, E. I. duPont de Nemours & Co., Wilmington, Delaware - 19880-0402. -FAU - Wierzbicki, A -AU - Wierzbicki A -FAU - Aegerter, M -AU - Aegerter M -FAU - Caster, C S -AU - Caster CS -FAU - Perez-Grau, L -AU - Perez-Grau L -FAU - Kinney, A J -AU - Kinney AJ -FAU - Hitz, W D -AU - Hitz WD -FAU - Booth, J R Jr -AU - Booth JR Jr -FAU - Schweiger, B -AU - Schweiger B -FAU - Stecca, K L -AU - Stecca KL -AU - et al. -LA - eng -SI - GENBANK/L22931 -SI - GENBANK/L22961 -SI - GENBANK/L22962 -SI - GENBANK/L22963 -SI - GENBANK/L22964 -SI - GENBANK/L22965 -PT - Comparative Study -PT - Journal Article -PT - Research Support, U.S. Gov't, Non-P.H.S. -PL - United States -TA - Plant Physiol -JT - Plant physiology -JID - 0401224 -RN - 0 (DNA, Bacterial) -RN - 0 (DNA, Complementary) -RN - 0 (T-DNA) -RN - EC 1.14.19.- (Fatty Acid Desaturases) -RN - EC 1.14.99.- (omega-3 fatty acid desaturase) -SB - IM -MH - Algorithms -MH - Amino Acid Sequence -MH - Arabidopsis/*enzymology/genetics -MH - Brassica/*enzymology/genetics -MH - Cloning, Molecular -MH - DNA, Bacterial/metabolism -MH - DNA, Complementary/analysis -MH - Fatty Acid Desaturases/*biosynthesis -MH - Gene Conversion -MH - Gene Library -MH - Molecular Sequence Data -MH - *Phylogeny -MH - Restriction Mapping -MH - Sequence Homology, Amino Acid -MH - Soybeans/*enzymology/genetics -MH - Transformation, Genetic -MH - Vegetables/genetics -PMC - PMC159005 -EDAT- 1993/10/01 00:00 -MHDA- 2001/03/28 10:01 -CRDT- 1993/10/01 00:00 -PHST- 1993/10/01 00:00 [pubmed] -PHST- 2001/03/28 10:01 [medline] -PHST- 1993/10/01 00:00 [entrez] -AID - 10.1104/pp.103.2.467 [doi] -PST - ppublish -SO - Plant Physiol. 1993 Oct;103(2):467-76. doi: 10.1104/pp.103.2.467. - - -##### PUB RECORD ##### -## 10.1270/jsbbs.64.371 25914592 PMC4267312 Hoshino, Watanabe, et al., 2014 "Hoshino T, Watanabe S, Takagi Y, Anai T. A novel GmFAD3-2a mutant allele developed through TILLING reduces α-linolenic acid content in soybean seed oil. Breed Sci. 2014 Dec;64(4):371-7. doi: 10.1270/jsbbs.64.371. Epub 2014 Dec 1. PMID: 25914592; PMCID: PMC4267312." ## - -PMID- 25914592 -OWN - NLM -STAT- PubMed-not-MEDLINE -DCOM- 20150427 -LR - 20201001 -IS - 1344-7610 (Print) -IS - 1347-3735 (Electronic) -IS - 1344-7610 (Linking) -VI - 64 -IP - 4 -DP - 2014 Dec -TI - A novel GmFAD3-2a mutant allele developed through TILLING reduces alpha-linolenic - acid content in soybean seed oil. -PG - 371-7 -LID - 10.1270/jsbbs.64.371 [doi] -AB - Soybean (Glycine max (L.) Merr.) oil typically contains 8% alpha-linolenic acid that - is highly unstable and easily oxidized. This property is undesirable in many food - and industrial applications. Genetic strategies for reducing alpha-linolenic acid - content would enhance the commercial value. However, genetic resources for low - alpha-linolenic acid content are limited among natural soybean variations. Microsomal - omega-3-fatty acid desaturase (FAD3) is responsible for the synthesis of - alpha-linolenic acid in the polyunsaturated fatty acid pathway. There are four FAD3 - homologs (Glyma02g39230, Glyma11g27190, Glyma14g37350 and Glyma18g06950) in the - soybean genome. While non-functional alleles have been reported for Glyma02g39230 - (GmFAD3-1a) and Glyma14g37350 (GmFAD3-1b), little variation is seen in - Glyma18g06950 (GmFAD3-2a). We isolated seven mutant GmFAD3-2a alleles, each - containing a single-nucleotide substitution, from 39,100 independent mutant lines - by using targeting induced local lesions in genomes (TILLING). Analysis of - GmFAD3-2a transcripts and enzyme activities revealed that one missense mutant, - 'P1-A9', contains a non-functional allele of GmFAD3-2a. By combining three - non-functional alleles (GmFAD3-1a, GmFAD3-1b, and GmFAD3-2a), we generated - soybean lines containing <2% alpha-linolenic acid in their seeds. The - reverse-genetics-based development of novel mutant alleles in the fatty acid - metabolic pathway will allow the improvement of soybean with better oil quality - through conventional breeding. -FAU - Hoshino, Tomoki -AU - Hoshino T -AD - Laboratory of Plant Genetics and Breeding, Faculty of Agriculture, Saga - University , Honjyo-machi 1, Saga 840-8502 , Japan ; Laboratory of Plant Genetics - and Breeding, Faculty of Agriculture, Yamagata University , Wakaba-machi 1, - Tsuruoka, Yamagata 997-8555 , Japan. -FAU - Watanabe, Satoshi -AU - Watanabe S -AD - Laboratory of Plant Genetics and Breeding, Faculty of Agriculture, Saga - University , Honjyo-machi 1, Saga 840-8502 , Japan. -FAU - Takagi, Yutaka -AU - Takagi Y -AD - Laboratory of Plant Genetics and Breeding, Faculty of Agriculture, Saga - University , Honjyo-machi 1, Saga 840-8502 , Japan. -FAU - Anai, Toyoaki -AU - Anai T -AD - Laboratory of Plant Genetics and Breeding, Faculty of Agriculture, Saga - University , Honjyo-machi 1, Saga 840-8502 , Japan. -LA - eng -PT - Journal Article -DEP - 20141201 -PL - Japan -TA - Breed Sci -JT - Breeding science -JID - 9888571 -PMC - PMC4267312 -OTO - NOTNLM -OT - TILLING -OT - reverse genetics -OT - soybean oil quality -OT - alpha-linolenic acid -EDAT- 2015/04/29 06:00 -MHDA- 2015/04/29 06:01 -CRDT- 2015/04/28 06:00 -PHST- 2014/07/11 00:00 [received] -PHST- 2014/10/05 00:00 [accepted] -PHST- 2015/04/28 06:00 [entrez] -PHST- 2015/04/29 06:00 [pubmed] -PHST- 2015/04/29 06:01 [medline] -AID - 64_371 [pii] -AID - 10.1270/jsbbs.64.371 [doi] -PST - ppublish -SO - Breed Sci. 2014 Dec;64(4):371-7. doi: 10.1270/jsbbs.64.371. Epub 2014 Dec 1. - - -##### PUB RECORD ##### -## 10.1186/s12864-017-3778-3 28549456 PMC5446728 Mao, Li, et al., 2017 "Mao T, Li J, Wen Z, Wu T, Wu C, Sun S, Jiang B, Hou W, Li W, Song Q, Wang D, Han T. Association mapping of loci controlling genetic and environmental interaction of soybean flowering time under various photo-thermal conditions. BMC Genomics. 2017 May 26;18(1):415. doi: 10.1186/s12864-017-3778-3. PMID: 28549456; PMCID: PMC5446728." ## - -PMID- 28549456 -OWN - NLM -STAT- MEDLINE -DCOM- 20180122 -LR - 20181113 -IS - 1471-2164 (Electronic) -IS - 1471-2164 (Linking) -VI - 18 -IP - 1 -DP - 2017 May 26 -TI - Association mapping of loci controlling genetic and environmental interaction of - soybean flowering time under various photo-thermal conditions. -PG - 415 -LID - 10.1186/s12864-017-3778-3 [doi] -LID - 415 -AB - BACKGROUND: Soybean (Glycine max (L.) Merr.) is a short day plant. Its flowering - and maturity time are controlled by genetic and environmental factors, as well - the interaction between the two factors. Previous studies have shown that both - genetic and environmental factors, mainly photoperiod and temperature, control - flowering time of soybean. Additionally, these studies have reported gene x gene - and gene x environment interactions on flowering time. However, the effects of - quantitative trait loci (QTL) in response to photoperiod and temperature have not - been well evaluated. The objectives of the current study were to identify the - effects of loci associated with flowering time under different photo-thermal - conditions and to understand the effects of interaction between loci and - environment on soybean flowering. METHODS: Different photoperiod and temperature - combinations were obtained by adjusting sowing dates (spring sowing and summer - sowing) or day-length (12 h, 16 h). Association mapping was performed on 91 - soybean cultivars from different maturity groups (MG000-VIII) using 172 SSR - markers and 5107 SNPs from the Illumina SoySNP6K iSelectBeadChip. The effects of - the interaction between QTL and environments on flowering time were also analysed - using the QTXNetwork. RESULTS: Large-effect loci were detected on Gm 11, Gm 16 - and Gm 20 as in previous reports. Most loci associated with flowering time are - sensitive to photo-thermal conditions. Number of loci associated with flowering - time was more under the long day (LD) than under the short day (SD) condition. - The variation of flowering time among the soybean cultivars mostly resulted from - the epistasis x environment and additive x environment interactions. Among the - three candidate loci, i.e. Gm04_4497001 (near GmCOL3a), Gm16_30766209 (near - GmFT2a and GmFT2b) and Gm19_47514601 (E3 or GmPhyA3), the Gm04_4497001 may be the - key locus interacting with other loci for controlling soybean flowering time. - CONCLUSION: The effects of loci associated with the flowering time of soybean - were dependent upon the photo-thermal conditions. This study facilitates the - understanding of the genetic mechanism of soybean flowering and molecular - breeding for the improvement of soybean adaptability to specific and/or broad - regions. -FAU - Mao, Tingting -AU - Mao T -AD - College of Agriculture, Northeast Agricultural University, Harbin, 150030, - Heilongjiang, China. -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 - Li, Jinyu -AU - Li J -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 - Wen, Zixiang -AU - Wen Z -AD - Department of Plant, Soil and Microbial Sciences, Michigan State University, 1066 - Bogue St., Rm. A384-E, East Lansing, MI, 48824-1325, USA. -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 - 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 - 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 - 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 - Li, Wenbin -AU - Li W -AD - College of Agriculture, Northeast Agricultural University, Harbin, 150030, - Heilongjiang, China. -FAU - Song, Qijian -AU - Song Q -AD - Soybean Genomics and Improvement Laboratory, US Department of Agriculture, - Agricultural Research Service (USDA-ARS), 10300 Baltimore Ave, Beltsville, MD, - 20705, USA. -FAU - Wang, Dechun -AU - Wang D -AD - Department of Plant, Soil and Microbial Sciences, Michigan State University, 1066 - Bogue St., Rm. A384-E, East Lansing, MI, 48824-1325, USA. wangdech@msu.edu. -FAU - Han, Tianfu -AU - Han T -AD - College of Agriculture, Northeast Agricultural University, Harbin, 150030, - Heilongjiang, China. hantianfu@caas.cn. -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. hantianfu@caas.cn. -LA - eng -PT - Journal Article -PT - Research Support, Non-U.S. Gov't -DEP - 20170526 -PL - England -TA - BMC Genomics -JT - BMC genomics -JID - 100965258 -SB - IM -MH - *Chromosome Mapping -MH - Flowers/*growth & development -MH - *Gene-Environment Interaction -MH - Genotype -MH - Linkage Disequilibrium -MH - *Photoperiod -MH - Polymorphism, Single Nucleotide -MH - Soybeans/*genetics/*growth & development -MH - *Temperature -PMC - PMC5446728 -OTO - NOTNLM -OT - Flowering time -OT - Gene by environment interaction -OT - Genetic architecture -OT - Photo-thermal condition -OT - Soybean (Glycine max) -EDAT- 2017/05/28 06:00 -MHDA- 2018/01/23 06:00 -CRDT- 2017/05/28 06:00 -PHST- 2016/06/03 00:00 [received] -PHST- 2017/05/10 00:00 [accepted] -PHST- 2017/05/28 06:00 [entrez] -PHST- 2017/05/28 06:00 [pubmed] -PHST- 2018/01/23 06:00 [medline] -AID - 10.1186/s12864-017-3778-3 [pii] -AID - 3778 [pii] -AID - 10.1186/s12864-017-3778-3 [doi] -PST - epublish -SO - BMC Genomics. 2017 May 26;18(1):415. doi: 10.1186/s12864-017-3778-3. - - -##### PUB RECORD ##### -## 10.1021/jf2033939 22107112 null Kovinich, Saleem, et al., 2012 "Kovinich N, Saleem A, Arnason JT, Miki B. Identification of two anthocyanidin reductase genes and three red-brown soybean accessions with reduced anthocyanidin reductase 1 mRNA, activity, and seed coat proanthocyanidin amounts. J Agric Food Chem. 2012 Jan 18;60(2):574-84. doi: 10.1021/jf2033939. Epub 2012 Jan 4. PMID: 22107112." ## - -PMID- 22107112 -OWN - NLM -STAT- MEDLINE -DCOM- 20120820 -LR - 20220310 -IS - 1520-5118 (Electronic) -IS - 0021-8561 (Linking) -VI - 60 -IP - 2 -DP - 2012 Jan 18 -TI - Identification of two anthocyanidin reductase genes and three red-brown soybean - accessions with reduced anthocyanidin reductase 1 mRNA, activity, and seed coat - proanthocyanidin amounts. -PG - 574-84 -LID - 10.1021/jf2033939 [doi] -AB - Anthocyanidin reductase (ANR; EC 1.3.1.77) catalyzes a key step in the - biosynthesis of proanthocyanidins (PAs; also known as condensed tannins), - flavonoid metabolites responsible for the brown pigmentation of seeds. Here, two - ANR genes (ANR1 and ANR2) from the seed coat of brown soybean (Glycine max (L.) - Merr.) have been isolated and their enzymatic function confirmed for the - reduction of cyanidin to (-)-epicatechin in vitro. Biochemical and genetic - comparisons of soybean lines differing in seed coat color revealed three - red-brown lines to exhibit major reductions in the amounts of soluble PAs in the - seed coat compared to brown soybean lines. Two spontaneous mutants with red-brown - grain color had reduced ANR1 gene expression in the seed coat, and an - EMS-mutagenized red-brown mutant had nonsynonymous substitutions that resulted in - slightly reduced ANR1 activity in vitro. These results suggest that defects in - the ANR1 gene can be associated with red-brown soybean grain color. These results - suggest that suppressing ANR1 gene expression or activity may be a rational - approach toward engineering seed coat color to enable the visual identification - of genetically modified soybean grains. -FAU - Kovinich, Nik -AU - Kovinich N -AD - Bioproducts and Bioprocesses, Research Branch, Agriculture and Agri-Food Canada, - Ottawa, Ontario, Canada. -FAU - Saleem, Ammar -AU - Saleem A -FAU - Arnason, John T -AU - Arnason JT -FAU - Miki, Brian -AU - Miki B -LA - eng -PT - Journal Article -PT - Research Support, Non-U.S. Gov't -DEP - 20120104 -PL - United States -TA - J Agric Food Chem -JT - Journal of agricultural and food chemistry -JID - 0374755 -RN - 0 (Proanthocyanidins) -RN - 0 (RNA, Messenger) -RN - 0 (Recombinant Proteins) -RN - 8R1V1STN48 (Catechin) -RN - EC 1.6.- (NADH, NADPH Oxidoreductases) -SB - IM -MH - Catechin/metabolism -MH - Color -MH - Gene Expression Regulation, Plant -MH - Genes, Plant -MH - Multigene Family -MH - Mutation -MH - NADH, NADPH Oxidoreductases/*genetics/*metabolism -MH - Phylogeny -MH - Proanthocyanidins/genetics/metabolism -MH - RNA, Messenger/genetics -MH - Recombinant Proteins/genetics/metabolism -MH - Seeds/genetics/metabolism/*physiology -MH - Soybeans/*genetics/metabolism -EDAT- 2011/11/24 06:00 -MHDA- 2012/08/21 06:00 -CRDT- 2011/11/24 06:00 -PHST- 2011/11/24 06:00 [entrez] -PHST- 2011/11/24 06:00 [pubmed] -PHST- 2012/08/21 06:00 [medline] -AID - 10.1021/jf2033939 [doi] -PST - ppublish -SO - J Agric Food Chem. 2012 Jan 18;60(2):574-84. doi: 10.1021/jf2033939. Epub 2012 - Jan 4. - - -##### PUB RECORD ##### -## 10.3390/ijms23052497 35269637 PMC8910378 Su, Chen, et al., 2022 "Su Q, Chen L, Cai Y, Chen Y, Yuan S, Li M, Zhang J, Sun S, Han T, Hou W. Functional Redundancy of FLOWERING LOCUS T 3b in Soybean Flowering Time Regulation. Int J Mol Sci. 2022 Feb 24;23(5):2497. doi: 10.3390/ijms23052497. PMID: 35269637; PMCID: PMC8910378." ## - -PMID- 35269637 -OWN - NLM -STAT- MEDLINE -DCOM- 20220408 -LR - 20220408 -IS - 1422-0067 (Electronic) -IS - 1422-0067 (Linking) -VI - 23 -IP - 5 -DP - 2022 Feb 24 -TI - Functional Redundancy of FLOWERING LOCUS T 3b in Soybean Flowering Time - Regulation. -LID - 10.3390/ijms23052497 [doi] -LID - 2497 -AB - Photoperiodic flowering is an important agronomic trait that determines - adaptability and yield in soybean and is strongly influenced by FLOWERING LOCUS T - (FT) genes. Due to the presence of multiple FT homologs in the genome, their - functions in soybean are not fully understood. Here, we show that GmFT3b exhibits - functional redundancy in regulating soybean photoperiodic flowering. - Bioinformatic analysis revealed that GmFT3b is a typical floral inducer FT - homolog and that the protein is localized to the nucleus. Moreover, GmFT3b - expression was induced by photoperiod and circadian rhythm and was more - responsive to long-day (LD) conditions. We generated a homozygous ft3b knockout - and three GmFT3b-overexpressing soybean lines for evaluation under different - photoperiods. There were no significant differences in flowering time between the - wild-type, the GmFT3b overexpressors, and the ft3b knockouts under natural - long-day, short-day, or LD conditions. Although the downstream flowering-related - genes GmFUL1 (a, b), GmAP1d, and GmLFY1 were slightly down-regulated in ft3b - plants, the floral inducers GmFT5a and GmFT5b were highly expressed, indicating - potential compensation for the loss of GmFT3b. We suggest that GmFT3b acts - redundantly in flowering time regulation and may be compensated by other FT - homologs in soybean. -FAU - Su, Qiang -AU - Su Q -AUID- ORCID: 0000-0002-3506-5395 -AD - National Center for Transgenic Research in Plants, Institute of Crop Sciences, - Chinese Academy of Agricultural Sciences, Beijing 100081, China. -AD - Ministry of Agriculture Key Laboratory of Soybean Biology (Beijing), Institute of - Crop Sciences, Chinese Academy of Agricultural Sciences, Beijing 100081, China. -FAU - Chen, Li -AU - Chen L -AD - National Center for Transgenic Research in Plants, Institute of Crop Sciences, - Chinese Academy of Agricultural Sciences, Beijing 100081, China. -AD - Ministry of Agriculture Key Laboratory of Soybean Biology (Beijing), Institute of - Crop Sciences, Chinese Academy of Agricultural Sciences, Beijing 100081, China. -FAU - Cai, Yupeng -AU - Cai Y -AD - National Center for Transgenic Research in Plants, Institute of Crop Sciences, - Chinese Academy of Agricultural Sciences, Beijing 100081, China. -AD - Ministry of Agriculture Key Laboratory of Soybean Biology (Beijing), Institute of - Crop Sciences, Chinese Academy of Agricultural Sciences, Beijing 100081, China. -FAU - Chen, Yingying -AU - Chen Y -AD - National Center for Transgenic Research in Plants, Institute of Crop Sciences, - Chinese Academy of Agricultural Sciences, Beijing 100081, China. -AD - Ministry of Agriculture Key Laboratory of Soybean Biology (Beijing), Institute of - Crop Sciences, Chinese Academy of Agricultural Sciences, Beijing 100081, China. -FAU - Yuan, Shan -AU - Yuan S -AD - Ministry of Agriculture Key Laboratory of Soybean Biology (Beijing), Institute of - Crop Sciences, Chinese Academy of Agricultural Sciences, Beijing 100081, China. -FAU - Li, Min -AU - Li M -AD - Ministry of Agriculture Key Laboratory of Soybean Biology (Beijing), Institute of - Crop Sciences, Chinese Academy of Agricultural Sciences, Beijing 100081, China. -FAU - Zhang, Jialing -AU - Zhang J -AD - National Center for Transgenic Research in Plants, Institute of Crop Sciences, - Chinese Academy of Agricultural Sciences, Beijing 100081, China. -AD - Ministry of Agriculture Key Laboratory of Soybean Biology (Beijing), Institute of - Crop Sciences, Chinese Academy of Agricultural Sciences, Beijing 100081, China. -FAU - Sun, Shi -AU - Sun S -AUID- ORCID: 0000-0003-1422-5334 -AD - Ministry of Agriculture Key Laboratory of Soybean Biology (Beijing), Institute of - Crop Sciences, Chinese Academy of Agricultural Sciences, Beijing 100081, China. -FAU - Han, Tianfu -AU - Han T -AUID- ORCID: 0000-0002-2362-2414 -AD - Ministry of Agriculture Key Laboratory of Soybean Biology (Beijing), Institute of - Crop Sciences, Chinese Academy of Agricultural Sciences, Beijing 100081, China. -FAU - Hou, Wensheng -AU - Hou W -AD - National Center for Transgenic Research in Plants, Institute of Crop Sciences, - Chinese Academy of Agricultural Sciences, Beijing 100081, China. -AD - Ministry of Agriculture Key Laboratory of Soybean Biology (Beijing), Institute of - Crop Sciences, Chinese Academy of Agricultural Sciences, Beijing 100081, China. -LA - eng -GR - 31871644/National Natural Science Foundation of China/ -GR - 2016ZX08010-004/Major Science and Technology Projects of China/ -PT - Journal Article -DEP - 20220224 -PL - Switzerland -TA - Int J Mol Sci -JT - International journal of molecular sciences -JID - 101092791 -RN - 0 (Plant Proteins) -SB - IM -MH - *Flowers/metabolism -MH - Gene Expression Regulation, Plant -MH - Phenotype -MH - Photoperiod -MH - Plant Proteins/genetics/metabolism -MH - *Soybeans/metabolism -PMC - PMC8910378 -OTO - NOTNLM -OT - GmFT3b -OT - flowering time -OT - functional redundancy -OT - photoperiod -OT - soybean -COIS- The authors declare no conflict of interest. -EDAT- 2022/03/11 06:00 -MHDA- 2022/04/09 06:00 -CRDT- 2022/03/10 15:35 -PHST- 2022/01/24 00:00 [received] -PHST- 2022/02/21 00:00 [revised] -PHST- 2022/02/22 00:00 [accepted] -PHST- 2022/03/10 15:35 [entrez] -PHST- 2022/03/11 06:00 [pubmed] -PHST- 2022/04/09 06:00 [medline] -AID - ijms23052497 [pii] -AID - ijms-23-02497 [pii] -AID - 10.3390/ijms23052497 [doi] -PST - epublish -SO - Int J Mol Sci. 2022 Feb 24;23(5):2497. doi: 10.3390/ijms23052497. - - -##### 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 ##### -## 10.1186/1471-2229-11-155 22070454 PMC3229458 Gillman, Tetlow, et al., 2011 "Gillman JD, Tetlow A, Lee JD, Shannon JG, Bilyeu K. Loss-of-function mutations affecting a specific Glycine max R2R3 MYB transcription factor result in brown hilum and brown seed coats. BMC Plant Biol. 2011 Nov 9;11:155. doi: 10.1186/1471-2229-11-155. PMID: 22070454; PMCID: PMC3229458." ## - -PMID- 22070454 -OWN - NLM -STAT- MEDLINE -DCOM- 20120418 -LR - 20220408 -IS - 1471-2229 (Electronic) -IS - 1471-2229 (Linking) -VI - 11 -DP - 2011 Nov 9 -TI - Loss-of-function mutations affecting a specific Glycine max R2R3 MYB - transcription factor result in brown hilum and brown seed coats. -PG - 155 -LID - 10.1186/1471-2229-11-155 [doi] -AB - BACKGROUND: Although modern soybean cultivars feature yellow seed coats, with the - only color variation found at the hila, the ancestral condition is black seed - coats. Both seed coat and hila coloration are due to the presence of - phenylpropanoid pathway derivatives, principally anthocyanins. The genetics of - soybean seed coat and hilum coloration were first investigated during the - resurgence of genetics during the 1920s, following the rediscovery of Mendel's - work. Despite the inclusion of this phenotypic marker into the extensive genetic - maps developed for soybean over the last twenty years, the genetic basis behind - the phenomenon of brown seed coats (the R locus) has remained undetermined until - now. RESULTS: In order to identify the gene responsible for the r gene effect - (brown hilum or seed coat color), we utilized bulk segregant analysis and - identified recombinant lines derived from a population segregating for two - phenotypically distinct alleles of the R locus. Fine mapping was accelerated - through use of a novel, bioinformatically determined set of Simple Sequence - Repeat (SSR) markers which allowed us to delimit the genomic region containing - the r gene to less than 200 kbp, despite the use of a mapping population of only - 100 F6 lines. Candidate gene analysis identified a loss of function mutation - affecting a seed coat-specific expressed R2R3 MYB transcription factor gene - (Glyma09g36990) as a strong candidate for the brown hilum phenotype. We observed - a near perfect correlation between the mRNA expression levels of the functional R - gene candidate and an UDP-glucose:flavonoid 3-O-glucosyltransferase (UF3GT) gene, - which is responsible for the final step in anthocyanin biosynthesis. In contrast, - when a null allele of Glyma09g36990 is expressed no upregulation of the UF3GT - gene was found. CONCLUSIONS: We discovered an allelic series of four loss of - function mutations affecting our R locus gene candidate. The presence of any one - of these mutations was perfectly correlated with the brown seed coat/hilum - phenotype in a broadly distributed survey of soybean cultivars, barring the - presence of the epistatic dominant I allele or gray pubescence, both of which can - mask the effect of the r allele, resulting in yellow or buff hila. These findings - strongly suggest that loss of function for one particular seed coat-expressed - R2R3 MYB gene is responsible for the brown seed coat/hilum phenotype in soybean. -FAU - Gillman, Jason D -AU - Gillman JD -AD - USDA-ARS, Plant Genetics Research Unit, 110 Waters Hall, Columbia, MO 65211, USA. - Jason.Gillman@ars.usda.gov -FAU - Tetlow, Ashley -AU - Tetlow A -FAU - Lee, Jeong-Deong -AU - Lee JD -FAU - Shannon, J Grover -AU - Shannon JG -FAU - Bilyeu, Kristin -AU - Bilyeu K -LA - eng -PT - Journal Article -DEP - 20111109 -PL - England -TA - BMC Plant Biol -JT - BMC plant biology -JID - 100967807 -RN - 0 (DNA, Plant) -RN - 0 (Soybean Proteins) -RN - 0 (Transcription Factors) -SB - IM -MH - Alleles -MH - Chromosome Mapping -MH - DNA, Plant/genetics -MH - Gene Expression Regulation, Plant -MH - Genes, Plant -MH - Microsatellite Repeats -MH - Mutation -MH - Phenotype -MH - Pigmentation/*genetics -MH - Seeds/*genetics/physiology -MH - Soybean Proteins/*genetics -MH - Soybeans/*genetics -MH - Transcription Factors/*genetics -PMC - PMC3229458 -EDAT- 2011/11/11 06:00 -MHDA- 2012/04/19 06:00 -CRDT- 2011/11/11 06:00 -PHST- 2011/07/15 00:00 [received] -PHST- 2011/11/09 00:00 [accepted] -PHST- 2011/11/11 06:00 [entrez] -PHST- 2011/11/11 06:00 [pubmed] -PHST- 2012/04/19 06:00 [medline] -AID - 1471-2229-11-155 [pii] -AID - 10.1186/1471-2229-11-155 [doi] -PST - epublish -SO - BMC Plant Biol. 2011 Nov 9;11:155. doi: 10.1186/1471-2229-11-155. - - -##### PUB RECORD ##### -## 10.1534/genetics.108.092742 18780733 PMC2567397 Liu, Kanazawa, et al., 2008 "Liu B, Kanazawa A, Matsumura H, Takahashi R, Harada K, Abe J. Genetic redundancy in soybean photoresponses associated with duplication of the phytochrome A gene. Genetics. 2008 Oct;180(2):995-1007. doi: 10.1534/genetics.108.092742. Epub 2008 Sep 9. PMID: 18780733; PMCID: PMC2567397." ## - -PMID- 18780733 -OWN - NLM -STAT- MEDLINE -DCOM- 20090105 -LR - 20220408 -IS - 0016-6731 (Print) -IS - 0016-6731 (Linking) -VI - 180 -IP - 2 -DP - 2008 Oct -TI - Genetic redundancy in soybean photoresponses associated with duplication of the - phytochrome A gene. -PG - 995-1007 -LID - 10.1534/genetics.108.092742 [doi] -AB - Gene and genome duplications underlie the origins of evolutionary novelty in - plants. Soybean, Glycine max, is considered to be a paleopolyploid species with a - complex genome. We found multiple homologs of the phytochrome A gene (phyA) in - the soybean genome and determined the DNA sequences of two paralogs designated - GmphyA1 and GmphyA2. Analysis of the GmphyA2 gene from the lines carrying a - recessive allele at a photoperiod insensitivity locus, E4, revealed that a - Ty1/copia-like retrotransposon was inserted in exon 1 of the gene, which resulted - in dysfunction of the gene. Mapping studies suggested that GmphyA2 is encoded by - E4. The GmphyA1 gene was mapped to a region of linkage group O, which is - homeologous to the region harboring E4 in linkage group I. Plants homozygous for - the e4 allele were etiolated under continuous far red light, but the - de-etiolation occurred partially, indicating that the mutation alone did not - cause a complete loss of phyA function. The genetic redundancy suggests that the - presence of duplicated copies of phyA genes accounts for the generation of - photoperiod insensitivity, while protecting against the deleterious effects of - mutation. Thus, this phenomenon provides a link between gene duplication and - establishment of an adaptive response of plants to environments. -FAU - Liu, Baohui -AU - Liu B -AD - Research Faculty of Agriculture, Hokkaido University, Sapporo, Japan. -FAU - Kanazawa, Akira -AU - Kanazawa A -FAU - Matsumura, Hisakazu -AU - Matsumura H -FAU - Takahashi, Ryoji -AU - Takahashi R -FAU - Harada, Kyuya -AU - Harada K -FAU - Abe, Jun -AU - Abe J -LA - eng -SI - GENBANK/AB370252 -SI - GENBANK/AB370253 -SI - GENBANK/AB370254 -PT - Journal Article -PT - Research Support, Non-U.S. Gov't -DEP - 20080909 -PL - United States -TA - Genetics -JT - Genetics -JID - 0374636 -RN - 0 (Phytochrome A) -RN - 0 (Retroelements) -SB - IM -MH - *Gene Duplication -MH - Genes, Plant/*genetics -MH - Genetic Linkage -MH - Genome, Plant -MH - Molecular Sequence Data -MH - *Photoperiod -MH - Phytochrome A/*genetics -MH - Polymorphism, Genetic -MH - Retroelements -MH - Soybeans/*genetics -PMC - PMC2567397 -EDAT- 2008/09/11 09:00 -MHDA- 2009/01/06 09:00 -CRDT- 2008/09/11 09:00 -PHST- 2008/09/11 09:00 [pubmed] -PHST- 2009/01/06 09:00 [medline] -PHST- 2008/09/11 09:00 [entrez] -AID - genetics.108.092742 [pii] -AID - gen1802995 [pii] -AID - 10.1534/genetics.108.092742 [doi] -PST - ppublish -SO - Genetics. 2008 Oct;180(2):995-1007. doi: 10.1534/genetics.108.092742. Epub 2008 - Sep 9. - - -##### PUB RECORD ##### -## 10.1186/1471-2229-10-195 20828382 PMC2956544 Pham, Lee, et al., 2010 "Pham AT, Lee JD, Shannon JG, Bilyeu KD. Mutant alleles of FAD2-1A and FAD2-1B combine to produce soybeans with the high oleic acid seed oil trait. BMC Plant Biol. 2010 Sep 9;10:195. doi: 10.1186/1471-2229-10-195. PMID: 20828382; PMCID: PMC2956544." ## - -PMID- 20828382 -OWN - NLM -STAT- MEDLINE -DCOM- 20101123 -LR - 20220331 -IS - 1471-2229 (Electronic) -IS - 1471-2229 (Linking) -VI - 10 -DP - 2010 Sep 9 -TI - Mutant alleles of FAD2-1A and FAD2-1B combine to produce soybeans with the high - oleic acid seed oil trait. -PG - 195 -LID - 10.1186/1471-2229-10-195 [doi] -AB - BACKGROUND: The alteration of fatty acid profiles in soybean [Glycine max (L.) - Merr.] to improve soybean oil quality is an important and evolving theme in - soybean research to meet nutritional needs and industrial criteria in the modern - market. Soybean oil with elevated oleic acid is desirable because this - monounsaturated fatty acid improves the nutrition and oxidative stability of the - oil. Commodity soybean oil typically contains 20% oleic acid and the target for - high oleic acid soybean oil is approximately 80% of the oil; previous - conventional plant breeding research to raise the oleic acid level to just 50-60% - of the oil was hindered by the genetic complexity and environmental instability - of the trait. The objective of this work was to create the high oleic acid trait - in soybeans by identifying and combining mutations in two delta-twelve fatty acid - desaturase genes, FAD2-1A and FAD2-1B. RESULTS: Three polymorphisms found in the - FAD2-1B alleles of two soybean lines resulted in missense mutations. For each of - the two soybean lines, there was one unique amino acid change within a highly - conserved region of the protein. The mutant FAD2-1B alleles were associated with - an increase in oleic acid levels, although the FAD2-1B mutant alleles alone were - not capable of producing a high oleic acid phenotype. When existing FAD2-1A - mutations were combined with the novel mutant FAD2-1B alleles, a high oleic acid - phenotype was recovered only for those lines which were homozygous for both of - the mutant alleles. CONCLUSIONS: We were able to produce conventional soybean - lines with 80% oleic acid in the oil in two different ways, each requiring the - contribution of only two genes. The high oleic acid soybean germplasm developed - contained a desirable fatty acid profile, and it was stable in two production - environments. The presumed causative sequence polymorphisms in the FAD2-1B - alleles were developed into highly efficient molecular markers for tracking the - mutant alleles. The resources described here for the creation of high oleic acid - soybeans provide a framework to efficiently develop soybean varieties to meet - changing market demands. -FAU - Pham, Anh-Tung -AU - Pham AT -AD - University of Missouri, Division of Plant Sciences, 110 Waters Hall, Columbia, MO - 65211, USA. -FAU - Lee, Jeong-Dong -AU - Lee JD -FAU - Shannon, J Grover -AU - Shannon JG -FAU - Bilyeu, Kristin D -AU - Bilyeu KD -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 - 20100909 -PL - England -TA - BMC Plant Biol -JT - BMC plant biology -JID - 100967807 -RN - 0 (DNA, Plant) -RN - 0 (Oleic Acids) -RN - 0 (Plant Proteins) -RN - 8001-22-7 (Soybean Oil) -RN - EC 1.14.19.- (Fatty Acid Desaturases) -SB - IM -MH - Alleles -MH - Amino Acid Sequence -MH - DNA, Plant/genetics -MH - Fatty Acid Desaturases/genetics/*metabolism -MH - Molecular Sequence Data -MH - Mutation, Missense -MH - Oleic Acids/*biosynthesis -MH - Phenotype -MH - Plant Proteins/genetics/*metabolism -MH - Polymorphism, Genetic -MH - Seeds/*chemistry -MH - Sequence Analysis, DNA -MH - Soybean Oil/chemistry -MH - Soybeans/chemistry/enzymology/*genetics -PMC - PMC2956544 -EDAT- 2010/09/11 06:00 -MHDA- 2010/12/14 06:00 -CRDT- 2010/09/11 06:00 -PHST- 2010/05/03 00:00 [received] -PHST- 2010/09/09 00:00 [accepted] -PHST- 2010/09/11 06:00 [entrez] -PHST- 2010/09/11 06:00 [pubmed] -PHST- 2010/12/14 06:00 [medline] -AID - 1471-2229-10-195 [pii] -AID - 10.1186/1471-2229-10-195 [doi] -PST - epublish -SO - BMC Plant Biol. 2010 Sep 9;10:195. doi: 10.1186/1471-2229-10-195. - - -##### PUB RECORD ##### -## 10.1590/1678-4685-gmb-2021-0016 34919115 PMC8679260 Molinari, Fuganti-Pagliarini, et al., 2021 "Molinari MDC, Fuganti-Pagliarini R, Barbosa DA, Marin SRR, Marin DR, Rech EL, Mertz-Henning LM, Nepomuceno AL. Flowering process in soybean under water deficit conditions: A review on genetic aspects. Genet Mol Biol. 2021 Dec 13;45(1):e20210016. doi: 10.1590/1678-4685-GMB-2021-0016. PMID: 34919115; PMCID: PMC8679260." ## - -PMID- 34919115 -OWN - NLM -STAT- PubMed-not-MEDLINE -LR - 20211229 -IS - 1415-4757 (Print) -IS - 1678-4685 (Electronic) -IS - 1415-4757 (Linking) -VI - 45 -IP - 1 -DP - 2021 -TI - Flowering process in soybean under water deficit conditions: A review on genetic - aspects. -PG - e20210016 -LID - S1415-47572022000100301 [pii] -LID - 10.1590/1678-4685-GMB-2021-0016 [doi] -LID - e20210016 -AB - Soybean is a key crop in many countries, being used from human food to the animal - industry due to its nutritional properties. Financially, the grain chain moves - large sums of money into the economy of producing countries. However, like other - agricultural commodities around the world, it can have its final yield seriously - compromised by abiotic environmental stressors, like drought. As flowers imply in - pods and in grains inside it to minimize damages caused by water restriction, - researchers have focused on understanding flowering-process related genes and - their interactions. Here a review dedicated to the soybean flowering process and - gene network involved in it is presented, describing gene interactions and how - genes act in this complex mechanism, also ruled by environmental triggers such as - day-light and circadian cycle. The objective was to gather information and - insights on the soybean flowering process, aiming to provide knowledge useful to - assist in the development of drought-tolerant soybean lines, minimizing losses - due to delays or anticipation of flowering and, consequently, restraining - financial and productivity losses. -FAU - Molinari, Mayla Daiane Correa -AU - Molinari MDC -AUID- ORCID: 0000-0002-9135-0422 -AD - Universidade Estadual de Londrina, Departamento de Biologia Geral, Londrina, PR, - Brazil. -AD - Embrapa Soja, Londrina, PR, Brazil. -FAU - Fuganti-Pagliarini, Renata -AU - Fuganti-Pagliarini R -AUID- ORCID: 0000-0001-9282-2826 -AD - Embrapa Soja, Londrina, PR, Brazil. -FAU - Barbosa, Daniel de Amorim -AU - Barbosa DA -AD - Universidade Estadual de Londrina, Departamento de Biologia Geral, Londrina, PR, - Brazil. -AD - Embrapa Soja, Londrina, PR, Brazil. -FAU - Marin, Silvana Regina Rockenbach -AU - Marin SRR -AD - Embrapa Soja, Londrina, PR, Brazil. -FAU - Marin, Daniel Rockenbach -AU - Marin DR -AD - Embrapa Soja, Londrina, PR, Brazil. -FAU - Rech, Elibio Leopoldo -AU - Rech EL -AD - Embrapa Recursos Geneticos e Biotecnologia, Instituto Nacional de Ciencia e - Tecnologia em Biologia Sintetica, Brasilia, DF, Brazil. -FAU - Mertz-Henning, Liliane Marcia -AU - Mertz-Henning LM -AD - Embrapa Soja, Londrina, PR, Brazil. -FAU - Nepomuceno, Alexandre Lima -AU - Nepomuceno AL -AD - Embrapa Soja, Londrina, PR, Brazil. -LA - eng -PT - Journal Article -DEP - 20211213 -PL - Brazil -TA - Genet Mol Biol -JT - Genetics and molecular biology -JID - 100883590 -PMC - PMC8679260 -COIS- Conflict of interest: The authors declare that there is no conflict of interest - that could be perceived as prejudicial to the impartiality of the reported - research. -EDAT- 2021/12/18 06:00 -MHDA- 2021/12/18 06:01 -CRDT- 2021/12/17 12:21 -PHST- 2021/01/24 00:00 [received] -PHST- 2021/09/30 00:00 [accepted] -PHST- 2021/12/17 12:21 [entrez] -PHST- 2021/12/18 06:00 [pubmed] -PHST- 2021/12/18 06:01 [medline] -AID - S1415-47572022000100301 [pii] -AID - 10.1590/1678-4685-GMB-2021-0016 [doi] -PST - epublish -SO - Genet Mol Biol. 2021 Dec 13;45(1):e20210016. doi: - 10.1590/1678-4685-GMB-2021-0016. eCollection 2021. - - -##### PUB RECORD ##### -## 10.1093/jxb/ers039 22357599 PMC3350928 Pandurangan, Pajak, et al., 2012 "Pandurangan S, Pajak A, Molnar SJ, Cober ER, Dhaubhadel S, Hernández-Sebastià C, Kaiser WM, Nelson RL, Huber SC, Marsolais F. Relationship between asparagine metabolism and protein concentration in soybean seed. J Exp Bot. 2012 May;63(8):3173-84. doi: 10.1093/jxb/ers039. Epub 2012 Feb 22. PMID: 22357599; PMCID: PMC3350928." ## - -PMID- 22357599 -OWN - NLM -STAT- MEDLINE -DCOM- 20120907 -LR - 20211021 -IS - 1460-2431 (Electronic) -IS - 0022-0957 (Print) -IS - 0022-0957 (Linking) -VI - 63 -IP - 8 -DP - 2012 May -TI - Relationship between asparagine metabolism and protein concentration in soybean - seed. -PG - 3173-84 -LID - 10.1093/jxb/ers039 [doi] -AB - The relationship between asparagine metabolism and protein concentration was - investigated in soybean seed. Phenotyping of a population of recombinant inbred - lines adapted to Illinois confirmed a positive correlation between free - asparagine levels in developing seeds and protein concentration at maturity. - Analysis of a second population of recombinant inbred lines adapted to Ontario - associated the elevated free asparagine trait with two of four quantitative trait - loci determining population variation for protein concentration, including a - major one on chromosome 20 (linkage group I) which has been reported in multiple - populations. In the seed coat, levels of asparagine synthetase were high at 50 mg - and progressively declined until 150 mg seed weight, suggesting that nitrogenous - assimilates are pre-conditioned at early developmental stages to enable a high - concentration of asparagine in the embryo. The levels of asparaginase B1 showed - an opposite pattern, being low at 50 mg and progressively increased until 150 mg, - coinciding with an active phase of storage reserve accumulation. In a pair of - genetically related cultivars, approximately 2-fold higher levels of asparaginase B1 protein - and activity in seed coat, were associated with high protein concentration, - reflecting enhanced flux of nitrogen. Transcript expression analyses attributed - this difference to a specific asparaginase gene, ASPGB1a. These results - contribute to our understanding of the processes determining protein - concentration in soybean seed. -FAU - Pandurangan, Sudhakar -AU - Pandurangan S -AD - Department of Biology, University of Western Ontario, London, Ontario, N6A 5B7, - Canada. -FAU - Pajak, Agnieszka -AU - Pajak A -FAU - Molnar, Stephen J -AU - Molnar SJ -FAU - Cober, Elroy R -AU - Cober ER -FAU - Dhaubhadel, Sangeeta -AU - Dhaubhadel S -FAU - Hernandez-Sebastia, Cinta -AU - Hernandez-Sebastia C -FAU - Kaiser, Werner M -AU - Kaiser WM -FAU - Nelson, Randall L -AU - Nelson RL -FAU - Huber, Steven C -AU - Huber SC -FAU - Marsolais, Frederic -AU - Marsolais F -LA - eng -PT - Journal Article -PT - Research Support, Non-U.S. Gov't -DEP - 20120222 -PL - England -TA - J Exp Bot -JT - Journal of experimental botany -JID - 9882906 -RN - 0 (Plant Proteins) -RN - 0 (RNA, Messenger) -RN - 7006-34-0 (Asparagine) -RN - EC 3.5.1.1 (Asparaginase) -RN - EC 6.3.1.1 (Aspartate-Ammonia Ligase) -SB - IM -MH - Asparaginase/genetics/metabolism -MH - Asparagine/*metabolism -MH - Aspartate-Ammonia Ligase/genetics/metabolism -MH - Blotting, Western -MH - Gene Expression Regulation, Plant -MH - Inbreeding -MH - Plant Proteins/genetics/*metabolism -MH - Quantitative Trait Loci/genetics -MH - Quantitative Trait, Heritable -MH - RNA, Messenger/genetics/metabolism -MH - Recombination, Genetic/genetics -MH - Seeds/enzymology/growth & development/*metabolism -MH - Soybeans/enzymology/genetics/growth & development/*metabolism -PMC - PMC3350928 -EDAT- 2012/02/24 06:00 -MHDA- 2012/09/08 06:00 -CRDT- 2012/02/24 06:00 -PHST- 2012/02/24 06:00 [entrez] -PHST- 2012/02/24 06:00 [pubmed] -PHST- 2012/09/08 06:00 [medline] -AID - ers039 [pii] -AID - 10.1093/jxb/ers039 [doi] -PST - ppublish -SO - J Exp Bot. 2012 May;63(8):3173-84. doi: 10.1093/jxb/ers039. Epub 2012 Feb 22. - - -##### 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. - - diff --git a/Glycine/max/wip_steven/Oellrich_Walls_2015_glyma.traits.yml b/Glycine/max/wip_steven/Oellrich_Walls_2015_glyma.traits.yml deleted file mode 100644 index bfc63aa..0000000 --- a/Glycine/max/wip_steven/Oellrich_Walls_2015_glyma.traits.yml +++ /dev/null @@ -1,651 +0,0 @@ ---- -gene_symbols: - - AMDH2 - - BADH2 -gene_symbol_long: GmAMDH2 -gene_model_pub_name: Glyma06g19820 -gene_model_full_id: ~ -confidence: 5 -phenotype_synopsis: fragrant seeds -traits: - - entity_name: enzyme activity trait - entity: TO:0000599 - - entity_name: seed - entity: PO:0009010 -references: - - citation: Qian, Jin, et al., 2022 - doi: 10.3390/ijms23084116 - pmid: 35456933 - - citation: Oellrich, Walls et al., 2015 - doi: 10.1186/s13007-015-0053-y - pmid: 25774204 ---- -gene_symbols: - - ANR1 -gene_symbol_long: Anthocyanin Reductase activitiy reduced -gene_model_pub_name: Glyma08g06630 -gene_model_full_id: ~ -confidence: 5 -phenotype_synopsis: Red-brown seed coat color -traits: - - entity_name: enzyme activity trait - entity: TO:0000599 - - entity_name: anthocyanin content - entity: TO:0000071 - - entity_name: seed coat - entity: PO:0009088 -references: - - citation: Kovinich, Saleem, et al., 2012 - doi: 10.1021/jf2033939 - pmid: 22107112 - - citation: Oellrich, Walls et al., 2015 - doi: 10.1186/s13007-015-0053-y - pmid: 25774204 ---- -gene_symbols: - - E1-1 -gene_symbol_long: Early flowering under long days -gene_model_pub_name: Glyma06g23026 -gene_model_full_id: ~ -confidence: 5 -phenotype_synopsis: Early flowering -traits: - - entity_name: photoperiod-sensitive flowering time trait - entity: TO:0000934 -references: - - citation: Xia, Watanabe, et al., 2012 - doi: 10.1073/pnas.1117982109 - pmid: 22619331 - - citation: Oellrich, Walls et al., 2015 - doi: 10.1186/s13007-015-0053-y - pmid: 25774204 ---- -classical_locus: E2 -gene_symbols: - - E2-1 -gene_symbol_long: Early flowering -gene_model_pub_name: Glyma01g36600 -gene_model_full_id: ~ -confidence: 5 -phenotype_synopsis: Early flowering -traits: - - entity_name: flowering time trait - entity: TO:0002616 -references: - - citation: Watanabe, Xia, et al., 2011 - doi: 10.1534/genetics.110.125062 - pmid: 21406680 - - citation: Oellrich, Walls et al., 2015 - doi: 10.1186/s13007-015-0053-y - pmid: 25774204 ---- -gene_symbols: - - E3-1 -gene_symbol_long: Early flowering -gene_model_pub_name: Glyma19g41210 -gene_model_full_id: ~ -confidence: 5 -phenotype_synopsis: Early flowering -traits: - - entity_name: flowering time trait - entity: TO:0002616 - - entity_name: far red light sensitivity - entity: TO:0000130 -references: - - citation: Mao, Li, et al., 2017 - doi: 10.1186/s12864-017-3778-3 - pmid: 28549456 - - citation: Oellrich, Walls et al., 2015 - doi: 10.1186/s13007-015-0053-y - pmid: 25774204 ---- -gene_symbols: - - Eu1-1 -gene_symbol_long: ESU -gene_model_pub_name: Glyma05g27840 -gene_model_full_id: ~ -confidence: 5 -phenotype_synopsis: Embryo urease activity -traits: - - entity_name: enzyme activity trait - entity: TO:0000599 - - entity_name: plant embryo - entity: PO:0009009 -references: - - citation: Polacco, Hyten, et al., 2011 - doi: 10.1093/jxb/err054 - pmid: 21430294 - - citation: Oellrich, Walls et al., 2015 - doi: 10.1186/s13007-015-0053-y - pmid: 25774204 ---- -gene_symbols: - - Eu2-1 -gene_symbol_long: GmUreF -gene_model_pub_name: Glyma14g04380 -gene_model_full_id: ~ -confidence: 5 -phenotype_synopsis: Urease activity -traits: - - entity_name: enzyme activity trait - entity: TO:0000599 - - entity_name: whole plant - entity: PO:0000003 -references: - - citation: Polacco, Hyten, et al., 2011 - doi: 10.1093/jxb/err054 - pmid: 21430294 - - citation: Oellrich, Walls et al., 2015 - doi: 10.1186/s13007-015-0053-y - pmid: 25774204 ---- -gene_symbols: - - Eu3-1 -gene_symbol_long: GmUreG -gene_model_pub_name: Glyma08g08970 -gene_model_full_id: ~ -confidence: 5 -phenotype_synopsis: Urease activity -traits: - - entity_name: enzyme activity trait - entity: TO:0000599 - - entity_name: whole plant - entity: PO:0000003 -references: - - citation: Polacco, Hyten, et al., 2011 - doi: 10.1093/jxb/err054 - pmid: 21430294 - - citation: Oellrich, Walls et al., 2015 - doi: 10.1186/s13007-015-0053-y - pmid: 25774204 ---- -gene_symbols: - - EU4-1 -gene_symbol_long: UU -gene_model_pub_name: Glyma11g37250 -gene_model_full_id: ~ -confidence: 5 -phenotype_synopsis: Urease activity -traits: - - entity_name: enzyme activity trait - entity: TO:0000599 - - entity_name: whole plant - entity: PO:0000003 -references: - - citation: Polacco, Hyten, et al., 2011 - doi: 10.1093/jxb/err054 - pmid: 21430294 - - citation: Oellrich, Walls et al., 2015 - doi: 10.1186/s13007-015-0053-y - pmid: 25774204 ---- -gene_symbols: - - Glyma09g36983 -gene_symbol_long: R2R MYB Transcription Factor -gene_model_pub_name: Glyma09g36983 -gene_model_full_id: ~ -confidence: 5 -phenotype_synopsis: Brown hilum, brown seed coat color -traits: - - entity_name: hilum - entity: PO:0020063 - - entity_name: seed coat - entity: PO:0009088 -references: - - citation: Zabala, Vodkin, et al., 2014 - doi: 10.1371/journal.pone.0111959 - pmid: 25369033 - - citation: Oellrich, Walls et al., 2015 - doi: 10.1186/s13007-015-0053-y - pmid: 25774204 ---- -gene_symbols: - - GmAS1-A -gene_symbol_long: Asparagine synthase 1 -gene_model_pub_name: Glyma11g27480 -gene_model_full_id: ~ -confidence: 5 -phenotype_synopsis: High asparagine synthase activity in seed coats -traits: - - entity_name: endosperm storage protein content - entity: TO:0002653 - - entity_name: enzyme activity trait - entity: TO:0000599 - - entity_name: seed coat - entity: PO:0009088 - - entity_name: seed - entity: PO:0009010 -references: - - citation: Lauter, Peiffer, et al., 2014 - doi: 10.1186/1471-2164-15-702 - pmid: 25149281 - - citation: Oellrich, Walls et al., 2015 - doi: 10.1186/s13007-015-0053-y - pmid: 25774204 ---- -gene_symbols: - - GmASPGB1-A -gene_symbol_long: Asparaginase B1 -gene_model_pub_name: Glyma14g09510 -gene_model_full_id: ~ -confidence: 5 -phenotype_synopsis: High asparaginase activity in seed coats -traits: - - entity_name: endosperm storage protein content - entity: TO:0002653 - - entity_name: enzyme activity trait - entity: TO:0000599 - - entity_name: seed coat - entity: PO:0009088 - - entity_name: seed - entity: PO:0009010 -references: - - citation: Pandurangan, Pajak, et al., 2012 - doi: 10.1093/jxb/ers039 - pmid: 22357599 - - citation: Oellrich, Walls et al., 2015 - doi: 10.1186/s13007-015-0053-y - pmid: 25774204 ---- -gene_symbols: - - GmCRY1 -gene_symbol_long: Late flowering under short day -gene_model_pub_name: Glyma04g11010 -gene_model_full_id: ~ -confidence: 5 -phenotype_synopsis: Late flowering under short day -traits: - - entity_name: photoperiod-sensitive flowering time trait - entity: TO:0000934 - - entity_name: blue light sensitivity - entity: TO:0000159 -references: - - citation: Molinari, Fuganti-Pagliarini, et al., 2021 - doi: 10.1590/1678-4685-GMB-2021-0016 - pmid: 34919115 - - citation: Oellrich, Walls et al., 2015 - doi: 10.1186/s13007-015-0053-y - pmid: 25774204 ---- -gene_symbols: - - GmFAB2-3 -gene_symbol_long: FAB2-3 -gene_model_pub_name: Glyma14g27990 -gene_model_full_id: ~ -confidence: 5 -phenotype_synopsis: High seed stearic acid content -traits: - - entity_name: stearic acid content - entity: TO:0005003 - - entity_name: seed - entity: PO:0009010 -references: - - citation: Carrero-Colón, Abshire, et al., 2014 - doi: 10.1371/journal.pone.0097891 - pmid: 24846334 - - citation: Oellrich, Walls et al., 2015 - doi: 10.1186/s13007-015-0053-y - pmid: 25774204 ---- -gene_symbols: - - GmFAD2-1 -gene_symbol_long: FAD2-1 -gene_model_pub_name: Glyma10g42470 -gene_model_full_id: ~ -confidence: 5 -phenotype_synopsis: High seed oleic acid content -traits: - - entity_name: oleic acid content - entity: TO:0005002 - - entity_name: seed - entity: PO:0009010 -references: - - citation: Pham, Lee, et al., 2010 - doi: 10.1186/1471-2229-10-195 - pmid: 20828382 - - citation: Oellrich, Walls et al., 2015 - doi: 10.1186/s13007-015-0053-y - pmid: 25774204 ---- -gene_symbols: - - GmFAD2-2 -gene_symbol_long: FAD2-2 -gene_model_pub_name: Glyma20g24530 -gene_model_full_id: ~ -confidence: 5 -phenotype_synopsis: High seed oleic acid content -traits: - - entity_name: oleic acid content - entity: TO:0005002 - - entity_name: seed - entity: PO:0009010 -references: - - citation: Pham, Lee, et al., 2010 - doi: 10.1186/1471-2229-10-195 - pmid: 20828382 - - citation: Oellrich, Walls et al., 2015 - doi: 10.1186/s13007-015-0053-y - pmid: 25774204 ---- -gene_symbols: - - GmFAD3-1 -gene_symbol_long: FAD3-1 -gene_model_pub_name: Glyma14g37350 -gene_model_full_id: ~ -confidence: 5 -phenotype_synopsis: High seed oleic acid content -traits: - - entity_name: oleic acid content - entity: TO:0005002 - - entity_name: seed - entity: PO:0009010 -references: - - citation: Hoshino, Watanabe, et al., 2014 - doi: 10.1270/jsbbs.64.371 - pmid: 25914592 - - citation: Oellrich, Walls et al., 2015 - doi: 10.1186/s13007-015-0053-y - pmid: 25774204 ---- -gene_symbols: - - GmFAD3-2 -gene_symbol_long: FAD3-2 -gene_model_pub_name: Glyma02g39230 -gene_model_full_id: ~ -confidence: 5 -phenotype_synopsis: High seed oleic acid content -traits: - - entity_name: oleic acid content - entity: TO:0005002 - - entity_name: seed - entity: PO:0009010 -references: - - citation: Yadav, Wierzbicki, et al., 1993 - doi: 10.1104/pp.103.2.467 - pmid: 8029334 - - citation: Oellrich, Walls et al., 2015 - doi: 10.1186/s13007-015-0053-y - pmid: 25774204 ---- -gene_symbols: - - GmFAD3-3 -gene_symbol_long: FAD3-3 -gene_model_pub_name: Glyma18g06950 -gene_model_full_id: ~ -confidence: 5 -phenotype_synopsis: High seed oleic acid content -traits: - - entity_name: oleic acid content - entity: TO:0005002 - - entity_name: seed - entity: PO:0009010 -references: - - citation: Hoshino, Watanabe, et al., 2014 - doi: 10.1270/jsbbs.64.371 - pmid: 25914592 - - citation: Oellrich, Walls et al., 2015 - doi: 10.1186/s13007-015-0053-y - pmid: 25774204 ---- -gene_symbols: - - GmFT2-A -gene_symbol_long: FT-2A -gene_model_pub_name: Glyma16g26660 -gene_model_full_id: ~ -confidence: 5 -phenotype_synopsis: Photoperiod insensitivity -traits: - - entity_name: flowering time trait - entity: TO:0002616 - - entity_name: photoperiod-sensitive flowering time trait - entity: TO:0000934 - - entity_name: whole plant flowering stage - entity: PO:0007016 -references: - - citation: Su, Chen, et al., 2022 - doi: 10.3390/ijms23052497 - pmid: 35269637 - - citation: Oellrich, Walls et al., 2015 - doi: 10.1186/s13007-015-0053-y - pmid: 25774204 ---- -gene_symbols: - - GmFT5-A -gene_symbol_long: FT-5A -gene_model_pub_name: Glyma16g04830 -gene_model_full_id: ~ -confidence: 5 -phenotype_synopsis: Photoperiod insensitivity -traits: - - entity_name: flowering time trait - entity: TO:0002616 - - entity_name: photoperiod-sensitive flowering time trait - entity: TO:0000934 - - entity_name: whole plant flowering stage - entity: PO:0007016 -references: - - citation: Su, Chen, et al., 2022 - doi: 10.3390/ijms23052497 - pmid: 35269637 - - citation: Oellrich, Walls et al., 2015 - doi: 10.1186/s13007-015-0053-y - pmid: 25774204 ---- -gene_symbols: - - GmLHY1 -gene_symbol_long: MYB Transcription Factor -gene_model_pub_name: Glyma16g01980 -gene_model_full_id: ~ -confidence: 5 -phenotype_synopsis: Elongated hypocotyl -traits: - - entity_name: seedling hypocotyl length - entity: TO:0006065 - - entity_name: photoperiod-sensitive flowering time trait - entity: TO:0000934 - - entity_name: photoperiod sensitivity trait - entity: TO:0000229 - - entity_name: hypocotyl - entity: PO:0020100 - - entity_name: whole plant flowering stage - entity: PO:0007016 -references: - - citation: Li, Cao, et al., 2019 - doi: 10.1073/pnas.1708508116 - pmid: 31676549 - - citation: Oellrich, Walls et al., 2015 - doi: 10.1186/s13007-015-0053-y - pmid: 25774204 ---- -gene_symbols: - - GmLPA1-1 -gene_symbol_long: LPA1-1 -gene_model_pub_name: Glyma03g32500 -gene_model_full_id: ~ -confidence: 5 -phenotype_synopsis: low phytic acid concentration in seeds -traits: - - entity_name: seed phosphorus content - entity: TO:0002666 - - entity_name: seed - entity: PO:0009010 -references: - - citation: Gillman,, Pantalone,, et al., 2009 - doi: 10.3835/plantgenome2008.03.0013 - pmid: 31676549 - - citation: Oellrich, Walls et al., 2015 - doi: 10.1186/s13007-015-0053-y - pmid: 25774204 ---- -gene_symbols: - - GmLPA1-2 -gene_symbol_long: LPA1-2 -gene_model_pub_name: Glyma19g35230 -gene_model_full_id: ~ -confidence: 5 -phenotype_synopsis: low phytic acid concentration in seeds -traits: - - entity_name: seed phosphorus content - entity: TO:0002666 - - entity_name: seed - entity: PO:0009010 -references: - - citation: Gillman,, Pantalone,, et al., 2009 - doi: 10.3835/plantgenome2008.03.0013 - pmid: 31676549 - - citation: Oellrich, Walls et al., 2015 - doi: 10.1186/s13007-015-0053-y - pmid: 25774204 ---- -gene_symbols: - - Ln -gene_symbol_long: GmJagged1 -gene_model_pub_name: Glyma20g25000 -gene_model_full_id: ~ -confidence: 5 -phenotype_synopsis: Narow leaflet -traits: - - entity_name: fruit seed number - entity: TO:0000445 - - entity_name: vascular leaf morphology trait - entity: TO:0000419 - - entity_name: leaflet - entity: PO:0020049 - - entity_name: whole plant - entity: PO:0000003 -references: - - citation: Sayama, Tanabata, et al., 2017 - doi: 10.1270/jsbbs.16201 - pmid: 29085246 - - citation: Oellrich, Walls et al., 2015 - doi: 10.1186/s13007-015-0053-y - pmid: 25774204 ---- -gene_symbols: - - MIPS1 -gene_symbol_long: GmMIPS1 -gene_model_pub_name: Glyma18g02210 -gene_model_full_id: ~ -confidence: 5 -phenotype_synopsis: Reduced emergence -traits: - - entity_name: seedling growth and development trait - entity: TO:0000949 - - entity_name: seedling shoot emergence stage - entity: PO:0007030 -references: - - citation: Yuan, Zhao, et al., 2007 - doi: 10.1007/s00122-007-0621-2 - pmid: 17701395 - - citation: Oellrich, Walls et al., 2015 - doi: 10.1186/s13007-015-0053-y - pmid: 25774204 ---- -gene_symbols: - - PhyA2 -gene_symbol_long: Photoperiod insensitivity -gene_model_pub_name: Glyma20g22160 -gene_model_full_id: ~ -confidence: 5 -phenotype_synopsis: photoperiod insensitivity to short day conditions -traits: - - entity_name: photoperiod-sensitive flowering time trait - entity: TO:0000934 -references: - - citation: Liu, Kanazawa, et al., 2008 - doi: 10.1534/genetics.108.092742 - pmid: 18780733 - - citation: Oellrich, Walls et al., 2015 - doi: 10.1186/s13007-015-0053-y - pmid: 25774204 ---- -classical_locus: R -gene_symbols: - - R -gene_symbol_long: Brown seed coat color -gene_model_pub_name: Glyma09g36983 -gene_model_full_id: ~ -confidence: 5 -phenotype_synopsis: Brown hilum, brown seed coat color -traits: - - entity_name: seed coat color - entity: TO:0000190 -references: - - citation: Zabala, Vodkin, et al., 2014 - doi: 10.1371/journal.pone.0111959 - pmid: 25369033 - - citation: Oellrich, Walls et al., 2015 - doi: 10.1186/s13007-015-0053-y - pmid: 25774204 ---- -gene_symbols: - - RS2 -gene_symbol_long: Raffinose synthase -gene_model_pub_name: Glyma06g18890 -gene_model_full_id: ~ -confidence: 5 -phenotype_synopsis: Seed raffinose concentration -traits: - - entity_name: raffinose content - entity: TO:0006004 - - entity_name: enzyme activity trait - entity: TO:0000599 - - entity_name: seed - entity: PO:0009010 -references: - - citation: Qiu, Vuong, et al., 2015 - doi: 10.1007/s00122-015-2575-0 - pmid: 26179337 - - citation: Oellrich, Walls et al., 2015 - doi: 10.1186/s13007-015-0053-y - pmid: 25774204 ---- -classical_locus: T -gene_symbols: - - T -gene_symbol_long: Tawny -gene_model_pub_name: Glyma06g21920 -gene_model_full_id: ~ -confidence: 5 -phenotype_synopsis: Gray pubescence at maturity -traits: - - entity_name: hilum color - entity: TO:0000968 - - entity_name: trichome morphology trait - entity: TO:0000911 - - entity_name: hilum - entity: PO:0020063 - - entity_name: trichome - entity: PO:0000282 -references: - - citation: Gillman, Tetlow, et al., 2011 - doi: 10.1186/1471-2229-11-155 - pmid: 22070454 - - citation: Oellrich, Walls et al., 2015 - doi: 10.1186/s13007-015-0053-y - pmid: 25774204 ---- -classical_locus: Wp -gene_symbols: - - Wp -gene_symbol_long: ~ -gene_model_pub_name: Glyma02g05450 -gene_model_full_id: ~ -confidence: 5 -phenotype_synopsis: Pink flowers -traits: - - entity_name: flower color - entity: TO:0000537 - - entity_name: seed coat color - entity: TO:0000190 - - entity_name: seed coat - entity: PO:0009088 - - entity_name: flower - entity: PO:0009046 -references: - - citation: Cheng, Wang, et al., 2013 - doi: 10.1371/journal.pone.0054154 - pmid: 23342093 - - citation: Oellrich, Walls et al., 2015 - doi: 10.1186/s13007-015-0053-y - pmid: 25774204 diff --git a/Glycine/max/wip_wei/Head_Galos_2012_traits.yml b/Glycine/max/wip_wei/Head_Galos_2012_traits.yml deleted file mode 100644 index 1c315d2..0000000 --- a/Glycine/max/wip_wei/Head_Galos_2012_traits.yml +++ /dev/null @@ -1,33 +0,0 @@ ---- -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 -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: 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 - ---- -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 -confidence: 3 -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 diff --git a/Glycine/max/wip_will/README.md b/Glycine/max/wip_will/README.md deleted file mode 100644 index e2ac2a2..0000000 --- a/Glycine/max/wip_will/README.md +++ /dev/null @@ -1,15 +0,0 @@ -# Using gene_model_full_id_finder.py - -#### Purpose -The purpose of this script is to take in your .traits.yml file that is missing gene_model_full_ids and output an updated file with the correct gene_model_full_ids. - -#### Requirements -1. This script requires the corresponding `.tsv` file for species you are looking at. i.e. `Glycine.pan3.YWTW.clust.tsv` for Glycine Max. This file can be found at https://data.legumeinfo.org/Glycine/GENUS/pangenes/Glycine.pan3.YWTW/. You will need to unzip this file using `gunzip Glycine.pan3.YWTW.clust.tsv.gz`. Additionally, you want this file to be in the same directory as the `gene_model_full_id_finder.py` script. -2. Then open up the file `gene_model_full_id_finder.py`in a text editor or IDE. -3. Look for the variable name on lines 48 and 49 `GLYMA_YAML_PATH` and `GLYMA_TSV_PATH`. You should make those varaibles the path to the `.yml` file and and `.tsv` file respectively. -4. Then locate (line 52) where it says `gene_model_full_id_finder(GLYMA_TSV_PATH, GLYMA_YAML_PATH, 'g_outfile.yml')`. `g_outfile.yml` is the name of the output file, but you can change this to be whatever path you want. -5. Save and Run the script by running - -```bsh - python gene_model_full_id_finder.py -``` diff --git a/Glycine/max/wip_will/gene_model_full_id_finder.py b/Glycine/max/wip_will/gene_model_full_id_finder.py deleted file mode 100644 index fe1aaba..0000000 --- a/Glycine/max/wip_will/gene_model_full_id_finder.py +++ /dev/null @@ -1,60 +0,0 @@ -import yaml - - -def gene_model_full_id_finder(tsv_path, yaml_path, output_path): - """# finds gene_model_full_id in tsv file based on gene_model_pub_name and adds it to the yaml file""" - with open(tsv_path, 'r') as tsv_file: - # Open the YAML file and load its contents as separate Python objects - with open(yaml_path, 'r') as file: - documents = yaml.load_all(file, Loader=yaml.Loader) - tsv_file_read = tsv_file.read() - output_data = [] - for document in documents: - # Process each YAML document delimited by '---' - gene_model_pub_name = document['gene_model_pub_name'] - for row in tsv_file_read.split('\n'): - items = row.split('\t') - for item in items: - if gene_model_pub_name in item: - gene_model_full_id = item - document['gene_model_full_id'] = gene_model_full_id - output_data.append(document) - - # Write the output data to outfile.yml - with open(output_path, 'w') as outfile: - yaml.dump_all(output_data, outfile) - - -def get_gene_model_full_id_dictionary(tsv_path, yaml_path): - """returns a dictionary of gene_model_pub_name:gene_model_full_id""" - with open(tsv_path, 'r') as tsv_file: - # Open the YAML file and load its contents as separate Python objects - with open(yaml_path, 'r') as file: - documents = yaml.load_all(file, Loader=yaml.Loader) - tsv_file_read = tsv_file.read() - output_data = {} - for document in documents: - # Process each YAML document delimited by '---' - gene_model_pub_name = document['gene_model_pub_name'] - for row in tsv_file_read.split('\n'): - items = row.split('\t') - for item in items: - if gene_model_pub_name in item: - gene_model_full_id = item - output_data[gene_model_pub_name] = gene_model_full_id - return output_data - - -GLYMA_YAML_PATH = 'FILE.traits.yml' -GLYMA_TSV_PATH = 'Glycine.pan3.YWTW.clust.tsv' - -# find the gene model full id in the tsv file for GLYMA -gene_model_full_id_finder(GLYMA_TSV_PATH, GLYMA_YAML_PATH, 'g_outfile.yml') - - -# find the gene model full id in the tsv file for Medicago - -# MEDICAGO_YAML_PATH = 'wip_steven/Oellrich_Walls_2015_medtr.medtr.traits.yml' -# MEDICAGO_TSV_PATH = 'Medicago.pan1.XXQ6.clust.tsv' - -# gmfi_finder(MEDICAGO_TSV_PATH, MEDICAGO_YAML_PATH, 'm_outfile.yml') diff --git a/Glycine/soja/wip_greg/Jin_Sun_2021.yml b/Glycine/soja/studies/Jin_Sun_2021.yml similarity index 100% rename from Glycine/soja/wip_greg/Jin_Sun_2021.yml rename to Glycine/soja/studies/Jin_Sun_2021.yml diff --git a/Glycine/soja/wip_greg/Qi_Li_2014.yml b/Glycine/soja/studies/Qi_Li_2014.yml similarity index 100% rename from Glycine/soja/wip_greg/Qi_Li_2014.yml rename to Glycine/soja/studies/Qi_Li_2014.yml diff --git a/Lotus/japonicus/wip_marlene/Soyano_Hirakawa_2014.yml b/Lotus/japonicus/studies/Soyano_Hirakawa_2014.yml similarity index 100% rename from Lotus/japonicus/wip_marlene/Soyano_Hirakawa_2014.yml rename to Lotus/japonicus/studies/Soyano_Hirakawa_2014.yml diff --git a/Medicago/truncatula/wip_steven/done/Oellrich_Walls_2015.traits.yml b/Medicago/truncatula/studies/Oellrich_Walls_2015.traits.yml similarity index 100% rename from Medicago/truncatula/wip_steven/done/Oellrich_Walls_2015.traits.yml rename to Medicago/truncatula/studies/Oellrich_Walls_2015.traits.yml diff --git a/Medicago/truncatula/wip_wei/Wang_Lu_2022.MtGSTF7.yml b/Medicago/truncatula/studies/Wang_Lu_2022.MtGSTF7.yml similarity index 100% rename from Medicago/truncatula/wip_wei/Wang_Lu_2022.MtGSTF7.yml rename to Medicago/truncatula/studies/Wang_Lu_2022.MtGSTF7.yml diff --git a/Medicago/truncatula/wip_steven/done/Oellrich_Walls_2015.citations.txt b/Medicago/truncatula/wip_steven/done/Oellrich_Walls_2015.citations.txt deleted file mode 100644 index 02384bb..0000000 --- a/Medicago/truncatula/wip_steven/done/Oellrich_Walls_2015.citations.txt +++ /dev/null @@ -1,31 +0,0 @@ -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. 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PMID: 25406544." diff --git a/Phaseolus/vulgaris/wip_marlene/phavu_Davila-Delgado_Flores-Canul_2023.yml b/Phaseolus/vulgaris/studies/Davila-Delgado_Flores-Canul_2023.yml similarity index 100% rename from Phaseolus/vulgaris/wip_marlene/phavu_Davila-Delgado_Flores-Canul_2023.yml rename to Phaseolus/vulgaris/studies/Davila-Delgado_Flores-Canul_2023.yml diff --git a/Pisum/sativum/wip_marlene/Sato_Morita_2007.yml b/Pisum/sativum/studies/Sato_Morita_2007.yml similarity index 100% rename from Pisum/sativum/wip_marlene/Sato_Morita_2007.yml rename to Pisum/sativum/studies/Sato_Morita_2007.yml diff --git a/README.md b/README.md deleted file mode 100644 index 89dda9e..0000000 --- a/README.md +++ /dev/null @@ -1,84 +0,0 @@ -# Gene Function and Phenotype - -## Files -Experimentally-based information about gene function and plant phenotype, and the associated supporting references, are stored in three files per species, in a **gene_functions** directory. -Those files are the following - with "gensp" being the abbreviation for the present **gen**us and **sp**ecies: -- gensp.traits.yml -- gensp.citations.txt (Note the "txt" extension; this file will be left uncompressed). -- gensp.references.txt (Note the "txt" extension; this file will be left uncompressed). - -The **gensp.traits.yml** file is produced by a curator (with some assistance from the get_citations.pl script; see below*), and represents minimal essential information about a gene and its function as described by literature cited in the file. - -The **gensp.citations.txt** file is generated by the script **get_citations.pl**, which takes gensp.traits.yml as input. This file has five fields: DOI, PubMedID, PubMedCentralID, Author-Author-Year, and full citation. (\*Note that the **get_citations.pl** script can help fill in reference elements in gensp.traits.yml -- specifically, adding doi given the pmid, or the pmid given the doi.) - -The **gensp.references.txt** file is generated by the script **get_references.pl**, which takes the gensp.citations.txt as input. This file has the [MEDLINE-format](https://www.nlm.nih.gov/bsd/mms/medlineelements.html) publication information (authors, title, abstract, etc.) for the citations in gensp.citations.txt. - -The traits.yml file contains one or more yaml "documents", indicated by three leading dashes (`---`) at the top of each document. Each holds information about one gene with experimentally-established function or trait association. A document might also be thought of as a "function card", with information about one gene for which a phenotypic effect has been established. - -## Curation and review process -Because the curation process for this type of data involves close reading and review of scientific literature, and because several curators will be doing this work, we will prepare the files away from the main Data Store. After review and revision if needed, new gene records (as yaml documents) will be added to the appropriate gensp.traits.yml file in the Data Store. Draft curation work will go into the [gene-function-registry](https://github.com/legumeinfo/gene-function-registry) repository, and then go into the Data Store file system -- and from there, into the [datastore-metadata](https://github.com/legumeinfo/datastore-metadata) repository. - -Protocols for the curation process will be maintained at the [datastore-specifications](https://github.com/legumeinfo/datastore-specifications) repository -- specifically, in [PROTOCOLS/gene_functions](https://github.com/legumeinfo/datastore-specifications/tree/main/PROTOCOLS/gene_functions). The other relevant working document is the [tracking spreadsheet](https://docs.google.com/spreadsheets/d/1iDdaIQNqK8jvkyQZHATSC1gI-FVhlKv5xde4yPR-Rzs/edit#gid=1914121906), where we'll note who is working on what manuscripts, and their status. - -## Content of the **gensp.traits.yml** file -There are ten top-level keys - four of which contain an array of key-value pairs. Note that if a value is not available for a (non-required) key, the key should simply be omitted (i.e. don't include the key without a value or with a blank or null in the value field). - -``` ---- -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 -comments: - - Mutational and association analysis relative to classical locus. -phenotype_synopsis: GmGI modulates flowering time, delaying expression of GmFT2a under long days. -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 -``` - -The **classical_locus** block is optional. It holds the name of a locus that has been defined in literature about this species, typically naming a mapped phenotype. For example, in soybean, the "E2" locus is one of several named "earliness" loci. In pea, the "I" locus was used by Mendel to name the yellow-or-green seed-color locus ("I" indicating yellow and "i" indicating green). This block holds a single value. - -The **gene_symbols** block is optional. It holds the name of a locus as described in literature about a mapped trait. This block may hold multiple values, since it is not uncommon for different publications to use different locus names. The first listed name will be considered "preferred." - -The **gene_symbol_long** block is optional. It holds the "spelled out" or descriptive name of the gene symbol. - -The **gene_model_pub_name** block is required. It holds the name of a gene as identified in the first citation from the "references" section. This gene name may be from any annotation. It will typically be "bare," without indication of assembly or annotation versions. - -The **gene_model_full_id** block is required. It holds the fully-qualified gene ID, with components "gensp.Accession.gnm#.ann#.gene_ID". The "gene_ID" may be the same as **gene_model_pub_name**, but may be different if a corresponding and preferable gene model is available from another assembly and/or annotation. The purpose of this ID is to enable linking this gene to other resources at SoyBase/LIS/PeanutBase. - -The **confidence** block is to have values [1-5]. This field indicates level of experimental support, with 5 being the strongest -- typically consisting of evidence at the level of a genetic complementation test, or otherwise observed as a mutant phenotype (experimental evidence code IMP) associated with the mutated form of the indicated gene. A level of 3 would be strong associational support, but lacking experimental lab validation such as genetic complementation. Levels 1 and 2 would be high-throughput evidence, and generally will NOT be collected in the SoyBase/LIS/PeanutBase projects. Papers that report lists of "candidate genes" in the vicinity of a GWAS or QTL region would be level 1 or 2 support, and should generally not be collected here. - -The **comments** block is for unstructured text, if needed for curatorial comments or other purposes. Comments must be entered as an array - i.e. with leading spaces and dash before each comment string. - -The **phenotype_synopsis** block is for unstructured text, to give a brief human-readable description of the main phenotype associated with this gene (either through its wildtype or mutant form, but inferred relative to the mutant phenotype). - -The **traits** block must contain at least one "entity" key with a valid ontology accession. Trait or Plant ontologies (TO and PO) are preferred where possible. Optionally (and generally discouraged due to the complexity and difficulty of getting this right), a modifying ontology term may be added to a trait block, in association with (listed underneath) an entity term. A modifier could be a "quality" or a "relation" key with a relation ontology may be associated with the entity ontology. Quality terms typically come from the Phenotype And Trait Ontology, [https://www.ebi.ac.uk/ols4/ontologies/pato](PATO) , and relation terms typically come from the Relations Ontology, [RP](https://www.ebi.ac.uk/ols4/ontologies/ro) The association between entity and relation ontology terms is established by proximity: entity and term followed by relation and term. However, to reiterate: focus on the primary entities, from TO or PO, and don't get bogged down with selecting modifiers. - -The **references** block contains one or more blocks of citations, each containing three key-value pairs: "citation", "doi", and "pmid". Of these, the doi is required (some publications lack a pmid, but all should have a doi). The pmid should be provided if available (the **get_citations.pl** will do this if the curator does not). The citation should be in one of the following forms (depending on whether there are one, two, or three-or-more authors): -``` - LastName, YEAR - LastName, LastName, YEAR - LastName, LastName et al., YEAR -``` - - diff --git a/Vicia/faba/studies/Jayakodi_Golicz_2023.yml b/Vicia/faba/studies/Jayakodi_Golicz_2023.yml new file mode 100644 index 0000000..cbb7aeb --- /dev/null +++ b/Vicia/faba/studies/Jayakodi_Golicz_2023.yml @@ -0,0 +1,35 @@ +--- +gene_symbols: +gene_model_pub_name: Vfaba.Hedin2.R1.4g051440.1 +gene_model_full_id: vicfa.Hedin2.gnm1.ann1.4g051440.1 +confidence: 4 +comments: + - Evidence based on GWAS, allele analysis, and homology to an Arabidopsis gene (CYP78A) involved in seed size regulation +phenotype_synopsis: Seed size regulation +traits: + - entity_name: seed size + entity: TO:0000391 +references: + - citation: Jayakodi, Golicz et al., 2023 + doi: 10.1038/s41586-023-05791-5 + pmid: 36890232 +--- +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 +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.\ +phenotype_synopsis: Control of hilum color +traits: + - entity_name: hilum color + entity: TO:0000968 +references: + - citation: Jayakodi, Golicz et al., 2023 + doi: 10.1038/s41586-023-05791-5 + pmid: 36890232 + + diff --git a/Vigna/radiata/wip_marlene/vigra_Liu_Zhang_2022.yml b/Vigna/radiata/studies/Liu_Zhang_2022.yml similarity index 100% rename from Vigna/radiata/wip_marlene/vigra_Liu_Zhang_2022.yml rename to Vigna/radiata/studies/Liu_Zhang_2022.yml