Alterations to glyma.Zhang_Sun_2018.yml (#91)

* Rename glyma.Zhang_Sun_2017.yml to glyma.Zhang_Sun_2018.yml and alter the contents of this gene function file

* Alterations to glyma.Zhang_Sun_2018.yml on 23 December 2024

* Alterations to glyma.Zhang_Sun_2018.yml on 27 December 2024

* Alterations Part Deux to glyma.Zhang_Sun_2018.yml on 27 December 2024

* Alterations Part Trois to glyma.Zhang_Sun_2018.yml on 27 December 2024

* Eliminate Trailing Spaces on Line 35 in glyma.Zhang_Sun_2018.yml on 27 December 2024

Glycine/max/studies/glyma.Zhang_Sun_2018.yml

@@ -0,0 +1,55 @@
+---
+scientific_name: Glycine max
+gene_symbols:
+  - GmB1
+gene_symbol_long: Bloom 1
+gene_model_pub_name: Glyma.13G241700
+gene_model_full_id: glyma.Wm82.gnm4.ann1.Glyma.13G241700
+confidence: 4
+curators:
+  - Marlene Dorneich-Hayes
+  - Scott Kalberer
+comments:
+  - Seed coat bloom proteins are synthesized within the pod endocarp and adhere
+    to the surface of the seed coat. During Glycine max domestication, selection
+    for the recessive mutant allele bloom 1 (Gmb1) gave rise to both the shiny
+    no-bloom coat phenotype and elevated seed oil content.
+  - A point mutation from C to T in the coding sequence of the dominant allele
+    Bloom 1 (GmB1) causes an amino acid change from cysteine to arginine
+    resulting in a loss of helix protein structure.
+  - Gene expression levels of B1 were higher than b1 in transgenic Williams82,
+    which suggests the C to T polymorphism impacts transcription.
+  - Gene expression levels of the allele B1 in developing pods, pod endocarp,
+    seeds, and seed coats were positively correlated with the amount of bloom
+    deposition. The C to T polymorphism was associated with different seed coat
+    bloom phenotypes among Glycine soja and G. max accessions.
+  - High B1-allele expression in transgenic soybean plants was associated with
+    reduced seed oil accumulation relative to b1 controls. Genome-wide SNP data
+    from G. max accessions revealed a seed oil QTL associated with bloom in the
+    410 kb selective sweep region, suggesting the B1 locus may have pleiotropic
+    effects on oil content.
+  - The transcription factors GmWRI1a, GmLEC1a, GmLEC1b and GmABI3b upregulate
+    fatty acid biosynthesis in soybean seeds. Overexpression of B1 was
+    associated with reductions in gene expression for all four transcription
+    factors in developing pods and pod endocarp, but didn't impact transcription
+    or fatty acid biosynthesis in developing seed coat and seeds.
+phenotype_synopsis:
+  - Bloom 1 (GmB1) encodes a transmembrane transporter-like protein that not
+    only controls seed coat bloom but also exerts pleiotropic effects on seed
+    oil content following up-regulated oil biosynthesis in pods.
+traits:
+  - entity_name: regulation of seed growth
+    entity: GO:0080113
+  - entity_name: seed development
+    entity: GO:0048316
+  - entity_name: fat and essential oil content
+    entity: TO:0000604
+  - entity_name: seed coat luster
+    entity: TO:0000888
+references:
+  - citation: Zhang, Sun et al., 2018
+    doi: 10.1038/s41477-017-0084-7
+    pmid: 29292374
+  - citation: Zuo, Ikram et al., 2022
+    doi: 10.1016/j.csbj.2022.06.014
+    pmid: 35782726