LegumeIP V3: From Models to Crops - An Integrative Gene Discovery Platform for Translational Genomics in Legumes

  • [G. max (gene)]
  • Detail of Experiment mapped on Glycine max Wm82 Gm275Wm82a2V1

Details

NameTranscriptomic comparison reveals genetic variation potentially underlying seed developmental evolution of soybeans
DescriptionSoybean (Glycine max) was domesticated from its wild relative Glycine soja. However, the genetic variations underlying soybean domestication are not well known. Comparative transcriptomics revealed that a small portion of the orthologous genes might have been fast-evolving. In contrast, three gene expression clusters were identified as divergent by their expression patterns, which occupied 37.44% of the total genes, hinting at an essential role for gene expression alteration in soybean domestication. Moreover, the most divergent stage in gene expression between wild and cultivated soybeans occurred during seed development around the cotyledon stage (15 days after fertilization, G15). A module in which the coexpressed genes were significantly downregulated at G15 of wild soybeans was identified. The divergent clusters and modules included substantial differentially expressed genes (DEGs) between wild and cultivated soybeans related to cell division, storage compound accumulation, hormone-response, and seed maturation processes. Chromosomal-linked DEGs, quantitative trait loci controlling seed weight and oil content, and selection sweeps revealed candidate DEGs at G15 in the fruit-related divergence of G. max and G. soja. Our work establishes a transcriptomic selection mechanism for altering gene expression during soybean domestication, thus shedding light on the molecular networks underlying soybean seed development and breeding strategy.
ContactChinese Academy of Sciences
XrefPRJNA481793
Reference
Conditions20
SpeciesGlycine max
Metadata export .CSV   .JSON

Analysis

Mapped Genomes Gm275Wm82a2V1     Gm508Wm82a4V1    
Expression Analysis Expression Profile /  Differential Expression /  Co-expression

Conditions

Name Genotype Mutation Stage Tissue Treatment Level Time Samples Xref Download alignments
DN_G15 DN pods at 15 day pod
  • DN_G15_1
 .bam    .bai    .csi   
DN_G5 DN pods at 5 day pod
  • DN_G5_1
 .bam    .bai    .csi   
DN_H DN flower flower
  • DN_H_1
 .bam    .bai    .csi   
DN_JJ DN apical bud apical bud
  • DN_JJ_1
 .bam    .bai    .csi   
DN_WH DN flower bud flower bud
  • DN_WH_1
 .bam    .bai    .csi   
HF_G15 HF pods at 15 day pod
  • HF_G15_1
 .bam    .bai    .csi   
HF_G5 HF pods at 5 day pod
  • HF_G5_1
 .bam    .bai    .csi   
HF_H HF flower flower
  • HF_H_1
 .bam    .bai    .csi   
HF_JJ HF apical bud apical bud
  • HF_JJ_1
 .bam    .bai    .csi   
HF_WH HF flower bud flower bud
  • HF_WH_1
 .bam    .bai    .csi   
HN_G15 HN pods at 15 day pod
  • HN_G15_1
 .bam    .bai    .csi   
HN_G5 HN pods at 5 day pod
  • HN_G5_1
 .bam    .bai    .csi   
HN_H HN flower flower
  • HN_H_1
 .bam    .bai    .csi   
HN_JJ HN apical bud apical bud
  • HN_JJ_1
 .bam    .bai    .csi   
HN_WH HN flower bud flower bud
  • HN_WH_1
 .bam    .bai    .csi   
NF_G15 NF pods at 15 day pod
  • NF_G15_1
 .bam    .bai    .csi   
NF_G5 NF pods at 5 day pod
  • NF_G5_1
 .bam    .bai    .csi   
NF_H NF flower flower
  • NF_H_1
 .bam    .bai    .csi   
NF_JJ NF apical bud apical bud
  • NF_JJ_1
 .bam    .bai    .csi   
NF_WH NF flower bud flower bud
  • NF_WH_1
 .bam    .bai    .csi