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

  • [G. soja (gene)]
  • Detail of Experiment mapped on Glycine soja W05 GsW05V1

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 soja
Metadata export .CSV   .JSON

Analysis

Mapped Genomes GsW05V1    
Expression Analysis Expression Profile /  Differential Expression /  Co-expression

Conditions

Name Genotype Mutation Stage Tissue Treatment Level Time Samples Xref Download alignments
Y1_G15 Y1 pods at 15 day pod
  • Y1_G15_1
 .bam    .bai    .csi   
Y1_G5 Y1 pods at 5 day pod
  • Y1_G5_1
 .bam    .bai    .csi   
Y1_H Y1 flower flower
  • Y1_H_1
 .bam    .bai    .csi   
Y1_JJ Y1 apical bud apical bud
  • Y1_JJ_1
 .bam    .bai    .csi   
Y1_WH Y1 flower bud flower bud
  • Y1_WH_1
 .bam    .bai    .csi   
Y2_G15 Y2 pods at 15 day pod
  • Y2_G15_1
 .bam    .bai    .csi   
Y2_G5 Y2 pods at 5 day pod
  • Y2_G5_1
 .bam    .bai    .csi   
Y2_H Y2 flower flower
  • Y2_H_1
 .bam    .bai    .csi   
Y2_JJ Y2 apical bud apical bud
  • Y2_JJ_1
 .bam    .bai    .csi   
Y2_WH Y2 flower bud flower bud
  • Y2_WH_1
 .bam    .bai    .csi   
Y3_G15 Y3 pods at 15 day pod
  • Y3_G15_1
 .bam    .bai    .csi   
Y3_G5 Y3 pods at 5 day pod
  • Y3_G5_1
 .bam    .bai    .csi   
Y3_H Y3 flower flower
  • Y3_H_1
 .bam    .bai    .csi   
Y3_JJ Y3 apical bud apical bud
  • Y3_JJ_1
 .bam    .bai    .csi   
Y3_WH Y3 flower bud flower bud
  • Y3_WH_1
 .bam    .bai    .csi   
Y4_G15 Y4 pods at 15 day pod
  • Y4_G15_1
 .bam    .bai    .csi   
Y4_G5 Y4 pods at 5 day pod
  • Y4_G5_1
 .bam    .bai    .csi   
Y4_H Y4 flower flower
  • Y4_H_1
 .bam    .bai    .csi   
Y4_JJ Y4 apical bud apical bud
  • Y4_JJ_1
 .bam    .bai    .csi   
Y4_WH Y4 flower bud flower bud
  • Y4_WH_1
 .bam    .bai    .csi