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 Gm508Wm82a4V1


NameMutations in Argonaute5 Illuminate Epistatic Interactions of the K1 and I Loci Leading to Saddle Seed Color Patterns in Glycine max
DescriptionThe soybean (Glycine max) seed coat has distinctive, genetically programmed patterns of pigmentation and the recessive k1 mutation can epistatically overcome the dominant I and i-i alleles, which inhibit seed color by producing small interfering RNAs (siRNAs) targeting chalcone synthase (CHS) mRNAs. Small RNA sequencing of dissected regions of immature seed coats demonstrated that CHS siRNA levels cause the patterns produced by the i-i and i-k alleles of the I locus, which restrict pigment to the hilum or saddle region of the seed coat, respectively. To identify the K1 locus, we compared RNA-Seq data from dissected regions of two Clark isolines having similar saddle phenotypes mediated by CHS siRNAs but different genotypes (homozygous i-k K1 versus homozygous i-i k1). By examining differentially expressed genes, mapping information, and genome resequencing, we identified a 129-bp deletion in Glyma.11G190900 encoding Argonaute5 (AGO5), a member of the Argonaute family. Amplicon sequencing of several independent saddle pattern mutants from different genetic backgrounds revealed independent lesions affecting AGO5, thus establishing Glyma.11G190900 as the K1 locus. Non-functional AGO5 from k1 alleles leads to altered distributions of CHS siRNAs, thus explaining how the k1 mutation reverses the phenotype of the seed coat regions from yellow to pigmented, even in the presence of the normally dominant I or i-i alleles. Overall design: Immature seed coats of 100-200 mg with chimeric pigmented phenotypes of Clark 8 (i-k, K1) or Clark 18a (i-i, k1) were separated into the regions destined to become either the black saddle region or the yellow sections. Extracted mRNAs were subjected to high throughput sequencing and analyzed for expression analyses to determine the genetic differences conferred by the K1 locus or the differences in expression in different dissected regions of the seed coat.
ContactLila Vodkin, Crop Sciences, University of Illinois
SpeciesGlycine max
Metadata export .CSV   .JSON


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


Name Genotype Mutation Stage Tissue Treatment Level Time Samples Xref Download alignments
black_saddle immature seed coat 100-200 mg fresh seed weight
  • black_saddle_1
  • black_saddle_2
  • black_saddle_3
  • black_saddle_4
  • black_saddle_5
  • black_saddle_6
.bam    .bai    .csi   
.bam    .bai    .csi   
.bam    .bai    .csi   
.bam    .bai    .csi   
.bam    .bai    .csi   
.bam    .bai    .csi   
yellow_region immature seed coat 100-200 mg fresh seed weight
  • yellow_region_1
  • yellow_region_2
  • yellow_region_3
  • yellow_region_4
  • yellow_region_5
  • yellow_region_6
.bam    .bai    .csi   
.bam    .bai    .csi   
.bam    .bai    .csi   
.bam    .bai    .csi   
.bam    .bai    .csi   
.bam    .bai    .csi