Abstract
BackgroundWater permeability governed by seed coat is a major facet of seed crops, especially soybean, whose seeds lack physiological dormancy and experience rapid deterioration in seed viability under prolonged storage. Moreover, the physiological and chemical characteristics of soybean seeds are known to vary with seed coat color. Thus, to underpin the genes controlling water permeability in soybean seeds, we carried out an in-depth characterization of the associated genomic variation.ResultsIn the present study, we have analyzed genomic variation between cultivated soybean and its wild progenitor with implications on seed permeability, a trait related to seed storability. Whole genome resequencing of G.max and G. soja, identified SNPs and InDels which were further characterized on the basis of their genomic location and impact on gene expression. Chromosomal density distribution of the variation was assessed across the genome and genes carrying SNPs and InDels were characterized into different metabolic pathways. Seed hardiness is a complex trait that is affected by the allelic constitution of a genetic locus as well as by a tricky web of plant hormone interactions. Seven genes that hold a probable role in the determination of seed permeability were selected and their expression differences at different stages of water imbibition were analyzed. Variant interaction network derived 205 downstream interacting partners of 7 genes confirmed their role in seed related traits. Interestingly, genes encoding for Type I- Inositol polyphosphate 5 phosphatase1 and E3 Ubiquitin ligase could differentiate parental genotypes, revealed protein conformational deformations and were found to segregate among RILs in coherence with their permeability scores. The 2 identified genes, thus showed a preliminary association with the desirable permeability characteristics.ConclusionIn the light of above outcomes, 2 genes were identified that revealed preliminary, but a relevant association with soybean seed permeability trait and hence could serve as a primary material for understanding the molecular pathways controlling seed permeability traits in soybean.
Highlights
Water permeability governed by seed coat is a major facet of seed crops, especially soybean, whose seeds lack physiological dormancy and experience rapid deterioration in seed viability under prolonged storage
Identification and chromosomal distribution of Single nucleotide polymorphism (SNP) and Insertion deletions (InDels) A total of 77,339 and 215932 SNPs as well as 451,522 and 697,295 InDels were identified in G. max and G. soja, respectively, upon comparison with the reference genome after filtering
Mapping of maximum SNPs and InDels on chromosome 18 of soybean cultivars with contrasting mungbean yellow mosaic India virus resistance traits has been earlier reported [26] and is consistent with variation distribution observed for G. max in the present study
Summary
Water permeability governed by seed coat is a major facet of seed crops, especially soybean, whose seeds lack physiological dormancy and experience rapid deterioration in seed viability under prolonged storage. The physiological and chemical characteristics of soybean seeds are known to vary with seed coat color. To underpin the genes controlling water permeability in soybean seeds, we carried out an in-depth characterization of the associated genomic variation. Wild (G. soja) and cultivated soybean (G. max) differ in various morphological and physiological characteristics. Large seeds with variable seed coat colors are characteristic of cultivated varieties and referred to as permeable seeds, whereas wild species possess small, coarse black and hard seeds that display water impermeability. Wild and cultivated soybean differ in the extent of hardseededness, though considerable variation exists in the later for water permeability [1,2,3]. Moderately impermeable seed cultivars are desirable as they can maintain their post-harvest viability and quality
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