Abstract
Seed size/weight is a major agronomic trait which determine crop productivity in legumes. To understand the genetic basis of seed size determination, we sought to identify DNA polymorphisms between two small (Himchana 1 and Pusa 362) and two large-seeded (JGK 3 and PG 0515) chickpea cultivars via whole genome resequencing. We identified a total of 75535 single nucleotide polymorphisms (SNPs), 6486 insertions and deletions (InDels), 1938 multi-nucleotide polymorphisms (MNPs) and 5025 complex variants between the two small and two large-seeded chickpea cultivars. Our analysis revealed 814, 244 and 72 seed-specific genes harboring DNA polymorphisms in promoter or non-synonymous and large-effect DNA polymorphisms, respectively. Gene ontology analysis revealed enrichment of cell growth and division related terms in these genes. Among them, at least 22 genes associated with quantitative trait loci, and those involved in cell growth and division and encoding transcription factors harbored promoter and/or large-effect/non-synonymous DNA polymorphisms. These also showed higher expression at late-embryogenesis and/or mid-maturation stages of seed development in the large-seeded cultivar, suggesting their role in seed size/weight determination in chickpea. Altogether, this study provided a valuable resource for large-scale genotyping applications and a few putative candidate genes that might play crucial role in governing seed size/weight in chickpea.
Highlights
Chickpea seed is enriched in essential amino acids, which can serve as readily and cheaply available source of dietary proteins
To understand the functional relevance of DNA polymorphisms in seed size/weight determination, we analyzed the effect of DNA polymorphisms on differential expression of seed-specific genes, genes involved in cell growth and division based on gene ontology (GO) terms, genes encoding transcription factors and those associated with QTLs
We identified a total of 355155 single nucleotide polymorphisms (SNPs), 10340 multi-nucleotide polymorphisms (MNPs), 32355 insertions and deletions (InDels) and 24847 complex variants among the small and large-seeded chickpea cultivars in one to one comparison (Supplementary file 1)
Summary
Chickpea seed is enriched in essential amino acids, which can serve as readily and cheaply available source of dietary proteins. We identified a total of 75535 SNPs, 1938 MNPs, 6486 InDels and 5025 complex variants that differentiated both small and large-seeded chickpea cultivars (Fig. 1a). (a) Percentage distribution of different types of DNA polymorphisms (SNPs, MNPs, InDels and complex) identified between the two small and two large-seeded chickpea cultivars in different genomic regions are shown in bar graphs.
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