Genome-wide generation and genotyping of informative SNPs to scan molecular signatures for seed yield in chickpea

Udita Basu,Naveen Malik,Swarup K. Parida,Rishi Srivastava,Deepak Bajaj,Hari D. Upadhyaya,Virevol Thakro,Anurag Daware

doi:10.1038/s41598-018-29926-1

Abstract

We discovered 2150 desi and 2199 kabuli accessions-derived SNPs by cultivar-wise individual assembling of sequence-reads generated through genotyping-by-sequencing of 92 chickpea accessions. Subsequent large-scale validation and genotyping of these SNPs discovered 619 desi accessions-derived (DAD) SNPs, 531 kabuli accessions-derived (KAD) SNPs, 884 multiple accessions-derived (MAD) SNPs and 1083 two accessions (desi ICC 4958 and kabuli CDC Frontier)-derived (TAD) SNPs that were mapped on eight chromosomes. These informative SNPs were annotated in coding/non-coding regulatory sequence components of genes. The MAD-SNPs were efficient to detect high intra-specific polymorphic potential and wide natural allelic diversity level including high-resolution admixed-population genetic structure and precise phylogenetic relationship among 291 desi and kabuli accessions. This signifies their effectiveness in introgression breeding and varietal improvement studies targeting useful agronomic traits of chickpea. Six trait-associated genes with SNPs including quantitative trait nucleotides (QTNs) in combination explained 27.5% phenotypic variation for seed yield per plant (SYP). A pentatricopeptide repeat (PPR) gene with a synonymous-coding SNP/QTN significantly associated with SYP trait was found most-promising in chickpea. The essential information delineated can be of immense utility in genomics-assisted breeding applications to develop high-yielding chickpea cultivars.

Highlights

Chickpea (Cicer arietinum) is a self-pollinated, diploid (2n = 16) and economically important legume food crop rich in human dietary proteins[1]
The sequence reads generated by sequencing and genotyping of 92 desi and kabuli chickpea accessions using GBS assay were assembled cultivar-wise individually. This exertion successfully discovered various types of informative single nucleotide polymorphism (SNPs) including desi accessions-derived (DAD), kabuli accessions-derived (KAD)- and multiple accessions-derived (MAD)-SNPs which were further compared with two accessions (ICC 4958 and CDC Frontier) derived (TAD) SNPs for evaluating the potential of these developed markers in large-scale genetic analysis in chickpea (Fig. 1)
The optimized multiplex assay successfully validated 619 DAD, 531 KAD- and 1083 TAD-SNPs based on their homozygous and heterozygous allele discrimination as evident from the call cluster plots of low and high mass homo- and hetero-zygote yields with a 92–94% genotyping success rate (Tables 1 and S1–S4). The comparison of both DAD- and KAD-SNPs identified 884 MAD-SNPs differentiating all 92 desi and kabuli accessions together which were physically mapped on eight chickpea chromosomes (Tables 1 and S3)

Summary

Introduction

In view of aforementioned prospects, efforts were made in the current study for large-scale validation and high-throughput genotyping of informative SNPs, discovered by desi and kabuli cultivar-wise individual assembling of the sequence reads, generated from 92 accessions using GBS assay at a genome-wide scale in chickpea (Fig. 1) The efficacy of these validated whole genome/gene-derived SNPs to detect intra-specific polymorphism, molecular diversity and domestication pattern among 291 desi and kabuli cultivated chickpea accessions and for establishing marker-trait association with seed yield per plant were determined

Methods

Results

Conclusion