An Integrated Genome-Wide Strategy for Genetic Dissection of Complex Seed and Pod Yield Component Traits in Chickpea

Large-scale discovery and high-throughput genotyping of SNPs (single nucleotide polymorphisms) in diverse natural and mapping populations is required at genome-wide level for high-resolution association analysis and QTL (quantitative trait loci) mapping to accelerate genomics-assisted crop improvement in chickpea. The genotyping-by-sequencing (GBS) of 92 diverse desi and kabuli chickpea accessions representing a diverse seed and pod trait-specific association panel and individuals belonging to an intra-specific RIL (recombinant inbred line) mapping population (desi cv. ICC12299 × kabuli cv. ICC8261) discovered 44,844 and 43,358 genome-wide high quality SNPs, respectively. These SNPs were structurally and functionally annotated in diverse coding and non-coding sequence components of genes and genomes (chromosomes). Further, a genome-wide association study (GWAS) (using 44,844 SNPs) was integrated with ultra-high resolution genetic linkage map (inter-marker distance; 0.20-0.37 cM)-based QTL mapping (using 43,358 SNPs), differential expression profiling, gene-specific molecular haplotyping/linkage disequilibrium (LD) mapping and QTL-region specific haplotype/LD-based trait association analysis for quantitative dissection of complex seed and pod yield component traits in chickpea. This enabled us to delineate novel natural allelic variants and superior haplotypes in the potential candidate genes harbouring major QTLs specifically regulating seed/pod number and seed weight/size in chickpea. The efficacy of ultra-high resolution QTL region-specific haplotype-based association analysis as compared to conventional map-based positional cloning in rapid scale-down of the major QTLs into specific candidate gene(s) governing seed and pod traits was apparent. Collectively, the functionally relevant molecular tags scanned using integrated genomic strategies have potential to expedite marker-assisted genetic enhancement of crop plants, including chickpea.