Whole Genome Re-sequencing Based GWAS Identifies Candidate Genes Leading to Development of KASP Marker for Seed Size Traits in Lentil (Lens Culinaris Medik.)

Abstract

Lentil (Lens culinaris Medik.) has emerged as a protein-rich, abiotic stress-resilient, cool-season legume grown in arid and semi-arid areas of Asia, Middle-East, Asian countries, and Canada. Seed size plays a crucial role in deciding its monetary value and classification in the international market, along with key attributes such as cooking time and post-harvest milling quality. Therefore, the present study performs whole genome re-sequencing (WGRS) based genome-wide association study (GWAS) to narrow down genomic regions/candidate genes associated with seed size traits i.e. seed weight, seed diameter and seed thickness, using 170 lentil core set accessions from the National Genebank of India. Sequencing of these accessions on Illumina seq platform followed by stringent filtering, revealed 23,593 SNPs having genome-wide distribution with a linkage disequilibrium (LD) decay of 59,604 bp. In parallel, the accessions were phenotyped for seed size traits at three different locations for two consecutive years. GWAS integrating genotypic and phenotypic data using different multi-locus GWAS models identified 9 SNPs significantly associated with seed size traits. Among these, a SNP (CHR6_174959614) was anchored to a gene encoding the Photosystem II D2 protein, known to have a role in regulating seed size in other plant species. Further, the Kompetitive Allele Specific PCR marker developed from associated SNP CHR6_174959614 showed significant allelic association with seed size traits in an independent lentil germplasm panel of 91 accessions. The results of this study could potentially accelerate the marker-assisted breeding programs to enhance seed size and in turn yield of lentil.