Genetic loci underlying seed size and yield-related traits in cowpea

Abstract

Understanding the genetic bases of seed size and yield-related traits in cowpea is important for enhancing the development of market demanded varieties. The objective of this study was to identify genomic regions associated with seed size and yield-related traits in cowpea. In this study, an F_6:7 recombinant inbred line (RIL) population consisting of 248 genotypes derived from a biparental cross involving RP270 (small seed in size) and BRSImponente (extra-large seed in size), was evaluated for two consecutive years in the field and in the glasshouse to identify quantitative trait loci (QTLs) with effects on these cowpea traits. The RILs were genotyped using a 2602 cowpea mid-density SNP panel, that was filtered down to 916 informative SNPs for the linkage analysis A total of 36 QTLs were associated with seed size, and eight with grain-yield related traits. Eight of the QTLs were found to be stable for seed size because of their presence in the same regions of the genome across the four environments. Two regions on chromosomes 7 and 11 contained QTL clusters for all evaluated traits. Gene annotations, gene ontology, and available literature on the genomic regions of QTL clusters and stable QTLs revealed 13 possible genes that might be participating in the regulation of seed-related traits of cowpea. Some SNPs were linked to multiple traits thereby reinforcing evidence of pleiotropy. These SNPs serve as valuable tools for marker-assisted selection (MAS) and genomic selection (GS), offering practical applications for developing cowpea varieties with market desired seed related traits and grain yield.