Genome-Wide Association Study on Cowpea seed coat color using RGB images

Abstract

This study delves into the genetic mechanisms underlying seed coat color variation in cowpeas (Vigna unguiculata [L.] Walp.), a trait with significant implications for nutritional value, consumer preference, and adaptation to environmental stresses. Through a genome-wide association study (GWAS) involving cowpea accessions exhibiting red, green, and blue seed coats, we identified 16 significant single nucleotide polymorphisms (SNPs) distributed across chromosomes 3, 4, 5, 9, 10, and 11. Our analysis highlighted the polygenic nature of seed coat color, emphasizing the shared SNP loci across different colors, suggesting integrated genetic influence or linked inheritance patterns, especially on chromosomes 9 and 10. We highlighted candidate genes, including Pentatricopeptide repeat family (PPR), Lupus La-related protein/La-related protein 1, and Udp-glycosyltransferase 71b2-related genes on chromosome 9, and MYB-like DNA-binding (MYB) genes on chromosome 10, all of which are implicated in pigment biosynthesis and regulatory pathways crucial to seed coat coloration and plant physiological processes. Our results corroborate previous findings linking seed coat color to the anthocyanin biosynthesis pathway and reveal the complex genetic architecture and phenotypic plasticity inherent in cowpeas. The overlap in quantitative trait loci (QTL) regions across different seed coat colors points to a shared genetic basis, potentially enabling the manipulation of seed coat color to enhance the nutritional profile and marketability of cowpeas.

Supplementary information: The online version contains supplementary material available at 10.1007/s11032-024-01516-2.

Keywords: Cowpea; Fiji ImageJ; GWAS; Seed coat color.