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

Liny Lay; Waleed Khan; Hyun Jo; Seong-Hoon Kim; Yoonha Kim

doi:10.1007/s11032-024-01516-2

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

Mol Breed. 2024 Nov 19;44(12):80. doi: 10.1007/s11032-024-01516-2. eCollection 2024 Dec.

Authors

Liny Lay¹, Waleed Khan¹, Hyun Jo¹, Seong-Hoon Kim², Yoonha Kim¹

Affiliations

¹ Department of Applied Biosciences, Kyungpook National University, Daegu, 41566 Republic of Korea.
² National Agrobiodiversity Center, National Institute of Agricultural Sciences, RDA, Jeonju, 54874 Republic of Korea.

PMID: 39574799
PMCID: PMC11576706 (available on 2025-11-19)
DOI: 10.1007/s11032-024-01516-2

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.

© The Author(s), under exclusive licence to Springer Nature B.V. 2024. Springer Nature or its licensor (e.g. a society or other partner) holds exclusive rights to this article under a publishing agreement with the author(s) or other rightsholder(s); author self-archiving of the accepted manuscript version of this article is solely governed by the terms of such publishing agreement and applicable law.