Identification of Candidate Genes Controlling Red Seed Coat Color in Cowpea (Vigna unguiculata [L.] Walp)

Abstract

Seed coat color is an important consumer-related trait of the cowpea (Vigna unguiculata [L.] Walp.) and has been a subject of study for over a century. Utilizing newly available resources, including mapping populations, a high-density genotyping platform, and several genome assemblies, the red seed coat color has been mapped to two loci, Red-1 (R-1) and Red-2 (R-2), on Vu03 and Vu07, respectively. A gene model (Vigun03g118700) encoding a dihydroflavonol 4-reductase, a homolog of anthocyanidin reductase 1, which catalyzes the biosynthesis of epicatechin from cyanidin, has been identified as a candidate gene for R-1. Possible causative variants have also been identified for Vigun03g118700. A gene model on Vu07 (Vigun07g118500), with predicted nucleolar function and high relative expression in the developing seed, has been identified as a candidate for R-2. The observed red color is believed to be the result of a buildup of cyanidins in the seed coat.

The pattern of genetic variability in a core collection of 2,021 cowpea accessions

“…Thus, we consider Vigun03g118700 to be the likely causal locus for the red seed coat color phenotype. This candidate gene was also independently proposed as regulating red seed coat color based on the results of QTL mapping in a biparental F2 population and GWAS in the UCR minicore population ( Herniter et al . 2024 ).…”

Seed-Coat Pigmentation Plays a Crucial Role in Partner Selection and N2 Fixation in Legume-Root–Microbe Associations in African Soils

“…Chromosome Pv08 therefore plays a key role in the phenylpropanoid pathway, with significant effects on common bean seed-coat pigmentation. The genetic basis of the red seed-coat color in cowpea was found to involve two loci, Red-1 (R-1) on chromosome Vu03 and Red-2 (R-2) on chromosome Vu07 [ 35 ]. The candidate gene for R-1 was Vigun03g118700 , encoding dihydroflavonol 4-reductase, which is a cyanidin biosynthesis catalyst, while the candidate gene for R-2 was Vigun07g118500 , with a nucleolar function and elevated expression in developing seeds.…”

“…The candidate gene for R-1 was Vigun03g118700 , encoding dihydroflavonol 4-reductase, which is a cyanidin biosynthesis catalyst, while the candidate gene for R-2 was Vigun07g118500 , with a nucleolar function and elevated expression in developing seeds. The red color was attributed to the accumulation of cyanidin in the seed coat [ 35 ].…”

“…These molecules include flavonoids, proteins, peptides, amino acids, alkaloids, and terpenoids [ 65 , 75 ]. Flavonoids are phenolic secondary metabolites that confer color on seeds, flowers, and fruits [ 35 ]. They play many important roles in plant development, including defense against insect pests and diseases, as well as nodulation in symbiotic legumes ( Table 1 ; Figure 1 ) [ 65 , 77 , 78 , 79 ].…”