Identification of a Candidate Gene Controlling Black Color in Cowpea Seed Coats

Cowpea (Vigna unguiculata) is a major source of calories in sub-Saharan Africa, as well as an important diet component in southeast Asia and elsewhere. One of the most important traits of cowpea from the perspective of consumer acceptance is the seed coat color and pattern. In marketplaces all across the world different seed coat colors are sold, with the preferred colors and patterns for different uses, such as ground for flour or cooked whole, highly localized. This means that consumer acceptance is much more easily achieved if new varieties appear similar to previously preferred varieties. In this study, we put forward a candidate gene for controlling presence of black color in the cowpea seed coat. This gene is homologous to the soybean gene Glyma.09G235100, which encodes a MYB transcription factor regulating anthocyanin production. The candidate gene was identified through QTL analyses in two RIL populations of 95 and 121 lines, respectively, and GWAS in a minicore collection containing 370 world-wide accessions. Genotyping of these populations was conducted using the Cowpea iSelect Consortium Array containing 51,128 SNPs. Expression of the gene appears to be controlled by a presence/absence variation, with the candidate gene deleted in varieties not expressing black color in the seed coat.