Identification of Candidate Genes Controlling Black Seed Coat and Pod Tip Color in Cowpea (Vigna unguiculata [L.] Walp)

Walp) is a diploid warm-season legume, primarily consumed as a grain, vegetable, or fodder for livestock. The seeds are used for cooking as whole beans or ground into flour, while immature pods and leaves are consumed as green vegetables. Most cowpeas are grown by smallholder farmers under marginal conditions in sub-Saharan Africa, often as an intercrop. In the United States, cowpeas are part of the traditional cuisine of the Southern states and are consumed as both fresh and dry beans. Seed coat color is an important consumer-related trait in cowpea, with previous research indicating that consumers make decisions on the acceptability, quality, and presumed taste of a product depending on appearance, especially color. Color preferences vary across and within markets as consumers prefer specific seed coat traits for different uses. Newly developed cultivars will be more easily integrated into markets if the seeds are more visually similar to presently accepted cultivars. Research on the inheritance of seed coat traits in cowpea began in the early 20th century, with a factor called Black seed color (Bl) identified through the study of F2 populations. However, previous mapping efforts were hampered by the lack of high-resolution mapping technologies and a reference genome. This study makes use of available resources, including mapping populations, a reference genome, and a high-density single nucleotide polymorphism genotyping platform, to map the black seed coat and purple pod tip color traits, with the gene symbol Bl, in cowpea. Four populations were used for mapping: two biparental populations of recombinant inbred lines (RILs), an eight-parent Multiparent Advanced Generation Inter-Cross (MAGIC) population, and a minicore population representing the worldwide diversity of cultivated cowpea. One biparental population consists of 94 F6-8 RILs developed at the University of California, Riverside, derived from a cross between "California Blackeye 27" and "IT82E-18." The other biparental RIL population was provided by the International Institute for Tropical Agriculture and consists of 121 F6-8 RILs derived from a cross between "Sanzi" and "Vita 7." The seeds of each of these four parents show great phenotypic diversity, including in seed coat color traits. Phenotypic data for seed coat color were collected through visual examination of the seeds. Both biparental RIL populations and the MAGIC population segregated for black seed coat color. In the CB27 by IT82E-18 population, lines were scored as "black" or "brown." In the Sanzi by Vita 7 population, lines were scored as "purple-black" or "tan." In both the MAGIC and the minicore populations, lines were scored as "black" or "non-black." Segregation distortion of the phenotypic data was observed in all four populations, with black-seeded lines given the score "1" and non-black-seeded lines given the score "0."