Genome-Wide Association Study of Pod Nutritional-Quality Traits in Cowpea (Vigna unguiculata [L.] Walp)

Cowpea is a multipurpose leguminous crop that plays an important role in human dietary nutrition and agricultural sustainability due to its rich nutritional quality. Improving the nutritional quality of pods in new cultivars has become a priority objective in cowpea breeding. However, the genetic architecture of pod nutritional quality in the cowpea remains unclear. In the current study, five cowpea pod nutritional quality traits, including the amino acid content (AA), cellulose content (CC), crude protein content (PR), starch content (PTS), and soluble sugar content (PSS), were evaluated in a diversity panel of 215 cowpea landraces. It was found that all five traits showed substantial variation in this population, and the two subspecies, vegetable cowpea and grain cowpea, had different nutritional patterns in fresh pods. Using GWAS, a total of 20 genomic regions were identified as significantly associated with the five nutritional quality traits. Haplotype analysis further determined the corresponding favorable haplotype for each locus. In addition, 275 predicted genes were identified as the candidate genes for the selected regions, of which three predicted genes—VuG9806G012380, encoding an oligopeptide transporter protein, VuG9806G016720, encoding an α-glucosidase-like protein, and VuG9811G017840, encoding a glycoside hydrolase protein—were regarded as the likely candidate genes for AA_6.2, AA_6.3, and PSS_11.1, respectively. These results unravel the genetic basis of pod nutritional quality and will facilitate the molecular breeding of high-nutritional-quality cowpea varieties.