Single and multi-trait genome-wide association studies identify genomic regions associated with phenological traits in cowpea

Understanding the genetic control of traits linked to phenology is essential to address strategies and efforts in the development of resilient cultivars capable of adapting to climate change. In this study, we performed genome-wide association studies on a cowpea [Vigna unguiculata (L.) Walp] mini-core collection to dissect the genetic architecture and identify genomic regions associated with days to flowering, days from flowering to pod maturity, and days to pod maturity. Phenotypic data were collected in 2 years and used to test associations with 41,533 single-nucleotide polymorphism markers by single and multi-trait analysis. In addition, we searched for candidate genes putatively involved in phenological traits within genome-associated regions. The single-trait approach identified 28 significant marker-trait associations for the three traits, while the multi-trait identified 18 significant associations, both evidencing pleiotropic associations. Five of these markers were associated with phenological traits reported in previous studies. Candidate genes were identified, including genes involved in phosphorylation and encoding the maternal effect embryo arrest 60, known to be associated with pod maturity and flowering, respectively. Functional validation of these genes will further improve our understanding of the variation of phenological traits in cowpea and other related crops. Substantial genetic variation for phenological traits was found in the cowpea mini-core collection.A total of 46 single nucleotide polymorphisms (SNPs) were detected for days to flowering, days from flowering to pod maturity, and days to pod maturity.Some SNPs were significant for two traits simultaneously, suggesting a pleiotropic effect.Gene annotation identified 39 unique genes, of which 18 were characterized according to biological processes.