The GWAS outputs for Cowpea (Vigna unguiculata) responses to drought stress at early vegetative stress. The cowpea seedlings (miniCore population) were exposed to drought stress at 17 days after germination using the weight of the pot and AAWEsmo device, developed in Julkowska Lab, Boyce Thompson Institute. The seedlings were kept at 60 and 10% of soil water holding capacity for 2 weeks and the data on cowpea shoot size, evapotranspiration and photosystem II efficiency was collected. The data was assembled and curated (https://rpubs.com/mjulkowska/Cowpea2022alltraits), and subsequently used for GWAS. The GWAS data was analyzed, and the most interesting associations were selected (https://rpubs.com/mjulkowska/Cowpea2022Gwas). The raw data was collected by Hayley Sussman, with help of Olga Khmelnitsky, while GWAS was performed by Magdalena Julkowska, using ASReml script developed by Arthur Korte (https://github.com/arthurkorte/GWAS), adapted for cowpea.