Genetic Dissection of Protein Content in Cowpea Using Custom-made NIRS equations and GWAS as a Model for Nutritional Breeding and Undergraduate Research Training

As the demand for plant-based nutrition increases, improving the protein profile of legumes like cowpea has become a breeding priority. Cowpea, a multi-use legume and staple in many low-income regions, provides important dietary protein that can help meet the demand in our growing population. Our research used genome-wide association studies (GWAS) and phenomic tools to investigate the genetic architecture of seed protein content in cowpea and integrated four cohorts of undergraduate researchers through a USDA-AFRI REEU program. Using wet chemistry and near-infrared spectroscopy (NIRS), we assessed crude protein within the UCR Minicore collection, developed and validated a customed-made NIRS calibration equation for crude protein (R² = 0.86), and performed GWAS with ∼41k single nucleotide polymorphisms (SNPs). Significant SNPs associated with protein content were identified on chromosomes 1, 3, 7, 10, and 11, and candidate genes were linked to functions including nutrient transport, stress response, and seed storage protein regulation. These results provide a foundation for future marker validation and functional studies, and demonstrate the value of pairing trait discovery with undergraduate training.