Genome-wide association studies of nutritional traits in peas (Pisum sativum L.) for biofortification

Pea (Pisum sativum L.) is a high-nutrient, cool-season legume of increasing relevance in plant-based nutrition and sustainable agriculture. As demand for alternative protein sources increases, improving pea seeds’ nutritional content and quality through genomics-assisted breeding has become a priority. Despite its importance, limited research has explored the genetic basis of nutritional traits in pea. In this study, 267 accessions from the United States Department of Agriculture (USDA) Pea Single Plant Plus Collection were evaluated across 3 years at two USDA-certified organic farms in South Carolina to (1) assess phenotypic variation, (2) characterize the population structure and origin, and (3) perform a genome-wide association study (GWAS) using 54,316 single-nucleotide polymorphism markers on five nutritional traits: protein concentration, sulfur-containing amino acids (SAAs), dietary fiber, total starch, and protein digestibility (PDg). Population structure analysis using ADMIXTURE and principal components analyses identified 10 ancestral subpopulations. GWAS identified 17 marker-trait associations for protein, SAA, and PDg, including a genomic hotspot on the proximal end of chromosome 5 associated with both protein and SAA. This region harbors candidate genes involved in seed development, germination, and protein biosynthesis, suggesting potential roles in protein and SAAs accumulation. These findings provide valuable insights into the genetic architecture underlying key nutritional traits and highlight candidate target genes for breeding high-quality, biofortified pea cultivars. This research expands the genetic potential of pea as a sustainable and nutritious crop alternative for plant-based food systems.