Identification of significant genome-wide associations and QTL underlying variation in seed protein composition in pea (Pisum sativum L.)

Pea seeds are a valuable source of plant proteins for human and animal nutrition and have various industrial applications. The relative abundance of different seed storage proteins affects protein quality, including digestibility and functional properties of protein extracts. Thus, understanding the genetic basis of seed protein composition is crucial to enhance protein quality and nutritional value through breeding. In this study, we employed two complementary approaches, Genome-Wide Association Study (GWAS) and Quantitative Trait Locus (QTL) mapping, to identify genetic loci underlying seed protein composition in pea. Sodium dodecyl sulfate-polyacrylamide gel electrophoresis (SDS-PAGE) was used to separate the seed proteins, and their relative abundance was quantified using densitometric analysis. For GWAS, we analysed a diverse panel of 209 accessions genotyped with an 84,691 SNP array and identified genetic loci significantly associated with globulins, such as convicilin, vicilin, legumins; and non-globulins, including lipoxygenase, late embryogenesis abundant protein (LEA), and annexin-like protein. Additionally, using QTL mapping with 96 recombinant inbred lines (RILs), we mapped 11 QTL, including five that overlapped with regions identified by GWAS for the same proteins. Within these regions, we identified structural genes for seed proteins and other genes with predicted functions in protein biosynthesis, trafficking, and modification. This comprehensive genetic mapping study serves as a foundation for future breeding efforts to improve protein quality in pea and other legumes.