Association study of crude seed protein and fat concentration in a USDA pea diversity panel

Pea (Pisum sativum L.) is a key rotational crop and is increasingly important in the food processing sector for its protein. This study focused on identifying diverse high seed protein concentration (SPC) lines in pea plant genetic resources. Objectives included identifying high-protein pea lines, exploring genetic architecture across environments, pinpointing genes and metabolic pathways associated with high protein, and documenting information for single nucleotide polymorphism (SNP)-based marker-assisted selection. From 2019 to 2021, a 487-accession pea diversity panel, More protein, More pea, More profit, was evaluated in a randomized complete block design. DNA was extracted for genomic analysis via genotype-by-sequencing. Phenotypic analysis included protein and fat measurements in seeds and flower color. Genome-wide association study (GWAS) used multiple models, and the Pathways Association Study Tool was used for metabolic pathway analysis. Significant associations were found between SNPs and pea seed protein and fat concentration. Gene Psat7g216440 on chromosome 7, which targets proteins to cellular destinations, including seed storage proteins, was identified as associated with SPC. Genes Psat4g009200, Psat1g199800, Psat1g199960, and Psat1g033960, all involved in lipid metabolism, were associated with fat concentration. GWAS also identified genes annotated for storage proteins associated with fat concentration, indicating a complex relationship between fat and protein. Metabolic pathway analysis identified 20 pathways related to fat and seven to protein concentration, involving fatty acids, amino acid and protein metabolism, and the tricarboxylic acid cycle. These findings will assist in breeding of high-protein, diverse pea cultivars, and SNPs that can be converted to breeder-friendly molecular marker assays are identified for genes associated with high protein.