Regional Differences in Soybean Protein and Amino Acid Profiles: A Genetic Exploration Using a Novel GWAS Panel

ABSTRACT Regional differences in soybean seed protein and amino acid content in Canada present significant challenges for crop improvement and the market value of high‐protein livestock feed. This study employed genome‐wide association studies (GWAS) using a novel panel of 206 cultivars to investigate the genetic basis of regional variations. Field trials were conducted across six site years in Eastern and Western Canada in 2021 and 2022. Phenotypic analysis revealed lower protein and amino acid content in Western regions, with an average decrease of 0.9% in protein compared with Eastern regions. Using 31,362 SNPs, we identified 370 significant marker trait associations (MTAs), consolidated into 175 quantitative trait loci (QTL), 27 of which are novel. Differences in reporting methodology for amino acid content, whether on a dry matter or protein basis, resulted in different results in phenotypic correlation and detected MTAs. Gene ontology analysis of novel QTL revealed pathways related to amino acid metabolism, cold stress response, and auxin biosynthesis. Previously reported QTL on Chromosomes 14, 15, and 20 were validated through detection in this panel. Stable critical amino acid values (CAAVs) across regions and only one detected MTA suggest that an amino acid–specific and not CAAV‐targeted approach should be used in breeding strategies. The novel association panel assembled here will be a resource for crop improvement efforts. This study provides valuable insights into the genetic architecture of regional protein and amino acid variation in Canadian soybean and identifies promising targets for breeding programs aimed at improving seed protein content and amino acid profiles in specific growing regions.