Soybean, a primary vegetable protein source, boasts favorable amino acid profiles; however, its composition still falls short of meeting human nutritional demands. The soybean amino acid content is a quantitative trait controlled by multiple genes. In this study, an F2 population of 186 individual plants derived from the cross between ChangJiangChun2 and JiYu166 served as the mapping population. Based on the previously published genetic map of our lab, we increased the density of the genetic map and constructed a new genetic map containing 518 SSR (simple sequence repeats) markers and 64 InDel (insertion-deletion) markers, with an average distance of 5.27 cm and a total length of 2881.2 cm. The content of eight essential amino acids was evaluated in the F2:5, F2:6, and BLUP (best linear unbiased prediction). A total of 52 QTLs (quantitative trait loci) were identified, and 13 QTL clusters were identified, among which loci02.1 and loci11.1 emerged as stable QTL clusters, exploring candidate genes within these regions. Through GO enrichment and gene annotation, 16 candidate genes associated with soybean essential amino acid content were predicted. This study would lay the foundation for elucidating the regulatory mechanisms of essential amino acid content and contribute to germplasm innovation in soybeans.
