Identification of Loci and Candidate Genes Associated with Arginine Content in Soybean

Soybean (Glycine max) seeds are rich in amino acids, offering key nutritional and physiological benefits. In this study, 290 soybean accessions from the USDA-ARS Germplasm Resources Information Network (GRIN) were analyzed. Four genome-wide association study (GWAS) models—Bayesian-information and Linkage-disequilibrium Iteratively Nested Keyway (BLINK), Mixed Linear Model (MLM), Fixed and Random Model Circulating Probability Unification (FarmCPU), and Multi-Locus Mixed Model (MLMM)—identified two significant single nucleotide polymorphisms (SNPs) associated with arginine content: Gm06_19014194_ss715593808 (LOD = 9.91, 3.91% variation) at 19,014,194 bp on chromosome 6 and Gm11_2054710_ ss715609614 (LOD = 9.05, 19% variation) at 2,054,710 bp on chromosome 11. Two candidate genes Glyma.06g203200 and Glyma.11G028600 were founded in the two SNP marker regions, respectively. Genomic prediction was performed for arginine content using several models: Bayes A (BA), Bayes B (BB), Bayesian LASSO (BL), Bayesian Ridge Regression (BRR), Ridge Regression Best Linear Unbiased Prediction (rrBLUP), Random Forest (RF), and Support Vector Machine (SVM). High genomic prediction accuracy were observed in both across- and cross-populations, supporting genomic selection (GS) for breeding high-arginine soybean cultivars.