Soybean is a primary global vegetable oil source, yet modern South American cultivars often exhibit superior oil content compared to those from China, the center of origin. Elucidating the genetic basis of this differentiation is crucial for enhancing production efficiency. In this study, we systematically evaluated 98 representative accessions, comprising Chinese germplasm (CN) and Uruguayan germplasm. The latter included Uruguayan conventional germplasm (UY_N, where ‘N’ indicates ‘Normal’, meaning non-transgenic) and Uruguayan transgenic germplasm (UY_T). Using the “Zhongdouxin No. 1” SNP array and multi-environment phenotypic data. Uruguayan germplasm exhibited significantly higher mean oil content (21.48%) than Chinese germplasm (19.42%, p < 0.001), with high heritability (H² ranging from 0.78 to 0.92). Genetic analysis revealed significant differentiation (mean F_ST = 0.14), with Uruguayan lines showing reduced diversity due to breeding bottlenecks. Genome-wide scans identified differentiation in genomic regions harboring known lipid biosynthesis genes; notably, the high-oil allele frequency of GmDGAT1 was 78.3% in Uruguayan germplasm versus 25.7% in Chinese lines, and the favorable GmbZIP123 haplotype was fixed in the Uruguayan population. Uruguayan accessions also carried significantly more favorable alleles (18.3) than Chinese accessions (14.8). We conclude that high-oil traits in Uruguayan soybean result from the systematic stacking of favorable haplotypes at key loci via directional selection. Consequently, we propose incorporating South American high-oil allelic modules into the broadly adapted genetic backgrounds of Chinese cultivars to bridge the oil content gap.

Plant height is a key agronomic trait in soybeans, directly influencing yield potential and agronomic performance. In this study, the tall-stem cultivar Heinong 63 and the dwarf-stem cultivar Longken 3077, along with their F₂ populations, were used as experimental materials. A preliminary mapping using the bulk segregant analysis sequencing (BSA-Seq) approach enabled us to locate the target locus within a 1.8 Mb interval, which was subsequently narrowed to a 48.3 kb region using simple sequence repeat (SSR) and insertion and deletion (InDel) markers. The interval was designated as PH19-31 and contained nine annotated genes. One InDel marker, PL7, was developed within this fine-mapped region. Based on an expression analysis of the nine candidate genes, Glyma.19G230000 and Glyma.19G230200 were identified as potential regulators of plant height in soybeans. This study provides valuable materials and technical support for the cloning of plant height-related genes and the molecular breeding of soybeans.