Soybean (Glycine max L.) is a globally important source of plant proteins, oils, and amino acids for both humans and livestock. Wild soybean (Glycine soja Sieb. and Zucc.), the ancestor of cultivated soybean, could be a useful genetic source for increasing these components in soybean crops. In this study, 96,432 single-nucleotide polymorphisms (SNPs) across 203 wild soybean accessions from the 180K Axiom^® Soya SNP array were investigated using an association analysis. Protein and oil content exhibited a highly significant negative correlation, while the 17 amino acids exhibited a highly significant positive correlation with each other. A genome-wide association study (GWAS) was conducted on the protein, oil, and amino acid content using the 203 wild soybean accessions. A total of 44 significant SNPs were associated with protein, oil, and amino acid content. Glyma.11g015500 and Glyma.20g050300, which contained SNPs detected from the GWAS, were selected as novel candidate genes for the protein and oil content, respectively. In addition, Glyma.01g053200 and Glyma.03g239700 were selected as novel candidate genes for nine of the amino acids (Ala, Asp, Glu, Gly, Leu, Lys, Pro, Ser, and Thr). The identification of the SNP markers related to protein, oil, and amino acid content reported in the present study is expected to help improve the quality of selective breeding programs for soybeans.

Soybean seeds consist of approximately 40% protein and 20% oil, making them one of the world’s most important cultivated legumes. However, the levels of these compounds are negatively correlated with each other and regulated by quantitative trait loci (QTL) that are controlled by several genes. In this study, a total of 190 F₂ and 90 BC₁F₂ plants derived from a cross of Daepung (Glycine max) with GWS-1887 (G. soja, a source of high protein), were used for the QTL analysis of protein and oil content. In the F_2:3 populations, the average protein and oil content was 45.52% and 11.59%, respectively. A QTL associated with protein levels was detected at Gm20_29512680 on chr. 20 with a likelihood of odds (LOD) of 9.57 and an R² of 17.2%. A QTL associated with oil levels was also detected at Gm15_3621773 on chr. 15 (LOD: 5.80; R²: 12.2%). In the BC₁F_2:3 populations, the average protein and oil content was 44.25% and 12.14%, respectively. A QTL associated with both protein and oil content was detected at Gm20_27578013 on chr. 20 (LOD: 3.77 and 3.06; R² 15.8% and 10.7%, respectively). The crossover to the protein content of BC₁F_3:4 population was identified by SNP marker Gm20_32603292. Based on these results, two genes, Glyma.20g088000 (S-adenosyl-l-methionine-dependent methyltransferases) and Glyma.20g088400 (oxidoreductase, 2-oxoglutarate-Fe(II) oxygenase family protein), in which the amino acid sequence had changed and a stop codon was generated due to an InDel in the exon region, were identified.

The agronomic traits of soybean are important because they are directly or indirectly related to its yield. Cultivated soybean (Glycine max (L.) Merr) has lost genetic diversity during domestication and selective breeding. However, wild soybean (G. soja) represents a useful breeding material because it has a diverse gene pool. In this study, a total of 96,432 single-nucleotide polymorphisms (SNPs) across 203 wild soybean accessions from the 180K Axiom^® Soya SNP array were employed in the association analysis. Wild soybean accessions were divided into four clusters based on their genetic distance using ADMIXTURE, principal component analysis, and neighbor-joining clusters. The linkage disequilibrium decayed rapidly in wild soybean. A genome-wide association study was conducted for days to flowering (DtF), days to maturity (DtM), the number of pods (NoP), and the 100-seed weight (100SW), which are major agronomic traits for wild soybean accessions. A total of 22 significant SNPs were found to be associated with DtF, DtM, and the 100SW. Based on the detected SNP markers, Glyma.12g210400, a gene related to DtF, Glyma.17g115300, a gene related to DtM, and Glyma.14g140200, a gene related to the 100SW, were selected as candidate genes. The SNP markers related to agronomic traits identified in this study are expected to help improve the quality of soybean cultivars through selective breeding.

Trypsin inhibitors (TIs) in soybean seeds reduce the availability of processed soybean foods and animal feed. This study aimed to evaluate the trypsin inhibitor activity (TIA) in 999 Korean soybean accessions and conduct molecular characterization of soybean accessions with low TIA. TIA was evaluated using colorimetric analysis through a substrate–enzyme reaction. The average TIA of the 999 soybean accessions was 90.31%, ranging from 43.70% to 99.51%. Kunitz trypsin inhibitor 3 (KTi-3) gene target sequencing analysis was performed on seven soybean germplasm accessions (IT105782, IT170889, IT273590, IT274513, IT274515, IT276197, and IT022891) showing less than 60% TIA. Four soybean accessions (IT274513, IT274515, IT276197, and IT022891) exhibited the same mutations (a G-to-T transversion and an AG deletion) in the KTi-3 gene (Glyma.08g341500) in PI542044. In addition, whole-genome re-sequencing was performed on three soybean accessions with no mutations in the KTi-3 gene. Compared with the reference soybean genome, an in-frame insertion and five missense mutations were identified in the coding sequencing of the KTi-1 gene (Glyma.01g09500) in IT105782. A RT-qPCR analysis showed that the mRNA expression level of KTi-1 was reduced by approximately 17% in IT105782 during seed development. In this study, we identified a previously unreported mutation in the KTi-1 gene and developed a KASP marker using this new KTi-1 variant.

Sucrose is a desirable component of processed soybean foods and animal feed, and thus, its content is used as an important characteristic for assessing the quality of soybean seeds. However, few studies have focused on the quantitative trait loci (QTLs) associated with sucrose regulation in soybean seeds. This study aims to measure the sucrose content of 1014 soybean accessions and identify genes related to high sucrose levels using QTL analysis. Colorimetric analysis based on the enzymatic reaction of invertase (INV) and glucose oxidase (GOD) was employed to test the germplasms. A total of six high-sucrose genetic resources (IT186230, IT195321, IT263138, IT263276, IT263286, and IT276521) and two low-sucrose genetic resources (IT025668 and IT274054) were identified. Two F_2:3 populations, IT186230 × IT025668 and Ilmi × IT186230, were then established from these germplasms. QTL analysis identified four QTLs (qSUC6.1, qSUC11.1, qSUC15.1, and qSUC17.1), explaining 7.3–27.6% of the phenotypic variation in the sugar content. Twenty candidate genes were found at the four QTLs. Notably, Glyma.17G152300, located in the qSUC17.1 QTL region, exhibited a 17-fold higher gene expression in the high-sucrose germplasm IT186230 compared to the control germplasm Ilmi, confirming its role as a major gene regulating the sucrose content in soybean. These results may assist in marker-assisted selection for breeding programs that aim to develop soybean lines with a higher sucrose content.