Soybean vegetable oil is an important source of the human diet. However, the analysis of the genetic mechanism leading to changes in soybean oil content is still incomplete. In this study, a total of 227 soybean materials were applied and analyzed by a genome-wide association study (GWAS). There are 44 quantitative trait nucleotides (QTNs) that were identified as associated with oil content. A total of six, four, and 34 significant QTN loci were identified in Xiangyang, Hulan, and Acheng, respectively. Of those, 26 QTNs overlapped with or were near the known oil content quantitative trait locus (QTL), and 18 new QTNs related to oil content were identified. A total of 594 genes were located near the peak single nucleotide polymorphism (SNP) from three tested environments. These candidate genes exhibited significant enrichment in tropane, piperidine, and pyridine alkaloid biosynthesiss (ko00960), ABC transporters (ko02010), photosynthesis-antenna proteins (ko00196), and betalain biosynthesis (ko00965). Combined with the GWAS and weighted gene co-expression network analysis (WGCNA), four candidate genes (Glyma.18G300100, Glyma.11G221100, Glyma.13G343300, and Glyma.02G166100) that may regulate oil content were identified. In addition, Glyma.18G300100 was divided into two main haplotypes in the studied accessions. The oil content of haplotype 1 is significantly lower than that of haplotype 2. Our research findings provide a theoretical basis for improving the regulatory mechanism of soybean oil content.

Fatty acid transporters (FAXs) play an important role in fatty acid synthesis by facilitating transport fatty acids from the plastid to the endoplasmic reticulum. This process is essential for providing precursor substances necessary for triglycerides (TAGs). Although FAX genes have been identified in variety of plant species, the identification and molecular functions of the GmFAX gene members in soybean are still unclear. In this study, soybean FAX genes were identified through the utilization of the Phytozome (v13) and NCBI online websites. Subsequently, phylogenetic trees, expression patterns, gene structures, and qRT-PCR were analyzed. A total of eight GmFAX members were identified at the whole genome level, and further phylogenetic analysis revealed that these members can be categorized into four subfamilies. In addition, all members of GmFAX contain a highly conserved domain Tmemb_14. Through qRT-PCR analysis, it was found that the expression level of the GmFAX8 gene is relatively high in leaves and stems. Further investigation revealed that the total fatty acid content in hairy roots overexpressing the GmFAX8 gene was significantly greater than that observed in the control strain. The results presented above suggest that the GmFAX8 gene may play an important role in the accumulation of oil within soybeans.

Phosphofructokinase (PFK), a core metabolic enzyme conserved across all organisms, plays a pivotal role in plant growth and development as well as in the regulation of responses to abiotic stresses. While the PFK gene family has been characterized in a variety of plant species and a partial identification in soybean has been reported recently, the complete repertoire and the functional roles of this gene family in soybean remain to be fully elucidated, with inconsistencies in gene number observed across different studies. In this study, we further performed a systematic genome-wide screening of soybean and identified a total of 27 GmPFK family members. Phylogenetic tree analysis further classified these members into three distinct subfamilies. Conserved structure analysis revealed that all GmPFKs contain the PFK domain (PF00365). Real-time quantitative PCR (qRT-PCR) analysis demonstrated that the GmPFK6 gene exhibited a significant upregulation of expression under salt stress. Furthermore, the GmPFK6 gene was cloned and introduced into soybean hairy roots. The results demonstrated that under salt stress, the root length and fresh weight of hairy roots from the control lines were significantly greater than those from the transgenic lines. In addition, under salt stress, the superoxide dismutase (SOD) activity in the control lines was significantly higher than that in the transgenic lines, while the malondialdehyde (MDA) content in the transgenic lines was significantly lower than that in the control lines.

Lipid phosphate phosphatases (LPPs) are critical regulatory factors in plant membrane lipid metabolism and lipid signal transduction, exerting key roles in membrane lipid remodeling, signal attenuation, and adaptation to abiotic stresses. However, the systematic identification of the soybean GmLPP gene family and its expression profiles in response to abiotic stresses remains largely unclear. In this study, a total of nine GmLPP family members were identified in the soybean genome, which were further classified into three subgroups based on their phylogenetic relationships. qRT-PCR analysis demonstrated that the majority of GmLPP genes responded to NaCl, PEG6000, NaHCO₃, JA, and SA treatments to varying extents, among which GmLPP7 exhibited the most pronounced response to salt stress. Subcellular localization assays demonstrated that the GmLPP7 protein is primarily localized to the cell membrane. Further haplotype analysis was performed on 160 soybean germplasm accessions, leading to the identification of five SNP loci within the GmLPP7 gene region. Among these, two SNPs were significantly associated with the relative germination index (STGI) and formed two distinct haplotypes. Notably, Hap2 exhibited a significantly higher STGI value, thus representing a superior salt-tolerant haplotype. In summary, this study systematically elucidates the evolutionary and expression profiles of the GmLPP gene family, identifies GmLPP7 as a candidate gene significantly associated with salt tolerance during soybean germination, and its superior haplotype Hap2, thereby providing novel genetic resources for the molecular improvement of salt tolerance in soybean.

Fructose-1,6-bisphosphate aldolase (FBA), as a key enzyme in energy metabolism, is widely present in organisms. Although FBA genes have been characterized in numerous plant species, their functional roles in soybean remain poorly understood. In this study, a total of 14 GmFBA genes were identified at the genome-wide level. Additionally, phylogenetic analysis divided all GmFBA family members into two divergent subclades. qRT-PCR analysis revealed that most GmFBA genes were markedly responsive to PEG6000 and salt stresses, among which GmFBA5 exhibited the strongest induction under salinity treatment. The heterologous expression of GmFBA5 in yeast was performed. The results showed that GmFBA5 markedly enhanced salt tolerance of yeast cells. Association analysis identified two distinct haplotypes of GmFBA5, and Haplotype 2 significantly enhances salt tolerance in soybean. These findings provide new insights into the potential role of GmFBA5 in soybean salt stress responses and provide candidate genetic resources for salt tolerance improvement.

Soybean is the world’s foremost oilseed crop, and leaf morphology significantly influences yield potential by affecting light interception, canopy structure, and photosynthetic efficiency. In this study, leaf length, leaf width, maximum leaf width, leaf apex opening angle, and leaf area were measured in 216 soybean accessions, and genome-wide association studies (GWAS) were conducted using genomic resequencing data to identify genetic variants associated with leaf morphological traits. A total of 824 SNP loci were found to be significantly associated with leaf shape, and 130 candidate genes were identified in the genomic regions flanking these significant loci. KEGG enrichment analysis revealed that the above candidate genes were significantly enriched in arginine biosynthesis (ko00220), nitrogen metabolism (ko00910), carbon metabolism (ko01200), pyruvate metabolism (ko00620), glycolysis/glycogenolysis (ko00010), starch and sucrose metabolism (ko00500), plant–pathogen interaction (ko04626), and amino acid biosynthesis (ko01230). By combining KEGG and GO enrichment analysis as well as expression level analysis, four candidate genes related to leaf shape (Glyma.10G141600, Glyma.13G062700, Glyma.16G041200 and Glyma.20G115500) were identified. Further, through candidate gene association analysis, it was found that the Glyma.10G141600 gene was divided into two major haplotypes. The leaf area of haplotype 1 was significantly smaller than that of haplotype 2. Subsequently, the cutting amplification polymorphism sequence (CAPS) molecular marker was developed. The marker Chr.10:37502955 can effectively distinguish the differences in leaf size through enzymatic digestion technology, and has excellent typing ability and application potential. The above results can provide a theoretical basis for molecular-assisted selection (MAS) of soybean leaf morphology.