Soybeans, a crucial grain and oil crop, are valued for their high protein and oil content. Soil salinization is a significant abiotic stress that negatively impacts soybean growth and development, resulting in reduced yield and quality. The germination period represents a critical phase in soybean development. This study evaluated salt tolerance in 165 soybean mutant lines during germination, identifying five elite salt-tolerant germplasm resources. Multi-environment genome-wide association studies (GWASs) identified 11 significantly associated and 44 suggestive single nucleotide polymorphisms, alongside five novel quantitative trait loci linked to salt tolerance. Analysis of candidate regions qtl5-1 and qtl5-2 identified Glyma.05G097200 and Glyma.05G240200 as promising candidate genes, exhibiting distinct expression patterns between salt-tolerant and -sensitive genotypes. Functional characterization in Arabidopsis demonstrated that overexpression of the soybean gene GmMACPF1 induced salt sensitivity, while the macpf1 mutant of Arabidopsis displayed enhanced salt tolerance. Additionally, GmMACPF1 underwent selection during soybean domestication, with haplotypes Hap1 and Hap3 conferring improved salt tolerance. These results indicate that GmMACPF1 functions as a negative regulator of salt tolerance during germination, offering novel insights into the molecular mechanisms governing soybean response to salt stress during this crucial developmental stage.

Roots are vital for crop growth, development, yield, and tolerance to various types of environmental stress. Numerous genetic loci associated with soybean root morphological traits have been identified, but few genes associated with these traits have been reported. This study identified seven quantitative trait loci (QTLs) containing stable SNPs significantly associated with the root dry weight in soybeans through a genome-wide association study. Among these QTLs, qRDW14-2 presented the greatest significance. In qRDW14-2, the gene GmRGD14, encoding the lysophosphatidic acid acyltransferase LPAT4, was identified as a candidate. GmRGD14, in block63, which contained the significant SNP S14_6521715, had the highest expression level in soybean roots, and its Arabidopsis homologous mutant lpat4 presented more lateral roots than did the control Col-0. GmRGD14 was localized primarily to the cell membrane and endoplasmic reticulum. The heterologous overexpression of GmRGD14 in Arabidopsis significantly increased the lateral root number, which was similar to the phenotype of atlpat4. Furthermore, overexpression of GmRGD14 resulted in a greater total root length, root tip number, root surface area, and root volume in the hairy roots of transgenic soybean plants than in those of control soybean plants, whereas knockdown of the gene via RNA interference in soybean hairy roots resulted in the opposite phenotype. GmRGD14, which is highly genetically variable in wild soybean, has been gradually utilized during soybean domestication. Overall, this study revealed that GmRGD14 is a new key gene involved in root growth, providing a promising genetic target for breeding elite soybean varieties with strong root systems.