Soybean is sensitive to drought stress, and increasing tolerance to drought stresses is an important target for improving the performance of soybean in the field. The genetic mechanisms underlying soybean’s drought tolerance remain largely unknown. Via a genome-wide association study (GWAS) combined with linkage analysis, we identified 11 single-nucleotide polymorphisms (SNPs) and 22 quantitative trait locus (QTLs) that are significantly associated with soybean drought tolerance. One of these loci, namely qGI10-1, was co-located by GWAS and linkage mapping. The two intervals of qGI10-1 were differentiated between wild and cultivated soybean. A nuclear factor Y transcription factor, GmNFYB17, was located in one of the differentiated regions of qGI10-1 and thus selected as a candidate gene for further analyses. The analysis of 29 homologous genes of GmNFYB17 in soybean showed that most of the genes from this family were involved in drought stress. The over-expression of GmNFYB17 in soybean enhanced drought resistance and yield accumulation. The transgenic plants grew better than control under limited water conditions and showed a lower degree of leaf damage and MDA content but higher RWC, SOD activity and proline content compared with control. Moreover, the transgenic plants showed a fast-growing root system, especially regarding a higher root–top ratio and more branching roots and lateral roots. The better agronomic traits of yield were also found in GmNFYB17 transgenic plants. Thus, the GmNFYB17 gene was proven to positively regulate drought stress resistance and modulate root growth in soybean. These results provide important insights into the molecular mechanisms underlying drought tolerance in soybean.

Fusarium oxysporum root rot (FORR) is an important disease threatening soybean production. The development of marker-assisted selection (MAS) molecular markers will help accelerate the disease resistance breeding process and achieve the breeding goal of improving soybean disease resistance. This study evaluated the FORR disease resistance of 356 soybean germplasm accessions (SGAs) and screened resistance-related loci using genome-wide association analysis (GWAS) to develop molecular markers for MAS. A total of 1,355,930 high-quality SNPs were analyzed, 150 SNP sites significantly associated with FORR resistance were identified, and these sites were distributed within 41 QTLs. Additionally, 240 candidate genes were screened near these QTL regions, involving multiple functions such as hormone metabolism, signal transduction, stress defense, and growth regulation. Cleaved amplified polymorphic sequence (CAPS) and Kompetitive Allele-Specific PCR (KASP) molecular markers were developed based on candidate genes with significant SNP loci and beneficial haplotypes. The CAPS markers, S15_50486939-CAPS1 and S15_50452626-CAPS2, can effectively distinguish resistant and sensitive genotypes through enzyme digestion. The KASP marker is based on S07_19078765-G/T and exhibits a genotype clustering pattern consistent with disease resistance, demonstrating its application value in breeding. The CAPS and KASP markers developed in this study can provide reliable tools for MAS in FORR disease-resistant varieties. The research results will help reveal the genetic structure of FORR disease resistance and provide support for efficient breeding.

The utilization of saline land is a global challenge, and cultivating salt-tolerant soybean varieties is beneficial for improving the efficiency of saline land utilization. Exploring the genetic basis of salt-tolerant soybean varieties and developing salt-tolerant molecular markers can effectively promote the process of soybean salt-tolerant breeding. In the study, the membership function method was used to evaluate seven traits related to salt tolerance and comprehensive salt tolerance at the soybean seedling stage; genome-wide association analysis (GWAS) was performed in a natural population containing 200 soybean materials; and linkage analysis was performed in 112 recombinant inbred lines (RIL) population to detect quantitative trait loci (QTLs) of salt tolerance. In the GWAS, 147 SNPs were mapped, explaining 5.28–17.16% of phenotypic variation. In the linkage analysis, 10 QTLs were identified, which could explain 6.9–16.16% of phenotypic variation. And it was found that there were two co-located regions between the natural population and the RIL population, containing seven candidate genes of salt tolerance in soybean. In addition, one colocalization interval was found to contain qZJS-15-1, rs47665107, and rs4793412, all of which could explain more than 10% of phenotypic variation rates, making it suitable for molecular marker development. The physical positions of rs47665107 and rs47934112 were included in qZJS-15-1. Therefore, a KASP marker was designed and developed using Chr. 15:47907445, which was closely linked to the qZJS-15-1. This marker could accurately and clearly cluster the materials of salt-tolerant genotypes in the heterozygous population tested. The QTLs and KASP markers found in the study provide a theoretical and technical basis for accelerating the salt-tolerant breeding of soybean.