Salt is recognized as one of the most major factors that limits soybean yield in acidic soils. Soil enzyme activity and bacterial community have a critical function in improving the tolerance to soybean. Our aim was to assess the activities of soil enzyme, the structure of bacteria and their potential functions for salt resistance between Salt-tolerant (Salt-T) and -sensitive (Salt-S) soybean genotypes when subject to salt stress. Plant biomass, soil physicochemical properties, soil catalase, urease, sucrase, amylase, and acid phosphatase activities, and rhizosphere microbial characteristics were investigated in Salt-T and Salt-S soybean genotypes under salt stress with a pot experiment. Salt stress significantly decreased the soil enzyme activities and changed the rhizosphere microbial structure in a genotype-dependent manner. In addition, 46 ASVs which were enriched in the Salt-T geotype under the salt stress, such as ASV19 (Alicyclobacillus), ASV132 (Tumebacillus), ASV1760 (Mycobacterium) and ASV1357 (Bacillus), which may enhance the tolerance to soybean under salt stress. Moreover, the network structure of Salt-T soybean was simplified by salt stress, which may result in soil bacterial communities being susceptible to external factors. Salt stress altered the strength of soil enzyme activities and the assembly of microbial structure in Salt-T and Salt-S soybean genotypes. Na⁺, NO₃⁻–N, NH₄⁺–N and Olsen-P were the most important driving factors in the structure of bacterial community in both genotypes. Salt-T genotypes enriched several microorganisms that contributed to enhance salt tolerance in soybeans, such as Alicyclobacillus, Tumebacillus, and Bacillus. Nevertheless, the simplified network structure of salt-T genotype due to salt stress may render its bacterial community structure unstable and susceptible.

Soybean is a crucial crop globally, serving as a significant source of unsaturated fatty acids and protein in the human diet. However, further enhancements are required for the related genes that regulate soybean oil synthesis. In this study, 155 soybean germplasms were cultivated under three different environmental conditions, followed by phenotypic identification and genome-wide association analysis using simplified sequencing data. Genome-wide association analysis was performed using SLAF-seq data. A total of 36 QTLs were significantly associated with oil content (−log10(p) > 3). Out of the 36 QTLs associated with oil content, 27 exhibited genetic overlap with previously reported QTLs related to oil traits. Further transcriptome sequencing was performed on extreme high–low oil soybean varieties. Combined with transcriptome expression data, 22 candidate genes were identified (|log2FC| ≥ 3). Further haplotype analysis of the potential candidate genes showed that three potential candidate genes had excellent haplotypes, including Glyma.03G186200, Glyma.09G099500, and Glyma.18G248900. The identified loci harboring beneficial alleles and candidate genes likely contribute significantly to the molecular network’s underlying marker-assisted selection (MAS) and oil content.

The number of four-seed pods (NFSP) in soybean is an important yield trait and a quantitative trait regulated by multiple genes. Mapping quantitative trait nucleotide (QTN), mining major genes, and screening excellent breeding schemes for NFSP are of great significance for breeding high-yielding soybean varieties. In this study, a germplasm population (GP) containing 455 soybean varieties was planted in five environments to investigate NFSP. Single-nucleotide polymorphism (SNP) genotype data were obtained based on the Axiom_SoyaSNP 180K chip, and a genome-wide association study (GWAS) was used to locate QTNs, which were used to predict candidate genes and simulate breeding. The results showed that there was genetic variation in NFSP and different gene expression in various environments. The broad-sense heritability of NFSP over multiple environments was 72.7%. A total of 89 QTNs correlated with the number of four pods were identified on 20 chromosomes, including 34 stable QTNs repeatedly detected by multiple methods or in multiple environments and four QTNs with an additive by environment interaction effect. In the decay regions of 34 stable QTNs, three genes related to NFSP in soybean were screened and verified by haplotype analysis, namely, Glyma.13G105400, Glyma.04G063700, and Glyma.04G063100. Multiple regression analysis of 89 QTNs on NFSP was used to establish molecular-assisted selection models for five environments, which could explain 44.82%–55.06% of the phenotypic variation in NFSP. Based on this model, 153 breeding schemes were selected for five environments, which could achieve the breeding goals of NFSP over 43, 43, 25, 31, and 40 under 21AC, 21XY, 23WD, 23QQHE, and 23AC environments, respectively. These results laid the foundation for understanding the genetic mechanism of pod formation in soybean and molecular breeding of high-yielding varieties.

Expanding soybean planting is vital for food security both in China and globally. The 50° N latitude serves as the northern boundary of major soybean regions. However, enhancing the adaptability of soybean to photothermal conditions enables the potential to extend cultivation to higher latitudes and altitudes. Understanding the genetic basis of super-early maturity of soybean is crucial to achieving this goal. In this study, 438 soybean germplasms collected from high-latitude regions were evaluated in Heihe (HH) (50°15′ N, 127°28′ E, 154 m), Beijicun (BJC) (53°28′ N, 122°21′ E, 295 m) and Labudalin (LBDL) (50°15′ N, 120°19′ E, 577 m). Using resequencing data, we analyzed natural variation and haplotypes in 35 key genes associated with flowering time and maturity. The results showed that the relative maturity groups (RMGs) for BJC, HH, and LBDL were −1.0, 0.0, and −1.2, respectively. Among the 35 genes analyzed, 23 had identical allelic variations, while 12 genes exhibited 19 SNPs and four InDels. Functional mutations were identified in E1, E2, E3, and E4. Notably, all cultivars carried the e1-as allele of E1, which is likely critical for high-latitude adaptation. Additional mutations included a single-base substitution in E2 (16142 A > T) and E3 (5203 C > T), causing premature codon termination, along with frameshift mutations in E4 (3726 and 4099) and E3 (2649). Haplotype analysis revealed significant differences in growth stages among nine gene haplotypes. The higher frequency of early-maturing haplotypes in BJC and LBDL highlights the role of gene accumulation in soybean adaptation. These findings offer valuable insights for improving soybean maturity and expanding its cultivation in high-latitude regions of China.

Soybean–maize rotation is an effective strategy for addressing the challenges associated with continuous soybean cropping. However, the effects of maize frequency in cropping sequences on soil fungal functions and their associations with soybean yields remain unclear. Through a 12-year field study comparing continuous soybean (CS), maize–soybean (MS), and maize–maize–soybean (MMS) systems, fungal community functions, system-specific taxa, and bacterial–fungal inter-kingdom co-occurrence patterns were analyzed. In contrast to conventional assumptions, CS enriched symbiotic fungi and suppressed pathogens, suggesting adaptive disease resilience. Integrating maize into soybean cropping systems increased the complexity of bacterial–fungal cross-kingdom co-occurrence networks. While the MS system increased the relative abundances of plant pathogens and saprotrophs, the MMS system stabilized fungal functions and inhibited plant pathogen accumulation. The system-specific taxa identified in the CS and MMS systems included potential plant growth-promoting microbes and were associated with the relative abundances of pathogens and saprotrophic fungi as well as soybean yield. This relationship may represent a critical link between fungal function and soybean production. These findings indicate that integrating maize into soybean rotations, especially in the MMS system, can stabilize fungal functions and mitigate pathogen accumulation, ultimately increasing soybean yield. These results underscore the importance of tailored crop rotation practices to optimize soil microbial communities for sustainable agricultural production.

Soybean ( Glycine max ) is a globally important staple oilseed crop, yet its yield is severely limited by saline-alkaline stress. Developing soybean cultivars with enhanced saline-alkaline tolerance is therefore crucial for sustainable agriculture. To identify candidate genes associated with saline-alkaline stress tolerance in soybean, this study evaluated the saline-alkaline tolerance of a core panel of 198 soybean accessions at the germination stage, focusing on four key germination-related traits: germination energy (GE), germination rate (GR), radicle length (RL), and hypocotyl length (HL). Phenotypic analysis revealed significant variation in stress tolerance among the 198 accessions, with a subset exhibiting robust saline-alkaline tolerance and others showing significant sensitivity. This finding confirms substantial genetic diversity in saline-alkaline stress adaptability within the panel. Subsequently, whole-genome resequencing was performed on the panel, generating 385, 087 high-quality single nucleotide polymorphisms (SNPs). A genome-wide association study (GWAS) was conducted by integrating these SNP data with phenotypic traits under saline-alkaline stress, resulting in the identification of 428 candidate genes potentially associated with saline-alkaline tolerance. Notably, two previously reported salinity tolerance-related genes, GmLecRlk ( Glyma.07G005700 ) and GmERF34 ( Glyma.07G074200 ), were successfully validated in this study. Additionally, the superior haplotypes of Glyma.07G004400 and Glyma.15G022000 —which showed significant associations with improved saline-alkaline tolerance—were characterized. Collectively, through phenotypic evaluation of 198 soybean accessions under saline-alkaline stress and genome-wide genetic dissection, this study provides a theoretical foundation and technical support for elucidating the molecular regulatory network of saline-alkaline tolerance in soybean and accelerating the breeding of saline-alkaline tolerant soybean cultivars.