Salinized soil can significantly hinder soybean growth, leading to a reduction in overall yield. To address this issue, identifying key genes related to salt tolerance in soybeans is essential for improving their resistance to salinity and ensuring sustainable development of soybean production. While current research predominantly focuses on salt tolerance during the seedling stage, there is still a lack of comprehensive studies on the genes involved in salt tolerance during the germination stage. This study established the optimal screening criteria by phenotyping the salt-tolerant variety R063 and the salt-sensitive variety W82 during the germination stage under salt stress. RNA-seq analysis was performed on 24 samples from both varieties at 36 and 48 hours under two different salt concentrations (0 and 150 mM/L NaCl). Differential expression analysis revealed that the salt-tolerant variety R063 exhibited the fewest differentially expressed genes (DEGs) compared to its control after 48 hours of salt stress. A total of 305 DEGs were commonly identified between the salt-tolerant variety R063 and the salt-sensitive variety W82 under salt stress at both time points. Additionally, 187 DEGs were commonly identified between R063 under salt stress and its corresponding control group across the two time points. Gene ontology (GO) enrichment analysis revealed that the differentially expressed genes were significantly enriched in ADP binding, monooxygenase activity, oxidoreductase activity, defense response, and protein phosphorylation signaling pathways. The weighted gene co-expression network analysis (WGCNA) method was employed to identify modules strongly correlated with salt tolerance during soybean germination. Candidate genes associated with soybean sprouting salt tolerance were identified by evaluating the connectivity and expression profiles of genes within these modules. These findings provide a theoretical foundation for further elucidating the molecular mechanisms underlying salt tolerance during soybean germination and present new genetic resources for studying this trait.

Soil salinity is rapidly spreading across agricultural regions and has become one of the most critical constraints on soybean growth, yield, and sustainable production. Despite the central role of transcription factors (TFs) in coordinating plant responses to abiotic stresses, the molecular mechanisms by which RWP-RK domain-containing TFs regulate salt-tolerant responses in soybean remain poorly understood. Our previous genome-wide characterization identified 28 RWP-RK TFs in soybean exhibiting abiotic stress-responsive expression, yet their biological functions under salt stress have not been experimentally validated. Here, we investigated a 981-bp GmRWP-RK1 encoding region and demonstrated its regulatory role in enhancing salt tolerance by activating antioxidant defence, Na⁺/K⁺ homeostasis, and transcriptional control of salt-responsive genes using a cross-species overexpression approach. The two Arabidopsis lines (OE1 & OE4) overexpressing GmRWP-RK1 demonstrated significantly improved salt tolerance, as evidenced by ~18% greater survival and enhanced germination compared to non-transgenic plants under salinity stress. This phenotype was supported by stronger antioxidant protection, as indicated by elevated proline levels, reduced MDA accumulation, and increased SOD and POD activities. At the molecular level, the transgenic lines also showed up-regulated expression of key stress-responsive genes (AtACS10, AtSUMO1, AtGBF1), confirming the regulatory influence of GmRWP-RK1 on salt-adaptation pathways. Consistent with the Arabidopsis results, GmRWP-RK1 overexpression in soybean hairy roots also led to improved salt-stress tolerance by accumulating significantly reduced ROS contents (27.38% lower H₂O₂ and 33.98% lower O₂⁻), and maintained a balanced Na⁺/K⁺ ratio compared to that of non-transgenic hairy roots under salinity. Furthermore, GmRWP-RK1-overexpressing transgenic soybean hairy roots showed increased expression of stress-responsive genes, especially GmATG-5, GmOLP-1, and GmOLP-2. Overall, our results support a possible role of GmRWP-RK1 in soybean salt tolerance and provide a foundation for future functional and breeding-oriented studies.

Phytophthora root and stem rot caused by Phytophthora sojae (P. sojae) is a globally prevalent oomycete disease. The use of resistant cultivars is an effective and environmentally friendly strategy to manage this disease. It is important to understand the molecular mechanisms underlying the response of Glycine max (soybean) to P. sojae infection. In this study, we demonstrated that an isoflavonoid-specific prenyltransferase gene (GmPT10d, Glyma.10G070300) was significantly upregulated in the soybean cultivar Williams 82 with high resistance to P. sojae infection. Transgenic soybean seedlings overexpressing GmPT10d exhibited enhanced resistance to P. sojae, and those subjected to RNA interference showed increased susceptibility to the pathogen. Yeast-one-hybrid and electrophoretic mobility shift assays revealed that GmARF15 could directly bind to the promoter of GmPT10d. Further analysis of the GmARF15 function showed that transgenic soybean seedlings overexpressing GmARF15 also exhibited enhanced resistance to P. sojae. Transactivation assay, luciferase assay, and qPCR analysis showed that GmARF15 could promote the expression of GmPT10d. Further analysis indicated that elevated salicylic acid levels were associated with increased expression of GmARF15 and GmPT10d. Taken together, these findings reveal a regulatory mechanism by which GmARF15 enhances soybean resistance to P. sojae, potentially by promoting the expression of GmPT10d through the salicylic acid signaling pathway.

Saline–alkali stress severely limits crop production worldwide. Soybean [Glycine max (L.) Merr.] is particularly sensitive during seed germination, a stage critical for stand establishment. This complex stress environment encompasses two distinct yet equally critical dimensions: neutral salt stress and alkaline salt stress, each eliciting specialized physiological and metabolic responses. Here, a comparative assessment of four genotypes (tolerant: CN16, CN17; sensitive: Williams 82, K18) under 100 mmol/L Na⁺ revealed that alkaline salt stress exerts a significantly more potent inhibitory effect than neutral salt stress. Tolerant cultivars maintained 75–80% germination under alkaline conditions, whereas sensitive ones dropped below 15%, a divergence primarily driven by superior oxidative mitigation capacity. Integrated multi-omics analysis of the tolerant variety CN16 identified stage-specific regulatory shifts: early alkaline salt stress (60 h) triggers extensive transcriptional reprogramming focused on physical barrier reinforcement, including cell walls and lipid remodeling. By 96 h, regulatory modes between the two stress types diverged: neutral salt elicited a transcriptional surge, while alkaline salt transitioned to a metabolically dominant regulation, shifting flux from growth-related isoflavonoids to defense-related anthocyanins. Crucially, this study uncovers the distinct bioenergetic trade-offs governing these responses: whereas adaptation to neutral salt relies on low-energy galactose metabolism, tolerance to alkaline salt demands energy-intensive processes, specifically the active vacuolar compartmentalization of organic acids and anthocyanins for intracellular buffering. This obligatory energy expenditure restricts biomass accumulation, explaining the severe growth penalties observed in complex saline-alkali environments. Finally, the identification of a core regulatory module driven by key genes, including GmPHOT2b, GmLOG, and GmSHMT08, enriches the metabolic regulatory network under saline-alkali stress, providing core targets and a theoretical framework for precisely balancing metabolic expenditure with biomass accumulation in breeding practice.

Soybean (Glycine max) germination is highly sensitive to neutral salt stress. Although sodium chloride (NaCl) and sodium sulfate (Na₂SO₄) co-exist in nature, their distinct phytotoxic mechanisms remain severely under-investigated. In this study, 50 germplasm accessions were systematically screened, identifying R014 as highly salt-tolerant and R120 as highly sensitive. Phenotypic and dynamic antioxidant monitoring (0–72 h) established 48 h as the critical tolerance window, revealing that Na₂SO₄ induces complex physical damage (crystallization) and osmotic injury, with its ionic toxicity significantly exceeding that induced by NaCl. Crucially, R014 effectively maintained peak activities of antioxidant enzymes (SOD, POD, CAT) to combat these specific stressors. By integrating deep RNA sequencing with weighted gene co-expression network analysis (WGCNA) using 48 h radicle data, significant transcriptomic reprogramming was revealed. WGCNA robustly isolated 35 functional modules, located five key phenotypic clusters, and defined three major hub genes (Glyma.11G101900, Glyma.17G185000, and Glyma.20G247850) that regulate calcium signaling. Verified by qRT-PCR, this study suggests the differential physiological and molecular architectural characteristics between chloride and sulfate toxicities, providing precisely targeted genetic loci for the breeding of salt-tolerant soybean.