Comparative Transcriptomic Analysis and WGCNA Suggest Differential Salt Tolerance Mechanisms of Soybean at Germination Stage Under NaCl and Na2SO4 Stresses

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.