Integrative Analysis of Physiology, Transcriptomics, and Metabolomics Unveils Mechanisms in Soybean ( Glycine max (Linn.) Merr) Response to Salt Stress

Salt stress is a major factor limiting the growth, development, and yield of soybeans ( Glycine max (Linn.) Merr), yet the regulatory networks underlying soybean resistance to salt stress remain largely unresolved. This study aimed to elucidate the mechanisms of soybean resistance to salt stress by integrating phenotypic, physiological, transcriptomic, and metabolomic analyses of the salt‐tolerant soybean cultivar HD6 and the salt‐sensitive cultivar ZH929. We found that HD6 exhibited significantly stronger osmotic regulation capacity, enhanced antioxidant capacity, and greater photosynthetic efficiency compared with ZH929. Transcriptomic analysis revealed that differentially expressed genes under salt stress were primarily enriched in pathways related to arginine biosynthesis and isoflavone biosynthesis. Consistently HD6 accumulated higher levels of amino acids and flavonoids. Integrated analysis of transcriptomic and metabolomic data further underscored the critical roles of amino acid and flavonoid biosynthesis regulatory networks in conferring salt resistance. Notably, genes LOC547724 ( glutamate decarboxylase, GAD ), LOC102661752 ( succinate dehydrogenase [ubiquinone] iron–sulfur subunit 2 , SDH2 ), and CHS10 ( chalcone synthase 10 , CHS ), along with metabolites including L‐glutamine and rutin, were identified as central components of these networks. Additionally, weighted gene co‐expression network analysis highlighted the importance of hub genes such as LOC100820620 ( peroxidase ) in the salt stress response. Collectively, these findings demonstrate that amino acids and flavonoids are crucial for soybean resistance to salt stress.