Sucrose and starch metabolism pathways as candidate regulatory pathways in the salt stress response revealed by transcriptomic and metabolomic analysis during soybean (Glycine max) germination.

Soybean is a globally important grain and oil crop, and salt stress severely restricts its germination and seedling establishment, ultimately reducing yields. However, the core metabolic regulatory network underlying its salt-stress response and during seed germination remains poorly understood. In this study, the soybean cultivar 'Heihe 91' was cultivated under control (0 mmol/L NaCl) and 150 mmol/L NaCl salt treatments. Phenotypic and physiological assays combined with transcriptomic and non-targeted metabolomic analyses were performed to explore the salt response mechanism during germination. Salt stress significantly inhibited seedling growth, induced oxidative damage, and activated the antioxidant enzyme system. A total of 6,410 differentially expressed genes and numerous differentially accumulated metabolites were identified, both of which were significantly enriched for annotations to the starch and sucrose metabolism pathway. Salt stress significantly reduced starch content by 32.74% and increased sucrose content, with upregulation of key rate-limiting enzyme genes, including sucrose synthase, β-amylase, and glycogen phosphorylase. RT-qPCR and physiological quantification confirmed the reliability of the omics results. This study demonstrates that the starch and sucrose metabolism pathway is the core regulatory pathway through which soybeans respond to salt stress during germination, thus mediating carbon partitioning reprogramming from storage substance accumulation to osmotic adjustment and stress defense. These findings provide key candidate genes and an empirical basis for salt tolerance genetic improvement of soybean at the germination stage.