Integrated Transcriptome and Metabolome Analysis Elucidates the Regulatory Networks of Salt Stress Response During Cotton Seed Germination

Background/Objectives: Soil salinization constitutes a critical threat to global agriculture, with cotton (Gossypium spp.) being highly susceptible. This abiotic stress most severely impacts cotton during the early sowing and seedling stages, compromising stand establishment and early growth. Manifestations of this stress include reduced germination rates, uneven emergence, stunted seedlings, and, ultimately, diminished boll set and fiber yield. Methods: To investigate the molecular basis of salt tolerance in cotton seed germination, we performed integrated transcriptomic and metabolomic profiling of Gossypium hirsutum cv. ST022-1056m5 under 150 mM NaCl stress at 24 h, 48 h, and 72 h, finding that salt stress significantly inhibited germination. Differentially expressed genes (DEGs) and differentially accumulated metabolites (DAMs) were identified, followed by functional enrichment and Weighted Gene Co-expression Network Analysis (WGCNA) to construct regulatory networks. Results: Transcriptomics revealed stage-specific differentially expressed genes, with predominant downregulation and enrichment in catalytic/transporter activities. Metabolomics showed distinct reprogramming, with 210 shared differentially accumulated metabolites enriched in lipids, organic acids, terpenoids, and phenolic acids. KEGG analysis highlighted time-dependent pathway shifts: sucrose metabolism and MAPK signaling at 24 h, photosynthesis at 48 h, and cuticular lipid biosynthesis at 72 h. Weighted Gene Co-expression Network Analysis (WGCNA) identified stage-associated modules and hub genes (GH_A02G0892, GH_A08G2853), and multi-omics integration indicated the strongest transcript–metabolite coordination at 24 h. Conclusion: Our study reveals dynamic molecular reprogramming underpinning stage-specific salt adaptation in germinating cotton seeds. These identified DEGs, DAMs, and hub genes represent promising candidate targets for molecular breeding and offer a crucial genetic basis for improving salt tolerance in cotton.