Induction of glutathione and flavonoid biosynthesis activates antioxidant enzymes to enhance drought tolerance in rice

Drought stress during early seed germination severely impacts rice establishment and productivity, yet the molecular and metabolic mechanisms underlying drought tolerance at this stage remain poorly understood. In this study, Luying 46 (LY46), a drought-tolerant genotype, and Haogenai (HGN), a drought-sensitive genotype, were used to investigate key adaptive traits and regulatory networks that confer drought resilience during germination. LY46 showed higher germination rates, better shoot and root growth under drought stress compared to HGN. Integrated transcriptomic and metabolomic analyses revealed enhanced glycolysis, glutathione metabolism, and phenylpropanoid biosynthesis as central pathways supporting drought adaptation in LY46. Upregulation of genes involved in starch mobilization and sugar metabolism facilitated energy production under water deficit, while elevated antioxidant enzyme activities, flavonoids, phenolic acid and prolines, mitigated oxidative damage. Metabolite profiling further revealed accumulation of peptides, amines, nucleotides, alkaloids, lipids and fatty acids in LY46 under drought. Weighted gene coexpression network analysis (WGCNA) revealed the coordinated regulation of antioxidant, osmoprotectant, and metabolic pathways involved in alleviating drought stress. Biochemical assays confirmed LY46’s maintenance of membrane integrity by effectively reducing lipid peroxidation under stress. Collectively, our comprehensive multiomics approach revealed a coordinated molecular and metabolic network regulated by transcription factors that underpins drought tolerance during rice germination, providing valuable insights into drought resilience in rice.