Multi-omics profiling unravels the synergistic roles of defence priming and metabolic remodeling in wheat waterlogging tolerance.
Waterlogging severely restricts wheat seed germination and seedling growth, but the underlying tolerance mechanisms remain poorly understood. Using two tolerant (T1, T2) and two sensitive (S1, S2) wheat genotypes, we analyzed phenotypic, physiological, metabolic and transcriptional responses to waterlogging stress. Tolerant genotypes maintained high seed viability and germination rate and showed accelerated seedling growth after waterlogging, whereas sensitive genotypes suffered severe germination inhibition and loss of embryo viability. Tolerant genotypes exhibited more stable antioxidant enzyme activities and glutathione content, which alleviated hypoxia-induced oxidative damage. Integrated omics revealed tissue-specific adaptive strategies: shoots activated glutathione metabolism and primary carbon metabolism to maintain redox balance and energy supply, whereas roots enhanced secondary metabolism, such as flavonoid biosynthesis, for stress defense. Conserved pathways, including lysine degradation and phenylpropanoid metabolism, contributed to antioxidant capacity, cell wall reinforcement and immune priming. Stress memory also promoted rapid recovery during reoxygenation. In contrast, sensitive genotypes lacked such coordinated responses and suffered irreversible damage. This study clarifies the multi-level mechanisms of waterlogging tolerance and provides potential targets for breeding waterlogging-resistant wheat.