Integrated transcriptome and metabolome analysis reveals the mechanisms of hydrogen-rich water in mitigating salt stress in peach seeds (Prunus davidiana)

Salt stress is a major abiotic stress that impairs plant growth and development, affecting gene transcription, metabolite profiles, and overall phenotypes. However, the underlying molecular response mechanisms, especially those mediated by hydrogen-rich water (HRW), remain unclear. In this study, we integrated physiological, transcriptomic, and metabolomic analyses to explore the effects of HRW on salt stress tolerance in Prunus davidiana seeds. The results showed that, compared with salt stress alone, exogenous hydrogen-rich water (HRW) treatment significantly reduced oxidative damage in peach seeds. Specifically, HRW decreased the accumulation of superoxide anion (O₂⁻) and the content of malondialdehyde (MDA), while increasing the activities of superoxide dismutase (SOD) and peroxidase (POD). Integrated transcriptomic and metabolomic analyses revealed significant reprogramming of genes and metabolites, particularly those involved in the phenylpropanoid and flavonoid biosynthesis pathways. Salt stress markedly suppressed the biosynthesis and accumulation of secondary metabolites such as flavonoids, alkaloids, and chlorogenic acid by downregulating key rate-limiting genes (PAL, C4H, HCT). Exogenous HRW treatment effectively reversed the repression of these genes and restored related metabolite levels to nearly those of the control group. In summary, hydrogen-rich water acts as an alleviator of salt stress, and the identified metabolites and key rate-limiting genes offer potential targets for improving salt tolerance in mountain peach seeds.