Integrated transcriptomics and metabolomics analysis revealed the molecular mechanism of Paeonia rockii to saline-alkali stress tolerance

• The study identified 7118 differentially expressed genes and 75 differentially accumulated metabolites in Paeonia rockii under saline-alkali stress. Crucial genes in glutathione metabolism were highlighted for their role in enhancing stress tolerance. • P. rockii showed increased osmoregulatory substances and antioxidant enzyme activities. Significant morphological changes were noted at a 300 mM stress concentration, indicating strong adaptive mechanisms. • Enhanced enzyme activities in the glutathione pathway, such as glutathione peroxidase and glutathione S-transferase, were vital for detoxifying reactive oxygen species and maintaining redox balance under stress conditions. Saline-alkali stress significantly hinders plant growth and distribution. Paeonia rockii demonstrates remarkable tolerance to such conditions. This research aimed to uncover the molecular bases of saline-alkali stress tolerance in P. rockii through transcriptomic and metabolomic analyses. We observed several stress responses in P. rockii , including leaf curling, discoloration, enhanced osmoregulatory substance content, and increased antioxidant enzyme activity, particularly at a 300 mM stress concentration. The study identified 7,118 differentially expressed genes (DEGs) and 75 differentially accumulated metabolites (DAMs) post-stress exposure. Notably, KEGG pathway enrichment revealed glutathione metabolism as a pivotal mechanism in stress adaptation. Activation of genes such as gpx, GR, G6PD, E1.11.1.11 , and GST enhances glutathione signaling, improving the plant's antioxidant capacity and overall stress tolerance. Additionally, the activation of the ODC1 gene family and the suppression of the speE gene family contribute to the accumulation of polyamine antistress factors, facilitating better adaptation. This research highlights the dual roles of glutathione and polyamine pathways in saline-alkali stress tolerance, presenting novel insights into P. rockii 's adaptive strategies. These findings insight into the molecular mechanisms of P. rockii and offers a theoretical foundation for screening genes related to saline tolerance, thus expanding planting areas and breeding resistant varieties.