Transcriptomic and metabolomic profiling reveals key mechanisms of alkaline stress tolerance in rice

Alkaline stress severely restricts rice growth and yield by disrupting ion balance, nutrient uptake, and oxidative metabolism. Clarifying the molecular mechanisms of tolerance is vital for breeding resilient varieties. This study explores transcriptional and metabolic adaptations in an alkali-tolerant (Qijing 10, LD) and sensitive (Tengxi 138, WL) rice variety under alkaline stress. Transcriptomic analysis revealed 1,297 differentially expressed genes (DEGs) in the sensitive variety under alkaline stress (TWL), primarily enriched in pathways related to antioxidant enzyme synthesis (e.g., peroxidase genes), transmembrane ion transport, and membrane lipid stabilization pathways. In contrast, the tolerant variety (TLD) exhibited only 38 DEGs, suggesting transcriptional homeostasis achieved via suppression of stress-related gene overactivation. Metabolomic profiling demonstrated stable levels of key lipids (phosphatidic acid, galactolipids) and osmolytes (proline, betaine) in the tolerant variety under stress, whereas the sensitive variety accumulated lipid peroxidation products (malondialdehyde, MDA) and displayed dysregulated carbohydrate metabolic dysregulation. Integrated multi-omics analysis indicated that the tolerant variety coordinated lipid metabolism gene modulation with antioxidant metabolite accumulation, establishing dual barriers for ROS scavenging and membrane protection. Conversely, transcriptional dysregulation in the sensitive variety led to metabolic collapse. Alkaline tolerance in rice hinges on the synergistic modulation of stress-responsive genes and metabolic networks to preserve redox equilibrium and membrane function. The tolerant variety’s capacity to stabilize transcriptional activity and metabolic flux underlies its resilience. These results elucidate key molecular and metabolic determinants of alkaline tolerance, offering strategic targets for breeding rice cultivars adapted to alkaline environments.