Integrated multi-omics analysis reveals a lipid–redox regulatory network underlying drought tolerance and yield stability in rice

BACKGROUND: Upland conditions in agroecosystems severely constrain rice productivity. To elucidate the molecular and physiological mechanisms underlying drought tolerance and yield stability in rice, integrated analyses of field phenotyping, transcriptomics, metabolomics, and whole-genome resequencing were conducted using two contrasting rice cultivars, DB46 and LK23. RESULTS: Field evaluations showed that DB46 maintained superior yield stability under upland conditions, which was associated with increased leaf width, whereas LK23 exhibited pronounced leaf rolling that reduced transpiration but severely limited photosynthesis and biomass accumulation. Transcriptomic analyses revealed that DB46 coordinately up-regulated pathways related to fatty acid degradation, α-linolenic acid metabolism, and reactive oxygen species (ROS) detoxification, thereby supporting efficient energy mobilization and redox homeostasis. In contrast, these pathways were broadly suppressed in LK23, resulting in energy deficiency and oxidative stress. Metabolomic profiling further demonstrated significant enrichment of lipid- and secondary metabolism in DB46, including fatty acid biosynthesis, fatty acid metabolism, fatty acid elongation, fatty acid degradation, flavonoid biosynthesis, and phenylalanine metabolism, which collectively contributed to a robust antioxidant defense system. Whole-genome resequencing indicated a more conserved genomic architecture in DB46, whereas LK23 exhibited greater local polymorphism. Integrated multi-omics analyses identified 337 candidate genes associated with lipid metabolism and redox regulation, including lipoxygenase, protein phosphatase 1 L, and PP2C. CONCLUSIONS: Our findings uncover a lipid-redox regulatory network that underpins drought tolerance and yield stability in rice. These results provide valuable candidate genes and molecular targets for the genetic improvement and molecular design breeding of drought-resilient rice cultivars.