Integrated Multi-omics Analysis Reveals that Hybrid Rice Reprograms Carbon Metabolism to Confer Drought Resistance

Drought severely limits global rice production, and exploiting heterosis offers a promising route to improve drought resistance. However, the molecular mechanisms underlying drought resistance in hybrid rice remain largely unknown. Here, we integrated multi-omics analyses in flag leaves of elite hybrid rice Hanyou73 (HY73) and its parental lines, Hanhui3 (HH3) and Huhan7B (HH7B), during grain-filling under drought. We uncover a non-additive effect (NAE)-driven carbon metabolic reprogramming fundamental to HY73's superior drought resistance. Proteomic profiling revealed HY73 prioritizes carbon metabolism, selectively retaining monosaccharide (MOS) such as glucose-6-phosphate (G6P) and glucose-1-phosphate (G1P) to bolster stress-buffering processes. Subsequent metabolomic analysis identified this carbon retention fuels a hybrid-specific Monosaccharide-Acetyl-CoA-Fatty acyl/Prenol lipid (MOS-AcCoA-FA/PR) shunt, effectively diverting carbon into vital lipid-based hormonal, structural, and energetic functions. Importantly, NAE-driven AcCoA accumulation correlates with elevated lysine acetylation (Kac) in HY73, indicating a connection between metabolism and post-translational regulation. Acetylomic analyses pinpointed acetylation at lysine 155 (K155ac) on the phosphoglucomutase OsPGM3 as a pivotal regulatory switch in carbon metabolism. OsPGM3 governs the G6P/G1P balance under drought, coordinating local carbon usage for the sugar-lipid shunt and sugar export vital for yield potential. K155ac precisely fine-tunes OsPGM3 activity, acting as a post-translational checkpoint responsive to drought-induced carbon shifts. Together, our findings elucidate a hybrid-specific NAE-carbon flux-Kac regulatory axis that precisely balances drought adaptation with yield maintenance, offering new targets for breeding climate-resilient hybrid rice.