Improved Water Use Efficiency in Rice During Drought–Rewatering Cycles: Insights from Transcriptomics and Metabolomics

Alternate wetting and drying (AWD) is a crucial water-saving irrigation strategy in rice production, yet its regulatory mechanisms during drought–rewatering cycles remain unclear, particularly across recovery stages. Using a polyethylene glycol (PEG-6000) hydroponic system, we analyzed physiological, metabolomic, and transcriptomic responses of Oryza sativa L. ssp. japonica under control, continuous drought, and rewatering treatments. The net photosynthetic rate (Pn) recovered within one day after rewatering, and subsequently exceeded control levels, indicating a photosynthetic compensatory effect. In contrast, instantaneous water-use efficiency (WUE) showed only a transient increase before declining thereafter and remaining lower than under continuous drought, revealing an asynchronous recovery in which carbon assimilation precedes the recovery of transpiration. Metabolomic analysis indicated a shift from drought-induced accumulation to recovery-driven metabolic reprogramming, with coordinated up-regulation of central carbon metabolism and chlorophyll biosynthesis. Decreases in citrate, malate, and glutamate suggested their sustained utilization to support nitrogen assimilation and chlorophyll synthesis. Transcriptomic data further revealed large-scale reprogramming during late recovery, including up-regulation of nitrogen assimilation genes (e.g., NIA, NiR), linking carbon–nitrogen coordination with photosynthetic compensation. Overall, these results demonstrate that stage-specific integration of physiological recovery, metabolic restructuring, and transcriptional regulation underlies AWD-induced efficiency and identify early rewatering as a critical window for optimizing WUE.