Multi-omics Analysis Reveals the Hormonal Basis of Differential Response to Nighttime Heat Temperature Between Superior and Inferior Rice Grains

Nighttime high temperature (NHT) poses a significant threat to rice production, particularly during the grain-filling stage. However, its impact on grain development remains poorly understood. In this study, we investigated the effects of NHT on yield and quality in two japonica rice varieties (N5055 and YND1) during early grain-filling stage. We found that NHT significantly reduced the grain setting rate, hundred-grain weight and amylose content, with inferior grains (IGs) being more severely affected than superior grains (SGs). Metabolomic analysis revealed 670 differentially accumulated metabolites (DAMs), primarily associated with lipid, amino acid, and hormone metabolism. Notably, more hormone-related DAMs were detected in SGs than in IGs. Transcriptomic profiling identified 7750 differentially expressed genes (DEGs) under control conditions, but only 576 under NHT, indicating a dramatic disruption of transcriptional programs. Eight hormone-related genes were significantly differentially expressed in SGs, underscoring the crucial role of hormonal regulation in the SG-specific NHT response. Hormonal profiling further revealed 12 differentially accumulated hormones, six of which exhibited distinct accumulation patterns between SGs and IGs. This demonstrates that SGs undergo unique hormonal reprogramming under NHT stress, characterized by significant upregulation of cytokinins. The key cytokinin response regulators, OsRR3 and OsRR6, were specifically correlated with cytokinin levels in SGs, but not in IGs. Our integrated analysis reveals that differential hormonal and transcriptional regulation underpins the contrasting responses of SGs and IGs to NHT, providing new insights into the metabolic and molecular basis of NHT tolerance in rice.