Multi-omics analysis reveals distinct metabolic strategies associated with grain chalkiness variation between rice cultivars under naturally occurring high-temperature conditions

High temperature during the grain-filling stage negatively affects rice grain quality by promoting grain chalkiness formation. However, the molecular and metabolic factors associated with cultivar-dependent differences in chalkiness variation under high-temperature conditions remain poorly understood. In this study, two conventional indica rice cultivars with contrasting chalkiness phenotypes, a high-chalkiness cultivar ZZ35 (HC) and a low-chalkiness cultivar R1466 (LC), were compared under naturally occurring high-temperature conditions. Time-series transcriptomic and untargeted metabolomic analyses were performed to characterize the dynamic changes associated with chalkiness variation during grain development. Integrated transcriptome and metabolome analyses revealed distinct transcriptional and metabolic profiles between HC and LC cultivars during grain filling. Phenylpropanoid metabolism showed differential regulation between the two cultivars, with LC exhibiting enhanced expression of lignin biosynthesis-related genes and higher accumulation of lignin-associated metabolites, including coniferyl alcohol and sinapyl alcohol, suggesting cultivar-dependent differences in phenylpropanoid-related metabolic responses under high-temperature conditions. Consistently, LC showed higher levels of lignin monomers and stronger lignification signals in mature grain hulls under both temperature environments. In contrast, HC exhibited lower expression of phenylpropanoid-related genes and reduced accumulation of related metabolites, particularly under high-temperature conditions. Co-expression network analysis further identified candidate modules associated with phenolic metabolism, carbon metabolism, and stress-responsive processes. These findings suggest that cultivar-dependent differences in phenylpropanoid metabolism and other metabolic processes are associated with variation in rice chalkiness under high-temperature conditions. The identified metabolic signatures and co-expression modules provide potential clues for understanding the molecular factors underlying heat-associated grain quality variation and warrant further functional validation.