Abstract

The continuous rise in global temperatures and the increasing frequency of extreme heat events pose severe challenges to rice production due to heat stress. Exploring heat tolerance genes and developing heat-tolerant rice varieties represent effective strategies to address this issue. In this study, we identified a novel heat tolerance gene, OsClpI3 , through analysis of the Caseinolytic proteases (Clp) ATPase gene family. OsClpI3 is predominantly expressed in leaves, encodes a chloroplast-localized protein, and positively regulates heat tolerance during both the seedling and heading stages. OsClpI3 exhibits ATPase activity, which is markedly reduced in mutant lines. Integrated transcriptomic and metabolomic analyses revealed that OsClpI3 contributes to rice thermotolerance by maintaining photosynthetic electron transport efficiency and overall photosynthetic performance under high-temperature conditions. Furthermore, natural variation in OsClpI3 affects heat tolerance, and haplotype analysis revealed a superior haplotype, Type4. These findings provide new insights into the molecular mechanisms underlying heat tolerance in rice and offer valuable genetic resources for breeding heat-tolerant rice varieties.