The OsNTL3-WRKY53-CatA module confers thermotolerance in rice

High temperature is a major environmental constraint that severely limits rice (Oryza sativa) growth, yield potential, and geographical adaptability. The molecular mechanisms underlying rice adaptation to warm climates remain poorly understood. By integrating population genomic data with multi-scale phenotyping, we show that a single nucleotide polymorphism (SNP-1456) in the promoter of the defense transcription factor WRKY53 determines rice thermotolerance and grain yield. The thermotolerant allele strengthens the binding of the membrane-tethered NAC factor OsNTL3, which represses WRKY53 expression. Low WRKY53 derepresses catalase A (CatA), thereby lowering hydrogen peroxide (H₂O₂) levels. CRISPR knockout of WRKY53 boosts seed set and increases yield under field heat waves. Environmental-cline analysis of 4315 accessions reveals that the thermotolerant allele of WRKY53 is predominantly distributed in low-latitude regions with warm climates. Our findings reveal a previously uncharacterized WRKY53-centered regulatory network that mediates thermotolerance and facilitates rice adaptation to warm environments, offering promising targets for molecular breeding of climate-resilient rice varieties.