OsSPT38 encodes a novel SUMO E3 ligase that improves rice stress resilience and grain yield.

Abiotic stresses threaten global food security, underscoring the requirement for resilient crop varieties. In this study, we identified OsSPT38, a previously uncharacterized SUMO E3 ligase in rice, and discovered a gain-of-function mutation (Gly212Asp) of OsSPT38 that enhances rice stress resilience and yield. The phenotypic effects of this mutation were validated in 18 independent mutants and by base editing in the elite indica cultivar Huanghuazhan. Among 4774 rice accessions, the Gly212Asp mutation was identified exclusively in seven japonica varieties, demonstrating its rarity and recent evolutionary origin. Functional analyses showed that OsSPT38 interacts with the SUMO E2 enzyme OsSCE3 and stress-associated proteins to promote their SUMOylation, thereby stabilizing target proteins. The Gly212Asp allele (OsSPT38D) displayed greater activity than the wild-type allele. These findings uncover OsSPT38 as a key regulator of abiotic stress adaptation and underscore Gly212Asp as a promising molecular target for breeding high-yielding stress-resilient rice varieties.