Duplicated OsATG9 Genes Antagonise Autophagy to Balance Growth and Drought Tolerance in Rice

ABSTRACT Gene duplication events frequently occur during eukaryotic genome evolution, often leading to functional redundancy for organism survival in complex environments. However, whether duplicate genes evolve diverse functions remains unclear. In this study, we explored the roles of autophagy‐related gene 9 OsATG9a and OsATG9b in rice development and drought stress responses. Autophagy, an evolutionarily conserved degradation pathway, plays a critical role in multiple biological processes by recycling cellular components. We found both OsATG9a and OsATG9b involved in autophagy, with functional redundancy affecting traits like grain size, plant height, tiller number, primary branch number, and panicle length. Notably, OsATG9b exhibited a distinct response to drought stress. The osatg9a mutant displayed a lower survival rate than wild type (WT) after drought stress, similar to other osatg mutants, while the osatg9b mutant showed the opposite. Moreover, autophagy flux decreased in osatg9a mutant but increased in osatg9b , surpassing WT response. Overexpression of OsATG9b resulted in lower survival rates and reduced autophagy induction under drought stress. Moreover, the response of ABA related genes in osatg9a and in osatg9b were opposite compared with WT. These suggest that OsATG9a promotes autophagy during drought stress, while OsATG9b negatively impacts it, representing a newly evolved function in rice by differently regulating ABA pathway. Our findings provided insights into the functional divergence of duplicate genes during evolution.