Allelic variation in OsATG3 enhances nitrogen-responsive tillering to sustain rice productivity

Nitrogen (N) deficiency constrains crop productivity by limiting shoot growth, yet the adaptive mechanisms that reprogram shoot development under low N conditions remain largely elusive. Here, we identify a major locus, OsATG3 (autophagy-related protein 3), controlling tillering in response to N deficiency through a genome-wide association study in rice. OsATG3 functions as an essential autophagy component and promotes selective degradation of IDEAL PLANT ARCHITECTURE1 (IPA1) via OsATG8d-mediated autophagy in shoot apices, thereby enhancing N-responsive tillering. Natural variation in the promoter of OsATG3 modulates its transcriptional activity and underlies the adaptive range of tiller number under low N conditions. The elite haplotype OsATG3-H enhances both tillering and grain yield under N-limited supply and appears to contribute to geographical adaptation both in O. sativa and O. glaberrima. Our findings uncover a genetic and molecular mechanism that couples N deficiency to shoot developmental plasticity, providing a promising target for sustainable rice breeding with reduced fertilizer input.