Superior alleles of SEED-AGING GENE 9 enhance seed storability and dormancy in rice

High-quality seeds necessitate both appropriate dormancy to prevent preharvest sprouting and robust storability to preserve germination vigor, which serve as the fundamental guarantee for the successful production and safe storage of crops. As complex and quantitative traits, the improvement of seed quality has been impeded by limited understanding of their regulatory genes. Here, in rice, we identify SEED-AGING GENE 9 (SAG9), encoding a nuclear protein, as a negative regulator underlying the major seed-storability quantitative trait locus qSS-9, which also exerts a moderate effect on dormancy. Indeed, SAG9 physically interacts with selected bZIP transcription factors expressed in seeds, inhibiting their transcriptional activation of Late Embryogenesis Abundant genes-revealing a shared genetic pathway coordinating dormancy and storability. This has driven the differential local adaptation of SAG9 distinct haplotypes, thereby promoting balancing selection during rice domestication. Notably, the elite SAG9 haplotype Hap- has been largely lost during domestication, which is one of the causes for the reduction in seed dormancy and storability of modern varieties. Furthermore, strong-dormancy alleles (SD1, SDR3.1, Sdr4, SD6, and Rc) enhance storability and show additive effects with SAG9 Hap-. Diverse pyramiding combinations of these genes across regions reflect synergistic adaptation to environmental or breeding demands. Collectively, our study elucidates the molecular and domestication basis of seed quality traits, providing targets for precision breeding in modern rice varieties.