Large-scale genomic and phenomic analyses of modern cultivars empower future rice breeding design.

Modern cultivated rice plays a pivotal role in global food security. China accounts for nearly 30% of the world's rice production and has bred numerous cultivated varieties over the last decades that are well adapted to diverse growing regions. However, the genomic bases that underlie the phenotypes of modern cultivars are poorly characterized, limiting access to this vast resource for breeding of specialized, regionally adapted cultivars. In this study, we constructed a comprehensive genetic variation map of modern rice using resequencing datasets from 6044 representative cultivars from five major growing regions in China. Genomic and phenotypic analyses of this diversity panel revealed regional preferences for genomic backgrounds and specific traits, such as heading date, biotic/abiotic stress resistance, and grain shape, associated with adaptation to local growing conditions and consumer preferences. We identified 3131 QTLs associated with 53 phenotypes across 212 datasets under different environmental conditions through genome-wide association studies. Notably, we cloned and functionally verified a novel gene related to grain length, OsGL3.6. By integrating multiple datasets, we developed RiceAtlas, a versatile multi-scale toolkit for rice breeding design. We rapidly improved the grain shape of the Suigeng4 cultivar using the RiceAtlas breeding design function. These valuable resources enhance our understanding of the adaptability and breeding requirements of modern rice and can facilitate advances in future rice-breeding initiatives.