Ma Xiaoding, Wang Hao, Yan Shen, Zhou Chuanqing, Zhou Kunneng, Zhang Qiang, Li Maomao, Yang Yaolong, Li Danting, Song Peng, Tang Cuifeng, Geng Leiyue, Sun Jianchang, Ji Zhiyuan, Sun Xianjun, Zhou Yongli, Zhou Peng, Cui Di, Han Bing, Jing Xin, He Qiang, Fang Wei, Han Longzhi
State Key Laboratory of Crop Gene Resources and Breeding, Institute of Crop Sciences, Chinese Academy of Agricultural Sciences, Beijing 100081, China.
Smartgenomics Technology Institute, Tianjin 301700, China.
Mol Plant. 2025 Apr 7;18(4):651-668. doi: 10.1016/j.molp.2025.03.007. Epub 2025 Mar 13.
Modern cultivated rice plays a pivotal role in global food security. China accounts for nearly 30% of the world's rice production and has developed numerous cultivated varieties over the past decades that are well adapted to diverse growing regions. However, the genomic bases underlying the phenotypes of these modern cultivars remain poorly characterized, limiting the exploitation of this vast resource for breeding 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 rice-growing regions in China. Our genomic and phenotypic analyses of this diversity panel revealed regional preferences for specific genomic backgrounds and traits, such as heading date, biotic/abiotic stress resistance, and grain shape, which are crucial for adaptation to local conditions and consumer preferences. We identified 3131 quantitative trait loci associated with 53 phenotypes across 212 datasets under various 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 successfully utilized the RiceAtlas breeding design function to rapidly improve the grain shape of the Suigeng4 cultivar. These valuable resources enhance our understanding of the adaptability and breeding requirements of modern rice and can facilitate advances in future rice-breeding initiatives.
现代栽培稻在全球粮食安全中发挥着关键作用。中国的水稻产量占世界近30%，在过去几十年中培育出了众多适应不同种植区域的栽培品种。然而，这些现代品种表型的基因组基础仍未得到充分表征，限制了对这一庞大资源用于培育专门的、适应区域环境的品种的利用。在本研究中，我们利用来自中国五个主要水稻种植区的6044个代表性品种的重测序数据集构建了现代水稻的综合遗传变异图谱。我们对这个多样性群体的基因组和表型分析揭示了对特定基因组背景和性状的区域偏好，如抽穗期、生物/非生物胁迫抗性和粒形，这些对于适应当地环境和消费者偏好至关重要。通过全基因组关联研究，我们在各种环境条件下的212个数据集中鉴定出与53种表型相关的3131个数量性状位点。值得注意的是，我们克隆并功能验证了一个与粒长相关的新基因OsGL3.6。通过整合多个数据集，我们开发了RiceAtlas，这是一个用于水稻育种设计的多功能多尺度工具包。我们成功利用RiceAtlas育种设计功能快速改良了绥粳4品种的粒形。这些宝贵资源加深了我们对现代水稻适应性和育种需求的理解，并有助于推动未来水稻育种计划的进展。
