A pangenome reference of wild and cultivated rice

Dongling Guo, Yan Li, Hengyun Lu, Yan Zhao, Nori Kurata, Xinghua Wei, Ahong Wang, Yongchun Wang, Qilin Zhan, Danlin Fan, Congcong Zhou, Yiqi Lu, Qilin Tian, Qijun Weng, Qi Feng, Tao Huang, Lei Zhang, Zhoulin Gu, Changsheng Wang, Ziqun Wang, Zixuan Wang, Xuehui Huang, Qiang Zhao () and Bin Han ()
Additional contact information
Dongling Guo: Chinese Academy of Sciences
Yan Li: Chinese Academy of Sciences
Hengyun Lu: Chinese Academy of Sciences
Yan Zhao: Chinese Academy of Sciences
Nori Kurata: National Institute of Genetics
Xinghua Wei: Chinese Academy of Agricultural Sciences
Ahong Wang: Chinese Academy of Sciences
Yongchun Wang: Chinese Academy of Sciences
Qilin Zhan: Chinese Academy of Sciences
Danlin Fan: Chinese Academy of Sciences
Congcong Zhou: Chinese Academy of Sciences
Yiqi Lu: Chinese Academy of Sciences
Qilin Tian: Chinese Academy of Sciences
Qijun Weng: Chinese Academy of Sciences
Qi Feng: Chinese Academy of Sciences
Tao Huang: Chinese Academy of Sciences
Lei Zhang: Chinese Academy of Sciences
Zhoulin Gu: Chinese Academy of Sciences
Changsheng Wang: Chinese Academy of Sciences
Ziqun Wang: Chinese Academy of Sciences
Zixuan Wang: Chinese Academy of Sciences
Xuehui Huang: Shanghai Normal University
Qiang Zhao: Chinese Academy of Sciences
Bin Han: Chinese Academy of Sciences

Nature, 2025, vol. 642, issue 8068, 662-671

Abstract: Abstract Oryza rufipogon, the wild progenitor of Asian cultivated rice Oryza sativa, is an important resource for rice breeding1. Here we present a wild–cultivated rice pangenome based on 145 chromosome-level assemblies, comprising 129 genetically diverse O. rufipogon accessions and 16 diverse varieties of O. sativa. This pangenome contains 3.87 Gb of sequences that are absent from the O. sativa ssp. japonica cv. Nipponbare reference genome. We captured alternate assemblies that include heterozygous information missing in the primary assemblies, and identified a total of 69,531 pan-genes, with 28,907 core genes and 13,728 wild-rice-specific genes. We observed a higher abundance and a significantly greater diversity of resistance-gene analogues in wild rice than in cultivars. Our analysis indicates that two cultivated subpopulations, intro-indica and basmati, were generated through gene flows among cultivars in South Asia. We also provide strong evidence to support the theory that the initial domestication of all Asian cultivated rice occurred only once. Furthermore, we captured 855,122 differentiated single-nucleotide polymorphisms and 13,853 differentiated presence–absence variations between indica and japonica, which could be traced to the divergence of their respective ancestors and the existence of a larger genetic bottleneck in japonica. This study provides reference resources for enhancing rice breeding, and enriches our understanding of the origins and domestication process of rice.

Date: 2025
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DOI: 10.1038/s41586-025-08883-6

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