A pangenome reference of wild and cultivated rice

Oryza rufipogon, the wild progenitor of Asian cultivated rice Oryza sativa, is an important resource for rice breeding<sup>1</sup>. 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.

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Publication Details

Journal
Nature
Published
2025-04-16
DOI
https://doi.org/10.1038/s41586-025-08883-6
Citations
39
Primary Topic
Genetic Mapping and Diversity in Plants and Animals
Type
article
Field-Weighted Citation Impact
70.87
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article

A pangenome reference of wild and cultivated rice

Xuehui Huang, Zhoulin Gu, Qiang Zhao, Qijun Weng et al.
39 citations
Nature
Genetic Mapping and Diversity in Plants and Animals
70.87
article

A pangenome reference of wild and cultivated rice

Xuehui Huang, Zhoulin Gu, Qiang Zhao, Qijun Weng, Ahong Wang, Qi Feng, Yongchun Wang, Yiqi Lu, Xinghua Wei, Lei Zhang, Qilin Tian, Bin Han, Ziqun Wang, Hengyun Lu, Danlin Fan, Congcong Zhou, Qilin Zhan, Yán Li, Zixuan Wang, Changsheng Wang, Nori Kurata, Dongling Guo, Yan Zhao, Tao Huang
article en
39 citations

Abstract

Oryza rufipogon, the wild progenitor of Asian cultivated rice Oryza sativa, is an important resource for rice breeding<sup>1</sup>. 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.

NatureVol. 642(8068)
National Institute of Genetics (JP), Shanghai Normal University (CN), Chinese Academy of Agricultural Sciences (CN), Center for Excellence in Molecular Plant Sciences (CN), China National Rice Research Institute (CN), University of Chinese Academy of Sciences (CN)
Zero hunger
Openalex Percentile: Top 0%
Genetic Mapping and Diversity in Plants and Animals
70.87
DOIOpen Access PDFOpenAlex
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