中国科学院分子植物科学卓越创新中心韩斌小组近日取得一项新成果。经过不懈努力，他们提出了野生稻和栽培稻的全基因组参考资料。相关论文于2025年4月16日发表于国际顶尖学术期刊《自然》杂志上。

在这里，该课题组研究人员提出了一个基于145个染色体水平组装的野生栽培水稻泛基因组，其中包括129个遗传多样性的水稻品种和16个不同的水稻品种。这个泛基因组包含3.87在大豆中缺失的Gb的序列。Nipponbare参考基因组。该课题组人员捕获了包含原始组合中缺失的杂合子信息的替代组合，共鉴定出69531个泛基因，其中28907个核心基因和13728个野生水稻特异性基因。研究组观察到野生稻中抗性基因类似物的丰度和多样性明显高于栽培稻。他们的分析表明，两个可栽培的亚种群，即籼型和巴斯马蒂，是通过南亚栽培品种之间的基因流动产生的。该课题组人员还提供了强有力的证据来支持所有亚洲栽培水稻的最初驯化只发生过一次的理论。

此外，该课题组人员在籼稻和粳稻之间捕获了855122个分化的单核苷酸多态性和13853个分化的存在-缺失变异，这可以追溯到它们各自祖先的分歧和粳稻存在更大的遗传瓶颈。本研究为加强水稻育种提供了参考资料，丰富了他们对水稻起源和驯化过程的认识。

据了解，水稻（Oryza rufipogon）是亚洲栽培水稻（Oryza sativa）的野生祖先，是水稻育种中一种重要的抗性品种。

附：英文原文

Title: A pangenome reference of wild and cultivated rice

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

Issue&Volume: 2025-04-16

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 3.87Gb 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.

DOI: 10.1038/s41586-025-08883-6

Source: https://www.nature.com/articles/s41586-025-08883-6