Data from: Phylogeography of Asian wild rice, Oryza rufipogon: a genome-wide view

Asian wild rice (Oryza rufipogon) that ranges widely across the eastern and southern part of Asia is recognized as the direct ancestor of cultivated Asian rice (O. sativa). Studies of the geographic structure of O. rufipogon, based on chloroplast and low-copy nuclear markers, reveal a possible phylogeographic signal of subdivision in O. rufipogon. However, this signal of geographic differentiation is not consistently observed among different markers and studies, with often conflicting results. To more precisely characterize the phylogeography of O. rufipogon populations, a genome-wide survey of unlinked markers, intensively sampled from across the entire range of O. rufipogon is critical. In this study, we surveyed sequence variation at 42 genome-wide sequence tagged sites (STS) in 108 O. rufipogon accessions from throughout the native range of the species. Using Bayesian clustering, principal component analysis and amova, we conclude that there are two genetically distinct O. rufipogon groups, Ruf-I and Ruf-II. The two groups exhibit a clinal variation pattern generally from north-east to south-west. Different from many earlier studies, Ruf-I, which is found mainly in China and the Indochinese Peninsula, shows genetic similarity with one major cultivated rice variety, O. satvia indica, whereas Ruf-II, mainly from South Asia and the Indochinese Peninsula, is not found to be closely related to cultivated rice varieties. The other major cultivated rice variety, O. sativa japonica, is not found to be similar to either O. rufipogon groups. Our results support the hypothesis of a single origin of the domesticated O. sativa in China. The possible role of palaeoclimate, introgression and migration–drift balance in creating this clinal variation pattern is also discussed.

广泛分布于亚洲东部和南部的亚洲普通野生稻（Oryza rufipogon）被公认为亚洲栽培稻（O. sativa）的直接祖先。基于叶绿体及低拷贝核标记开展的亚洲普通野生稻群体地理结构研究，揭示了其群体存在分化的潜在系统地理信号。然而，该遗传分化信号在不同标记及研究中并不一致，研究结果常存在冲突。为更精准地解析亚洲普通野生稻群体的系统地理格局，对覆盖其整个分布范围的密集采样群体开展全基因组非连锁标记扫描至关重要。本研究对覆盖该物种原生分布全境的108份亚洲普通野生稻种质资源的42个全基因组序列标签位点（sequence tagged sites, STS）进行了序列变异分析。通过贝叶斯聚类、主成分分析及分子方差分析（Analysis of Molecular Variance, AMOVA），本研究确定亚洲普通野生稻存在两个遗传分化显著的类群：Ruf-I与Ruf-II。这两个类群整体呈现出从东北向西南的渐变变异模式。与诸多早期研究不同的是，主要分布于中国及印度支那半岛的Ruf-I类群，与主要栽培稻类群籼型栽培稻（O. sativa indica）具有较高的遗传相似性；而主要分布于南亚及印度支那半岛的Ruf-II类群，则未表现出与栽培稻类群的紧密亲缘关系。另一主要栽培稻类群粳型栽培稻（O. sativa japonica），与上述两个亚洲普通野生稻类群均未表现出遗传相似性。本研究结果支持亚洲栽培稻起源于中国的单一起源假说。本研究还探讨了古气候、基因渐渗以及迁移-漂变平衡在塑造该渐变变异模式中可能发挥的作用。