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与南部区域的普通野生稻（Oryza rufipogon），被公认为亚洲栽培稻（Oryza sativa）的直接祖先。基于叶绿体与低拷贝核标记开展的普通野生稻地理结构研究，已揭示其种群分化的潜在系统地理信号。然而，不同标记及不同研究中并未一致观测到该地理分化信号，结果往往相互矛盾。为更精准地解析普通野生稻种群的系统地理学特征，对覆盖其整个分布范围、经密集采样的全基因组非连锁标记开展序列变异分析，是至关重要的。本研究针对覆盖该物种原生分布全域的108份普通野生稻种质资源，对42个全基因组序列标签位点（sequence tagged sites, STS）的序列变异进行了检测。本研究采用贝叶斯聚类、主成分分析以及分子方差分析（AMOVA），最终确定存在两个遗传分化显著的普通野生稻类群：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，主要分布于中国及中南半岛的Ruf-I类群，与主要栽培稻品种之一的籼型稻（Oryza sativa indica）具有较高的遗传相似性；而主要分布于南亚及中南半岛的Ruf-II类群，则与现有栽培稻品种无显著亲缘关联。另一主要栽培稻品种——粳型稻（Oryza sativa japonica），则与两类普通野生稻类群均无明显遗传相似性。本研究结果支持“亚洲栽培稻起源于中国的单次驯化事件”这一假说。本研究还探讨了古气候、基因渐渗以及迁移-漂变平衡在形成该渐变变异模式中可能发挥的作用。