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.similar to sativa). Studies of the geographic structure of O.similar to rufipogon, based on chloroplast and low-copy nuclear markers, reveal a possible phylogeographic signal of subdivision in O.similar to 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.similar to rufipogon populations, a genome-wide survey of unlinked markers, intensively sampled from across the entire range of O.similar to rufipogon is critical. In this study, we surveyed sequence variation at 42 genome-wide sequence tagged sites (STS) in 108 O.similar to 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.similar to 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.similar to 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.similar to sativa japonica, is not found to be similar to either O.similar to rufipogon groups. Our results support the hypothesis of a single origin of the domesticated O.similar to sativa in China. The possible role of palaeoclimate, introgression and migrationdrift balance in creating this clinal variation pattern is also discussed.