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.