Phylogeography of Asian wild rice, Oryza rufipogon

A genome-wide view

Pu Huang, Jeanmaire Molina, Jonathan M. Flowers, Samara Rubinstein, Scott A. Jackson, Michael D. Purugganan, Barbara A. Schaal

Research output: Contribution to journalArticle

Abstract

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. See also the Perspective by Gross

Original languageEnglish (US)
Pages (from-to)4593-4604
Number of pages12
JournalMolecular Ecology
Volume21
Issue number18
DOIs
StatePublished - Sep 2012

Fingerprint

Phylogeography
Oryza rufipogon
wild rice
phylogeography
rice
genome
Genome
China
Sequence Tagged Sites
introgression
paleoclimate
chloroplast
ancestry
Chloroplasts
Principal Component Analysis
principal component analysis
Cluster Analysis
Oryza
South Asia
Oryza sativa

Keywords

  • domestication
  • Oryza rufipogon
  • Oryza sativa
  • phylogeography

ASJC Scopus subject areas

  • Ecology, Evolution, Behavior and Systematics
  • Genetics

Cite this

Huang, P., Molina, J., Flowers, J. M., Rubinstein, S., Jackson, S. A., Purugganan, M. D., & Schaal, B. A. (2012). Phylogeography of Asian wild rice, Oryza rufipogon: A genome-wide view. Molecular Ecology, 21(18), 4593-4604. https://doi.org/10.1111/j.1365-294X.2012.05625.x

Phylogeography of Asian wild rice, Oryza rufipogon : A genome-wide view. / Huang, Pu; Molina, Jeanmaire; Flowers, Jonathan M.; Rubinstein, Samara; Jackson, Scott A.; Purugganan, Michael D.; Schaal, Barbara A.

In: Molecular Ecology, Vol. 21, No. 18, 09.2012, p. 4593-4604.

Research output: Contribution to journalArticle

Huang, P, Molina, J, Flowers, JM, Rubinstein, S, Jackson, SA, Purugganan, MD & Schaal, BA 2012, 'Phylogeography of Asian wild rice, Oryza rufipogon: A genome-wide view', Molecular Ecology, vol. 21, no. 18, pp. 4593-4604. https://doi.org/10.1111/j.1365-294X.2012.05625.x
Huang, Pu ; Molina, Jeanmaire ; Flowers, Jonathan M. ; Rubinstein, Samara ; Jackson, Scott A. ; Purugganan, Michael D. ; Schaal, Barbara A. / Phylogeography of Asian wild rice, Oryza rufipogon : A genome-wide view. In: Molecular Ecology. 2012 ; Vol. 21, No. 18. pp. 4593-4604.
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