Phylogeography of Asian wild rice, <i>Oryza rufipogon</i>: a genome‐wide view

Molecular Ecology - Tập 21 Số 18 - Trang 4593-4604 - 2012
Pu Huang1, Jeanmaire Molina2, Jonathan M. Flowers2, Samara Rubinstein2, Scott A. Jackson3, Michael D. Purugganan2, Barbara A. Schaal1
1Department of Biology, Washington University, St. Louis, MO 63130 USA
2Department of Biology and Center for Genomics and Systems Biology, New York University, New York, NY 10003, USA
3Center for Applied Genetic Technologies, University of Georgia, Athens, GA, 30621, USA.

Tóm tắt

AbstractAsian 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.

Từ khóa


Tài liệu tham khảo

10.1002/bies.200800162

10.1371/journal.pgen.0030163

10.1111/j.1461-0248.2006.00974.x

10.1093/molbev/msg004

Chou CL, 1948, China is the place of origin of rice, Zhong Guo Dao Zuo, 7, 53

10.1126/science.1172873

10.1111/j.1365-294X.2006.02994.x

10.1016/j.mbs.2006.09.015

10.1186/1471-2105-9-539

10.1016/j.tree.2009.01.009

10.1038/nature01019

10.1016/j.cell.2006.12.006

10.1126/science.1143986

10.1111/j.1365-294X.2005.02553.x

10.1111/j.1755-0998.2010.02847.x

10.1093/genetics/155.3.1405

10.1038/ng1108-1264

10.1126/science.1166605

10.1007/s12520-010-0035-y

10.1111/j.1365-294X.2004.02108.x

10.1007/s00122-002-1027-9

10.1534/genetics.104.035642

10.1111/j.1558-5646.2008.00602.x

10.1016/j.tplants.2010.05.008

10.1111/j.1469-8137.2009.02957.x

10.1126/science.278.5341.1312

10.1093/genetics/116.1.153

10.1111/j.1365-294X.2007.03467.x

10.1023/A:1005810616885

10.1080/10635150701701091

10.1093/bioinformatics/btp187

10.1111/j.1365-294X.2007.03489.x

10.1073/pnas.0603152103

10.1073/pnas.0810108105

10.1007/s00122-002-1013-2

10.1007/s001220100694

10.1073/pnas.1104686108

10.2306/scienceasia1513-1874.2009.35.161

10.1111/j.1365-294X.2004.02396.x

R Development Core Team, 2011, R: A Language and Environment for Statistical Computing

Ray N, 2001, A GIS‐based vegetation map of the world at the last glacial maximum (25,000‐15,000 BP), Internet Archaeology, 11

10.1186/1471-2148-10-180

10.1266/jjg.57.25

SecondG MorishimaH(1981)Geographical and ecological pattern of variation ofOryza perennisat 7 isozyme loci.National Institute of Genetics Mishima Japan 1980 Annual Report 95–96.

Slatkin M, 1991, F st in hierarchical island model, Genetics, 127, 627, 10.1093/genetics/127.3.627

10.1046/j.1469-8137.2003.00699.x

10.1093/bioinformatics/btm069

10.1086/379378

10.1086/319501

Sun CQ, 1997, RFLP analysis of nuclear DNA in common wild rice (Oryza rufipogon Griff.) and cultivated rice (Oryza sativa L.), Scientia Agricultura Sinica, 30, 37

10.1093/aob/mcm128

10.1371/journal.pgen.0030133

10.1111/j.1365-294X.2005.02683.x

10.1046/j.1365-2915.1999.00189.x

Tanaka T, 2008, The rice annotation project database (RAP‐DB): 2008 update, Nucleic Acids Research, 36, D1028

10.1038/ng.197

10.1016/j.plantsci.2008.01.016

10.1093/genetics/144.3.1113

10.1038/18435

10.1038/hdy.2008.61

10.1016/0040-5809(75)90020-9

10.1111/j.1365-294X.2006.02870.x

Yuan LP, 1989, Progress in Irrigated Rice Research, 219

10.1534/genetics.106.061432

10.1111/j.1469-8137.2009.02984.x

10.1007/s00122-003-1251-y

10.1111/j.1469-8137.2005.01406.x

10.1093/molbev/msm005

10.1186/gb-2008-9-3-r49

Thông tin
Thông tin xuất bản

Molecular Ecology

Tập 21 Số 18

4593-4604

Thông tin tác giả