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Volumn 7, Issue 11, 2012, Pages

Origin of Oryza sativa in China Inferred by Nucleotide Polymorphisms of Organelle DNA

Author keywords

[No Author keywords available]

Indexed keywords

PLANT DNA;

EID: 84869217520     PISSN: None     EISSN: 19326203     Source Type: Journal    
DOI: 10.1371/journal.pone.0049546     Document Type: Article
Times cited : (13)

References (50)
  • 1
    • 33747595222 scopus 로고    scopus 로고
    • Eastern North America as an independent center of plant domestication
    • Smith BD, (2006) Eastern North America as an independent center of plant domestication. Proc Natl Acad Sci U S A 103: 12223-12228.
    • (2006) Proc Natl Acad Sci U S A , vol.103 , pp. 12223-12228
    • Smith, B.D.1
  • 2
    • 33749431393 scopus 로고    scopus 로고
    • New evidence for the origins of sedentism and rice domestication in the Lower Yangzi River, China
    • Jiang L, Liu L, (2006) New evidence for the origins of sedentism and rice domestication in the Lower Yangzi River, China. Antiquity 80: 355-361.
    • (2006) Antiquity , vol.80 , pp. 355-361
    • Jiang, L.1    Liu, L.2
  • 4
    • 0001513652 scopus 로고
    • The origin and evolution of cultivated rice in China
    • Ting Y, (1957) The origin and evolution of cultivated rice in China. Acta Agr Sinica 8: 243-260.
    • (1957) Acta Agr Sinica , vol.8 , pp. 243-260
    • Ting, Y.1
  • 5
    • 33745494845 scopus 로고
    • The origin and development of cultivated rice in China
    • Liu Z, (1975) The origin and development of cultivated rice in China. Acta Genet Sinica 2: 23-29.
    • (1975) Acta Genet Sinica , vol.2 , pp. 23-29
    • Liu, Z.1
  • 6
    • 34848893361 scopus 로고    scopus 로고
    • Fire and flood management of coastal swamp enabled first rice paddy cultivation in east China
    • Zong Y, Chen Z, Innes JB, Chen C, Wang Z, et al. (2007) Fire and flood management of coastal swamp enabled first rice paddy cultivation in east China. Nature 449: 459-462.
    • (2007) Nature , vol.449 , pp. 459-462
    • Zong, Y.1    Chen, Z.2    Innes, J.B.3    Chen, C.4    Wang, Z.5
  • 7
    • 62849117160 scopus 로고    scopus 로고
    • The domestication process and domestication rate in rice: spikelet bases from the Lower Yangtze
    • Fuller DQ, Qin L, Zheng Y, Zhao Z, Chen X, et al. (2009) The domestication process and domestication rate in rice: spikelet bases from the Lower Yangtze. Science 323: 1607-1610.
    • (2009) Science , vol.323 , pp. 1607-1610
    • Fuller, D.Q.1    Qin, L.2    Zheng, Y.3    Zhao, Z.4    Chen, X.5
  • 8
    • 49849083288 scopus 로고    scopus 로고
    • Nonindependent domestication of the two rice subspecies, Oryza sativa ssp. Indica and ssp. japonica, demonstrated by multilocus microsatellites
    • Gao LZ, Innan H, (2008) Nonindependent domestication of the two rice subspecies, Oryza sativa ssp. Indica and ssp. japonica, demonstrated by multilocus microsatellites. Genetics 179: 965-976.
    • (2008) Genetics , vol.179 , pp. 965-976
    • Gao, L.Z.1    Innan, H.2
  • 10
    • 84866241595 scopus 로고    scopus 로고
    • Phylogeography of Asian wild rice, Oryza rufipogon: a genome-wide view
    • Huang P, Molina J, Flowers JM, Rubinstein S, Jackson SA, et al. (2012) Phylogeography of Asian wild rice, Oryza rufipogon: a genome-wide view. Mol Ecol 21: 4593-4604.
    • (2012) Mol Ecol , vol.21 , pp. 4593-4604
    • Huang, P.1    Molina, J.2    Flowers, J.M.3    Rubinstein, S.4    Jackson, S.A.5
  • 11
    • 0037225254 scopus 로고    scopus 로고
    • Polyphyletic origin of cultivated rice: based on the interspersion pattern of SINEs
    • Cheng C, Motohashi R, Tsuchimoto S, Fukuta Y, Ohtsubo H, et al. (2003) Polyphyletic origin of cultivated rice: based on the interspersion pattern of SINEs. Mol Biol Evol 20: 67-75.
    • (2003) Mol Biol Evol , vol.20 , pp. 67-75
    • Cheng, C.1    Motohashi, R.2    Tsuchimoto, S.3    Fukuta, Y.4    Ohtsubo, H.5
  • 12
    • 33745439823 scopus 로고    scopus 로고
    • Phylogeography of Asian wild rice, Oryza rufipogon, reveals multiple independent domestications of cultivated rice, O. sativa
    • Londo JP, Chiang YC, Hung KH, Chiang TY, Schaal BA, (2006) Phylogeography of Asian wild rice, Oryza rufipogon, reveals multiple independent domestications of cultivated rice, O. sativa. Proc Natl Acad Sci U S A 103: 9578-9583.
    • (2006) Proc Natl Acad Sci U S A , vol.103 , pp. 9578-9583
    • Londo, J.P.1    Chiang, Y.C.2    Hung, K.H.3    Chiang, T.Y.4    Schaal, B.A.5
  • 13
    • 84862779339 scopus 로고    scopus 로고
    • Footprints of Natural and artificial selection for photoperiod pathway genes in Oryza
    • Huang CL, Hung CY, Chiang YC, Hwang CC, Hsu TW, et al. (2012) Footprints of Natural and artificial selection for photoperiod pathway genes in Oryza. Plant J 70: 769-782.
    • (2012) Plant J , vol.70 , pp. 769-782
    • Huang, C.L.1    Hung, C.Y.2    Chiang, Y.C.3    Hwang, C.C.4    Hsu, T.W.5
  • 14
    • 77954143052 scopus 로고    scopus 로고
    • Genetic diversity and evolutionary relationships in genus Oryza revealed by using highly variable regions of chloroplast DNA
    • Kumagai M, Wang L, Ueda S, (2010) Genetic diversity and evolutionary relationships in genus Oryza revealed by using highly variable regions of chloroplast DNA. Gene 462: 44-51.
    • (2010) Gene , vol.462 , pp. 44-51
    • Kumagai, M.1    Wang, L.2    Ueda, S.3
  • 15
    • 84869094459 scopus 로고    scopus 로고
    • Highly variable chloroplast markers for evaluating plant phylogeny at low taxonomic levels and for DNA barcoding
    • Dong WP, Liu J, Yu J, Wang L, Zhou SL, (2012) Highly variable chloroplast markers for evaluating plant phylogeny at low taxonomic levels and for DNA barcoding. PLoS One 7: e35071.
    • (2012) PLoS One , vol.7
    • Dong, W.P.1    Liu, J.2    Yu, J.3    Wang, L.4    Zhou, S.L.5
  • 16
    • 78651096904 scopus 로고    scopus 로고
    • A core collection and mini core collection of Oryza sativa L. in China
    • Zhang HL, Zhang DL, Wang MX, Sun JL, Qi YW, et al. (2011) A core collection and mini core collection of Oryza sativa L. in China. Theor Appl Genet 122: 49-61.
    • (2011) Theor Appl Genet , vol.122 , pp. 49-61
    • Zhang, H.L.1    Zhang, D.L.2    Wang, M.X.3    Sun, J.L.4    Qi, Y.W.5
  • 17
    • 70350618917 scopus 로고    scopus 로고
    • Efficient indica and japonica rice identification based on the InDel molecular method: Its implication in rice breeding and evolutionary research
    • Lu BR, Cai XX, Jin X, (2009) Efficient indica and japonica rice identification based on the InDel molecular method: Its implication in rice breeding and evolutionary research. Prog Nat Sci 19: 1241-1252.
    • (2009) Prog Nat Sci , vol.19 , pp. 1241-1252
    • Lu, B.R.1    Cai, X.X.2    Jin, X.3
  • 18
    • 0542399647 scopus 로고    scopus 로고
    • A method for isolation of chloroplast DNA and mitochondrial DNA from sunflower
    • Triboush SO, Danilenko NG, Davydenko OG, (1998) A method for isolation of chloroplast DNA and mitochondrial DNA from sunflower. Plant Mol Biol Rep 16: 183-189.
    • (1998) Plant Mol Biol Rep , vol.16 , pp. 183-189
    • Triboush, S.O.1    Danilenko, N.G.2    Davydenko, O.G.3
  • 19
    • 0031574072 scopus 로고    scopus 로고
    • The CLUSTAL_X windows interface: flexible strategies for multiple sequence alignment aided by quality analysis tools
    • Thompson JD, Gibson Plewniak F, Jeanmougin F, Higgins DG, (1997) The CLUSTAL_X windows interface: flexible strategies for multiple sequence alignment aided by quality analysis tools. Nucleic Acids Res 24: 4876-4882.
    • (1997) Nucleic Acids Res , vol.24 , pp. 4876-4882
    • Thompson, J.D.1    Gibson Plewniak, F.2    Jeanmougin, F.3    Higgins, D.G.4
  • 20
    • 0002051540 scopus 로고    scopus 로고
    • Bioedit: A user-friendly biological sequence alignment editor and analysis program for Windows 95/98/NT
    • Hall TA, (1999) Bioedit: A user-friendly biological sequence alignment editor and analysis program for Windows 95/98/NT. Nucleic Acids Symposium Series 41: 95-98.
    • (1999) Nucleic Acids Symposium Series , vol.41 , pp. 95-98
    • Hall, T.A.1
  • 22
    • 0016491430 scopus 로고
    • On the number of segregating sites in genetical models without recombination
    • Watterson GA, (1975) On the number of segregating sites in genetical models without recombination. Theor Popul Biol 7: 256-276.
    • (1975) Theor Popul Biol , vol.7 , pp. 256-276
    • Watterson, G.A.1
  • 23
    • 68049133091 scopus 로고    scopus 로고
    • DNA sequence polymorphism analysis using DnaSP
    • Rozas J, (2009) DNA sequence polymorphism analysis using DnaSP. Methods Mol Biol 537: 337-350.
    • (2009) Methods Mol Biol , vol.537 , pp. 337-350
    • Rozas, J.1
  • 24
    • 0026681074 scopus 로고
    • Analysis of molecular variance inferred from metric distances among DNA haplotypes: application to human mitochondrial DNA restriction data
    • Excoffier L, Smouse PE, Quattro JM, (1992) Analysis of molecular variance inferred from metric distances among DNA haplotypes: application to human mitochondrial DNA restriction data. Genetics 131: 471-491.
    • (1992) Genetics , vol.131 , pp. 471-491
    • Excoffier, L.1    Smouse, P.E.2    Quattro, J.M.3
  • 25
    • 0032900678 scopus 로고    scopus 로고
    • Median-joining networks for interring intraspecific phylogenies
    • Bandelt HJ, Forster P, Rohl A, (1999) Median-joining networks for interring intraspecific phylogenies. Mol Biol Evol 16: 37-48.
    • (1999) Mol Biol Evol , vol.16 , pp. 37-48
    • Bandelt, H.J.1    Forster, P.2    Rohl, A.3
  • 26
    • 0023375195 scopus 로고
    • The neighbor-joining method: a new method for reconstructing phylogenetic trees
    • Saitou N, Nei M, (1987) The neighbor-joining method: a new method for reconstructing phylogenetic trees. Mol Biol Evol 4: 406-425.
    • (1987) Mol Biol Evol , vol.4 , pp. 406-425
    • Saitou, N.1    Nei, M.2
  • 28
    • 0019296687 scopus 로고
    • A simple method for estimating evolutionary rates of base substitutions through comparative studies of DNA sequences
    • Kimura M, (1980) A simple method for estimating evolutionary rates of base substitutions through comparative studies of DNA sequences. J Mol Evol 16: 111-120.
    • (1980) J Mol Evol , vol.16 , pp. 111-120
    • Kimura, M.1
  • 29
    • 0041817568 scopus 로고    scopus 로고
    • Inference of population structure: extensions to linked loci and correlated allele frequencies
    • Falush D, Stephens M, Pritchard JK, (2003) Inference of population structure: extensions to linked loci and correlated allele frequencies. Genetics 164: 1567-1587.
    • (2003) Genetics , vol.164 , pp. 1567-1587
    • Falush, D.1    Stephens, M.2    Pritchard, J.K.3
  • 30
    • 0023462635 scopus 로고
    • Rates of nucleotide substitution vary greatly among plant mitochondrial, chloroplast, and nuclear DNAs
    • Wolfe KH, Li WH, Sharp PM, (1987) Rates of nucleotide substitution vary greatly among plant mitochondrial, chloroplast, and nuclear DNAs. Proc Natl Acad Sci U S A 84: 9054-9058.
    • (1987) Proc Natl Acad Sci U S A , vol.84 , pp. 9054-9058
    • Wolfe, K.H.1    Li, W.H.2    Sharp, P.M.3
  • 31
    • 0029812835 scopus 로고    scopus 로고
    • Substitution rate comparisons between grasses and palms: synonymous rate differences at the nuclear gene Adh parallel rate differences at the plastid gene rbcL
    • Gaut BS, Morton BR, McCaig BC, Clegg MT, (1996) Substitution rate comparisons between grasses and palms: synonymous rate differences at the nuclear gene Adh parallel rate differences at the plastid gene rbcL. Proc Natl Acad Sci U S A 93: 10274-10279.
    • (1996) Proc Natl Acad Sci U S A , vol.93 , pp. 10274-10279
    • Gaut, B.S.1    Morton, B.R.2    McCaig, B.C.3    Clegg, M.T.4
  • 32
    • 77953491820 scopus 로고    scopus 로고
    • Ecological divergence in the presence of gene flow in two closely related Oryza species (O. rufipogon and O. nivara)
    • Zheng XM, Ge S, (2010) Ecological divergence in the presence of gene flow in two closely related Oryza species (O. rufipogon and O. nivara). Mol Ecol 19: 2439-2454.
    • (2010) Mol Ecol , vol.19 , pp. 2439-2454
    • Zheng, X.M.1    Ge, S.2
  • 33
    • 0035121402 scopus 로고    scopus 로고
    • Comparison of the genetic diversity of common wild rice (Oryza rufipogon Griff.) and cultivated rice (Oryza sativa L.) using RFLP markers
    • Sun CQ, Wang XK, Li ZC, Yoshimura A, Iwata N, (2001) Comparison of the genetic diversity of common wild rice (Oryza rufipogon Griff.) and cultivated rice (Oryza sativa L.) using RFLP markers. Theor Appl Genet 102: 157-162.
    • (2001) Theor Appl Genet , vol.102 , pp. 157-162
    • Sun, C.Q.1    Wang, X.K.2    Li, Z.C.3    Yoshimura, A.4    Iwata, N.5
  • 34
    • 1942517957 scopus 로고    scopus 로고
    • Population structure and conservation genetics of wild rice Oryza rufipogon (Poaceae): a region-wide perspective from microsatellite variation
    • Gao LZ, (2004) Population structure and conservation genetics of wild rice Oryza rufipogon (Poaceae): a region-wide perspective from microsatellite variation. Mol Ecol 13: 1009-1024.
    • (2004) Mol Ecol , vol.13 , pp. 1009-1024
    • Gao, L.Z.1
  • 35
    • 56549115237 scopus 로고    scopus 로고
    • Genetic structure of Oryza rufipogon Griff. in China
    • Wang MX, Zhang HL, Zhang DL, Qi YW, Fan ZL, et al. (2008) Genetic structure of Oryza rufipogon Griff. in China. Heredity 101: 527-535.
    • (2008) Heredity , vol.101 , pp. 527-535
    • Wang, M.X.1    Zhang, H.L.2    Zhang, D.L.3    Qi, Y.W.4    Fan, Z.L.5
  • 36
    • 21244501403 scopus 로고    scopus 로고
    • Phylogenetic relationships among A-genome species of the genus Oryza revealed by intron sequences of four nuclear genes
    • Zhu QH, Ge S, (2005) Phylogenetic relationships among A-genome species of the genus Oryza revealed by intron sequences of four nuclear genes. New Phytol 167: 249-265.
    • (2005) New Phytol , vol.167 , pp. 249-265
    • Zhu, Q.H.1    Ge, S.2
  • 37
    • 33847661877 scopus 로고    scopus 로고
    • Multilocus analysis of nucleotide variation of Oryza sativa and its wild relatives: severe bottleneck during domestication of rice
    • Zhu Q, Zheng X, Luo J, Gaut BS, Ge S, (2007) Multilocus analysis of nucleotide variation of Oryza sativa and its wild relatives: severe bottleneck during domestication of rice. Mol Biol Evol 24: 875-888.
    • (2007) Mol Biol Evol , vol.24 , pp. 875-888
    • Zhu, Q.1    Zheng, X.2    Luo, J.3    Gaut, B.S.4    Ge, S.5
  • 38
    • 33846821972 scopus 로고    scopus 로고
    • Large-scale DNA polymorphism study of Oryza sativa and O. rufipogon reveals the origin and divergence of Asian rice
    • Rakshit S, Rakshit A, Matsumura H, Takahashi Y, Hasegawa Y, et al. (2007) Large-scale DNA polymorphism study of Oryza sativa and O. rufipogon reveals the origin and divergence of Asian rice. Theor Appl Genet 114: 731-743.
    • (2007) Theor Appl Genet , vol.114 , pp. 731-743
    • Rakshit, S.1    Rakshit, A.2    Matsumura, H.3    Takahashi, Y.4    Hasegawa, Y.5
  • 39
    • 79959824365 scopus 로고    scopus 로고
    • Two evolutionary histories in the genome of rice: the roles of domestication genes
    • He Z, Zhai W, Wen H, Tang T, Wang Y, et al. (2011) Two evolutionary histories in the genome of rice: the roles of domestication genes. PLoS Genet 7: e1002100.
    • (2011) PLoS Genet , vol.7
    • He, Z.1    Zhai, W.2    Wen, H.3    Tang, T.4    Wang, Y.5
  • 40
    • 84862854293 scopus 로고    scopus 로고
    • Independent domestication of Asian rice followed by gene flow from japonica to indica
    • Yang C, Kawahara Y, Mizuno H, Wu J, Matsumoto T, et al. (2011) Independent domestication of Asian rice followed by gene flow from japonica to indica. Mol Bio Evol 29: 1471-1479.
    • (2011) Mol Bio Evol , vol.29 , pp. 1471-1479
    • Yang, C.1    Kawahara, Y.2    Mizuno, H.3    Wu, J.4    Matsumoto, T.5
  • 41
    • 39749148897 scopus 로고    scopus 로고
    • The evolving story of rice evolution
    • Vaughan DA, Lu BR, Tomooka N, (2008) The evolving story of rice evolution. Plant Sci 174: 394-408.
    • (2008) Plant Sci , vol.174 , pp. 394-408
    • Vaughan, D.A.1    Lu, B.R.2    Tomooka, N.3
  • 42
    • 84867509029 scopus 로고    scopus 로고
    • Domestication and geographic origin of Oryza sativa in China: insights from multilocus analysis of nucleotide variation of O. sativa and O. rufipogon
    • Wei X, Qiao WH, Chen YT, Wang RS, Cao LR, et al. (2012) Domestication and geographic origin of Oryza sativa in China: insights from multilocus analysis of nucleotide variation of O. sativa and O. rufipogon. Mol Ecol 21: 5073-5087.
    • (2012) Mol Ecol , vol.21 , pp. 5073-5087
    • Wei, X.1    Qiao, W.H.2    Chen, Y.T.3    Wang, R.S.4    Cao, L.R.5
  • 43
    • 35348934368 scopus 로고    scopus 로고
    • The complex history of the domestication of rice
    • Sweeney M, McCouch S, (2007) The complex history of the domestication of rice. Ann Bot 100: 951-957.
    • (2007) Ann Bot , vol.100 , pp. 951-957
    • Sweeney, M.1    McCouch, S.2
  • 44
    • 35748969870 scopus 로고    scopus 로고
    • New insights into the history of rice domestication
    • Kovach MJ, Sweeney MT, McCouch SR, (2007) New insights into the history of rice domestication. Trends Genet 23: 578-587.
    • (2007) Trends Genet , vol.23 , pp. 578-587
    • Kovach, M.J.1    Sweeney, M.T.2    McCouch, S.R.3
  • 45
    • 36549064298 scopus 로고    scopus 로고
    • Genetics and phylogenetics of rice domestication
    • Sang T, Ge S, (2007a) Genetics and phylogenetics of rice domestication. Curr Opin Genet and Dev 17: 533-538.
    • (2007) Curr Opin Genet and Dev , vol.17 , pp. 533-538
    • Sang, T.1    Ge, S.2
  • 46
    • 34347262453 scopus 로고    scopus 로고
    • The puzzle of rice domestication
    • Sang T, Ge S, (2007b) The puzzle of rice domestication. J Integr Plant Biol 49: 760-768.
    • (2007) J Integr Plant Biol , vol.49 , pp. 760-768
    • Sang, T.1    Ge, S.2
  • 47
    • 2442645495 scopus 로고    scopus 로고
    • A comparison of rice chloroplast genomes
    • Tang J, Xia H, Cao M, Zhang X, Zeng W, et al. (2004) A comparison of rice chloroplast genomes. Plant physiol 135: 412-420.
    • (2004) Plant Physiol , vol.135 , pp. 412-420
    • Tang, J.1    Xia, H.2    Cao, M.3    Zhang, X.4    Zeng, W.5
  • 49
    • 77956295563 scopus 로고    scopus 로고
    • Genomic diversity and introgression in O. sativa reveal the impact of domestication and breeding on the rice genome
    • Zhao K, Wright M, Kimball J, Eizenga G, McClung A, et al. (2010) Genomic diversity and introgression in O. sativa reveal the impact of domestication and breeding on the rice genome. PLoS One 5: e10780.
    • (2010) PLoS One , vol.5
    • Zhao, K.1    Wright, M.2    Kimball, J.3    Eizenga, G.4    McClung, A.5
  • 50
    • 84862936211 scopus 로고    scopus 로고
    • Resequencing 50 accessions of cultivated and wild rice yields markers for identifying agronormically important genes
    • Xu X, Liu X, Ge S, Jensen DJ, Hu F, et al. (2012) Resequencing 50 accessions of cultivated and wild rice yields markers for identifying agronormically important genes. Nat Biotechnol 30: 105-111.
    • (2012) Nat Biotechnol , vol.30 , pp. 105-111
    • Xu, X.1    Liu, X.2    Ge, S.3    Jensen, D.J.4    Hu, F.5


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