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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, Kovach M, Tyagi W, Ali ML, Tung CW, Reynolds A, Bustamante CD, McCouch SR.

PLoS One. 2010 May 24;5(5):e10780. doi: 10.1371/journal.pone.0010780.


A map of rice genome variation reveals the origin of cultivated rice.

Huang X, Kurata N, Wei X, Wang ZX, Wang A, Zhao Q, Zhao Y, Liu K, Lu H, Li W, Guo Y, Lu Y, Zhou C, Fan D, Weng Q, Zhu C, Huang T, Zhang L, Wang Y, Feng L, Furuumi H, Kubo T, Miyabayashi T, Yuan X, Xu Q, Dong G, Zhan Q, Li C, Fujiyama A, Toyoda A, Lu T, Feng Q, Qian Q, Li J, Han B.

Nature. 2012 Oct 25;490(7421):497-501. doi: 10.1038/nature11532. Epub 2012 Oct 3.


Levels and patterns of nucleotide variation in domestication QTL regions on rice chromosome 3 suggest lineage-specific selection.

Xie X, Molina J, Hernandez R, Reynolds A, Boyko AR, Bustamante CD, Purugganan MD.

PLoS One. 2011;6(6):e20670. doi: 10.1371/journal.pone.0020670. Epub 2011 Jun 6.


New insights into the history of rice domestication.

Kovach MJ, Sweeney MT, McCouch SR.

Trends Genet. 2007 Nov;23(11):578-87. Epub 2007 Oct 25. Review.


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.

Mol Biol Evol. 2007 Mar;24(3):875-88. Epub 2007 Jan 11.


The complex history of the domestication of rice.

Sweeney M, McCouch S.

Ann Bot. 2007 Nov;100(5):951-7. Epub 2007 Jul 6. Review.


Natural selection in gene-dense regions shapes the genomic pattern of polymorphism in wild and domesticated rice.

Flowers JM, Molina J, Rubinstein S, Huang P, Schaal BA, Purugganan MD.

Mol Biol Evol. 2012 Feb;29(2):675-87. doi: 10.1093/molbev/msr225. Epub 2011 Sep 13.


Independent domestication of Asian rice followed by gene flow from japonica to indica.

Yang CC, Kawahara Y, Mizuno H, Wu J, Matsumoto T, Itoh T.

Mol Biol Evol. 2012 May;29(5):1471-9. doi: 10.1093/molbev/msr315. Epub 2011 Dec 22.


Evolutionary dynamics of the genomic region around the blast resistance gene Pi-ta in AA genome Oryza species.

Lee S, Costanzo S, Jia Y, Olsen KM, Caicedo AL.

Genetics. 2009 Dec;183(4):1315-25. doi: 10.1534/genetics.109.108266. Epub 2009 Oct 12.


Two evolutionary histories in the genome of rice: the roles of domestication genes.

He Z, Zhai W, Wen H, Tang T, Wang Y, Lu X, Greenberg AJ, Hudson RR, Wu CI, Shi S.

PLoS Genet. 2011 Jun;7(6):e1002100. doi: 10.1371/journal.pgen.1002100. Epub 2011 Jun 9.


SNP deserts of Asian cultivated rice: genomic regions under domestication.

Wang L, Hao L, Li X, Hu S, Ge S, Yu J.

J Evol Biol. 2009 Apr;22(4):751-61. doi: 10.1111/j.1420-9101.2009.01698.x. Epub 2009 Feb 23.


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, Zhang WX, Yuan NN, Li ZC, Zeng HL, Yang QW.

Mol Ecol. 2012 Oct;21(20):5073-87. doi: 10.1111/j.1365-294X.2012.05748.x. Epub 2012 Sep 18.


Genetic structure and diversity in Oryza sativa L.

Garris AJ, Tai TH, Coburn J, Kresovich S, McCouch S.

Genetics. 2005 Mar;169(3):1631-8. Epub 2005 Jan 16.


Genomic patterns of nucleotide diversity in divergent populations of U.S. weedy rice.

Reagon M, Thurber CS, Gross BL, Olsen KM, Jia Y, Caicedo AL.

BMC Evol Biol. 2010 Jun 15;10:180. doi: 10.1186/1471-2148-10-180.


The extent of linkage disequilibrium in rice (Oryza sativa L.).

Mather KA, Caicedo AL, Polato NR, Olsen KM, McCouch S, Purugganan MD.

Genetics. 2007 Dec;177(4):2223-32. Epub 2007 Oct 18.


Selection under domestication: evidence for a sweep in the rice waxy genomic region.

Olsen KM, Caicedo AL, Polato N, McClung A, McCouch S, Purugganan MD.

Genetics. 2006 Jun;173(2):975-83. Epub 2006 Mar 17.


Genomic variation in rice: genesis of highly polymorphic linkage blocks during domestication.

Tang T, Lu J, Huang J, He J, McCouch SR, Shen Y, Kai Z, Purugganan MD, Shi S, Wu CI.

PLoS Genet. 2006 Nov 17;2(11):e199.


Understanding rice domestication and implications for cultivar improvement.

Sang T, Ge S.

Curr Opin Plant Biol. 2013 May;16(2):139-46. doi: 10.1016/j.pbi.2013.03.003. Epub 2013 Mar 29. Review.

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