[1] Evolution D J. Consequences and future of plant and animal domestication[J]. Nature, 2002, 418(6898): 700-707.
[2] Godfray H C J, Beddington J R, Crute I R, et al. Food security: The challenge of feeding 9 billion people[J]. Science, 2010, 327(5967): 812-818.
[3] Sang T, Ge S. The puzzle of rice domestication[J]. Journal of Integrative Plant Biology, 2007, 49(6): 760-768.
[4] Sang T, Ge S. Genetics and phylogenetics of rice domestication[J]. Current Opinion in Genetics & Development, 2007, 17(6): 533-538.
[5] Konishi S, Ebana K, Izawa T. Inference of the japonica rice domestication process from the distribution of six functional nucleotide polymorphisms of domestication-related genes in various landraces and modern cultivars[J]. Plant & Cell Physiology, 2008, 49(9): 1283-1293.
[6] Tang H, Sezen U, Paterson A H. Domestication and plant genomes[J]. Current Opinion in Plant Biology, 2010, 13(2): 160-166.
[7] Khush G S. Origin, dispersal, cultivation and variation of rice[J]. Plant Molecular Biology, 1997, 35(1-2): 25-34.
[8] Kovach M J, Sweeney M T, McCouch S R. New insights into the history of rice domestication[J]. Trends in Genetics, 2007, 23(11): 578-587.
[9] Ge S, Sang T, Lu B R, et al. Phylogeny of rice genomes with emphasis on origins of allotetraploid species[J]. Proceedings of the National Academy of Sciences, 1999, 96(25): 14400-14405.
[10] Vaughan D A, Morishima H, Kadowaki K. Diversity in the Oryza genus[J]. Current Opinion in Plant Biology, 2003, 6(2): 139-146.
[11] Wang Y P, Bounphanousay C, Kanyavong K, et al. Population structural analysis of an in-situ conservation site for wild rice in Laos[J]. Genes & Genetic Systems, 2012, 87(5): 311-322.
[12] Grillo M A, Li C, Fowlkes A M, et al. Genetic architecture for the adaptive origin of annual wild rice, Oryza nivara[J]. Evolution, 2009, 63(4): 870-883.
[13] Vaughan D A, Lu B-R, Tomooka N. The evolving story of rice evolution[J]. Plant Science, 2008, 174(4): 394-408.
[14] Glaszmann J. Isozymes and classification of Asian rice varieties[J]. Theoretical and Applied Genetics, 1987, 74(1): 21-30.
[15] Oka H. Phylogenetic differentiation of the cultivated rice plant. I: Variation of various characters and character combinations among rice varieties[J]. Japanese Journal of Breeding, 1953, 3(2): 33-43.
[16] Zhang Q, Maroof M A S, Lu T Y, et al. Genetic diversity and differentiation of indica and japonica rice detected by RFLP analysis[J]. Theoretical and Applied Genetics, 1992, 83(4): 495-499.
[17] Sequencing Project International Rice G. The map-based sequence of the rice genome[J]. Nature, 2005, 436(7052): 793-800.
[18] Garris A J, Tai T H, Coburn J, et al. Genetic structure and diversity in Oryza sativa L.[J]. Genetics, 2005, 169(3): 1631-1638.
[19] Mizuta Y, Harushima Y, Kurata N. Rice pollen hybrid incompatibility caused by reciprocal gene loss of duplicated genes[J]. Proceedings of the National Academy of Sciences, 2010, 107(47): 20417-20422.
[20] Ouyang Y, Liu Y G, Zhang Q. Hybrid sterility in plant: Stories from rice[J]. Current Opinion in Plant Biology, 2010, 13(2): 186-192.
[21] Yang J, Zhao X, Cheng K, et al. A killer-protector system regulates both hybrid sterility and segregation distortion in rice[J]. Science, 2012, 337(6100): 1336-1340.
[22] Zhao Z J. The Middle Yangtze region in China is one place where rice was domesticated: Phytolith evidence from the Diaotonghuan Cave, Northern Jiangxi[J]. Antiquity, 1998, 72(278): 885-297.
[23] Jiang L, Liu L. New evidence for the origins of sedentism and rice domestication in the Lower Yangzi River, China[L]. Antiquity, 2006, 80(308): 355-361.
[24] Zhao Z, Zhang J. The report of flotation work at the Jiahu site[J]. Kaogu (Archaeology), 2009, 8: 84-93.
[25] Ellis J R, Pashley C H, Burke J M, et al. High genetic diversity in a rare and endangered sunflower as compared to a common congener[J]. Molecular Ecology, 2006, 15(9): 2345-2355.
[26] Fuller D Q, Qin L, Zheng Y, et al. The domestication process and domestication rate in rice: Spikelet bases from the Lower Yangtze[J]. Science, 2009, 323(5921): 1607-1610.
[27] Gross B L, Zhao Z. Archaeological and genetic insights into the origins of domesticated rice[J]. Proceedings of the National Academy of Sciences, 2014, 111(17): 6190-6197.
[28] Fuller D Q, Allaby R G, Stevens C. Domestication as innovation: the entanglement of techniques, technology and chance in the domestication of cereal crops[J]. World Archaeology, 2010, 42(1): 13-28.
[29] Fuller D Q. Agricultural origins and frontiers in south Asia: A working synthesis[J]. Journal of World Prehistory, 2006, 20(1): 1-86.
[30] Fuller D Q. Finding plant domestication in the Indian subcontinent[J]. Current Anthropology, 2011, 52(S4): S347-S62.
[31] Lu B R, Zheng K L, Qian H R, et al. Genetic differentiation of wild relatives of rice as assessed by RFLP analysis[J]. Theoretical and Applied Genetics, 2002, 106(1): 101-106.
[32] Gao L Z, Innan H. Nonindependent domestication of the two rice subspecies, Oryza sativa ssp. indica and ssp. japonica, demonstrated by multilocus microsatellites[J]. Genetics, 2008, 179(2): 965-976.
[33] Zhu Q, Ge S. Phylogenetic relationships among A-genome species of the genus Oryza revealed by intron sequences of four nuclear genes[J]. New Phytologist, 2005, 167(1): 249-265.
[34] Kawakami S-I, Ebana K, Nishikawa T, et al. Genetic variation in the chloroplast genome suggests multiple domestication of cultivated Asian rice (Oryza sativa L.)[J]. Genome, 2007, 50(2): 180-187.
[35] Wang Z Y, Second G, Tanksley S D. Polymorphism and phylogenetic relationships among species in the genus Oryza as determined by analysis of nuclear RFLPs[J]. Theoretical and Applied Genetics, 1992, 83(5): 565-581.
[36] Zhao X, Yang L, Zheng Y, et al. Subspecies-specific intron length polymorphism markers reveal clear genetic differentiation in common wild rice (Oryza rufipogon L.) in relation to the domestication of cultivated rice (O. sativa L.)[J]. Journal of Genetics and Genomics, 2009, 36(7): 435-442.
[37] Xu X, Liu X, Ge S, et al. Resequencing 50 accessions of cultivated and wild rice yields markers for identifying agronomically important genes[J]. Nature Biotechnology, 2012, 30(1): 105-111.
[38] Sun Q, Wang K, Yoshimura A, et al. Genetic differentiation for nuclear, mitochondrial and chloroplast genomes in common wild rice (Oryza rufipogon Griff.) and cultivated rice (Oryza sativa L.)[J]. Theoretical and Applied Genetics, 2002, 104(8): 1335-1345.
[39] Ma J, Bennetzen J L. Rapid recent growth and divergence of rice nuclear genomes[J]. Proceedings of the National Academy of Sciences, 2004, 101(34): 12404-12410.
[40] Vitte C, Ishii T, Lamy F, et al. Genomic paleontology provides evidence for two distinct origins of Asian rice (Oryza sativa L.)[J]. Molecular Genetics and Genomics, 2004, 272(5): 504-511.
[41] Londo J P, Chiang Y C, Hung K H, et al. Phylogeography of Asian wild rice, Oryza rufipogon, reveals multiple independent domestications of cultivated rice, Oryza sativa[J]. Proceedings of the National Academy of Sciences, 2006, 103(25): 9578-9583.
[42] Wei X, Qiao W H, Chen Y T, et al. Domestication and geographic origin of Oryza sativa in China: Insights from multilocus analysis of nucleotide variation of O. sativa and O. rufipogon[J]. Molecular Ecology, 2012, 21(20): 5073-5087.
[43] Li C, Zhou A, Sang T. Rice domestication by reducing shattering[J]. Science, 2006, 311(5769): 1936-1939.
[44] Sweeney M T, Thomson M J, Cho Y G, et al. Global dissemination of a single mutation conferring white pericarp in rice[J]. PLoS Genetics, 2007, 3(8): e133.
[45] Jin J, Huang W, Gao J P, et al. Genetic control of rice plant architecture under domestication[J]. Nature Genetics, 2008, 40(11): 1365-1369.
[46] Tan L, Li X, Liu F, et al. Control of a key transition from prostrate to erect growth in rice domestication[J]. Nature Genetics, 2008, 40(11): 1360-1364.
[47] Izawa T, Konishi S, Shomura A, et al. DNA changes tell us about rice domestication[J]. Current Opinion in Plant Biology, 2009, 12(2): 185-192.
[48] Sweeney M, McCouch S. The complex history of the domestication of rice[J]. Annals of Botany, 2007, 100(5): 951-957.
[49] Yang C C, Kawahara Y, Mizuno H, et al. Independent domestication of Asian rice followed by gene flow from japonica to indica[J]. Molecular Biology and Evolution, 2012, 29(5): 1471-1479.
[50] He Z, Zhai W, Wen H, et al. Two evolutionary histories in the genome of rice: The roles of domestication genes[J]. PLoS Genetics, 2011, 7 (6): e1002100.
[51] Huang X, Lu T, Han B. Resequencing rice genomes: An emerging new era of rice genomics[J]. Trends in Genetics, 2013, 29(4): 225-232.
[52] Molina J, Sikora M, Garud N, et al. Molecular evidence for a single evolutionary origin of domesticated rice[J]. Proceedings of the National Academy of Sciences, 2011, 108(20): 8351-8356.
[53] Ge S, Sang T. Inappropriate model rejects independent domestications of indica and japonica rice[J]. Proceedings of the National Academy of Sciences, 2011, 108(39): e755.
[54] Huang P, Molina J, Flowers J M, et al. Phylogeography of Asian wild rice, Oryza rufipogon: A genome-wide view[J]. Molecular Ecology, 2012, 21(18): 4593-4604.
[55] Huang X, Kurata N, Wei X, et al. A map of rice genome variation reveals the origin of cultivated rice[J]. Nature, 2012, 490(7421): 497-501.
[56] Yu J, Hu S, Wang J, et al. A draft sequence of the rice genome (Oryza sativa L. ssp. indica)[J]. Science, 2002, 296(5565): 79-92.
[57] McNally K L, Childs K L, Bohnert R, et al. Genomewide SNP variation reveals relationships among landraces and modern varieties of rice[J]. Proceedings of the National Academy of Sciences, 2009, 106(30): 12273-12278.
[58] Zhao K, Wright M, Kimball J, et al. Genomic diversity and introgression in O. sativa reveal the impact of domestication and breeding on the rice genome[J]. PLOS One, 2010, 5(5): e10780.
[59] Twyford A D, Ennos R A. Next-generation hybridization and introgression[J]. Heredity, 2012, 108(3): 179-189.
[60] Metzker M L. Sequencing technologies—The next generation[J]. Nature Reviews Genetics, 2010, 11(1): 31-46.
[61] Patterson N, Price A L, Reich D. Population structure and eigenanalysis[J]. PLoS Genetics, 2006, 2(12): e190.
[62] Falush D, Stephens M, Pritchard J K. Inference of population structure using multilocus genotype data: Linked loci and correlated allele frequencies[J]. Genetics, 2003, 164(4): 1567-1587.
[63] Alexander D H, Novembre J, Lange K. Fast model-based estimation of ancestry in unrelated individuals[J]. Genome Research, 2009, 19(9): 1655-1664.
[64] Pickrell J K, Pritchard J K. Inference of population splits and mixtures from genome-wide allele frequencydata[J]. PLoS Genetics, 2012, 8(11): e1002967.
[65] Lipson M, Loh P R, Patterson N, et al. Reconstructing Austronesian population history in Island Southeast Asia[J]. Nature Communications, 2014, 5: 4689.
[66] Patterson N J, Moorjani P, Luo Y, et al. Ancient admixture in human history[J]. Genetics, 2012, 192: 1065-1093.
[67] Sankararaman S, Mallick S, Dannemann M, et al. The genomic landscape of Neanderthal ancestry in present-day humans[J]. Nature, 2014, 507 (7492): 354-357.
[68] Plagnol V, Wall J D. Possible ancestral structure in human populations[J]. PLoS Genetics, 2006, 2(7): e105.
[69] Vernot B, Akey J M. Resurrecting surviving neandertal lineages from modern human genomes[J]. Science, 2014, 343(6174): 1017-1021.
[70] Liu K J, Dai J, Truong K, et al. An HMM-based comparative genomic framework for detecting introgression in eukaryotes[J]. PLOS Computational Biology, 2014, 10(6): e1003649.