水稻的起源与驯化——来自基因组学的证据
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摘要
水稻是世界上最重要的粮食作物,约1万年前开始被驯化。由于水稻与其祖先野生种存在一定的遗传分化,水稻的起源和驯化问题长期存在争议。本文综述了水稻起源和驯化方面的研究成果,特别是近年来基因组学方面的证据,认为水稻2个亚种独立起源于野生祖先种内很早就分化的不同类群,但一些驯化基因——控制重要农艺性状的基因,可能首先在一个亚种中被驯化,然后通过基因渐渗,扩散到另一个亚种中。因此,水稻驯化的关键是研究驯化基因的起源和扩散方式。随着大规模基因组测序技术的发展和相应数据分析方法的建立,在全基因组水平对水稻及其祖先进行大规模分析,已成为揭示水稻起源与驯化之谜的必由之路。
Rice(Oryza sativa L.) was domesticated about 10000 years ago and has been one of the most important food crops in the world. Owing to the genetic differentiations within and between rice and its wild ancestral species, the origin and domestication of rice have been controversial for a long time. Many previous investigations, especially recent genomic evidence suggested that two subspecies of rice originated independently from early differentiation populations of the wild ancestral species while quite a few domesticated genes associated with important agricultural traits might occur only in one subspecies at first and spread into the other one by introgression. Therefore, the origin and spreading mode of domesticated genes is crucial to understanding of the domestication of rice. Fortunately, the recent development of high-throughput genomic sequencing technologies and related approaches of population genomics offer us an opportunity to research population genetic differentiations within and between rice and its wild ancestral species at the genome scale, which has been the key to reveal the mystery of rice origin and domestication.
Rice(Oryza sativa L.) was domesticated about 10000 years ago and has been one of the most important food crops in the world. Owing to the genetic differentiations within and between rice and its wild ancestral species, the origin and domestication of rice have been controversial for a long time. Many previous investigations, especially recent genomic evidence suggested that two subspecies of rice originated independently from early differentiation populations of the wild ancestral species while quite a few domesticated genes associated with important agricultural traits might occur only in one subspecies at first and spread into the other one by introgression. Therefore, the origin and spreading mode of domesticated genes is crucial to understanding of the domestication of rice. Fortunately, the recent development of high-throughput genomic sequencing technologies and related approaches of population genomics offer us an opportunity to research population genetic differentiations within and between rice and its wild ancestral species at the genome scale, which has been the key to reveal the mystery of rice origin and domestication.
引文
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[2]Godfray H C J,Beddington J R,Crute I R,et al.Food security:Thechallenge 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 IntegrativePlant 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 domesticationprocess from the distribution of six functional nucleotide polymorphismsof domestication-related genes in various landraces and moderncultivars[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].PlantMolecular Biology,1997,35(1-2):25-34.
[8]Kovach M J,Sweeney M T,Mc Couch S R.New insights into the historyof 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 emphasison origins of allotetraploid species[J].Proceedings of the NationalAcademy 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 structuralanalysis 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 theadaptive 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 riceevolution[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 ricevarieties[J].Japanese Journal of Breeding,1953,3(2):33-43.
[16]Zhang Q,Maroof M A S,Lu T Y,et al.Genetic diversity anddifferentiation 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 ofthe rice genome[J].Nature,2005,436(7052):793-800.
[18]Garris A J,Tai T H,Coburn J,et al.Genetic structure and diversityin Oryza sativa L.[J].Genetics,2005,169(3):1631-1638.
[19]Mizuta Y,Harushima Y,Kurata N.Rice pollen hybrid incompatibilitycaused by reciprocal gene loss of duplicated genes[J].Proceedings ofthe National Academy of Sciences,2010,107(47):20417-20422.
[20]Ouyang Y,Liu Y G,Zhang Q.Hybrid sterility in plant:Stories fromrice[J].Current Opinion in Plant Biology,2010,13(2):186-192.
[21]Yang J,Zhao X,Cheng K,et al.A killer-protector system regulatesboth 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 ricewas 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 ricedomestication 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 arare 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 anddomestication 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 theorigins of domesticated rice[J].Proceedings of the National Academyof Sciences,2014,111(17):6190-6197.
[28]Fuller D Q,Allaby R G,Stevens C.Domestication as innovation:theentanglement of techniques,technology and chance in thedomestication of cereal crops[J].World Archaeology,2010,42(1):13-28.
[29]Fuller D Q.Agricultural origins and frontiers in south Asia:A workingsynthesis[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 wildrelatives of rice as assessed by RFLP analysis[J].Theoretical andApplied 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,demonstratedby multilocus microsatellites[J].Genetics,2008,179(2):965-976.
[33]Zhu Q,Ge S.Phylogenetic relationships among A-genome species ofthe 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 thechloroplast genome suggests multiple domestication of cultivatedAsian rice(Oryza sativa L.)[J].Genome,2007,50(2):180-187.
[35]Wang Z Y,Second G,Tanksley S D.Polymorphism and phylogeneticrelationships among species in the genus Oryza as determined byanalysis 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 lengthpolymorphism markers reveal clear genetic differentiation in commonwild rice(Oryza rufipogon L.)in relation to the domestication ofcultivated 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 cultivatedand wild rice yields markers for identifying agronomically importantgenes[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].Theoreticaland Applied Genetics,2002,104(8):1335-1345.
[39]Ma J,Bennetzen J L.Rapid recent growth and divergence of ricenuclear 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 evidencefor two distinct origins of Asian rice(Oryza sativa L.)[J].MolecularGenetics and Genomics,2004,272(5):504-511.
[41]Londo J P,Chiang Y C,Hung K H,et al.Phylogeography of Asianwild rice,Oryza rufipogon,reveals multiple independentdomestications of cultivated rice,Oryza sativa[J].Proceedings of theNational Academy of Sciences,2006,103(25):9578-9583.
[42]Wei X,Qiao W H,Chen Y T,et al.Domestication and geographicorigin of Oryza sativa in China:Insights from multilocus analysis ofnucleotide variation of O.sativa and O.rufipogon[J].MolecularEcology,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 ofa single mutation conferring white pericarp in rice[J].PLo S Genetics,2007,3(8):e133.
[45]Jin J,Huang W,Gao J P,et al.Genetic control of rice plantarchitecture 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 toerect 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 ricedomestication[J].Current Opinion in Plant Biology,2009,12(2):185-192.
[48]Sweeney M,Mc Couch S.The complex history of the domestication ofrice[J].Annals of Botany,2007,100(5):951-957.
[49]Yang C C,Kawahara Y,Mizuno H,et al.Independent domesticationof 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 genomeof rice:The roles of domestication genes[J].PLo S Genetics,2011,7(6):e1002100.
[51]Huang X,Lu T,Han B.Resequencing rice genomes:An emergingnew 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 singleevolutionary origin of domesticated rice[J].Proceedings of the NationalAcademy of Sciences,2011,108(20):8351-8356.
[53]Ge S,Sang T.Inappropriate model rejects independent domesticationsof indica and japonica rice[J].Proceedings of the National Academy ofSciences,2011,108(39):e755.
[54]Huang P,Molina J,Flowers J M,et al.Phylogeography of Asian wildrice,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 variationreveals 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]Mc Nally K L,Childs K L,Bohnert R,et al.Genomewide SNP variationreveals 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 introgressionin O.sativa reveal the impact of domestication and breeding on therice genome[J].PLOS One,2010,5(5):e10780.
[59]Twyford A D,Ennos R A.Next-generation hybridization andintrogression[J].Heredity,2012,108(3):179-189.
[60]Metzker M L.Sequencing technologies—The next generation[J].NatureReviews Genetics,2010,11(1):31-46.
[61]Patterson N,Price A L,Reich D.Population structure and eigenanalysis[J].PLo S Genetics,2006,2(12):e190.
[62]Falush D,Stephens M,Pritchard J K.Inference of population structureusing multilocus genotype data:Linked loci and correlated allelefrequencies[J].Genetics,2003,164(4):1567-1587.
[63]Alexander D H,Novembre J,Lange K.Fast model-based estimationof ancestry in unrelated individuals[J].Genome Research,2009,19(9):1655-1664.
[64]Pickrell J K,Pritchard J K.Inference of population splits andmixtures from genome-wide allele frequencydata[J].PLo S Genetics,2012,8(11):e1002967.
[65]Lipson M,Loh P R,Patterson N,et al.Reconstructing Austronesianpopulation history in Island Southeast Asia[J].NatureCommunications,2014,5:4689.
[66]Patterson N J,Moorjani P,Luo Y,et al.Ancient admixture in humanhistory[J].Genetics,2012,192:1065-1093.
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