水稻的起源及驯化相关基因克隆研究进展
摘要
现代遗传学已研究证实关键基因的变异与水稻驯化密切相关,研究水稻关键基因驯化过程,有助于弄清驯化过程中分子水平变异与自然选择间如何联系的问题。现对水稻起源及驯化相关的基因克隆研究进展进行综述,旨在为水稻驯化基因育种利用及分子设计改良育种提供参考。
引文
[1]Sang T,Ge S.The puzzle of rice domestication[J].Journal of Integrative Plant Biology,2007,49(6):760-768.
[2]Sweeney M,Mc Couch S.The complex history of the domestication of rice[J].Annals of Botany,2007,100(5):951-957.
[3]Vaughan D A,Balazs E,Heslop-Harrison J S.From crop domestication to super-domestication[J].Annals of Botany,2007,100(5):893-901.
[4]金亮,卢艳,包劲松.水稻落粒性基因定位与克隆研究进展[J].分子植物育种,2009,7(2):393-397.
[5]Sang T,Ge S.Genetics and phylogenetics of rice domestication[J].Current Opinion in Genetics&Development,2007,17(6):533-538.
[6]Konishi S,Ebana K,Izawa T.Inference of the japonica rice domesticationprocess 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.
[7]Tang H,Sezen U,Paterson A H.Domestication and plant genomes[J].Current Opinion in Plant Biology,2010,13(2):160-166.
[8]Kovach M J,Sweeney M T,Mc Couch S R.New insights into the history of rice domestication[J].Trends in Genetics,2007,23(11):578-587.
[9]Vaughan D A,Morishima H,Kadowaki K.Diversity in the Oryza genus[J].Current Opinion in Plant Biology,2003,6(2):139-146.
[10]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.
[11]Vaughan D A,Lu BR,Tomooka N.Was asian rice(Oryza sativa)domesticated more than once[J]Rice,2008,1(1):16-24.
[12]Oka H I,Chang W T.Rice varieties intermediate between wild and cultivated forms and the origin of the Japonica type[J].Botanical bulletin of academia sinica,1962(3):109-131.
[13]Oka H I,Morishima H.Phylogenetic differentiation of cultivated rice.Potentiality of wild progenitors to evolve the Indica and Japonica types of rice cultivars[J].Euphytica,1982(31):41-50.
[14]Morishima H,Hinata K,Oka H I.Comparison of modes of evolution of cultivated forms from two wild rice species,Oryza breviligulata and O.perennis[J].Evolution,1963(17):170-181.
[15]Oka H I.Experiment studies on the origin of cultivated rice[J].Genetics,1974(78):475-486.
[16]Sano Y,Morishima H,Oka H I.Intermediate perenniannual populations of Oryza perennis found in Thailand and their evolutionary sinificance[J].Botanical magazine Tokyo,1980(93):291-305.
[17]Sampath S,Govindaswami S.Wild rices of Orissa and their relationship to the cultivated varieties[J].Rice News Teller,1958,6(3):17-20.
[18]丁颖.中国栽培稻种的起源及其演变[J].农业学报,1957,8(3):243-260.
[19]王象坤,陈一午,程侃声,等.云南稻种资源的综合研究与利用Ⅲ.云南的光壳稻[J].中国农业大学学报,1984,10(4):333-344.
[20]程侃声,周季维,卢义宣,等.云南稻种资源的综合研究与利用Ⅱ.亚洲栽培稻分类的再认识[J].作物学报,1984,10(4):271-280.
[21]周拾禄.中国是稻之起源地[J].中国稻作,1948,5(5):53-54.
[22]周拾禄.水稻栽培科学与技术[M].北京:农业出版社,1981.
[23]Khush G S.Origin,dispersal,cultivation and variation of rice[J].Plant Molecuar Biology,1997,35(1):24-34.
[24]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.
[25]Ikehashi H.Why are there indica type and Japonica type in rice History of the studies and a view for origin of two types[J].Rice Science,2009,16(1):1-13.
[26]Li Z G,Hideki I.Nonindependent domestication of the two rice subspecies,Oryza sativa ssp.Indica and spp.Japonica,demonstrated by multilocus microsatellites[J].Genetics,2008,179(2):965-976.
[27]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.
[28]He Z,Zhai W,Wen H,et al.Two evolutionary histories in the genome of rice:The roles of domestication genes[J].PLo S Genetics,2011,7(6):e1002100.
[29]Konishi S,Izawa T,Lin S Y,et al.An SNP caused loss of seed shattering during rice domestication[J].Science,2006,312(5778):1392-1396.
[30]Li C,Zhou A,Sang T.Rice domestication by reducing shattering[J].Science,2006,311(5769):1936-1939.
[31]Sweeney M T,Thomson M J,Pfeil B E,et al.Caught red-handed:Rc encodes a basic helix-loop-helix protein conditioning red pericarp in rice[J].The Plant Cell,2006,18(2):283-294.
[32]Wang E,Wang J,Zhu X,et al.Control of rice grainfilling and yield by a gene with a potential signature of domestication[J].Nature Genetics,2008,40(11):1370-1374.
[33]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.
[34]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.
[35]Shomura A,Izawa T,Ebana K,et al.Deletion in a gene associated with grain size increased yields during rice domestication[J].Nature Genetics,2008,40(8):1023-1028.
[36]Olsen K M,Caicedo A L,Polato N,et al.Selection under domestication:evidence for a sweep in the rice waxy genomic region[J].Genetics,2006,173(2):975-983.
[37]Sweeney M T,Thomson M J,Cho Y G,et at.Global Dissemination of a Single Mutation Conferring White Pericarp in Rice[J].PLo S Genetics,2007,3(8):1418-1424.
[38]Furukawa T,Maekawa M,Oki T,et al.The Rc and Rd genes are involved in proanthocyanidin synthesis in rice pericarp[J].The Plant Journal,2006,49(1):91-102.
[39]Gu X Y,Foley M E,Horvath D P,et al.Association between seed dormancy and pericarp color is controlled by a pleiotropic gene that regulates abscisic acid and flavonoid synthesis in weedy red rice[J].Genetics,2011,189(4):1515-1524.
[40]Doi K,Izawa T,Fuse T,et al.Ehd1,a B-type response regulator in rice,confers short-day promotion of flowering and controls FT-like gene expression independently of Hd1[J].Genes and Development,2004,18(8):926-936.
[41]Yano M,Katayose Y,Ashikari M,et al.Hd1,a major photoperiod sensitivity quantitative trait locus in rice,is closely related to the Arabidopsis flowering time gene CONSTANS[J].The Plant Cell,2000,12(12):2473-2484.
[42]Takahashi Y,Shomura A,Sasaki T,et al.Hd6,a rice quantitative trait locus involved in photoperiod sensitivity,encodes the alpha subunit of protein kinase CK2[J].Proceedings of the National Academy of Sciences,2001,98(14):7922-7927.
[43]Ma Y,Dai XY,Xu YY,et al.COLD1 confers chilling colerance in Rice[J].Cell,2015,160(6):1209-1221.
[44]Nagano H,Onishi K,Ogasawara M,et al.Genealogy of the“Green Revolution”gene in rice[J].Genes and Genetic Systems,2005,80(5):351-356.
[45]Jiao Y Q,Wang Y H,Xue D W,et al.Regulation of Os SPL14 by Osmi R156 defines ideal plant architecture in rice[J].Nature Genetics,2010,42(6):541-544.
[46]Ashikari M,Sakakibara H,Lin S,et al.Cytokinin oxidase regulates rice grain production[J].Science,2005,309(5735):741-745.
[47]Huang X Z,Qian Q,Liu Z B,et at.Natural variation at the DEP1 locus enhances grain yield in rice[J].Nature Genetics,2009,41(4):494-497.
[48]Jones MK,Liu XY.Archaeology.Origins of agricul ture in East Asia[J].Science,2009,324(5928):730-731.
[49]区树俊,汪鸿儒,储成才.亚洲栽培稻主要驯化性状研究进展[J].遗传,2012,34(11):1379-1389.
[50]Wang Y,Li J.Rice,rising[J].Nature Genetics,2008,40(11):1273-1275.
[51]高清松,杨泽峰,徐辰武.水稻基因组进化的研究进展[J].扬州大学学报(农业与生命科学版),2009,30(2):34-41.
[52]Konishi S,Ebana K,Izawa T.Inference of the japonica rice domestication process from the distribution of six functional nucleotide polymorphisms of domesticationrelated genes in various landraces and modern cultivars[J].Plant and Cell Physiology,2008,49(9):1283-1293.
[53]Duncan A.V,Bao-R L,Norihiko Tomooka.The evolving story of rice evolution[J].Plant Science,2008(174):394-408.
[54]Project IRGS.The map-based sequence of the rice genome[J].Nature,2005,436(7052):793-800.
[55]Xu X,Liu X,Ge S,et al.Resequencing 50 accessions of cultivated and wild rice yields markers for identifying agronomically important genes[J].Nat Biotechnol,2011,30(1):105-111.
[2]Sweeney M,Mc Couch S.The complex history of the domestication of rice[J].Annals of Botany,2007,100(5):951-957.
[3]Vaughan D A,Balazs E,Heslop-Harrison J S.From crop domestication to super-domestication[J].Annals of Botany,2007,100(5):893-901.
[4]金亮,卢艳,包劲松.水稻落粒性基因定位与克隆研究进展[J].分子植物育种,2009,7(2):393-397.
[5]Sang T,Ge S.Genetics and phylogenetics of rice domestication[J].Current Opinion in Genetics&Development,2007,17(6):533-538.
[6]Konishi S,Ebana K,Izawa T.Inference of the japonica rice domesticationprocess 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.
[7]Tang H,Sezen U,Paterson A H.Domestication and plant genomes[J].Current Opinion in Plant Biology,2010,13(2):160-166.
[8]Kovach M J,Sweeney M T,Mc Couch S R.New insights into the history of rice domestication[J].Trends in Genetics,2007,23(11):578-587.
[9]Vaughan D A,Morishima H,Kadowaki K.Diversity in the Oryza genus[J].Current Opinion in Plant Biology,2003,6(2):139-146.
[10]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.
[11]Vaughan D A,Lu BR,Tomooka N.Was asian rice(Oryza sativa)domesticated more than once[J]Rice,2008,1(1):16-24.
[12]Oka H I,Chang W T.Rice varieties intermediate between wild and cultivated forms and the origin of the Japonica type[J].Botanical bulletin of academia sinica,1962(3):109-131.
[13]Oka H I,Morishima H.Phylogenetic differentiation of cultivated rice.Potentiality of wild progenitors to evolve the Indica and Japonica types of rice cultivars[J].Euphytica,1982(31):41-50.
[14]Morishima H,Hinata K,Oka H I.Comparison of modes of evolution of cultivated forms from two wild rice species,Oryza breviligulata and O.perennis[J].Evolution,1963(17):170-181.
[15]Oka H I.Experiment studies on the origin of cultivated rice[J].Genetics,1974(78):475-486.
[16]Sano Y,Morishima H,Oka H I.Intermediate perenniannual populations of Oryza perennis found in Thailand and their evolutionary sinificance[J].Botanical magazine Tokyo,1980(93):291-305.
[17]Sampath S,Govindaswami S.Wild rices of Orissa and their relationship to the cultivated varieties[J].Rice News Teller,1958,6(3):17-20.
[18]丁颖.中国栽培稻种的起源及其演变[J].农业学报,1957,8(3):243-260.
[19]王象坤,陈一午,程侃声,等.云南稻种资源的综合研究与利用Ⅲ.云南的光壳稻[J].中国农业大学学报,1984,10(4):333-344.
[20]程侃声,周季维,卢义宣,等.云南稻种资源的综合研究与利用Ⅱ.亚洲栽培稻分类的再认识[J].作物学报,1984,10(4):271-280.
[21]周拾禄.中国是稻之起源地[J].中国稻作,1948,5(5):53-54.
[22]周拾禄.水稻栽培科学与技术[M].北京:农业出版社,1981.
[23]Khush G S.Origin,dispersal,cultivation and variation of rice[J].Plant Molecuar Biology,1997,35(1):24-34.
[24]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.
[25]Ikehashi H.Why are there indica type and Japonica type in rice History of the studies and a view for origin of two types[J].Rice Science,2009,16(1):1-13.
[26]Li Z G,Hideki I.Nonindependent domestication of the two rice subspecies,Oryza sativa ssp.Indica and spp.Japonica,demonstrated by multilocus microsatellites[J].Genetics,2008,179(2):965-976.
[27]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.
[28]He Z,Zhai W,Wen H,et al.Two evolutionary histories in the genome of rice:The roles of domestication genes[J].PLo S Genetics,2011,7(6):e1002100.
[29]Konishi S,Izawa T,Lin S Y,et al.An SNP caused loss of seed shattering during rice domestication[J].Science,2006,312(5778):1392-1396.
[30]Li C,Zhou A,Sang T.Rice domestication by reducing shattering[J].Science,2006,311(5769):1936-1939.
[31]Sweeney M T,Thomson M J,Pfeil B E,et al.Caught red-handed:Rc encodes a basic helix-loop-helix protein conditioning red pericarp in rice[J].The Plant Cell,2006,18(2):283-294.
[32]Wang E,Wang J,Zhu X,et al.Control of rice grainfilling and yield by a gene with a potential signature of domestication[J].Nature Genetics,2008,40(11):1370-1374.
[33]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.
[34]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.
[35]Shomura A,Izawa T,Ebana K,et al.Deletion in a gene associated with grain size increased yields during rice domestication[J].Nature Genetics,2008,40(8):1023-1028.
[36]Olsen K M,Caicedo A L,Polato N,et al.Selection under domestication:evidence for a sweep in the rice waxy genomic region[J].Genetics,2006,173(2):975-983.
[37]Sweeney M T,Thomson M J,Cho Y G,et at.Global Dissemination of a Single Mutation Conferring White Pericarp in Rice[J].PLo S Genetics,2007,3(8):1418-1424.
[38]Furukawa T,Maekawa M,Oki T,et al.The Rc and Rd genes are involved in proanthocyanidin synthesis in rice pericarp[J].The Plant Journal,2006,49(1):91-102.
[39]Gu X Y,Foley M E,Horvath D P,et al.Association between seed dormancy and pericarp color is controlled by a pleiotropic gene that regulates abscisic acid and flavonoid synthesis in weedy red rice[J].Genetics,2011,189(4):1515-1524.
[40]Doi K,Izawa T,Fuse T,et al.Ehd1,a B-type response regulator in rice,confers short-day promotion of flowering and controls FT-like gene expression independently of Hd1[J].Genes and Development,2004,18(8):926-936.
[41]Yano M,Katayose Y,Ashikari M,et al.Hd1,a major photoperiod sensitivity quantitative trait locus in rice,is closely related to the Arabidopsis flowering time gene CONSTANS[J].The Plant Cell,2000,12(12):2473-2484.
[42]Takahashi Y,Shomura A,Sasaki T,et al.Hd6,a rice quantitative trait locus involved in photoperiod sensitivity,encodes the alpha subunit of protein kinase CK2[J].Proceedings of the National Academy of Sciences,2001,98(14):7922-7927.
[43]Ma Y,Dai XY,Xu YY,et al.COLD1 confers chilling colerance in Rice[J].Cell,2015,160(6):1209-1221.
[44]Nagano H,Onishi K,Ogasawara M,et al.Genealogy of the“Green Revolution”gene in rice[J].Genes and Genetic Systems,2005,80(5):351-356.
[45]Jiao Y Q,Wang Y H,Xue D W,et al.Regulation of Os SPL14 by Osmi R156 defines ideal plant architecture in rice[J].Nature Genetics,2010,42(6):541-544.
[46]Ashikari M,Sakakibara H,Lin S,et al.Cytokinin oxidase regulates rice grain production[J].Science,2005,309(5735):741-745.
[47]Huang X Z,Qian Q,Liu Z B,et at.Natural variation at the DEP1 locus enhances grain yield in rice[J].Nature Genetics,2009,41(4):494-497.
[48]Jones MK,Liu XY.Archaeology.Origins of agricul ture in East Asia[J].Science,2009,324(5928):730-731.
[49]区树俊,汪鸿儒,储成才.亚洲栽培稻主要驯化性状研究进展[J].遗传,2012,34(11):1379-1389.
[50]Wang Y,Li J.Rice,rising[J].Nature Genetics,2008,40(11):1273-1275.
[51]高清松,杨泽峰,徐辰武.水稻基因组进化的研究进展[J].扬州大学学报(农业与生命科学版),2009,30(2):34-41.
[52]Konishi S,Ebana K,Izawa T.Inference of the japonica rice domestication process from the distribution of six functional nucleotide polymorphisms of domesticationrelated genes in various landraces and modern cultivars[J].Plant and Cell Physiology,2008,49(9):1283-1293.
[53]Duncan A.V,Bao-R L,Norihiko Tomooka.The evolving story of rice evolution[J].Plant Science,2008(174):394-408.
[54]Project IRGS.The map-based sequence of the rice genome[J].Nature,2005,436(7052):793-800.
[55]Xu X,Liu X,Ge S,et al.Resequencing 50 accessions of cultivated and wild rice yields markers for identifying agronomically important genes[J].Nat Biotechnol,2011,30(1):105-111.