全基因组分析策略应用于水稻抗稻瘟病基因鉴定的研究和进展
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摘要
水稻是世界上最重要的粮食作物之一。稻瘟病严重危害水稻生产,每年可造成水稻大面积减产。利用水稻抗病基因资源,培育抗病水稻品种,是防治稻瘟病的经济有效、安全的方法。基于遗传定位及图位克隆,已有一百多个抗稻瘟病基因得到鉴定,其中有二十多个基因被克隆。近年来,全基因组分析策略进一步推动了水稻抗稻瘟病基因鉴定的发展。本研究简要总结了水稻抗稻瘟病基因的定位和克隆,并概述了全基因组分析策略应用于水稻抗稻瘟病基因鉴定的研究和进展。
Rice is one of the most important food crops in the world. Rice blast seriously endangers rice production, resulting in a large reduction in rice yield every year. Breeding resistant cultivars using blast resistance genes is an economically effective and environmentally-safe way of controlling blast disease. Based on genetic mapping and map-based cloning, over 100 resistance genes have been identified, of which more than 20 have been cloned. In recent years, genome-wide analysis approaches have further promoted the identification of rice blast resistance genes. This paper briefly introduced the mapping and cloning of rice blast resistance genes, and summarized the advances in identifying rice blast resistance genes by genome-wide analysis approaches.
Rice is one of the most important food crops in the world. Rice blast seriously endangers rice production, resulting in a large reduction in rice yield every year. Breeding resistant cultivars using blast resistance genes is an economically effective and environmentally-safe way of controlling blast disease. Based on genetic mapping and map-based cloning, over 100 resistance genes have been identified, of which more than 20 have been cloned. In recent years, genome-wide analysis approaches have further promoted the identification of rice blast resistance genes. This paper briefly introduced the mapping and cloning of rice blast resistance genes, and summarized the advances in identifying rice blast resistance genes by genome-wide analysis approaches.
引文
Abe A.,Kosugi S.,Yoshida K.,Natsume S.,Takagi H.,Kanzaki H.,Matsumura H.,Yoshida K.,Mitsuoka C.,Tamiru M.,Innan H.,Cano L.,Kamoun S.,and Terauchi R.,2012,Genome sequencing reveals agronomically important loci in rice using MutMap,Nat.Biotechnol.,30(2):174-178
Bryan G.T.,Wu K.S.,Farrall L.,Jia Y.,Hershey H.P.,McAdams S.A.,Faulk K.N.,Donaldson G.K.,Tarchini R.,and Valent B.,2000,t A single amino acid difference distinguishes resistant and susceptible alleles of the rice blast resistance gene Pi-ta,The Plant Cell,12(11):2033-2046
Chen H.,Xia F.,Wu X.R.,and Sun Y.H.,2016,The application of bulked segregant analysis in plant gene mapping,Jiy inzuxue Yu Yingyong Shengwuxue(Genomics and Applied Biology),35(6):1546-1551(陈浣,夏菲,吴新儒,孙玉合,2016,集群分离分析法在植物基因定位上的应用,基因组学与应用生物学,35(6):1546-1551)
Chen X.W.,Shang J.J.,Chen D.X.,Lei C.L.,Zou Y.,Zhai W.X.,Liu G.Z.,Xu J.C.,Ling Z.Z.,Cao G.,Ma B.T.,Wang Y.P.,Zhao X.F.,Li S.G.,and Zhu L.H.,2006,A B-lectin receptor kinase gene conferring rice blast resistance,Plant J.,46(5):794-804
Fukuoka S.,Saka N.,Koga H.,Shimizu T.,Ebana K.,Hayashi N.,Takahasi A.,Hirochika H.,Yano M.,and Okuno K.,2009,Loss of function of a proline-containing protein confers durable disease resistance in rice,Science,325(5943):998-1001
Huang X.H.,Wei X.H.,Sang T.,Zhao Q.,Feng Q.,Zhao Y.,Li C.Y.,Zhu C.R.,Lu T.T.,Zhang Z.W.,Li M.,Fan D.L.,Guo Y.L.,Wang A.H.,Wang L.,Deng L.W.,Li W.J.,Lu Y.Q.,Weng Q.J.,Liu K.Y.,Huang T.,Zhou T.Y.,Jing Y.F.,Li W.,Lin Z.,Buckler E.S.,Qian Q.,Zhang Q.F.,Li J.Y.,and Han B.,2010,Genome-wide association studies of 14 agronomic traits in rice landraces,Nat.Genet.,42(11):961-967
Huang X.H.,Zhao Y.,Wei X.H.,Li C.Y.,Wang A.H.,Zhao Q.,Li W.J.,Guo Y.L.,Deng L.W.,Zhu C.R.,Fan D.L.,Lu Y.Q.,Weng Q.J.,Liu K.Y.,Zhou T.Y.,Jing Y.F.,Si L.Z.,Dong G.J.,Huang T.,Lu T.T.,Feng Q.,Qian Q.,Li J.Y.,and Han B.,2011,Genome-wide association study of flowering time and grain yield traits in a worldwide collection of rice germplasm,Nat.Genet.,44(1):32-39
Kang H.X.,Wang Y.,Peng S.S.,Zhang Y.L.,Xiao Y.H.,Wang D.,Qu S.H.,Li Z.Q.,Yan S.Y.,Wang Z.L.,Liu W.D.,Ning Y.S.,Korniliev P.,Leung H.,Mezey J.,Mccouch S.R.,and Wang G.L.,2016,Dissection of the genetic architecture of rice resistance to the blast fungus Magnaporthe oryzae,Mol.Plant Pathol.,17(6):959-972
Klein R.J.,Zeiss C.,Chew E.Y.,Tsai J.Y.,Sackler R.S.,Haynes C.,Henning A.K.,SanGiovanni J.P.,Mane S.M.,Mayne S.T.,Bracken M.B.,Ferris F.L.,Ott J.,Barnstable C.,and Hoh J.,2005,Complement factor H polymorphism in age-related macular degeneration,Science,308(5720):385-389
Koide Y.,Kobayashi N.,Xu D.,and Fukuta Y.,2009,Resistance genes and selection DNA markers for blast disease in rice(Oryza sativa L.),Jpn.Agr.Res.Q.,43(4):255-280
Li W.T.,Zhu Z.W.,Chern M.,Yin J.J.,Yang C.,Ran L.,Cheng M.P.,He M.,Wang K.,Wang J.,Zhou X.A.,Zhu X.B.,Chen Z.X.,Wang J.C.,Zhao W.,Ma B.T.,Qin P.,ChenW.L.,Wang W.P.,Liu J.L.,Wang W.M.,Wu X.J.,Li P.,Wang J.R.,Zhu L.H.,Li S.J.,and Chen X.W.,2017,A natural allele of a transcription factor in rice confers broad-spectrum blast resistance,Cell,170(1):114-126
Liang T.M.,Guo X.R.,Chen Z.Q.,Tian D.G.,Chen Z.J.,Wang F.,and Chen S.B.,2018,Identification and gene mapping of a blast disease resistance gene in rice line IR65482,Fenzi Zhiwu Yuzhong(Molecular Plant Breeding),16(13):1-6(梁廷敏,郭新睿,陈子强,田大刚,陈在杰,王锋,陈松彪,2018,水稻材料IR65482抗稻瘟病基因鉴定与定位,分子植物育种,16(13):1-6)
Liang Z.,Wang L.,and Pan Q.,2016,A new recessive gene conferring resistance against rice blast,Rice,9(1):47
Liu J.,Wang X.J.,Mitchell T.,Hu Y.,Liu X.,Dai L.,and Wang G.L.,2010,Recent progress and understanding of the molecular mechanisms of the rice-Magnaporthe oryzae interaction,Mol.Plant Pathol.,11(3):419-427
Mgonja E.M.,Balimponya E.G.,Kang H.,Bellizzi M.,Park C.H.,Li Y.,Mabagala R.,Sneller C.,Correll J.,Opiyo S.,Talbot N.J.,Mitchell T.,and Wang G.L.,2016,Genome-wide association mapping of rice resistance genes against Magnaporthe oryzae isolates from four African countries,Phytopathology,106(11):1359-1365
Mgonja E.M.,Park C.H.,Kang H.,Balimponya E.G.,Opiyo S.,Bellizzi M.,Mutiga S.K.,Rotich F.,Ganeshan V.D.,Mabagala R.,Sneller C.,Correll J.,Zhou B.,Talbot N.J.,Mitchell T.K.,and Wang G.L.,2017,Genotyping-by-sequencing-based genetic analysis of African rice cultivars and association mapping of blast resistance genes against Magnaporthe oryzae populations in Africa,Phytopathology,107(9):1039-1046
Michelmore R.W.,Paran I.,and Kesseli R.V.,1991,Identification of markers linked to disease-resistance genes by bulked segregant analysis:a rapid method to detect markers in specific genomic regions by using segregating populations,Proc.Natl.Acad.Sci.USA,88(21):9828-9832
Raboin L.M.,Ballini E.,Tharreau D.,Ramanantsoanirina A.,Frouin J.,Courtois B.,and Ahmadi N.,2016,Association mapping of resistance to rice blast in upland field conditions,Rice,9(1):59-70
Risch N.,and Merikangas K.,1996,The future of genetic studies of complex human diseases,Science,273(5281):1516-1517
Sakamoto T.,and Matsuoka M.,2008,Identifying and exploiting grain yield genes in rice,Curr.Opin.Plant Biol.,11(2):209-214
Sharma T.R.,Rai A.K.,Gupta S.K.,Vijayan J.,Devanna B.N.,and Ray S.,2012,Rice blast management through host-plant resistance:retrospect and prospects,Agric.Res.,1(1):37-52
Singh W.H.,Kapila R.K.,Sharma T.R.,and Rathour R.,2015,Genetic and physical mapping of a new allele of Pik locus from japonica rice'Liziangxintuanheigu',Euphytica,205(3):889-901
Srivastava D.,Shamim M.,Kumar M.,Mishra A.,Pandey P.,Kumar D.,Yadav P.,Siddiqui M.H.,and Singh K.N.,2017,Current status of conventional and molecular interventions for blast resistance in rice,Rice Science,24(6):299-321
Takagi H.,Abe A.,Yoshida K.,Kosugi S.,Natsume S.,Mitsuoka C.,Uemura A.,Utsushi H.,Tamiru M.,Takuno S.,Innan H.,Cano L.M.,Kamoun S.,and Terauchi R.,2013a,QTL-seq:rapid mapping of quantitative trait loci in rice by whole genome resequencing of DNA from two bulked populations,Plant J.,74(1):174-183
Takagi H.,Uemura A.,Yaegashi H.,Tamiru M.,Abe A.,Mitsuoka C.,Utsushi H.,Natsume S.,Kanzaki H.,Matsumura H.,Saitoh H.,Yoshida K.,Cano L.M.,Kamoun S.,and Terauchi R.,2013b,MutMap-Gap:whole-genome resequencing of mutant F2progeny bulk combined with de novo assembly of gap regions identifies the rice blast resistance gene Pii,New Phytol.,200(1):276-283
Tian D.G.,Chen Z.J.,Chen Z.Q.,Zhou Y.C.,Wang Z.H.,Wang F.,and Chen S.B.,2016,Allele-specific marker-based assessment revealed that the rice blast resistance genes Pi2and Pi9 have not been widely deployed in Chinese indica rice cultivars,Rice,9(1):19-29
Wang C.H.,Yang Y.L.,Yuan X.P.,Xu Q.,Feng Y.,Yu H.Y.,Wang Y.P.,and Wei X.H.,2014,Genome-wide association study of blast resistance in indica rice,BMC Plant Biol.,14(1):311-321
Wang Z.X.,Yano M.,Yamanouchi U.,Iwamoto M.,Monna L.,Hayasaka H.,Katayose Y.,and Sasaki T.,1999,The Pib gene for rice blast resistance belongs to the nucleotide binding and leucine-rich repeat class of plant disease resistance genes,The Plant Journal,19(1):55-64
Zheng W.J.,Wang Y.,Wang L.L.,Ma Z.B.,Zhao J.M.,Wang P.,Zhang L.X.,Liu Z.H.,and Lu X.C.,2016,Genetic mapping and molecular marker development for Pi65(t),a novel broad-spectrum resistance gene to rice blast using next-generation sequencing,Theor.Appl.Genet.,129(5):1035-1044
Zhu D.,Kang H.X.,Li Z.Q.,Liu M.H.,Zhu X.L.,Wang Y.,Wang D.,Wang Z.L.,Liu W.D.,and Wang G.L.,2016,Agenome-wide association study of field resistance to Magnaporthe oryzae in rice,Rice,9(1):44-52
Bryan G.T.,Wu K.S.,Farrall L.,Jia Y.,Hershey H.P.,McAdams S.A.,Faulk K.N.,Donaldson G.K.,Tarchini R.,and Valent B.,2000,t A single amino acid difference distinguishes resistant and susceptible alleles of the rice blast resistance gene Pi-ta,The Plant Cell,12(11):2033-2046
Chen H.,Xia F.,Wu X.R.,and Sun Y.H.,2016,The application of bulked segregant analysis in plant gene mapping,Jiy inzuxue Yu Yingyong Shengwuxue(Genomics and Applied Biology),35(6):1546-1551(陈浣,夏菲,吴新儒,孙玉合,2016,集群分离分析法在植物基因定位上的应用,基因组学与应用生物学,35(6):1546-1551)
Chen X.W.,Shang J.J.,Chen D.X.,Lei C.L.,Zou Y.,Zhai W.X.,Liu G.Z.,Xu J.C.,Ling Z.Z.,Cao G.,Ma B.T.,Wang Y.P.,Zhao X.F.,Li S.G.,and Zhu L.H.,2006,A B-lectin receptor kinase gene conferring rice blast resistance,Plant J.,46(5):794-804
Fukuoka S.,Saka N.,Koga H.,Shimizu T.,Ebana K.,Hayashi N.,Takahasi A.,Hirochika H.,Yano M.,and Okuno K.,2009,Loss of function of a proline-containing protein confers durable disease resistance in rice,Science,325(5943):998-1001
Huang X.H.,Wei X.H.,Sang T.,Zhao Q.,Feng Q.,Zhao Y.,Li C.Y.,Zhu C.R.,Lu T.T.,Zhang Z.W.,Li M.,Fan D.L.,Guo Y.L.,Wang A.H.,Wang L.,Deng L.W.,Li W.J.,Lu Y.Q.,Weng Q.J.,Liu K.Y.,Huang T.,Zhou T.Y.,Jing Y.F.,Li W.,Lin Z.,Buckler E.S.,Qian Q.,Zhang Q.F.,Li J.Y.,and Han B.,2010,Genome-wide association studies of 14 agronomic traits in rice landraces,Nat.Genet.,42(11):961-967
Huang X.H.,Zhao Y.,Wei X.H.,Li C.Y.,Wang A.H.,Zhao Q.,Li W.J.,Guo Y.L.,Deng L.W.,Zhu C.R.,Fan D.L.,Lu Y.Q.,Weng Q.J.,Liu K.Y.,Zhou T.Y.,Jing Y.F.,Si L.Z.,Dong G.J.,Huang T.,Lu T.T.,Feng Q.,Qian Q.,Li J.Y.,and Han B.,2011,Genome-wide association study of flowering time and grain yield traits in a worldwide collection of rice germplasm,Nat.Genet.,44(1):32-39
Kang H.X.,Wang Y.,Peng S.S.,Zhang Y.L.,Xiao Y.H.,Wang D.,Qu S.H.,Li Z.Q.,Yan S.Y.,Wang Z.L.,Liu W.D.,Ning Y.S.,Korniliev P.,Leung H.,Mezey J.,Mccouch S.R.,and Wang G.L.,2016,Dissection of the genetic architecture of rice resistance to the blast fungus Magnaporthe oryzae,Mol.Plant Pathol.,17(6):959-972
Klein R.J.,Zeiss C.,Chew E.Y.,Tsai J.Y.,Sackler R.S.,Haynes C.,Henning A.K.,SanGiovanni J.P.,Mane S.M.,Mayne S.T.,Bracken M.B.,Ferris F.L.,Ott J.,Barnstable C.,and Hoh J.,2005,Complement factor H polymorphism in age-related macular degeneration,Science,308(5720):385-389
Koide Y.,Kobayashi N.,Xu D.,and Fukuta Y.,2009,Resistance genes and selection DNA markers for blast disease in rice(Oryza sativa L.),Jpn.Agr.Res.Q.,43(4):255-280
Li W.T.,Zhu Z.W.,Chern M.,Yin J.J.,Yang C.,Ran L.,Cheng M.P.,He M.,Wang K.,Wang J.,Zhou X.A.,Zhu X.B.,Chen Z.X.,Wang J.C.,Zhao W.,Ma B.T.,Qin P.,ChenW.L.,Wang W.P.,Liu J.L.,Wang W.M.,Wu X.J.,Li P.,Wang J.R.,Zhu L.H.,Li S.J.,and Chen X.W.,2017,A natural allele of a transcription factor in rice confers broad-spectrum blast resistance,Cell,170(1):114-126
Liang T.M.,Guo X.R.,Chen Z.Q.,Tian D.G.,Chen Z.J.,Wang F.,and Chen S.B.,2018,Identification and gene mapping of a blast disease resistance gene in rice line IR65482,Fenzi Zhiwu Yuzhong(Molecular Plant Breeding),16(13):1-6(梁廷敏,郭新睿,陈子强,田大刚,陈在杰,王锋,陈松彪,2018,水稻材料IR65482抗稻瘟病基因鉴定与定位,分子植物育种,16(13):1-6)
Liang Z.,Wang L.,and Pan Q.,2016,A new recessive gene conferring resistance against rice blast,Rice,9(1):47
Liu J.,Wang X.J.,Mitchell T.,Hu Y.,Liu X.,Dai L.,and Wang G.L.,2010,Recent progress and understanding of the molecular mechanisms of the rice-Magnaporthe oryzae interaction,Mol.Plant Pathol.,11(3):419-427
Mgonja E.M.,Balimponya E.G.,Kang H.,Bellizzi M.,Park C.H.,Li Y.,Mabagala R.,Sneller C.,Correll J.,Opiyo S.,Talbot N.J.,Mitchell T.,and Wang G.L.,2016,Genome-wide association mapping of rice resistance genes against Magnaporthe oryzae isolates from four African countries,Phytopathology,106(11):1359-1365
Mgonja E.M.,Park C.H.,Kang H.,Balimponya E.G.,Opiyo S.,Bellizzi M.,Mutiga S.K.,Rotich F.,Ganeshan V.D.,Mabagala R.,Sneller C.,Correll J.,Zhou B.,Talbot N.J.,Mitchell T.K.,and Wang G.L.,2017,Genotyping-by-sequencing-based genetic analysis of African rice cultivars and association mapping of blast resistance genes against Magnaporthe oryzae populations in Africa,Phytopathology,107(9):1039-1046
Michelmore R.W.,Paran I.,and Kesseli R.V.,1991,Identification of markers linked to disease-resistance genes by bulked segregant analysis:a rapid method to detect markers in specific genomic regions by using segregating populations,Proc.Natl.Acad.Sci.USA,88(21):9828-9832
Raboin L.M.,Ballini E.,Tharreau D.,Ramanantsoanirina A.,Frouin J.,Courtois B.,and Ahmadi N.,2016,Association mapping of resistance to rice blast in upland field conditions,Rice,9(1):59-70
Risch N.,and Merikangas K.,1996,The future of genetic studies of complex human diseases,Science,273(5281):1516-1517
Sakamoto T.,and Matsuoka M.,2008,Identifying and exploiting grain yield genes in rice,Curr.Opin.Plant Biol.,11(2):209-214
Sharma T.R.,Rai A.K.,Gupta S.K.,Vijayan J.,Devanna B.N.,and Ray S.,2012,Rice blast management through host-plant resistance:retrospect and prospects,Agric.Res.,1(1):37-52
Singh W.H.,Kapila R.K.,Sharma T.R.,and Rathour R.,2015,Genetic and physical mapping of a new allele of Pik locus from japonica rice'Liziangxintuanheigu',Euphytica,205(3):889-901
Srivastava D.,Shamim M.,Kumar M.,Mishra A.,Pandey P.,Kumar D.,Yadav P.,Siddiqui M.H.,and Singh K.N.,2017,Current status of conventional and molecular interventions for blast resistance in rice,Rice Science,24(6):299-321
Takagi H.,Abe A.,Yoshida K.,Kosugi S.,Natsume S.,Mitsuoka C.,Uemura A.,Utsushi H.,Tamiru M.,Takuno S.,Innan H.,Cano L.M.,Kamoun S.,and Terauchi R.,2013a,QTL-seq:rapid mapping of quantitative trait loci in rice by whole genome resequencing of DNA from two bulked populations,Plant J.,74(1):174-183
Takagi H.,Uemura A.,Yaegashi H.,Tamiru M.,Abe A.,Mitsuoka C.,Utsushi H.,Natsume S.,Kanzaki H.,Matsumura H.,Saitoh H.,Yoshida K.,Cano L.M.,Kamoun S.,and Terauchi R.,2013b,MutMap-Gap:whole-genome resequencing of mutant F2progeny bulk combined with de novo assembly of gap regions identifies the rice blast resistance gene Pii,New Phytol.,200(1):276-283
Tian D.G.,Chen Z.J.,Chen Z.Q.,Zhou Y.C.,Wang Z.H.,Wang F.,and Chen S.B.,2016,Allele-specific marker-based assessment revealed that the rice blast resistance genes Pi2and Pi9 have not been widely deployed in Chinese indica rice cultivars,Rice,9(1):19-29
Wang C.H.,Yang Y.L.,Yuan X.P.,Xu Q.,Feng Y.,Yu H.Y.,Wang Y.P.,and Wei X.H.,2014,Genome-wide association study of blast resistance in indica rice,BMC Plant Biol.,14(1):311-321
Wang Z.X.,Yano M.,Yamanouchi U.,Iwamoto M.,Monna L.,Hayasaka H.,Katayose Y.,and Sasaki T.,1999,The Pib gene for rice blast resistance belongs to the nucleotide binding and leucine-rich repeat class of plant disease resistance genes,The Plant Journal,19(1):55-64
Zheng W.J.,Wang Y.,Wang L.L.,Ma Z.B.,Zhao J.M.,Wang P.,Zhang L.X.,Liu Z.H.,and Lu X.C.,2016,Genetic mapping and molecular marker development for Pi65(t),a novel broad-spectrum resistance gene to rice blast using next-generation sequencing,Theor.Appl.Genet.,129(5):1035-1044
Zhu D.,Kang H.X.,Li Z.Q.,Liu M.H.,Zhu X.L.,Wang Y.,Wang D.,Wang Z.L.,Liu W.D.,and Wang G.L.,2016,Agenome-wide association study of field resistance to Magnaporthe oryzae in rice,Rice,9(1):44-52