抗稻瘟病位点LABR＿64的起源及其分布和序列多样性
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摘要
【目的】研究抗病基因在水稻种群中的分布特征是培育抗病品种的基础。【方法】以水稻第9染色体上与Pi3/Pi5/Pii/Pi15等位的抗病位点LABR_64为研究对象,结合稻瘟病抗性鉴定,对该位点中包含的两个抗病基因LABR_64-1和LABR_64-2在水稻群体中的分布特征进行了研究,并对其在单子叶植物中对应的直系同源序列进行了共线性分析。【结果】LABR_64位点在水稻中存在的频率约为16%,所有存在该位点的粳稻均表现高抗病性,缺失该位点的粳稻品种均表现出高感病性,而籼稻品种中LABR_64位点存在频率低于5%,虽然其存在情况下均表现出抗病性,但大部分缺失该位点品种也表现出抗性;存在LABR_64位点的品种中,LABR_64-2基因编码序列高度保守;LABR_64起源于单子叶与双子叶植物完全分离后及单子叶植物分化早期,其在不同的单子叶植物的分化过程中一直保持着良好的共线性。【结论】粳稻抗稻瘟病表型与LABR_64-1和LABR_64-2存在与否紧密关联,而籼稻的相关性不大,表明籼稻中其他抗性基因在稻瘟病抗性过程中起主导作用;鉴于LABR_64-2的高度保守性,可根据其编码序列设计分子标记,用于高效筛选抗稻瘟病粳稻品种;LABR_64可能在不同单子叶植物抗病过程中均具有重要作用。
【Objective】 A better understanding of the origin and distribution of disease resistance genes in rice germplasm is useful for breeding highly resistant varieties.【Method】We analyzed sequence diversity of the rice blast resistance locus LABR_64, which contains two homologous genes, LABR_64-1 and LABR_64-2, is located in the allelic region of Pi3/Pi5/Pii/Pi15 on rice chromosome 9. In addition, we analyzed the microsynteny of the LABR_64 orthologous region in different monocotyledons.【Result】The presence frequency(PF) of LABR_64 is 16%. All of the japonica rice cultivars carrying LABR_64 are highly resistant to rice blast and all of those without the locus are susceptible. In addition, the PF of LABR_64 in the indica subpopulation is lower than 5%. Although LABR_64 is correlated with the resistance to rice blast, many indica rice cultivars without LABR_64 are also resistant to rice blast. We also found that the LABR_64-2 sequence is much conserved. Moreover, the microsynteny analysis of the LABR_64 orthologous region in different monocotyledons indicated that LABR_64 originates after the separation of the monocotyledonous and dicotyledonous species, and at the early differentiation stage of monocotyledons.【Conclusion】The rice blast resistance phenotypes are closely correlated with the presence of the LABR_64 locus in japonicasubpopulation, but not in indica, indicating that there are many other resistance loci in the indica subpopulation. The LABR_64-2 sequence can be used for developing molecular markers in marker-assisted rice blast resistance breeding. It also indicated that LABR_64 may play a role in disease resistance in different monocotyledons.
【Objective】 A better understanding of the origin and distribution of disease resistance genes in rice germplasm is useful for breeding highly resistant varieties.【Method】We analyzed sequence diversity of the rice blast resistance locus LABR_64, which contains two homologous genes, LABR_64-1 and LABR_64-2, is located in the allelic region of Pi3/Pi5/Pii/Pi15 on rice chromosome 9. In addition, we analyzed the microsynteny of the LABR_64 orthologous region in different monocotyledons.【Result】The presence frequency(PF) of LABR_64 is 16%. All of the japonica rice cultivars carrying LABR_64 are highly resistant to rice blast and all of those without the locus are susceptible. In addition, the PF of LABR_64 in the indica subpopulation is lower than 5%. Although LABR_64 is correlated with the resistance to rice blast, many indica rice cultivars without LABR_64 are also resistant to rice blast. We also found that the LABR_64-2 sequence is much conserved. Moreover, the microsynteny analysis of the LABR_64 orthologous region in different monocotyledons indicated that LABR_64 originates after the separation of the monocotyledonous and dicotyledonous species, and at the early differentiation stage of monocotyledons.【Conclusion】The rice blast resistance phenotypes are closely correlated with the presence of the LABR_64 locus in japonicasubpopulation, but not in indica, indicating that there are many other resistance loci in the indica subpopulation. The LABR_64-2 sequence can be used for developing molecular markers in marker-assisted rice blast resistance breeding. It also indicated that LABR_64 may play a role in disease resistance in different monocotyledons.
引文
[1]Jiang N,Liu X L,Dai L Y,Wang G L.Advances on the mapping and cloning of blast resistance gene in rice.Chin Agric Sci Bull,2010,26(10):270-275.
[2]He X Y,Wang L,Wu W H,Chen Z M,Lin F,Chen Y S,Liu W,Chen Y H,Liao Y P.The progress of mapping,isolation of the genes resistance to blast and their breeding application in rice.Chin Agric Sci Bull,2014,30(6):1-12.
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[5]Kobe B,Deisenhofer J.A structural basis of the interactions between leucine-rich repeats and protein ligands.Nature,1995,374(6518):183-186.
[6]Tameling W I,Elzinga S D,Darmin P S,Vossen J H,Takken F L,Haring M A,Cornelissen B J.The tomato Rgene products I-2 and MI-1 are functional ATP binding proteins with ATPase activity.Plant Cell,2002,14(11):2929.
[7]Zhang X,Yang S,Wang J,Jia Y,Huang J,Tan S,Zhong Y,Wang L,Gu L,Chen J Q,Pan Q,Bergrelson J,Tian D.A genome-wide survey reveals abundant rice blast Rgenes in resistant cultivars.Plant J,2015,84(1):20-28.
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[9]Bryan G T,Wu K S,Farrall L,Jia Y,Hershey H P,McAdams S A,Faulk K N,Donaldson G K,Tarchini R,Valent B.A single amino acid difference distinguishes resistant and susceptible alleles of the rice blast resistance gene Pi-ta.Plant Cell,2000,12(11):2033-2046.
[10]Zhou B,Qu S,Liu G,Dolan M,Sakai H,Lu G,Bellizzi M,Wang G L.The eight amino-acid differences within three leucine-rich repeats between Pi2 and Piz-t resistance proteins determine the resistance specificity to Magnaporthe grisea.Mol Plant-Microbe Int,2006,19(11):1216-1228.
[11]Qu S H,Liu G F,Zhou B,Bellizzi M,Zeng L R,Dai L Y,Han B,Wang G L.The broad-spectrum blast resistance gene Pi9 encodes a nucleotide-binding site-leucine-rich repeat protein and is a member of a multigene family in rice.Genetics,2006,172(3):1901-1914.
[12]Lee S K,Song M Y,Seo Y S,Kim H K,Ko S,Cao P J,Suh J P,Yi G,Roh J H,Lee S,An G,Hahn T R,Wang GL,Ronald P,Jeon J S.Rice Pi5-mediated resistance to Magnaporthe oryzae requires the presence of two coiled-coil-nucleotide-binding-leucine-rich repeat genes.Genetics,2009,181(4):1627-1638.
[13]Fukuoka S,Saka N,Koga H,Ono K,Shimizu T,Ebana K,Hayashi N,Takahashi A,Hirochika H,Okuno K,Masahiro Yano.Loss of function of a proline-containing protein confers durable disease resistance in rice.Science,2009,325(5943):998-1001.
[14]Lin F,Chen S,Que Z Q,Wang L,Liu X Q,Pan Q H.The blast resistance gene Pi37 encodes a nucleotide binding site-leucine-rich repeat protein and is a member of a resistance gene cluster on rice chromosome 1.Genetics,2007,177(3):1871-1880.
[15]Ashikawa I,Hayashi N,Yamane H,Kanamori H,Wu J Z,Matsumoto T,Ono K,Yano M.Two adjacent nucleotide-binding site-leucine-rich repeat class genes are required to confer Pikm-specific rice blast resistance.Genetics,2008,180(4):2267-2276.
[16]Takahashi A,Hayashi N,Miyao A,Hirochika H.Unique features of the rice blast resistance Pish locus revealed by large scale retrotransposon-tagging.Bmc Plant Biol,2010,10(1):175-186.
[17]Zhai C,Lin F,Dong Z Q,He X Y,Yuan B,Zeng X S,Wang L,Pan Q H.The isolation and characterization of Pik,a rice blast resistance gene which emerged after rice domestication.New Phytol,2011,189(1):321-334.
[18]Deng Y,Zhai K,Xie Z,Yang D,Zhu X,Liu J,Wang X,Qin P,Yang Y,Zhang G,Li Q,Zhang J,Wu S,Millazzo J,Mao B,Wang E,Xie H,Tharreau D,He Z.Epigenetic regulation of antagonistic receptors confers rice blast resistance with yield balance.Science,2017,355(6328):962-966.
[19]Yi G,Lee S K,Hong Y K,Cho Y C,Nam M H,Kim S C,Han S S,Wang G L,Hahn T R,Ronald P C,Jeon J S.Use of Pi5(t)markers in marker-assisted selection to screen for cultivars with resistance to Magnaporthe grisea.Theor Appl Genet,2004,109(5):978-985.
[20]Jeon J S,Chen D,Yi G H,Wang G L,Ronald P C.Genetic and physical mapping of Pi5(t),a locus associated with broad-spectrum resistance to rice blast.Mol Genet Genom,2003,269(2):280-289.
[21]Inukai T,Zeigler R S,Sarkarung S,Bronson M,Dung LV,Kinoshita T,Nelson R J.Development of pre-isogenic lines for rice blast-resistance by marker-aided selection from a recombinant inbred population.Theor Appl Genet,1996,93(4):560-567.
[22]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,Wang G L.Dissection of the genetic architecture of rice resistance to the blast fungus Magnaporthe oryzae.Mol Plant Pathol,2015,17(6):959-972.
[23]ParK C H,Wang G L.The Magnaporthe oryzae effector AvrPiz-t Targets the RING E3 ubiquitin ligase APIP6 to suppress pathogen-associated molecular pattern-triggered immunity in rice.Plant Cell,2012,24(11):4748-4762.
[24]Wang B H,Zhen W,Lu G D,Zhang X B,Wang Z H.Screening on the spore-producing media of Pyricularia oryzae.Fujian Agric Sci Technol,2000(2):1-2.
[25]Huang X H,Yang S H,Gong J Y,Zhao Q,Feng Q,Zhan Q L,Zhao Y,Li W J,Cheng B Y,Xia J H,Chen N,Huang T,Zhang L,Fan D L,Chen J Y,Zhou C C,Lu YQ,Weng Q J,Han B.Genomic architecture of heterosis for yield traits in rice.Nature,2016,537(7622):629-633.
[26]Vogel J P,Garvin D F,Mockler T C.Genome sequencing and analysis of the model grass Brachypodium distachyon.Nature,2010,463(7282):763-768.
[27]Zhang L,Yu H,Ma B,Liu G F,Wang J J,Wang J M,Gao R C,Li J J,Liu J Y,Xu J,Zhang Y Y,Li Q,Huang X H,Xu J L,Li J M,Qian Q,Han B,He Z H,Li J Y.A natural tandem array alleviates epigenetic repression of IPA1 and leads to superior yielding rice.Nat Commun,2017,8(14789):1-14.
[28]Marschalek R,Silva M C,Santos S B D,Manke J R,Bieging C,Porto G,Wickert E,Andrade A D.Image-Rice Grain Scanner:A three-dimensional fully automated assessment of grain size and quality traits.Crop Breed Appl Biotechnol,2017,17:89-97.
[29]Luo C P,Ni L,Chen Z Y,Liu Y F,Liu Y Z,Nie Y F.Inoculation technology of rice blast and rice resistance to it in Jiangsu regional tests in 2009.Jiangsu Agric Sci,2009(6):178-179.
[30]Zhu Y Y,Chen H,Wang Y Y,Li Z S,Li Y,Fan J H,Chen J B,Yang S S,Ma G L,Hu L P,Zou J Y,Mundt C C,Borromeo E,Leung H,Mew T W.Diversifying variety for the control of rice blast in China.Biodiversity,2001,2(1):10-14.
[31]Lei C L,Wang J L,Jiang W R,Ling Z Z,George M L.Population structure and genetic variation of rice blast fungus in some rice-growing regions in northern China.Acta Phytopathol Sin,2002,32(3):219-226.
[32]Wang G L,Mackill D J,Bonman J M,McCouch S,Champoux M C,Nelson R J.RFLP Mapping of genes conferring complete and partial resistance to blast in a durably resistant rice cultivar.Genetics,1994,136(4):1421-1434.
[2]He X Y,Wang L,Wu W H,Chen Z M,Lin F,Chen Y S,Liu W,Chen Y H,Liao Y P.The progress of mapping,isolation of the genes resistance to blast and their breeding application in rice.Chin Agric Sci Bull,2014,30(6):1-12.
[3]Dangl J L,Jones J D G.Plant pathogens and integrated defense responses to infection.Nature,2001,411(6839):826-333.
[4]Iyer A S,Mccouch S R.The rice bacterial blight resistance gene xa5 encodes a novel form of disease resistance.Mol Plant-Microbe Int,2004,17(12):1348-1354.
[5]Kobe B,Deisenhofer J.A structural basis of the interactions between leucine-rich repeats and protein ligands.Nature,1995,374(6518):183-186.
[6]Tameling W I,Elzinga S D,Darmin P S,Vossen J H,Takken F L,Haring M A,Cornelissen B J.The tomato Rgene products I-2 and MI-1 are functional ATP binding proteins with ATPase activity.Plant Cell,2002,14(11):2929.
[7]Zhang X,Yang S,Wang J,Jia Y,Huang J,Tan S,Zhong Y,Wang L,Gu L,Chen J Q,Pan Q,Bergrelson J,Tian D.A genome-wide survey reveals abundant rice blast Rgenes in resistant cultivars.Plant J,2015,84(1):20-28.
[8]Wang Z X,Yano M,Yamanouchi U,Iwamoto M,Hayasaka H,Katayose Y,Sasaki T.The Pib gene for rice blast resistance belongs to the nucleotide binding and leucine-rich repeat class of plant disease resistance genes.Plant J,1999,19(1):55-64.
[9]Bryan G T,Wu K S,Farrall L,Jia Y,Hershey H P,McAdams S A,Faulk K N,Donaldson G K,Tarchini R,Valent B.A single amino acid difference distinguishes resistant and susceptible alleles of the rice blast resistance gene Pi-ta.Plant Cell,2000,12(11):2033-2046.
[10]Zhou B,Qu S,Liu G,Dolan M,Sakai H,Lu G,Bellizzi M,Wang G L.The eight amino-acid differences within three leucine-rich repeats between Pi2 and Piz-t resistance proteins determine the resistance specificity to Magnaporthe grisea.Mol Plant-Microbe Int,2006,19(11):1216-1228.
[11]Qu S H,Liu G F,Zhou B,Bellizzi M,Zeng L R,Dai L Y,Han B,Wang G L.The broad-spectrum blast resistance gene Pi9 encodes a nucleotide-binding site-leucine-rich repeat protein and is a member of a multigene family in rice.Genetics,2006,172(3):1901-1914.
[12]Lee S K,Song M Y,Seo Y S,Kim H K,Ko S,Cao P J,Suh J P,Yi G,Roh J H,Lee S,An G,Hahn T R,Wang GL,Ronald P,Jeon J S.Rice Pi5-mediated resistance to Magnaporthe oryzae requires the presence of two coiled-coil-nucleotide-binding-leucine-rich repeat genes.Genetics,2009,181(4):1627-1638.
[13]Fukuoka S,Saka N,Koga H,Ono K,Shimizu T,Ebana K,Hayashi N,Takahashi A,Hirochika H,Okuno K,Masahiro Yano.Loss of function of a proline-containing protein confers durable disease resistance in rice.Science,2009,325(5943):998-1001.
[14]Lin F,Chen S,Que Z Q,Wang L,Liu X Q,Pan Q H.The blast resistance gene Pi37 encodes a nucleotide binding site-leucine-rich repeat protein and is a member of a resistance gene cluster on rice chromosome 1.Genetics,2007,177(3):1871-1880.
[15]Ashikawa I,Hayashi N,Yamane H,Kanamori H,Wu J Z,Matsumoto T,Ono K,Yano M.Two adjacent nucleotide-binding site-leucine-rich repeat class genes are required to confer Pikm-specific rice blast resistance.Genetics,2008,180(4):2267-2276.
[16]Takahashi A,Hayashi N,Miyao A,Hirochika H.Unique features of the rice blast resistance Pish locus revealed by large scale retrotransposon-tagging.Bmc Plant Biol,2010,10(1):175-186.
[17]Zhai C,Lin F,Dong Z Q,He X Y,Yuan B,Zeng X S,Wang L,Pan Q H.The isolation and characterization of Pik,a rice blast resistance gene which emerged after rice domestication.New Phytol,2011,189(1):321-334.
[18]Deng Y,Zhai K,Xie Z,Yang D,Zhu X,Liu J,Wang X,Qin P,Yang Y,Zhang G,Li Q,Zhang J,Wu S,Millazzo J,Mao B,Wang E,Xie H,Tharreau D,He Z.Epigenetic regulation of antagonistic receptors confers rice blast resistance with yield balance.Science,2017,355(6328):962-966.
[19]Yi G,Lee S K,Hong Y K,Cho Y C,Nam M H,Kim S C,Han S S,Wang G L,Hahn T R,Ronald P C,Jeon J S.Use of Pi5(t)markers in marker-assisted selection to screen for cultivars with resistance to Magnaporthe grisea.Theor Appl Genet,2004,109(5):978-985.
[20]Jeon J S,Chen D,Yi G H,Wang G L,Ronald P C.Genetic and physical mapping of Pi5(t),a locus associated with broad-spectrum resistance to rice blast.Mol Genet Genom,2003,269(2):280-289.
[21]Inukai T,Zeigler R S,Sarkarung S,Bronson M,Dung LV,Kinoshita T,Nelson R J.Development of pre-isogenic lines for rice blast-resistance by marker-aided selection from a recombinant inbred population.Theor Appl Genet,1996,93(4):560-567.
[22]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,Wang G L.Dissection of the genetic architecture of rice resistance to the blast fungus Magnaporthe oryzae.Mol Plant Pathol,2015,17(6):959-972.
[23]ParK C H,Wang G L.The Magnaporthe oryzae effector AvrPiz-t Targets the RING E3 ubiquitin ligase APIP6 to suppress pathogen-associated molecular pattern-triggered immunity in rice.Plant Cell,2012,24(11):4748-4762.
[24]Wang B H,Zhen W,Lu G D,Zhang X B,Wang Z H.Screening on the spore-producing media of Pyricularia oryzae.Fujian Agric Sci Technol,2000(2):1-2.
[25]Huang X H,Yang S H,Gong J Y,Zhao Q,Feng Q,Zhan Q L,Zhao Y,Li W J,Cheng B Y,Xia J H,Chen N,Huang T,Zhang L,Fan D L,Chen J Y,Zhou C C,Lu YQ,Weng Q J,Han B.Genomic architecture of heterosis for yield traits in rice.Nature,2016,537(7622):629-633.
[26]Vogel J P,Garvin D F,Mockler T C.Genome sequencing and analysis of the model grass Brachypodium distachyon.Nature,2010,463(7282):763-768.
[27]Zhang L,Yu H,Ma B,Liu G F,Wang J J,Wang J M,Gao R C,Li J J,Liu J Y,Xu J,Zhang Y Y,Li Q,Huang X H,Xu J L,Li J M,Qian Q,Han B,He Z H,Li J Y.A natural tandem array alleviates epigenetic repression of IPA1 and leads to superior yielding rice.Nat Commun,2017,8(14789):1-14.
[28]Marschalek R,Silva M C,Santos S B D,Manke J R,Bieging C,Porto G,Wickert E,Andrade A D.Image-Rice Grain Scanner:A three-dimensional fully automated assessment of grain size and quality traits.Crop Breed Appl Biotechnol,2017,17:89-97.
[29]Luo C P,Ni L,Chen Z Y,Liu Y F,Liu Y Z,Nie Y F.Inoculation technology of rice blast and rice resistance to it in Jiangsu regional tests in 2009.Jiangsu Agric Sci,2009(6):178-179.
[30]Zhu Y Y,Chen H,Wang Y Y,Li Z S,Li Y,Fan J H,Chen J B,Yang S S,Ma G L,Hu L P,Zou J Y,Mundt C C,Borromeo E,Leung H,Mew T W.Diversifying variety for the control of rice blast in China.Biodiversity,2001,2(1):10-14.
[31]Lei C L,Wang J L,Jiang W R,Ling Z Z,George M L.Population structure and genetic variation of rice blast fungus in some rice-growing regions in northern China.Acta Phytopathol Sin,2002,32(3):219-226.
[32]Wang G L,Mackill D J,Bonman J M,McCouch S,Champoux M C,Nelson R J.RFLP Mapping of genes conferring complete and partial resistance to blast in a durably resistant rice cultivar.Genetics,1994,136(4):1421-1434.