用户名: 密码: 验证码:
Genome editing opens a new era of genetic improvement in polyploid crops
详细信息    查看全文 | 推荐本文 |
  • 英文篇名:Genome editing opens a new era of genetic improvement in polyploid crops
  • 作者:Qamar ; U.Zaman ; Chao ; Li ; Hongtao ; Cheng ; Qiong ; Hu
  • 英文作者:Qamar U.Zaman;Chao Li;Hongtao Cheng;Qiong Hu;Oil Crops Research Institute, Chinese Academy of Agricultural Sciences/Key Laboratory of Biology and Genetic Improvement of Oil Crops,Ministry of Agriculture;Graduate School of Chinese Academy of Agricultural Sciences;
  • 英文关键词:Genome editing;;CRISPR;;Site-specific mutagenesis;;Polyploid;;Crop improvement
  • 中文刊名:CROP
  • 英文刊名:作物学报(英文版)
  • 机构:Oil Crops Research Institute, Chinese Academy of Agricultural Sciences/Key Laboratory of Biology and Genetic Improvement of Oil Crops,Ministry of Agriculture;Graduate School of Chinese Academy of Agricultural Sciences;
  • 出版日期:2019-04-15
  • 出版单位:The Crop Journal
  • 年:2019
  • 期:v.7
  • 基金:supported by the National Natural Science Foundation of China(No.31700316);; the Science and Technology Innovation Project of Chinese Academy of Agricultural Sciences(Group No.118);; the Earmarked Fund for China Agriculture Research System(CARS-12);; the Fundamental Research Funds for Central Non-Profit Scientific Institution(1610172018009);; Graduate School of Chinese Academy of Agricultural Sciences
  • 语种:英文;
  • 页:CROP201902003
  • 页数:10
  • CN:02
  • ISSN:10-1112/S
  • 分类号:17-26
摘要
Sequence-specific nucleases(SSN) that generate double-stranded DNA breaks(DSBs) in genes of interest are the key to site-specific genome editing in plants. Genome editing has developed into one method of reducing undesirable traits in crops by the induction of knockout mutations. Different SSN-mediated genome-editing systems, including LAGLIDADG homing endonucleases or meganucleases, zinc-finger nucleases, transcription activator-like effector nucleases and clustered regularly interspaced short palindromic repeats, are emerging as robust tools for introducing functional mutations in polyploid crops including citrus, wheat, cotton, soybean, rapeseed, potato, grapes, Camelina sativa,dandelion, and tobacco. The approach utilizes knowledge of biological mechanisms for targeted induction of DSBs and their error-prone repair, allowing highly specific changes at designated genome loci. In this review, we briefly describe genome-editing technologies and their application to genetic improvement of polyploid crops.
        Sequence-specific nucleases(SSN) that generate double-stranded DNA breaks(DSBs) in genes of interest are the key to site-specific genome editing in plants. Genome editing has developed into one method of reducing undesirable traits in crops by the induction of knockout mutations. Different SSN-mediated genome-editing systems, including LAGLIDADG homing endonucleases or meganucleases, zinc-finger nucleases, transcription activator-like effector nucleases and clustered regularly interspaced short palindromic repeats, are emerging as robust tools for introducing functional mutations in polyploid crops including citrus, wheat, cotton, soybean, rapeseed, potato, grapes, Camelina sativa,dandelion, and tobacco. The approach utilizes knowledge of biological mechanisms for targeted induction of DSBs and their error-prone repair, allowing highly specific changes at designated genome loci. In this review, we briefly describe genome-editing technologies and their application to genetic improvement of polyploid crops.
引文
[1]D.A.Levin,Polyploidy and novelty in flowering plants,Am.Nat.122(1983)1-25.
    [2]G.J.Stebbins,Types of polyploids:their classification and significance,Adv.Genet.1(1947)403-429.
    [3]E.Mayr,Animal Species and Evolution,Harvard University Press,Cambridge,Massachusetts,USA,1963.
    [4]T.C.Osborn,J.C.Pires,J.A.Birchler,D.L.Auger,Z.J.Chen,H.S.Lee,L.Comai,A.Madlung,R.W.Doerge,V.Colot,R.A.Martienssen,Understanding mechanisms of novel gene expression in polyploids,Trends Genet.19(2003)141-147.
    [5]G.Li,R.Jain,M.Chern,N.T.Pham,J.A.Martin,T.Wei,W.S.Schackwitz,A.M.Lipzen,P.Q.Duong,K.C.Jones,The sequences of 1504 mutants in the model rice variety Kitaake facilitate rapid functional genomic studies,Plant Cell 29(2017)1218-1231.
    [6]J.Schell,M.V.Montagu,Transfer,maintenance and expression of bacterial Ti-plasmid DNA in plant cells transformed with A.tumefaciens,Brookhaven Symp.Biol.29(1977)36-49.
    [7]Y.Ishino,H.Shinagawa,K.Makino,M.Amemura,A.Nakata,Nucleotide sequence of the iap gene,responsible for alkaline phosphatase isozyme conversion in Escherichia coli,and identification of the gene product,J.Bacteriol.169(1987)5429-5433.
    [8]J.Smith,S.Grizot,S.Arnould,A.Duclert,J.C.Ephinat,P.Chames,J.Prieto,P.Redondo,F.J.Blanco,J.Bravo,Acombinatorial approach to create artificial homing endonucleases cleaving chosen sequences,Nucleic Acids Res.34(2006)e149.
    [9]J.H.Jung,F.Altpeter,TALEN mediated targeted mutagenesis of the caffeic acid O-methyltransferase in highly polyploid sugarcane improves cell wall composition for production of bioethanol,Plant Mol.Biol.92(2016)131-142.
    [10]A.Peng,S.Chen,T.Lei,L.Xu,Y.He,L.Wu,L.Yao,X.Zou,Engineering canker-resistant plants through CRISPR/Cas9-targeted editing of the susceptibility gene CsLOB1 promoter in citrus,Plant Biotechnol.J.15(2017)1509-1519.
    [11]C.Ren,X.Liu,Z.Zhang,Y.Wang,W.Duan,S.Li,Z.Liang,CRISPR/Cas9-mediated efficient targeted mutagenesis in Chardonnay(Vitis vinifera L.),Sci.Rep.6(2016),32289.
    [12]C.Morineau,Y.Bellec,F.Tellier,L.Gissot,Z.Kelemen,F.Nogue,J.D.Faure,Selective gene dosage by CRISPR-Cas9genome editing in hexaploid Camelina sativa,Plant Biotechnol.J.15(2017)729-739.
    [13]Y.Wang,X.Cheng,Q.Shan,Y.Zhang,J.Liu,C.Gao,J.L.Qiu,Simultaneous editing of three homoeoalleles in hexaploid bread wheat confers heritable resistance to powdery mildew,Nat.Biotechnol.32(2014)947-951.
    [14]Y.Zhang,Z.Liang,Y.Zong,Y.Wang,J.Liu,K.Chen,J.L.Qiu,C.Gao,Efficient and transgene-free genome editing in wheat through transient expression of CRISPR/Cas9 DNA or RNA,Nat.Commun.7(2016),12617.
    [15]W.Wang,Q.Pan,F.He,A.Akhunova,S.Chao,H.Trick,E.Akhunov,Transgenerational CRISPR-Cas9 activity facilitates multiplex gene editing in allopolyploid wheat,CRISPR J.1(2018)65-74.
    [16]X.C.Cui,Targeted Gene Editing Using CRISPR/Cas9 in a Wheat Protoplast System,(Master Thesis)Department of Biology,University of Ottawa,Canada,2017.
    [17]J.A.Townsend,D.A.Wright,R.J.Winfrey,F.Fu,M.L.Maeder,J.K.Joung,D.F.Voytas,High frequency modification of plant genes using engineered zinc finger nucleases,Nature 459(2009)442.
    [18]J.Gao,G.Wang,S.Ma,X.Xie,X.Wu,X.Zhang,Y.Wu,P.Zhao,Q.Xia,CRISPR/Cas9-mediated targeted mutagenesis in Nicotiana tabacum,Plant Mol.Biol.87(2015)99-110.
    [19]J.Li,T.J.Stoddard,Z.L.Demorest,P.O.Lavoie,S.Luo,B.M.Clasen,F.Cedrone,E.E.Ray,A.P.Coffman,A.Daulhac,Multiplexed,targeted gene editing in Nicotiana benthamiana for glyco-engineering and monoclonal antibody production,Plant Biotechnol.J.14(2016)533-542.
    [20]J.Gao,T.Zhang,B.Xu,L.Jia,B.Xiao,H.Liu,L.Liu,H.Yan,Q.Xia,CRISPR/Cas9-mediated mutagenesis of carotenoid cleavage dioxygenase 8(CCD8)in tobacco affects shoot and root architecture,Int.J.Mol.Sci.(2018)https://doi.org/10.3390/ijms19041062.
    [21]N.M.Butler,N.J.Baltes,D.F.Voytas,D.S.Douches,Geminivirus-mediated genome editing in potato(Solanum tuberosum L.)using sequence-specific nucleases,Front.Plant Sci.7(2016)1045.
    [22]B.M.Clasen,T.J.Stoddard,S.Luo,Z.L.Demorest,J.Li,F.Cedrone,R.Tibebu,S.Davison,E.E.Ray,A.Daulhac,Improving cold storage and processing traits in potato through targeted gene knockout,Plant Biotechnol.J.14(2016)169-176.
    [23]M.Andersson,H.Turesson,A.Nicolia,A.S.Falt,M.Samuelsson,P.Hofvander,Efficient targeted multiallelic mutagenesis in tetraploid potato(Solanum tuberosum)by transient CRISPR-Cas9 expression in protoplasts,Plant Cell Rep.36(2017)117-128.
    [24]N.J.Sauer,J.Narvaez-Vasquez,J.Mozoruk,R.B.Miller,Z.J.Warburg,M.J.Woodward,Y.A.Mihiret,T.A.Lincoln,R.E.Segami,S.L.Sanders,Oligonucleotide-mediated genome editing provides precision and function to engineered nucleases and antibiotics in plants,Plant Physiol.170(2016)1917-1928.
    [25]M.Gupta,R.C.Dekelver,A.Palta,C.Clifford,S.Gopalan,J.C.Miller,S.Novak,D.Desloover,D.Gachotte,J.Connell,Transcriptional activation of Brassica napusβ-ketoacyl-ACPsynthase II with an engineered zinc finger protein transcription factor,Plant Biotechnol.J.10(2012)783-791.
    [26]J.Braatz,H.J.Harloff,M.Mascher,N.Stein,A.Himmelbach,C.Jung,CRISPR-Cas9 induced mutations in polyploid oilseed rape,Plant Physiol.(2017)https://doi.org/10.1104/pp.17.00426.
    [27]L.Chao,M.Hao,W.Wang,H.Wang,F.Chen,W.Chu,B.Zhang,D.Mei,H.Cheng,Q.Hu,An efficient CRISPR/Cas9platform for rapidly generating simultaneous mutagenesis of multiple gene homoeologs in allotetraploid oilseed rape,Front.Plant Sci.9(2018)442.
    [28]A.Okuzaki,T.Ogawa,C.Koizuka,K.Kaneko,M.Inaba,J.Imamura,N.Koizuka,CRISPR/Cas9-mediated genome editing of the fatty acid desaturase 2 gene in Brassica napus,Plant Physiol.Biochem.(2018)https://doi.org/10.1016/j.plaphy.2018.04.025.
    [29]H.Yang,J.J.Wu,T.Tang,K.D.Liu,C.Dai,CRISPR/CAs9-mediated genome editing efficiently creates specfic mutations at multiple loci using one sgRNA in Braasica napus,Sci.Rep.7(2017)7489.
    [30]Y.Yang,K.Zhu,H.Li,S.Han,Q.Meng,S.U.Khan,C.Fan,K.Xie,Y.Zhou,Precise editing of CLAVATA genes in Brassica napus L.regulates multilocular silique development,Plant Biotechnol.J.(2018)https://doi.org/10.1111/pbi.12872.
    [31]B.Iaffaldano,Y.Zhang,K.Cornish,CRISPR/Cas9 genome editing of rubber producing dandelion Taraxacum kok-saghyz using Agrobacterium rhizogenes without selection,Ind.Crop.Prod.89(2016)356-362.
    [32]L.Wang,L.Wang,Q.Tan,Q.Fan,H.Zhu,Z.Hong,Z.Zhang,D.Duanmu,Efficient inactivation of symbiotic nitrogen fixation related genes in Lotus japonicus using CRISPR-Cas9,Front.Plant Sci.7(2016)1333.
    [33]H.Du,X.Zeng,M.Zhao,X.Cui,Q.Wang,H.Yang,H.Cheng,D.Yu,Efficient targeted mutagenesis in soybean by TALENs and CRISPR/Cas9,J.Biotechnol.217(2016)90-97.
    [34]W.Haun,A.Coffman,B.M.Clasen,Z.L.Demorest,A.Lowy,E.Ray,A.Retterath,T.Stoddard,A.Juillerat,F.Cedrone,Improved soybean oil quality by targeted mutagenesis of the fatty acid desaturase 2 gene family,Plant Biotechnol.J.12(2014)934-940.
    [35]Z.L.Demorest,A.Coffman,N.J.Baltes,T.J.Stoddard,B.M.Clasen,S.Luo,A.Retterath,A.Yabandith,M.E.Gamo,J.Bissen,Direct stacking of sequence-specific nucleaseinduced mutations to produce high oleic and low linolenic soybean oil,BMC Plant Biol.16(2016)225.
    [36]T.B.Jacobs,P.R.LaFayette,R.J.Schmitz,W.A.Parrott,Targeted genome modifications in soybean with CRISPR/Cas9,BMC Biotechnol.15(2015)16.
    [37]X.Sun,Z.Hu,R.Chen,Q.Jiang,G.Song,H.Zhang,Y.Xi,Targeted mutagenesis in soybean using the CRISPR-Cas9system,Sci.Rep.5(2015),10342.
    [38]G.Silva,L.Poirot,R.Galetto,J.Smith,G.Montooya,P.Duchateau,F.Paques,Meganucleases and other tools for targeted genome engineering:perspectives and challenges for gene therapy,Curr.Gene Ther.11(2011)11-27.
    [39]K.D'Halluin,C.Vanderstraeten,J.Hulle,J.Rosolowska,I.Den Brande,A.Pennewaert,K.D'Hont,M.Bossut,D.Jantz,R.Ruiter,Targeted molecular trait stacking in cotton through targeted double-strand break induction,Plant Biotechnol.J.11(2013)933-941.
    [40]S.Arnould,C.Delenda,S.Grizot,C.Desseaux,F.Paques,G.H.Silva,J.Smith,The I-CreI meganuclease and its engineered derivatives:applications from cell modification to gene therapy,Protein Eng.Des.Sel.24(2011)27-31.
    [41]L.Zhao,R.P.Bonocora,D.A.Shub,B.L.Stoddard,The restriction fold turns to the dark side:a bacterial homing endonuclease with a PD-(D/E)-XK motif,EMBO J.26(2007)2432-2442.
    [42]Y.S.Rong,K.G.Golic,Gene targeting by homologous recombination in Drosophila,Science 288(2000)2013-2018.
    [43]H.Puchta,Gene replacement by homologous recombination in plants,Plant Mol.Biol.48(2001)173-182.
    [44]A.Gouble,J.Smith,S.Bruneau,C.Perez,V.Guyot,J.P.Cabaniols,S.Leduc,L.Fiette,P.Ave,B.Micheau,Efficient in toto targeted recombination in mouse liver by meganuclease-induced double-strand break,J.Gene Med.8(2006)616-622.
    [45]N.Windbichler,M.Menichelli,P.Papath,A synthetic homing endonuclease-based gene drive system in the human malaria mosquito,Nature 473(2011)212-215.
    [46]R.S.Flannagan,T.Linn,M.A.Valvano,A system for the construction of targeted unmarked gene deletions in the genus Burkholderia,Environ.Microbiol.10(2008)1652-1660.
    [47]F.D.Urnov,E.J.Rebar,M.C.Holmes,H.S.Zhang,P.D.Gregory,Genome editing with engineered zinc finger nucleases,Nat.Rev.Genet.11(2010)636-646.
    [48]J.D.Sander,E.J.Dahlborg,M.J.Goodwin,L.Cade,F.Zhang,D.Cifuentes,S.J.Curtin,J.S.Blackburn,S.Thibodeau-Beganny,Y.Qi,Selection-free zinc-finger nuclease engineering by context-dependent assembly(CoDA),Nat.Methods 8(2011)67-69.
    [49]Y.G.Kim,J.Cha,S.Chandrasegaran,Hybrid restriction enzymes:zinc finger fusions to Fok I cleavage domain,Proc.Natl.Acad.Sci.U.S.A.93(1996)1156-1160.
    [50]E.Vanamee,S.Santagata,A.K.Aggarwal,Fok I requires two specific DNA sites for cleavage,J.Mol.Biol.309(2001)69-78.
    [51]C.L.Ramirez,J.E.Foley,D.A.Wright,F.Muller-Lerch,S.H.Rahman,T.I.Cornu,R.J.Winfrey,F.Fu,J.A.Townsend,Unexpected failure rates for modular assembly of engineered zinc fingers,Nat.Methods 5(2008)374-376.
    [52]J.Boch,U.Bonas,Xanthomonas AvrBs3 family-type IIIeffectors:discovery and function,Annu.Rev.Phytopathol.48(2010)419-436.
    [53]C.Mussolino,J.Alzubi,E.J.Fine,R.Morbitzer,T.J.Cradick,T.Lahaye,G.Bao,T.Cathomen,TALENs facilitate targeted genome editing in human cells with high specificity and low cytotoxicity,Nucleic Acids Res.42(2014)6762-6773.
    [54]S.J.Curtin,D.F.Voytas,R.M.Stupar,Genome engineering of crops with designer nucleases,Plant Genome 5(2012)42-50.
    [55]Y.Sun,J.Li,L.Xia,Precise genome modification via sequence-specific nucleases mediated gene targeting for crop improvement,Front.Plant Sci.7(2016)1928.
    [56]M.M.Mahfouz,L.Li,M.Shamimuzzaman,A.Wibowo,X.Fang,J.K.Zhu,De novo-engineered transcription activator-like effector(TALE)hybrid nuclease with novel DNA binding specificity creates double-strand breaks,Proc.Natl.Acad.Sci.U.S.A.108(2011)2623-2628.
    [57]J.C.Miller,S.Tan,G.Qiao,K.A.Barlow,J.Wang,D.F.Xia,X.Meng,D.E.Paschon,E.Leung,S.J.Hinkley,A TALE nuclease architecture for efficient genome editing,Nat.Biotechnol.29(2011)143-148.
    [58]J.D.Sander,J.K.Joung,CRISPR-Cas systems for genome editing,regulation and targeting,Nat.Biotechnol.32(2014)347-355.
    [59]K.Belhaj,A.Chaparro-Garcia,S.Kamoun,N.J.Patron,V.Nekrasov,Editing plant genomes with CRISPR/Cas9,Curr.Opin.Biotechnol.32(2015)76-84.
    [60]C.Mohan,Genome editing in sugarcane:challenges ahead,Front.Plant Sci.7(2016)1542.
    [61]J.Fletcher,C.Bender,B.Budowle,W.T.Cobb,S.E.Gold,C.A.Ishimaru,D.Luster,U.Melcher,R.Murch,H.Scherm,Plant pathogen forensics:capabilities,needs,and recommendations,Microbiol.Mol.Biol.Rev.70(2006)450-471.
    [62]Z.Ali,A.Abulfaraj,A.Idris,S.Ali,M.Tashkandi,M.M.Mahfouz,CRISPR/Cas9-mediated viral interference in plants,Genome Biol.16(2015)238.
    [63]S.Mercx,N.Smargiasso,F.Chaumont,E.De Pauw,M.Boutry,C.Navarre,Inactivation of theβ(1,2)-xylosyltransferase and theα(1,3)-fucosyltransferase genes in Nicotiana tabacum BY-2 cells by a multiplex CRISPR/Cas9 strategy results in glycoproteins without plant-specific glycans,Front.Plant Sci.8(2017)403.
    [64]X.Ma,Q.Zhu,Y.Chen,Y.G.Liu,CRISPR/Cas9 platforms for genome editing in plants:developments and applications,Mol.Plant 9(2016)961-974.
    [65]L.Yan,S.Wei,Y.Wu,R.Hu,H.Li,W.Yang,Q.Xie,High efficiency genome editing in Arabidopsis using Yao promoter-driven CRISPR/Cas9 system,Mol.Plant 8(2015)1820-1823.
    [66]Y.Mao,Z.Zhang,Z.Feng,P.Wei,H.Zhang,J.R.Botella,J.K.Zhu,Development of germ-line-specific CRISPR-Cas9systems to improve the production of heritable gene modifications in Arabidopsis,Plant Biotechnol.J.14(2016)519-532.
    [67]X.Ma,Q.Zhang,Q.Zhu,W.Liu,Y.Chen,R.Qiu,B.Wang,Z.Yang,H.Li,Y.Lin,Y.Xie,R.Shen,S.Chen,Z.Wang,Y.Chen,J.Guo,L.Chen,X.Zhao,Z.Dong,Y.G.Liu,A robust CRISPR/Cas9system for convenient,high-efficiency multiplex genome editing in monocot and dicot plants,Mol.Plant 8(2015)1274-1284.
    [68]H.Zhang,J.Zhang,P.Wei,B.Zhang,F.Guo,Z.Feng,Y.Mao,L.Yang,H.Zhang,N.Xu,J.K.Zhu,The CRISPR/Cas9 system produces specific and homozygous targeted gene editing in rice in one generation,Plant Biotechnol.J.12(2014)797-807.
    [69]Y.Lei,L.Lu,H.Y.Liu,S.Li,F.Xing,L.L.Chen,CRISPR-P:a web tool for synthetic single-guide RNA design of CRISPR-system in plants,Mol.Plant 7(2014)1494-1496.
    [70]H.Liu,Y.Ding,Y.Zhou,W.Jin,K.Xie,L.L.Chen,CRISPR-P 2.0:an improved CRISPR-Cas9 tool for genome editing in plants,Mol.Plant 10(2017)530-532.
    [71]L.Cong,F.A.Ran,D.Cox,S.Lin,R.Barretto,N.Habib,P.D.Hsu,X.Wu,W.Jiang,L.A.Marraffini,Multiplex genome engineering using CRISPR/Cas systems,Science 339(2013)819-823.
    [72]F.A.Ran,L.Cong,W.X.Yan,D.A.Scott,J.S.Gootenberg,A.J.Kriz,B.Zetsche,O.Shalem,X.Wu,K.S.Makarowa,E.V.Koonin,P.A.Sharp,F.Zhang,In vivo genome editing using Staphylococcus aureus Cas9,Nature 520(2015)186-198.
    [73]R.D.Fagerlund,R.H.J.Staals,P.C.Fineran,The Cpf1 CRISPR-Cas protein expands genome-editing tools,Genome Biol.16(2016)251.
    [74]A.C.Komor,Y.B.Kim,M.S.Packer,J.A.Zuris,D.R.Liu,Programmable editing of a target base in genomic DNAwithout double-stranded DNA cleavage,Nature 533(2016)420-424.
    [75]D.F.Voytas,C.Gao,Precision genome engineering and agriculture:opportunities and regulatory challenges.Multiplex genome engineering using CRISPR/Cas systems,PLoS Biol.12(2014),e1001877.
    [76]W.Gao,L.Long,X.Tian,F.Xu,J.Liu,P.K.Singh,J.R.Botella,C.Song,Genome editing in cotton with CRISPR/Cas9 system,Front.Plant Sci.8(2017)1364.
    [77]D.Zhang,H.Zhang,T.Li,K.Chen,J.L.Qiu,C.Gao,Perfectly matched 20-nucleotide guide RNA sequences enable robust genome editing using high fidelity SpCas9 nucleases,Genome Biol.18(2017)191.
    [78]Z.Liang,K.Chen,Y.Zhang,J.Liu,K.Yin,J.L.Qiu,C.Gao,Genome editing of bread wheat using biolistic delivery of CRISPR/Cas9 in vitro transcripts or ribonucleoproteins,Nat.Protoc.13(2018)413-430.

© 2004-2018 中国地质图书馆版权所有 京ICP备05064691号 京公网安备11010802017129号

地址:北京市海淀区学院路29号 邮编:100083

电话:办公室:(+86 10)66554848;文献借阅、咨询服务、科技查新:66554700