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Targeted genome modification technologies and their applications in crop improvements

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Abstract

Recent advances in genome engineering indicate that innovative crops developed by targeted genome modification (TGM) using site-specific nucleases (SSNs) have the potential to avoid the regulatory issues raised by genetically modified organisms. These powerful SSNs tools, comprising zinc-finger nucleases, transcription activator-like effector nucleases, and clustered regulatory interspaced short palindromic repeats/CRISPR-associated systems, enable precise genome engineering by introducing DNA double-strand breaks that subsequently trigger DNA repair pathways involving either non-homologous end-joining or homologous recombination. Here, we review developments in genome-editing tools, summarize their applications in crop organisms, and discuss future prospects. We also highlight the ability of these tools to create non-transgenic TGM plants for next-generation crop breeding.

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References

  • Alberts B (2012) The breakthroughs of 2012. Science 338:1511

    Article  PubMed  Google Scholar 

  • Bae K-H, Do Kwon Y, Shin H-C, Hwang M-S, Ryu E-H, Park K-S, Yang H-Y, D-k Lee, Lee Y, Park J (2003) Human zinc fingers as building blocks in the construction of artificial transcription factors. Nat Biotechnol 21:275–280

    Article  PubMed  CAS  Google Scholar 

  • Baker M (2012) Gene-editing nucleases. Nat Methods 9:23–26

    Article  PubMed  CAS  Google Scholar 

  • Barrangou R (2012) RNA-mediated programmable DNA cleavage. Nat Biotechnol 30:836–838

    Article  PubMed  CAS  Google Scholar 

  • Barrangou R (2013) CRISPR-Cas systems and RNA-guided interference. Wiley interdiscip Rev RNA 4:267–278

    Article  PubMed  CAS  Google Scholar 

  • Boch J, Bonas U (2010) Xanthomonas AvrBs3 family-type III effectors: discovery and function. Annu Rev Phytopathol 48:419–436

    Article  PubMed  CAS  Google Scholar 

  • Boch J, Scholze H, Schornack S, Landgraf A, Hahn S, Kay S, Lahaye T, Nickstadt A, Bonas U (2009) Breaking the code of DNA binding specificity of TAL-type III effectors. Science 326:1509–1512

    Article  PubMed  CAS  Google Scholar 

  • Bogdanove AJ, Voytas DF (2011) TAL effectors: customizable proteins for DNA targeting. Science 333:1843–1846

    Article  PubMed  CAS  Google Scholar 

  • Bogdanove AJ, Schornack S, Lahaye T (2010) TAL effectors: finding plant genes for disease and defense. Curr Opin Plant Biol 13:394–401

    Article  PubMed  CAS  Google Scholar 

  • Cai C, Doyon Y, Ainley WM, Miller J, DeKelver R, Moehle E, Rock J, Lee Y-L, Garrison R, Schulenberg L, Blue R, Worden A, Baker L, Faraji F, Zhang L, Holmes M, Rebar E, Collingwood T, Rubin-Wilson B, Gregory P, Urnov F, Petolino J (2009) Targeted transgene integration in plant cells using designed zinc finger nucleases. Plant Mol Biol 69:699–709

    Article  PubMed  CAS  Google Scholar 

  • Carroll D (2011) Genome engineering with zinc-finger nucleases. Genetics 188:773–782

    Article  PubMed Central  PubMed  CAS  Google Scholar 

  • Cermak T, Doyle EL, Christian M, Wang L, Zhang Y, Schmidt C, Baller JA, Somia NV, Bogdanove AJ, Voytas DF (2011) Efficient design and assembly of custom TALEN and other TAL effector-based constructs for DNA targeting. Nucleic Acids Res 39:e82

    Article  PubMed Central  PubMed  CAS  Google Scholar 

  • Chen K, Gao C (2013) TALENs: customizable molecular DNA scissors for genome engineering of plants. J Genet Genomics 40:271–279

    Article  PubMed  CAS  Google Scholar 

  • Christian M, Cermak T, Doyle EL, Schmidt C, Zhang F, Hummel A, Bogdanove AJ, Voytas DF (2010) Targeting DNA double-strand breaks with TAL effector nucleases. Genetics 186:757–761

    Article  PubMed Central  PubMed  CAS  Google Scholar 

  • Christian M, Qi Y, Zhang Y, Voytas DF (2013) Targeted mutagenesis of Arabidopsis thaliana using engineered TAL effector nucleases (TALENs). G3 (Bethesda). doi:10.1534/g3.113.007104

  • Cong L, Zhou R, Y-c Kuo, Cunniff M, Zhang F (2012) Comprehensive interrogation of natural TALE DNA-binding modules and transcriptional repressor domains. Nat Commun 3:968

    Article  PubMed Central  PubMed  CAS  Google Scholar 

  • Cong L, Ran FA, Cox D, Lin S, Barretto R, Habib N, Hsu PD, Wu X, Jiang W, Marraffini LA, Zhang F (2013) Multiplex genome engineering using CRISPR/Cas systems. Science 339:819–823

    Article  PubMed Central  PubMed  CAS  Google Scholar 

  • Curtin SJ, Zhang F, Sander JD, Haun WJ, Starker C, Baltes NJ, Reyon D, Dahlborg EJ, Goodwin MJ, Coffman AP, Dobbs D, Joung JK, Voytas DF, Stupar RM (2011) Targeted mutagenesis of duplicated genes in soybean with zinc-finger nucleases. Plant Physiol 156:466–473

    Article  PubMed Central  PubMed  CAS  Google Scholar 

  • Curtin SJ, Voytas DF, Stupar RM (2012) Genome engineering of crops with designer nucleases. Plant Genome 5:42–50

    Article  CAS  Google Scholar 

  • De Francesco L (2012) Erratum: Move over ZFNs. Nat Biotechnol 30:112

    Article  CAS  Google Scholar 

  • Deng D, Yan C, Pan X, Mahfouz M, Wang J, Zhu JK, Shi Y, Yan N (2012) Structural basis for sequence-specific recognition of DNA by TAL effectors. Science 335:720–723

    Article  PubMed Central  PubMed  CAS  Google Scholar 

  • Durai S, Mani M, Kandavelou K, Wu J, Porteus MH, Chandrasegaran S (2005) Zinc finger nucleases: custom-designed molecular scissors for genome engineering of plant and mammalian cells. Nucleic Acids Res 33:5978–5990

    Article  PubMed Central  PubMed  CAS  Google Scholar 

  • Feng Z, Zhang B, Ding W, Liu X, Yang DL, Wei P, Cao F, Zhu S, Zhang F, Mao Y, Zhu JK (2013) Efficient genome editing in plants using a CRISPR/Cas system. Cell Res 23:1229–1232

    Article  PubMed Central  PubMed  CAS  Google Scholar 

  • Gaj T, Gersbach CA, Barbas Iii CF (2013) ZFN, TALEN, and CRISPR/Cas-based methods for genome engineering. Trends Biotechnol 31:397–405

    Article  PubMed  CAS  Google Scholar 

  • Huang P, Xiao A, Zhou M, Zhu Z, Lin S, Zhang B (2011) Heritable gene targeting in zebrafish using customized TALENs. Nat Biotechnol 29:699–700

    Article  PubMed  CAS  Google Scholar 

  • Jiang WZ, Zhou HB, Bi HH, Fromm M, Yang B, Weeks DP (2013) Demonstration of CRISPR/Cas9/sgRNA-mediated targeted gene modification in Arabidopsis, tobacco, sorghum and rice. Nucleic Acids Res. doi:10.1093/nar/gkt780

    Google Scholar 

  • Jinek M, Chylinski K, Fonfara I, Hauer M, Doudna JA, Charpentier E (2012) A programmable dual-RNA-guided DNA endonuclease in adaptive bacterial immunity. Science 337:816–821

    Article  PubMed  CAS  Google Scholar 

  • Joung JK, Sander JD (2012) TALENs: a widely applicable technology for targeted genome editing. Nature reviews. Nat Rev Mol Cell Biol 14:49–55

    Article  PubMed Central  PubMed  CAS  Google Scholar 

  • Li T, Huang S, Zhao X, Wright DA, Carpenter S, Spalding MH, Weeks DP, Yang B (2011) Modularly assembled designer TAL effector nucleases for targeted gene knockout and gene replacement in eukaryotes. Nucleic Acids Res 39:6315–6325

    Article  PubMed Central  PubMed  CAS  Google Scholar 

  • Li T, Liu B, Spalding MH, Weeks DP, Yang B (2012) High-efficiency TALEN-based gene editing produces disease-resistant rice. Nat Biotechnol 30:390–392

    Article  PubMed  CAS  Google Scholar 

  • Li JF, Norville JE, Aach J, McCormack M, Zhang D, Bush J, Church GM, Sheen J (2013) Multiplex and homologous recombination-mediated genome editing in Arabidopsis and Nicotiana benthamiana using guide RNA and Cas9. Nat Biotechnol 31:688–691

    Article  PubMed  CAS  Google Scholar 

  • Lusser M, Parisi C, Plan D, Rodríguez-Cerezo E (2012) Deployment of new biotechnologies in plant breeding. Nature Biotechnol 30:231–239

    Article  CAS  Google Scholar 

  • Maeder ML, Thibodeau-Beganny S, Osiak A, Wright DA, Anthony RM, Eichtinger M, Jiang T, Foley JE, Winfrey RJ, Townsend JA (2008) Rapid “open-source” engineering of customized zinc-finger nucleases for highly efficient gene modification. Mol Cell 31:294–301

    Article  PubMed Central  PubMed  CAS  Google Scholar 

  • Mak AN, Bradley P, Cernadas RA, Bogdanove AJ, Stoddard BL (2012) The crystal structure of TAL effector PthXo1 bound to its DNA target. Science 335:716–719

    Article  PubMed Central  PubMed  CAS  Google Scholar 

  • Mali P, Yang L, Esvelt KM, Aach J, Guell M, DiCarlo JE, Norville JE, Church GM (2013) RNA-guided human genome engineering via Cas9. Science 339:823–826

    Article  PubMed Central  PubMed  CAS  Google Scholar 

  • Mao Y, Zhang H, Xu N, Zhang B, Gao F, Zhu JK (2013) Application of the CRISPR-Cas system for efficient genome engineering in plants. Mol Plant. doi:10.1093/mp/sst121

    PubMed  Google Scholar 

  • Marton I, Zuker A, Shklarman E, Zeevi V, Tovkach A, Roffe S, Ovadis M, Tzfira T, Vainstein A (2010) Nontransgenic genome modification in plant cells. Plant Physiol 154:1079–1087

    Article  PubMed Central  PubMed  CAS  Google Scholar 

  • Miao J, Guo D, Zhang J, Huang Q, Qin G, Zhang X, Wan J, Gu H, Qu L-J (2013) Targeted mutagenesis in rice using CRISPR-Cas system. Cell Res. doi:10.1038/cr.2013

    PubMed Central  Google Scholar 

  • Morbitzer R, Elsaesser J, Hausner J, Lahaye T (2011) Assembly of custom TALE-type DNA binding domains by modular cloning. Nucleic Acids Res 39:5790–5799

    Article  PubMed Central  PubMed  CAS  Google Scholar 

  • Moscou MJ, Bogdanove AJ (2009) A simple cipher governs DNA recognition by TAL effectors. Science 326:1501

    Article  PubMed  CAS  Google Scholar 

  • Nekrasov V, Staskawicz B, Weigel D, Jones JDG, Kamoun S (2013) Targeted mutagenesis in the model plant Nicotiana benthamiana using Cas9 RNA-guided endonuclease. Nat Biotechnol 31:691–693

    Article  PubMed  CAS  Google Scholar 

  • Osakabe K, Osakabe Y, Toki S (2010) Site-directed mutagenesis in Arabidopsis using custom-designed zinc finger nucleases. Proc Natl Acad Sci USA 107:12034–12039

    Article  PubMed Central  PubMed  Google Scholar 

  • Pabo CO, Peisach E, Grant RA (2001) Design and selection of novel Cys2His2 zinc finger proteins. Annu Rev Biochem 70:313–340

    Article  PubMed  CAS  Google Scholar 

  • Paszkowski J, Baur M, Bogucki A, Potrykus I (1988) Gene targeting in plants. EMBO J 7:4021

    PubMed Central  PubMed  CAS  Google Scholar 

  • Pennisi E (2013) The CRISPR craze. Science 341:833–836

    Article  PubMed  CAS  Google Scholar 

  • Podevin N, Davies HV, Hartung F, Nogué F, Casacuberta JM (2013) Site-directed nucleases: a paradigm shift in predictable, knowledge-based plant breeding. Trends Biotechnol 31:375–383

    Article  PubMed  CAS  Google Scholar 

  • Reyon D, Khayter C, Regan MR, Joung JK, Sander JD (2012a) Engineering designer transcription activator-like effector nucleases (TALENs) by REAL or REAL-Fast assembly. Curr Protoc Mol Biol 100:12151–121514

    Google Scholar 

  • Reyon D, Tsai SQ, Khayter C, Foden JA, Sander JD, Joung JK (2012b) FLASH assembly of TALENs for high-throughput genome editing. Nat Biotechnol 30:460–465

    Article  PubMed Central  PubMed  CAS  Google Scholar 

  • Sander JD, Dahlborg EJ, Goodwin MJ, Cade L, Zhang F, Cifuentes D, Curtin SJ, Blackburn JS, Thibodeau-Beganny S, Qi Y (2010) Selection-free zinc-finger-nuclease engineering by context-dependent assembly (CoDA). Nat Methods 8:67–69

    Article  PubMed Central  PubMed  CAS  Google Scholar 

  • Sander JD, Cade L, Khayter C, Reyon D, Peterson RT, Joung JK, Yeh JR (2011) Targeted gene disruption in somatic zebrafish cells using engineered TALENs. Nat Biotechnol 29:697–698

    Article  PubMed Central  PubMed  CAS  Google Scholar 

  • Shan Q, Wang Y, Chen K, Liang Z, Li J, Zhang Y, Zhang K, Liu J, Voytas DF, Zheng X, Zhang Y, Gao C (2013a) Rapid and efficient gene modification in rice and Brachypodium using TALENs. Mol Plant 6:1365–1368

    Article  PubMed  CAS  Google Scholar 

  • Shan Q, Wang Y, Li J, Zhang Y, Chen K, Liang Z, Zhang K, Liu J, Xi JJ, Qiu J-L, Gao C (2013b) Targeted genome modification of crop plants using a CRISPR-Cas system. Nat Biotechnol 31:686–688

    Article  PubMed  CAS  Google Scholar 

  • Shukla VK, Doyon Y, Miller JC, DeKelver RC, Moehle EA, Worden SE, Mitchell JC, Arnold NL, Gopalan S, Meng X, Choi VM, Rock JM, Wu YY, Katibah GE, Zhifang G, McCaskill D, Simpson MA, Blakeslee B, Greenwalt SA, Butler HJ, Hinkley SJ, Zhang L, Rebar EJ, Gregory PD, Urnov FD (2009) Precise genome modification in the crop species Zea mays using zinc-finger nucleases. Nature 459:437–441

    Article  PubMed  CAS  Google Scholar 

  • Streubel J, Blucher C, Landgraf A, Boch J (2012) TAL effector RVD specificities and efficiencies. Nat Biotechnol 30:593–595

    Article  PubMed  CAS  Google Scholar 

  • Townsend JA, Wright DA, Winfrey RJ, Fu F, Maeder ML, Joung JK, Voytas DF (2009) High-frequency modification of plant genes using engineered zinc-finger nucleases. Nature 459:442–445

    Article  PubMed Central  PubMed  CAS  Google Scholar 

  • Voytas DF (2013) Plant genome engineering with sequence-specific nucleases. Annu Rev Plant Biol 64:327–350

    Article  PubMed  CAS  Google Scholar 

  • Waltz E (2012) Tiptoeing around transgenics. Nat Biotechnol 30:215–217

    Article  PubMed  CAS  Google Scholar 

  • Weber E, Gruetzner R, Werner S, Engler C, Marillonnet S (2011) Assembly of designer TAL effectors by Golden Gate cloning. PLoS ONE 6:e19722

    Article  PubMed Central  PubMed  CAS  Google Scholar 

  • Wendt T, Holm PB, Starker CG, Christian M, Voytas DF, Brinch-Pedersen H, Holme IB (2013) TAL effector nucleases induce mutations at a pre-selected location in the genome of primary barley transformants. Plant Mol Biol 83:279–285

    Article  PubMed  CAS  Google Scholar 

  • Wright DA, Thibodeau-Beganny S, Sander JD, Winfrey RJ, Hirsh AS, Eichtinger M, Fu F, Porteus MH, Dobbs D, Voytas DF (2006) Standardized reagents and protocols for engineering zinc finger nucleases by modular assembly. Nat Protocols 1:1637–1652

    Article  Google Scholar 

  • Wyman C, Kanaar R (2006) DNA double-strand break repair: all’s well that ends well. Annu Rev Genet 40:363–383

    Article  PubMed  CAS  Google Scholar 

  • Zhang F, Maeder ML, Unger-Wallace E, Hoshaw JP, Reyon D, Christian M, Li X, Pierick CJ, Dobbs D, Peterson T, Joung JK, Voytas DF (2010) High frequency targeted mutagenesis in Arabidopsis thaliana using zinc finger nucleases. Proc Natl Acad Sci USA 107:12028–12033

    Article  PubMed Central  PubMed  CAS  Google Scholar 

  • Zhang Y, Zhang F, Li X, Baller JA, Qi Y, Starker CG, Bogdanove AJ, Voytas DF (2013) Transcription activator-like effector nucleases enable efficient plant genome engineering. Plant Physiol 161:20–27

    Article  PubMed Central  PubMed  CAS  Google Scholar 

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Acknowledgments

The work was supported by the Ministry of Agriculture of China (2013ZX08002-004 and 2013ZX08010-002) and the National Natural Science Foundation of China (Grant Nos. 201263, 383601, and 31200273).

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Correspondence to Caixia Gao.

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Communicated by N. Stewart.

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Chen, K., Gao, C. Targeted genome modification technologies and their applications in crop improvements. Plant Cell Rep 33, 575–583 (2014). https://doi.org/10.1007/s00299-013-1539-6

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