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Applications of Genome Engineering/Editing Tools in Plants

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Advances in Plant Transgenics: Methods and Applications

Abstract

The advent of engineered nucleases such as zinc finger nucleases (ZFNs), transcription activator-like effector nucleases (TALENs) and clustered regularly interspaced short palindromic repeats/Cas9 (CRISPR/Cas9) has revolutionized targeted genome editing. CRISPR/Cas9-based editing system has surpassed its predecessors owing to its simplicity, versatility and efficiency. Therefore, it has become the most promising genome-editing tool in recent years which is evident through the increasing number of publications and in several organisms. This technology has profound applications in areas of functional genomics and crop improvement. Recent studies have proved that multiplex genome editing is possible not only in model crops but in major crops too. Unlike transgenic crops which yield random insertions of target genes, genome-editing tools enable targeted gene insertion at a specified locus (knock-in), deletion of desired genes from the genome (knockout) and also genome modification (replacement). In this context, this chapter describes in detail the various applications of genome-editing technologies in crop improvement and highlights how this tool has outwitted transgenic technology in recent times.

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References

  • Alagoz Y, Gurkok T, Zhang B, Unver T (2016) Manipulating the biosynthesis of bioactive compound alkaloids for next-generation metabolic engineering in opium poppy using CRISPR-Cas 9 genome editing technology. Sci Rep 6:309–310

    Article  CAS  Google Scholar 

  • Ali Z, Abulfaraj A, Idris A, Ali S, Tashkandi M, Mahfouz MM (2015) CRISPR/Cas9-mediated viral interference in plants. Genome Biol 16:238–249

    Article  PubMed  PubMed Central  CAS  Google Scholar 

  • Anand P, Schug A, Wenzel W (2013) Structure based design of protein linkers for zinc finger nuclease. FEBS Lett 587(19):3231–3235

    Article  CAS  PubMed  Google Scholar 

  • Baltes NJ, Hummel AW, Konecna E, Cegan R, Bruns AN, Bisaro DM, Voytas DF (2015) Conferring resistance to geminiviruses with the CRISPR–Cas prokaryotic immune system. Nat Plants 1:15145

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • Barrangou R, Horvath P (2012) CRISPR: new horizons in phage resistance and strain identification. Annu Rev Food Sci Technol 3:143–162

    Article  CAS  PubMed  Google Scholar 

  • Bartel DP (2009) MicroRNAs: Target recognition and regulatory functions. Cell 136(2):215–233

    Article  CAS  PubMed  PubMed Central  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(5959):1509–1152

    Article  CAS  PubMed  Google Scholar 

  • Bortesi L, Fischer R (2014) The CRISPR/Cas9 system for plant genome editing and beyond. Biotechnol Adv 33(1):41–52

    Article  PubMed  CAS  Google Scholar 

  • Butler NM, Atkins PA, Voytas DF, Douches DS (2015) Generation and inheritance of targeted mutations in potato (Solanum tuberosum L.) using the CRISPR/Cas System. PLoS One 10:e0144591

    Article  PubMed  PubMed Central  CAS  Google Scholar 

  • Cai C, Doyon Y, Ainley W, Miller J, DeKelver R et al (2009) Targeted transgene integration in plant cells using designed zinc finger nucleases. Plant Mol Biol 69:699–709

    Article  CAS  PubMed  Google Scholar 

  • Cathomen T, Keith Joung J (2008) Zinc-finger Nucleases: The Next Generation Emerges. Mol Ther 16(7):1200–1207

    Article  CAS  PubMed  Google Scholar 

  • Cermak T, Doyle EC, 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(12):e82

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • Chandrasekaran J, Brumin M, Wolf D, Leibman D, Klap C, Pearlsman M et al (2016) Development of broad virus resistance in non-transgenic cucumber using CRISPR/Cas9 technology. Mol Plant Pathol 17:1140–1153

    Article  CAS  PubMed  PubMed Central  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(2):757–761

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • Christian M, Qi Y, Zhang Y, Voytas DF (2013) Targeted mutagenesis of Arabidopsis thaliana using engineered TAL Effector Nucleases (TALENs). G3 (Bethesda) 3:1697–1705

    Article  CAS  Google Scholar 

  • Clasen BM, Stoddard TJ, Luo S, Demorest ZL, Li J, Cedrone F, Tibebu R, Davison S, Ray EE, Daulhac A, Coffman A, Yabandith A, Retterath A, Haun W, Baltes NJ, Mathis L, Voytas DF, Zhang F (2016) Improving cold storage and processing traits in potato through targeted gene knockout. Plant Biotechnol J 14:169–176

    Article  CAS  PubMed  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(6121):819–823

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • Courtier-Orgogoz V, Morizot B, Boete C (2017) Agricultural pest control with CRISPR based gene drive: time for public debate: Should we use gene drive for pest control? EMBO Rep 18:878–880

    Article  CAS  Google Scholar 

  • Dreissig S, Schiml S, Schindele P, Weiss O, Rutten T, Schubert V, Gladilin E, Mette MF, Puchta H, Houben A (2017) Live-cell CRISPR imaging in plants reveals dynamic telomere movements. Plant J 91(4):565–573

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • Du H, Zeng X, Zhao M, Cui X, Wang Q, Yang H, Cheng H, Yu D (2016) Efficient targeted mutagenesis in soybean by TALENs and CRISPR/Cas9. J Biotechnol 217:90–97

    Article  CAS  PubMed  Google Scholar 

  • Engler C, Kandzia R, Marillonnet S (2008) A one pot, one step, precision cloning method with high throughput capability. PLoS One 3(11):e3647

    Article  PubMed  PubMed Central  CAS  Google Scholar 

  • Esvelt KM, Smidler AL, Catteruccia F, Church GM (2014) Concerning RNA-guided gene drives for the alteration of wild populations. elife 3:e03401

    Article  PubMed  PubMed Central  CAS  Google Scholar 

  • Gantz VM, Jasinskiene N, Tatarenkova O, Fazekas A, Macias VM, Bier E, James AA (2015) Highly efficient Cas9-mediated gene drive for population modification of the malaria vector mosquito Anopheles stephensi. Proc Natl Acad Sci U S A 112:6736–6743

    Article  CAS  Google Scholar 

  • Georges F, Ray H (2017) Genome editing of crops: a renewed opportunity for food security. In: (Ed.). GM Crops Food 8(1):1–12

    Article  PubMed  PubMed Central  Google Scholar 

  • Gilbert LA, Horlbeck MA, Adamson B (2014) Genome-scale CRISPR-mediated control of gene repression and activation. Cell 159(3):647–661

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • Greisman HA, Pabo CO (1997) A general strategy for selecting high-affinity zinc finger proteins for diverse DNA target sites. Science 275(5300):657–661

    Article  CAS  PubMed  Google Scholar 

  • Hahn F, Mantegazza O, Greiner A, Hegemann P, Eisenhut M, Weber APM (2017) An efficient visual screen for CRISPR/Cas9 activity in Arabidopsis thaliana. Front Plant Sci 8:39

    Article  PubMed  PubMed Central  Google Scholar 

  • Hanania U, Ariel T, Tekoah Y, Fux L, Sheva M, Gubbay Y, Weiss M, Oz D, Azulay Y, Turbovski A, Forster Y, Shaaltiel Y (2017) Establishment of a tobacco BY2 cell line devoid of plant-specific xylose and fucose as a platform for the production of biotherapeutic proteins. Plant Biotechnol J 15:1120–1129

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • Hilton IB, D’Ippolito AM, Vockley CM, Thakore PI, Crawford GE, Reddy TE et al (2015) Epigenome editing by a CRISPR-Cas9-based acetyltransferase activates genes from promoters and enhancers. Nat Biotechnol 33:510–517

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • Horvath P, Barrangou R (2010) CRISPR/Cas, the immune system of bacteria and archaea. Science 327(5962):167–170

    Article  CAS  PubMed  Google Scholar 

  • Hu Y, Zhang J, Jia H, Sosso D, Li T, Frommer WB, Yang B, White FF, Wang N, Jones JB (2014) Lateral organ boundaries 1 is a disease susceptibility gene for citrus bacterial canker disease. Proc Natl Acad Sci U S A 111:521–529

    Article  CAS  Google Scholar 

  • Huang S, Weigel D, Beachy RN, Li J (2016) A proposed regulatory framework for genome-edited crops. Nat Genet 48(2):109–111

    Article  CAS  PubMed  Google Scholar 

  • Hurt JA, Thibodeau SA, Hirsh AS, Pabo CO, Joung JK (2003) Highly specific zinc finger proteins obtained by directed domain shuffling and cell-based selection. Proc Natl Acad Sci U S A 14;100(21):12271–12276

    Article  CAS  Google Scholar 

  • Jacobs TB, LaFayette PR, Schmitz RJ, Parrott WA (2015) Targeted genome modifications in soybean with CRISPR/Cas9. BMC Biotechnol 15:16

    Article  PubMed  PubMed Central  CAS  Google Scholar 

  • Jacobs TB, Zhang N, Patel D, Martin GB (2017) Generation of a collection of mutant tomato lines using pooled CRISPR libraries. Plant Physiol 174:2033–2037

    Article  CAS  Google Scholar 

  • Jia H, Wang N (2014) Targeted genome editing of sweet orange using Cas9/sgRNA. PLoS One 9(4):e93806

    Article  PubMed  PubMed Central  CAS  Google Scholar 

  • Jia H, Zhang Y, Orbovic V, Xu J, White F, Jones J, Wang N (2017) Genome editing of the disease susceptibility gene CsLOB1 in citrus confers resistance to citrus canker. Plant Biotechnol J 15:817–823

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • Jiang W, Zhou H, Bi H, Fromm M, Yang B, Weeks DP (2013) Demonstration of CRISPR/Cas9/sgRNA-mediated targeted gene modification in Arabidopsis, tobacco, sorghum and rice. Nucl Acids Res 41:e188

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • Jiang WZ, Henry IM, Lynagh PG, Comai L, Cahoon EB, Weeks DP (2017) Significant enhancement of fatty acid composition in seeds of the allohexaploid, Camelina sativa, using CRISPR/Cas9 gene editing. Plant Biotechnol J 15:648–657

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • Karvelis T, Gasiunas G, Siksnys V (2013) Programmable DNA cleavage in vitro by Cas9. Biochem Soc Trans 41(6):1401–1406

    Article  CAS  PubMed  Google Scholar 

  • Kaur N, Alok A, Shivani KN, Pandey P, Awasthi P, Tiwari S (2018) CRISPR/Cas9-mediated efficient editing in phytoene desaturase (PDS) demonstrates precise manipulation in banana cv. Rasthali genome. Func Int Genomics 18(1):89–99

    Article  CAS  Google Scholar 

  • Kim YG, Cha J, Chandrasegaran S (1996) Hybrid restriction enzymes: zinc finger fusions to Fok I cleavage domain. Proc Natl Acad Sci U S A 93(3):1156–1160

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • Kim H, Kim S-T, Ryu J, Kang B-C, Kim J-S, Kim S-G (2017) CRISPR/Cpf1-mediated DNA-free plant genome editing. Nat Commun 8:14406

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • Komor AC, Kim YB, Packer MS, Zuris JA, Liu DR (2016) Programmable editing of a target base in genomic DNA without double-stranded DNA cleavage. Nature 33:420–424

    Article  CAS  Google Scholar 

  • Larson MH, Gilbert LA, Wang X, Lim WA, Weis JS (2013) CRISPR interference (CRISPRi) for sequence-specific control of gene expression. Nat Protoc 8:2180–2196

    Article  CAS  PubMed  PubMed Central  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  CAS  PubMed  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  CAS  PubMed  PubMed Central  Google Scholar 

  • Li Z, Liu ZB, Xing A, Moon BP, Koellhoffer JP, Huang L et al (2015) Cas9-guide RNA directed genome editing in soybean. Plant Physiol 169(2):960–970

    Article  PubMed  PubMed Central  CAS  Google Scholar 

  • Li J, Meng X, Zong Y, Chen K, Zhang H, Liu J, Li J, Gao C (2016) Gene replacements and insertions in rice by intron targeting using CRISPR-Cas9. Nat Plants 2:16139

    Article  CAS  PubMed  Google Scholar 

  • Li X, Zhou W, Ren Y, Tian X, Lv T, Wang Z, Fang J, Chu C, Yang J, Bu Q (2017) High-efficiency breeding of early-maturing rice cultivars via CRISPR/Cas9-mediated genome editing. J Genet Genomics 44(3):175–178

    Article  PubMed  Google Scholar 

  • Li C, Chen C, Chen H, Wang S, Chen X, Cui Y (2018a) Verification of DNA motifs in Arabidopsis using CRISPR/Cas9-mediated mutagenesis. Plant Biotechnol J 8:1446–1451

    Article  CAS  Google Scholar 

  • Li R, Fu D, Zhu B, Luo Y, Zhu H (2018b) CRISPR/Cas9-mediated mutagenesis of lncRNA1459 alters tomato fruit ripening. Plant J. (in press)

    Google Scholar 

  • Li R, Li R, Li X, Fu D, Zhu B, Tian H, Luo Y, Zhu H (2018c) Multiplexed CRISPR/Cas9-mediated metabolic engineering of γ-aminobutyric acid levels in Solanum lycopersicum. Plant Biotechnol J 16:415–427

    Article  CAS  PubMed  Google Scholar 

  • Liang Z, Chen K, Li T, Yi Zhang Y, Wang Y, Zhao Q, Liu J, Zhang H, Liu C, Ran Y, Gao C (2017) Efficient DNA-free genome editing of bread wheat using CRISPR/Cas9 ribonucleoprotein complexes. Nat Commun 8:14261

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • Liu C, Zhang L, Liu H, Cheng K (2017) Delivery strategies of the CRISPR-Cas9 gene-editing system for therapeutic applications. J Control Release 266:17–26

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • Liu P, Chen M, Liu Y, Qi LS, Ding S (2018) CRISPR-based chromatin remodeling of the endogenous Oct4 or Sox2 locus enables reprogramming to pluripotency cell. Stem Cell 22(2):252–261

    CAS  Google Scholar 

  • Lu Y, Zhu JK (2017) Precise editing of a target base in the rice genome using a modified CRISPR/Cas9 System. Mol Plant 10:523–525

    Article  CAS  PubMed  Google Scholar 

  • Ma X, Liu YG (2016) CRISPR/Cas9-based multiplex genome editing in monocot and dicot plants. Curr Protoc Mol Biol 115:31.6.1–31.6.21

    Article  Google Scholar 

  • Ma X, Zhang Q, Zhu Q, Liu W, Chen Y, Qiu R, Wang B, Yang Z, Li H, Lin Y, Xie Y, Shen R, Chen S, Wang Z, Chen Y, Guo J, Chen L, Zhao X, Dong Z, Liu YG (2015) A Robust CRISPR/Cas9 system for convenient, high-efficiency multiplex genome editing in monocot and dicot plants. Mol Plant 8(8):1274–1284

    Article  CAS  PubMed  Google Scholar 

  • Ma H, Tu LC, Naseri A, Huisman M, Zhang S, Grunwald D, Pederson T (2016a) Multiplexed labeling of genomic loci with dCas9 and engineered sgRNAs using CRISP Rainbow. Nat Biotechnol 34(5):528–531

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • Ma X, Zhu Q, Chen Y, Liu YG (2016b) CRISPR/Cas9 platforms for genome editing in plants: developments and applications. Mol Plant 9(7):961–974

    Article  CAS  PubMed  Google Scholar 

  • Mahfouz MM, Li L, Piatek M, Fang X, Mansour H, Bangarusamy DK, Zhu J-K (2012) Targeted transcriptional repression using a chimeric TALE-SRDX repressor protein. Plant Mol Biol 78(3):311–321

    Article  CAS  PubMed  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(6121):823–826

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • Malnoy M, Viola R, Jung MH, Koo OJ, Kim S, Kim JS et al (2016) DNA-free genetically edited grapevine and apple protoplast using CRISPR/Cas9 ribonucleoproteins. Front Plant Sci 7:1904

    Article  PubMed  PubMed Central  Google Scholar 

  • Mani M, Kandavelou K, Dy FJ, Durai S, Chandrasegaran S (2005) Design, engineering, and characterization of zinc finger nucleases. Biochem Biophys Res Commun 335(2):447–457

    Article  CAS  PubMed  Google Scholar 

  • Mazier M, Flamain F, Nicolaï M, Sarnette V, Caranta C (2011) Knock-down of both eIF4E1 and eIF4E2 genes confers broad-spectrum resistance against Potyviruses in Tomato. PLoS One 6(12):e29595

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • Meng X, Yu H, Zhang Y, Zhuang F, Song X, Gao S, Gao C, Li J (2017) Construction of a genome-wide mutant library in rice using CRISPR/Cas9. Mol Plant 10(9):1238–1241

    Article  CAS  PubMed  Google Scholar 

  • Moore M, Klug A, Choo Y (2001) Improved DNA binding specificity from polyzinc finger peptides by using strings of two-finger units. Proc Natl Acad Sci U S A 98(4):1437–1441

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • Morgan SL, Mariano NC, Bermudez A, Arruda NL, Wu F, Luo Y, Shankar G, Jia L, Chen H, Hu JF, Hoffman AR, Huang CC, Pitteri SJ, Wang KC (2017) Manipulation of nuclear architecture through CRISPR-mediated chromosomal looping. Nat Commun 8:15993

    Article  CAS  PubMed  PubMed Central  Google Scholar 

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

    Article  CAS  PubMed  Google Scholar 

  • Nakajima I, Ban Y, Azuma A, Onoue N, Moriguchi T, Yamamoto T et al (2017) CRISPR/Cas9-mediated targeted mutagenesis in grape. PLoS One 12(5):e0177966

    Article  PubMed  PubMed Central  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  CAS  PubMed  Google Scholar 

  • Nekrasov V, Wang C, Win J, Lanz C, Weigel D, Kamoun S (2017) Rapid generation of a transgene-free powdery mildew resistant tomato by genome deletion. Sci Rep 7:482

    Article  PubMed  PubMed Central  CAS  Google Scholar 

  • Nishitani C, Hirai N, Komori S, Wada M, Okada K, Osakabe K, Yamamoto T, Osakabe Y (2016) Efficient genome editing in apple using a CRISPR/Cas9 system. Sci Rep 6:31481

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • Odipio J, Alicai T, Ingelbrecht I, Nusinow DA, Bart R, Taylor NJ (2017) Efficient CRISPR/Cas9 genome editing of phytoene desaturase in cassava. Front Plant Sci 8:1780

    Article  PubMed  PubMed Central  Google Scholar 

  • Ordon J, Gantner J, Kemna J, Schwalgun L, Reschke M, Streubel J, Boch J, Stuttmann J (2017) Generation of chromosomal deletions in dicotyledonous plants employing a user-friendly genome editing toolkit. Plant J 89(1):155–168

    Article  CAS  PubMed  Google Scholar 

  • Osakabe Y, Watanabe T, Sugano SS, Ueta R, Ishihara R, Shinozaki K, Osakabe K (2016) Optimization of CRISPR/Cas9 genome editing to modify abiotic stress responses in plants. Sci Rep 6:26685

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • Pabo C, Peisach E, Grant R (2001) Design and selection of novel Cys2 His2 zinc finger proteins. Annu Rev Biochem 70:313–340

    Article  CAS  PubMed  Google Scholar 

  • Pan C, Ye L, Qin L, Liu X, He Y, Wang J, Chen L et al (2016) CRISPR/Cas9-mediated efficient and heritable targeted mutagenesis in tomato plants in the first and later generations. Sci Rep 6:24765

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • Peng A, Chen S, Lei T, Xu L, He Y, Wu L et al (2017) Engineering canker resistant plants through CRISPR/Cas9-targeted editing of the susceptibility gene CsLOB1 promoter in citrus. Plant Biotechnol J 15(12):1509–1519

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • Piatek A, Ali Z, Baazim H, Li L, Abulfaraj A, Al-Shareef S (2015) RNA-guided transcriptional regulation in planta via synthetic dCas9-based transcription factors. Plant Biotechnol J 13:578–589

    Article  CAS  PubMed  Google Scholar 

  • Porteus MH, Carroll D (2005) Gene targeting using zinc finger nucleases. Nat Biotechnol 23(8):967–973

    Article  CAS  PubMed  Google Scholar 

  • Pyott DE, Sheehan E, Molnar A (2016) Engineering of CRISPR/ Cas9- mediated potyvirus resistance in transgene-free Arabidopsis plants. Mol Plant Path 17:1276–1288

    Article  CAS  Google Scholar 

  • Qi LS, Larson MH, Gilbert LA, Doudna JA, Weissman JS, Arkin AP et al (2013) Repurposing CRISPR as an RNA-guided platform for sequence specific control of gene expression. Cell 152:1173–1183

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • Ren B, Yan F, Kuang Y, Li N, Zhang D, Zhou X, Lin H, Zhou H (2018) Improved base editor for efficiently inducing genetic variations in rice with CRISPR/Cas9-guided hyperactive hAID mutant. Mol Plant doi 11:623. https://doi.org/10.1016/j.molp.2018.01.005

    Article  CAS  Google Scholar 

  • Rodríguez-Leal D, Lemmon ZH, Man J, Bartlett ME, Lippman ZB (2017) Engineering quantitative trait variation for crop improvement by genome editing. Cell 171(2):470–480

    Article  PubMed  CAS  Google Scholar 

  • Sander JD, Joung JK (2014) CRISPR-Cas systems for editing, regulating and targeting genomes. Nat Biotechnol 32(4):347–355

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • Schiml S, Fauser F, Puchta H (2014) The CRISPR/Cas system can be used as nuclease for in planta gene targeting and as paired nickases for directed mutagenesis in Arabidopsis resulting in heritable progeny. Plant J 80:1139–1150

    Article  CAS  PubMed  Google Scholar 

  • Scholze H, Boch J (2010) TAL effector-DNA specificity. Virulence 1(5):428–432

    Article  PubMed  Google Scholar 

  • Scott MJ, Gould F, Lorenzen MD, Grubbs N, Edwards OR, O’Brochta DA (2017) Agricultural production: assessment of the potential use of Cas9-mediated gene drive systems for agricultural pest control. J Respon Innov 5:98–120

    Article  Google Scholar 

  • Shalem O, Sanjana NE, Zhang F (2015) High-throughput functional genomics using CRISPR-Cas9. Nat Rev Genet 16:299–311

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • Shan Q, Wang Y, Li J, Zhang Y, Chen K, Liang Z, Zhang K, Liu J, Xi JJ, Qiu JL, Gao C (2013) Targeted genome modification of crop plants using a CRISPR-Cas system. Nat Biotechnol 31(8):686–688

    Article  CAS  PubMed  Google Scholar 

  • Shan Q, Zhang Y, Chen K, Zhang K, Gao C (2015) Creation of fragrant rice by targeted knockout of the OsBADH2 gene using TALEN technology. Plant Biotechnol J 13:791–800

    Article  CAS  PubMed  Google Scholar 

  • Shen C, Que Z, Xia Y, Tang N, Li D, He R, Cao M (2017) Knock out of the annexin gene OsAnn3 via CRISPR/Cas9-mediated genome editing decreased cold tolerance in rice. J Plant Biol 60(6):539–547

    Article  CAS  Google Scholar 

  • Shi J, Habben JE, Archibald RL, Drummond BJ, Chamberlin MA, Williams RW, Lafitte HR et al (2015) Overexpression of ARGOS genes modifies plant sensitivity to ethylene, leading to improved drought tolerance in both Arabidopsis and maize. Plant Physiol 169:266–282

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • Shi J, Gao H, Wang H, Lafitte HR, Archibald RL, Yang M, Hakimi SM, Mo H, Habben JE (2017) ARGOS8 variants generated by CRISPR-Cas9 improve maize grain yield under field drought stress conditions. Plant Biotechnol J 15:207–216

    Article  CAS  PubMed  Google Scholar 

  • Shimatani Z, Kashojiya S, Takayama M, Terada R, Arazoe T, Ishii H, Teramura H, Yamamoto T, Komatsu H, Miura K (2017) Targeted base editing in rice and tomato using a CRISPR-Cas9 cytidine deaminase fusion. Nat Biotechnol 35:441

    Article  CAS  PubMed  Google Scholar 

  • Shukla VK, Doyon Y, Miller JC, DeKelver RC, Moehle EA, Worden SE, Mitchell JC et al (2009) Precise genome modification in the crop Zea mays using zinc finger nucleases. Nature 459:437–441

    Article  CAS  PubMed  Google Scholar 

  • Sonoda E, Hochegger H, Saberi A, Taniguchi Y, Takeda S (2006) Differential usage of non-homologous end-joining and homologous recombination in double strand break repair. DNA Repair (Amst) 5(9–10):1021–1029

    Article  CAS  Google Scholar 

  • Sun Y, Zhang X, Wu C, He Y, Ma Y, Hou H, Guo X et al (2016) Engineering herbicide-resistant rice plants through CRISPR/Cas9-mediated homologous recombination of acetolactate synthase. Mol Plant 9:628–631

    Article  CAS  PubMed  Google Scholar 

  • Sun Y, Jiao G, Liu Z, Zhang X, Li J, Guo X, Du W, Du J, Francis F, Zhao Y et al (2017) Generation of high-amylose rice through CRISPR/Cas9-mediated targeted mutagenesis of starch branching enzymes. Front Plant Sci 8:298

    PubMed  PubMed Central  Google Scholar 

  • Svitashev S, Young JK, Schwartz C, Gao H, Falco SC, Cigan AM (2015) Targeted mutagenesis, precise gene editing and site-specific gene insertion in maize using Cas9 and guide RNA. Plant Physiol 169:931–945

    Article  PubMed  PubMed Central  CAS  Google Scholar 

  • Svitashev S, Schwartz C, Lenderts B, Young JK, Cigan AM (2016) Genome editing in maize directed by CRISPR-Cas9 ribonucleoprotein complexes. Nat Commun 7:13274

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • Thompson DB, Aboulhouda S, Hysolli E, Smith CJ, Wang S, Castanon O, Church GM (2017) The future of multiplexed eukaryotic genome engineering. ACS Chem Biol 13(2):313–325

    Article  PubMed  PubMed Central  CAS  Google Scholar 

  • Tian S, Jiang L, Gao Q, Zhang J, Zong M, Zhang H, Ren Y, Guo S, Gong G, Liu F, Xu Y (2017) Efficient CRISPR/Cas9-based gene knockout in watermelon. Plant Cell Rep 36(3):399–406

    Article  CAS  PubMed  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  CAS  PubMed  PubMed Central  Google Scholar 

  • Upadhyay SK, Kumar J, Alok A, Tuli R (2013) RNA-Guided Genome Editing for Target Gene Mutations in Wheat. G3: Genes, Genomes. Genetics 3(12):2233–2238

    CAS  Google Scholar 

  • USDA (2018). Available at https://www.usda.gov/media/press-releases/2018/03/28/secretary-perdue-issues-usda-statement-plant-breeding-innovation

  • Wang H, Yang H, Shivalila CS, Dawlaty MM, Cheng AW, Zhang F, Jaenisch R (2013) One-step generation of mice carrying mutations in multiple genes by CRISPR/Cas-mediated genome engineering. Cell 153(4):910–918

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • Wang Y, Cheng X, Shan Q, Zhang Y, Liu J, Gao C, Qiu JL (2014) Simultaneous editing of three homoeoalleles in hexaploid bread wheat confers heritable resistance to powdery mildew. Nat Biotechnol 32:947–951

    Article  CAS  PubMed  Google Scholar 

  • Wang S, Zhang S, Wang W, Xiong X, Meng F, Cui X (2015) Efficient targeted mutagenesis in potato by the CRISPR/Cas9 system. Plant Cell Rep 34(9):1473–1476

    Article  CAS  PubMed  Google Scholar 

  • Wang F, Wang C, Liu P, Lei C, Hao W, Gao Y, Liu YG, Zhao K (2016) Enhanced rice blast resistance by CRISPR/Cas9-targeted mutagenesis of the ERF transcription factor gene OsERF922. PLoS One 11:e0154027

    Article  PubMed  PubMed Central  CAS  Google Scholar 

  • Weinthal D, Tovkach A, Zeevi V, Tzfira T (2010) Genome editing in plant cells by zinc finger nucleases. Trends Plant Sci 15(6):308–321

    Article  CAS  PubMed  Google Scholar 

  • Weinthal DM, Taylor RA, Tzfira T (2013) Non homologous end joining-mediated gene replacement in plant cells. Plant Physiol 162:390–400

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • Woo JW, Kim J, Kwon SI, Corvalán C, Cho SW, Kim H, Kim SG, Kim ST, Choe S, Kim JS (2015) DNA-free genome editing in plants with preassembled CRISPR-Cas9 ribonucleoproteins. Nat Biotechnol 33(11):1162–1164

    Article  CAS  PubMed  Google Scholar 

  • Xie K, Minkenberg B, Yang Y (2015) Boosting CRISPR/Cas9 multiplex editing capability with the endogenous tRNA-processing system. Proc Natl Acad Sci U S A 112(11):3570–3575

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • Xing HL, Dong L, Wang ZP, Zhang HY, Han CY, Liu B, Wang XC, Chen QJ (2014) A CRISPR/Cas9 toolkit for multiplex genome editing in plants. BMC Plant Biol 14:327

    Article  PubMed  PubMed Central  CAS  Google Scholar 

  • Xu R, Yang Y, Qin R, Hao L, Qiu C, Li L, Wei P, Yang J (2016) Rapid improvement of grain weight via highly efficient CRISPR/Cas9-mediated multiplex genome editing in rice. J Genet Genomics 43:529–532

    Article  PubMed  Google Scholar 

  • Zaidi SS, Mansoor S (2017) Viral vectors for plant genome engineering. Front Plant Sci 11(8):539

    Google Scholar 

  • Zhang Y, Zhang F, Li X, Baller JA, Qi Y, Starker CG, Bogdanove AJ, Voytas DF (2013) TALENs enable efficient plant genome engineering. Plant Physiol 161(1):20–27

    Article  CAS  PubMed  Google Scholar 

  • Zhang Z, Mao Y, Ha S, Liu W, Botella JR, Zhu JK (2015) A multiplex CRISPR/Cas9 platform for fast and efficient editing of multiple genes in Arabidopsis. Plant Cell Rep 35(7):1519–1533

    Article  PubMed  PubMed Central  CAS  Google Scholar 

  • Zhang Y, Liang Z, Zong Y, Wang Y, Liu J, Chen K et al (2016a) Efficient and transgene-free genome editing in wheat through transient expression of CRISPR/Cas9 DNA or RNA. Nat Commun 7:12617

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • Zhang B, Yang X, Yang C, Li M, Guo Y (2016b) Exploiting the CRISPR/Cas9 System for targeted genome mutagenesis in Petunia. Sci Rep 6:20315

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • Zhao Y, Zhang C, Liu W, Gao W, Liu C, Song G, Li WX et al (2016a) An alternative strategy for targeted gene replacement in plants using a dual-sgRNA/Cas9 design. Sci Rep 6:23890

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • Zhao C, Zhang Z, Xie S, Si T, Li Y, Zhu JK (2016b) Mutational evidence for the critical role of CBF genes in cold acclimation in Arabidopsis. Plant Physiol 171:2744–2759

    CAS  PubMed  PubMed Central  Google Scholar 

  • Zhou H, Liu B, Weeks DP, Spalding MH, Yang B (2014) Large chromosomal deletions heritable small genetic changes induced by CRISPR/Cas9 in rice. Nucleic Acids Res 42:10903–10914

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • Zhou J, Deng K, Cheng Y, Zhong Z, Tian L, Tang X, Tang A, Zheng X, Zhang T, Qi Y, Zhang Y (2017) CRISPR-Cas9 based genome editing reveals new insights into MicroRNA function and regulation in rice. Front Plant Sci 8:1598

    Article  PubMed  PubMed Central  Google Scholar 

  • Zong Y, Wang Y, Li C, Zhang R, Chen K, Ran Y, Qiu JL, Wang D, Gao C (2017) Precise base editing in rice, wheat and maize with a Cas9- cytidine deaminase fusion. Nat Biotechnol 35:438–440

    Article  CAS  PubMed  Google Scholar 

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Acknowledgements

CM and PYTS gratefully acknowledge the São Paulo Research Foundation (FAPESP) for the postdoctoral research grant (Proc. 2015/10855-9) and doctoral grant (Proc. No. 2017/16118-1), respectively. FHS is a recipient of a Research Productivity Scholarship from the National Council for Research and Development (CNPq #311745/2013-0).

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Authors and Affiliations

  1. Molecular Biology Laboratory, Department of Genetics and Evolution, Federal University of São Carlos, São Carlos, SP, Brazil

    Chakravarthi Mohan, Priscila Yumi Tanaka Shibao & Flavio Henrique Silva

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  1. Chakravarthi Mohan
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  2. Priscila Yumi Tanaka Shibao
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  3. Flavio Henrique Silva
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Correspondence to Flavio Henrique Silva .

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Editors and Affiliations

  1. Plant Genetic Engineering Laboratory, Department of Biotechnology, Bharathiar University, Coimbatore, Tamil Nadu, India

    Ramalingam Sathishkumar

  2. String Bio Private Ltd, IBAB Campus, Bangalore, India

    Sarma Rajeev Kumar

  3. Department of Biotechnology, PSG College of Technology, Coimbatore, Tamil Nadu, India

    Jagadeesan Hema

  4. Plant Genetic Engineering Laboratory, Department of Biotechnology, Bharathiar University, Coimbatore, Tamil Nadu, India

    Venkidasamy Baskar

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Mohan, C., Shibao, P.Y.T., Silva, F.H. (2019). Applications of Genome Engineering/Editing Tools in Plants. In: Sathishkumar, R., Kumar, S., Hema, J., Baskar, V. (eds) Advances in Plant Transgenics: Methods and Applications. Springer, Singapore. https://doi.org/10.1007/978-981-13-9624-3_7

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