CRISPR/Cas9 for plant genome editing: accomplishments, problems and prospects

Abstract

The increasing burden of the world population on agriculture requires the development of more robust crops. Dissecting the basic biology that underlies plant development and stress responses will inform the design of better crops. One powerful tool for studying plants at the molecular level is the RNA-programmed genome editing system composed of a clustered regularly interspaced short palindromic repeats (CRISPR)-encoded guide RNA and the nuclease Cas9. Here, some of the recent advances in CRISPR/Cas9 technology that have profound implications for improving the study of plant biology are described. These tools are also paving the way towards new horizons for biotechnologies and crop development.

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References

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

    Article  PubMed  PubMed Central  Google Scholar 

  2. Aouida M, Eid A, Ali Z, Cradick T, Lee C, Deshmukh H, Atef A, AbuSamra D, Gadhoum SZ, Merzaban J et al (2015) Efficient fdCas9 synthetic endonuclease with improved specificity for precise genome engineering. PLoS One 10:e0133373

    Article  PubMed  PubMed Central  Google Scholar 

  3. Aragão FJL, Faria JC (2009) First transgenic geminivirus-resistant plant in the field. Nat Biotechnol 27:1086–1088 (author reply 1088–1089)

    Article  PubMed  Google Scholar 

  4. Baltes NJ, Gil-Humanes J, Cermak T, Atkins PA, Voytas DF (2014) DNA replicons for plant genome engineering. Plant Cell 26:151–163

    CAS  Article  PubMed  PubMed Central  Google Scholar 

  5. Baltes NJ, Hummel AW, Konecna E, Cegan R (2015) Conferring resistance to geminiviruses with the CRISPR-Cas prokaryotic immune system. Nat Plants 1:15145

    CAS  Article  Google Scholar 

  6. Bortesi L, Fischer R (2014) The CRISPR/Cas9 system for plant genome editing and beyond. Biotechnol Adv 33:1–28

    Google Scholar 

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

    CAS  Article  PubMed  PubMed Central  Google Scholar 

  8. Cermak T, Baltes NJ, Čegan R, Zhang Y, Voytas DF (2015) High-frequency, precise modification of the tomato genome. Genome Biol 16:232

    Article  PubMed  PubMed Central  Google Scholar 

  9. Cho SW, Kim S, Kim Y, Kweon J, Kim HS, Bae S, Kim J-S (2014) Analysis of off-target effects of CRISPR/Cas-derived RNA-guided endonucleases and nickases. Genome Res 24:132–141

    CAS  Article  PubMed  PubMed Central  Google Scholar 

  10. 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

    CAS  Article  PubMed  PubMed Central  Google Scholar 

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

    CAS  Article  PubMed  PubMed Central  Google Scholar 

  12. Crosetto N, Mitra A, Silva MJ, Bienko M, Dojer N, Wang Q, Karaca E, Chiarle R, Skrzypczak M, Ginalski K et al (2013) Nucleotide-resolution DNA double-strand break mapping by next-generation sequencing. Nat Methods 10:361–365

    CAS  Article  PubMed  PubMed Central  Google Scholar 

  13. Engler C, Gruetzner R, Kandzia R, Marillonnet S (2009) Golden gate shuffling: a one-pot DNA shuffling method based on type IIs restriction enzymes. PLoS One 4:e5553

    Article  PubMed  PubMed Central  Google Scholar 

  14. Esvelt KM, Mali P, Braff JL, Moosburner M, Yaung SJ, Church GM (2013) Orthogonal Cas9 proteins for RNA-guided gene regulation and editing. Nat Methods 10:1116–1121

    CAS  Article  PubMed  PubMed Central  Google Scholar 

  15. Fauser F, Roth N, Pacher M, Ilg G (2012) In planta gene targeting. Proc Nat Acad Sci 109:7535–7540

    CAS  Article  PubMed  PubMed Central  Google Scholar 

  16. Fauser F, Schiml S, Puchta H (2014) Both CRISPR/Cas-based nucleases and nickases can be used efficiently for genome engineering in Arabidopsis thaliana. Plant J 79:348–359

    CAS  Article  PubMed  Google Scholar 

  17. Feng Z, Mao Y, Xu N, Zhang B, Wei P, Yang DL, Wang Z, Zhang Z, Zheng R, Yang L et al (2014) Multigeneration analysis reveals the inheritance, specificity, and patterns of CRISPR/Cas-induced gene modifications in Arabidopsis. Proc Natl Acad Sci 111:4632–4637

    CAS  Article  PubMed  PubMed Central  Google Scholar 

  18. Fu Y, Foden JA, Khayter C, Maeder ML, Reyon D, Joung JK, Sander JD (2013) High-frequency off-target mutagenesis induced by CRISPR-Cas nucleases in human cells. Nat Biotechnol 31:822–826

    CAS  Article  PubMed  PubMed Central  Google Scholar 

  19. Fu Y, Sander JD, Reyon D, Cascio VM, Joung JK (2014) Improving CRISPR-Cas nuclease specificity using truncated guide RNAs. Nat Biotechnol 32:279–284

    CAS  Article  PubMed  PubMed Central  Google Scholar 

  20. Fujita T, Fujii H (2013) Efficient isolation of specific genomic regions and identification of associated proteins by engineered DNA-binding molecule-mediated chromatin immunoprecipitation (eChIP) using CRISPR. Biochem Biophys Res Commun 439:1–25

    Article  Google Scholar 

  21. Gao Y, Zhao Y (2014) Self-processing of ribozyme-flanked RNAs into guide RNAs in vitroand in vivofor CRISPR-mediated genome editing. J Integr Plant Biol 56:343–349

    CAS  Article  PubMed  Google Scholar 

  22. Gelvin SB (2003) Agrobacterium-mediated plant transformation: the biology behind the “gene-jockeying” tool. Microbiol Mol Biol Rev 67:16–37

    CAS  Article  PubMed  PubMed Central  Google Scholar 

  23. Gibson DG, Young L, Chuang R-Y, Venter JC, Hutchison CA, Smith HO (2009) Enzymatic assembly of DNA molecules up to several hundred kilobases. Nat Methods 6:343–345

    CAS  Article  PubMed  Google Scholar 

  24. Gilbert LA, Horlbeck MA, Adamson B, Villalta JE, Chen Y, Whitehead EH, Guimaraes C, Panning B, Ploegh HL, Bassik MC et al (2014) Genome-scale CRISPR-mediated control of gene repression and activation. Cell 159:647–661

    CAS  Article  PubMed  PubMed Central  Google Scholar 

  25. Guilinger JP, Thompson DB, Liu DR (2014) Fusion of catalytically inactive Cas9 to FokI nuclease improves the specificity of genome modification. Nat Biotechnol 32:577–582

    CAS  Article  PubMed  PubMed Central  Google Scholar 

  26. Gutierrez C (1999) Geminivirus DNA replication. Cell Mol Life Sci 56:313–329

    CAS  Article  PubMed  Google Scholar 

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

    CAS  Article  PubMed  PubMed Central  Google Scholar 

  28. Hiratsu K, Matsui K, Koyama T, Ohme-Takagi M (2003) Dominant repression of target genes by chimeric repressors that include the EAR motif, a repression domain, in Arabidopsis. Plant J 34:733–739

    CAS  Article  PubMed  Google Scholar 

  29. Honda A, Hirose M, Sankai T, Yasmin L, Yuzawa K, Honsho K, Izu H, Iguchi A, Ikawa M, Ogura A (2015) Single-step generation of rabbits carrying a targeted allele of the tyrosinase gene using CRISPR/Cas9. Exp Anim 64:31–37

    CAS  Article  PubMed  Google Scholar 

  30. Hsu PD, Scott DA, Weinstein JA, Ran FA, Konermann S, Agarwala V, Li Y, Fine EJ, Wu X, Shalem O et al (2013) DNA targeting specificity of RNA-guided Cas9 nucleases. Nat Biotechnol 31:827–832

    CAS  Article  PubMed  PubMed Central  Google Scholar 

  31. Jayathilaka K, Sheridan SD, Bold TD, Bochenska K, Logan HL, Weichselbaum RR, Bishop DK, Connell PP (2008) A chemical compound that stimulates the human homologous recombination protein RAD51. Proc Natl Acad Sci USA 105:15848–15853

    CAS  Article  PubMed  PubMed Central  Google Scholar 

  32. Ji X, Zhang H, Zhang Y, Wang Y, Gao C (2015) Establishing a CRISPR-Cas-like immune system conferring DNA virus resistance in plants. Nat Plants 1:1–5

    Google Scholar 

  33. 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

    CAS  Article  PubMed  Google Scholar 

  34. Kleinstiver BP, Pattanayak V, Prew MS, Tsai SQ, Nguyen NT, Zheng Z, Keith Joung J (2016) High-fidelity CRISPR-Cas9 nucleases with no detectable genome-wide off-target effects. Nature 529:490–495

    CAS  Article  PubMed  Google Scholar 

  35. Konermann S, Brigham MD, Trevino AE, Joung J, Abudayyeh OO, Barcena C, Hsu PD, Habib N, Gootenberg JS, Nishimasu H et al (2015) Genome-scale transcriptional activation by an engineered CRISPR-Cas9 complex. Nature 517:583–588

    CAS  Article  PubMed  Google Scholar 

  36. Krouk G, Lingeman J, Colon AM, Coruzzi G, Shasha D (2013) Gene regulatory networks in plants: learning causality from time and perturbation. Genome Biol 14:123

    Article  PubMed  PubMed Central  Google Scholar 

  37. Li T, Huang S, Jiang WZ, Wright D, Spalding MH, Weeks DP, Yang B (2011) TAL nucleases (TALNs): hybrid proteins composed of TAL effectors and FokI DNA-cleavage domain. Nucleic Acids Res 39:359–372

    Article  PubMed  Google Scholar 

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

    CAS  Article  PubMed  PubMed Central  Google Scholar 

  39. Li J, Blue R, Zeitler B, Strange TL, Pearl JR, Huizinga DH, Evans S, Gregory PD, Urnov FD, Petolino JF (2013b) Activation domains for controlling plant gene expression using designed transcription factors. Plant Biotechnol J 11:671–680

    CAS  Article  PubMed  Google Scholar 

  40. Li Z, Liu Z-B, Xing A, Moon BP, Koellhoffer JP, Huang L, Ward RT, Clifton E, Falco SC, Cigan AM (2015) Cas9-Guide RNA directed genome editing in soybean. Plant Physiol 169:960–970

    Article  PubMed  PubMed Central  Google Scholar 

  41. Lowder LG, Zhang D, Baltes NJ, Paul JW, Tang X, Zheng X, Voytas DF, Hsieh T-F, Zhang Y, Qi Y (2015) A CRISPR/Cas9 toolbox for multiplexed plant genome editing and transcriptional regulation. Plant Physiol 169:971–985

    Article  PubMed  PubMed Central  Google Scholar 

  42. Ma H, Naseri A, Reyes-Gutierrez P, Wolfe SA, Zhang S, Pederson T (2015a) Multicolor CRISPR labeling of chromosomal loci in human cells. Proc Natl Acad Sci 112:3002–3007

    CAS  Article  PubMed  PubMed Central  Google Scholar 

  43. Ma X, Zhang Q, Zhu Q, Liu W, Chen Y, Qiu R, Wang B, Yang Z, Li H, Lin Y et al (2015b) A robust CRISPR/Cas9 system for convenient, high-efficiency multiplex genome editing in monocot and dicot plants. Mol Plant 8:1274–1284

    CAS  Article  PubMed  Google Scholar 

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

    CAS  Article  PubMed  PubMed Central  Google Scholar 

  45. Mali P, Aach J, Stranges PB, Esvelt KM, Moosburner M, Kosuri S, Yang L, Church GM (2013b) CAS9 transcriptional activators for target specificity screening and paired nickases for cooperative genome engineering. Nat Biotechnol 31:833–838

    CAS  Article  PubMed  PubMed Central  Google Scholar 

  46. Mansoor S, Zafar Y, Briddon RW (2006) Geminivirus disease complexes: the threat is spreading. Trends Plant Sci 11:209–212

    CAS  Article  PubMed  Google Scholar 

  47. Mao Y, Zhang Z, Feng Z, Wei P, Zhang H, Botella JR, Zhu JK (2015) Development of germ-line-specific CRISPR-Cas9 systems to improve the production of heritable gene modifications in Arabidopsis. Plant Biotechnol J 14:519–532

    Article  PubMed  Google Scholar 

  48. Maruyama T, Dougan SK, Truttmann MC, Bilate AM, Ingram JR, Ploegh HL (2015) Increasing the efficiency of precise genome editing with CRISPR-Cas9 by inhibition of nonhomologous end joining. Nat Biotechnol 33:538–542

    CAS  Article  PubMed  PubMed Central  Google Scholar 

  49. Mikami M, Toki S, Endo M (2016) Precision targeted mutagenesis via Cas9 paired nickases in rice. Plant Cell Physiol. doi:10.1093/pcp/pcw049 (epub ahead of print)

    PubMed  PubMed Central  Google Scholar 

  50. Miller JC, Tan S, Qiao G, Barlow KA, Wang J, Xia DF, Meng X, Paschon DE, Leung E, Hinkley SJ et al (2010) A TALE nuclease architecture for efficient genome editing. Nat Biotechnol 29:143–148

    Article  PubMed  Google Scholar 

  51. Moffat AS (1999) Geminiviruses emerge as serious crop threat. Science 286:1835

    CAS  Article  Google Scholar 

  52. 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

    CAS  Article  PubMed  Google Scholar 

  53. Nishizawa-Yokoi A, Cermak T, Hoshino T, Sugimoto K, Saika H, Mori A, Osakabe K, Hamada M, Katayose Y, Starker C et al (2015) A defect in DNA ligase 4 enhances the frequency of TALEN-mediated targeted mutagenesis in rice. Plant Physiol 170:653–666

    Article  PubMed  PubMed Central  Google Scholar 

  54. Nissim L, Perli SD, Fridkin A, Perez-Pinera P, Lu TK (2014) Multiplexed and programmable regulation of gene networks with an integrated RNA and CRISPR/Cas toolkit in human cells. Mol Cell 54:698–710

    CAS  Article  PubMed  PubMed Central  Google Scholar 

  55. Pattanayak V, Lin S, Guilinger JP, Ma E, Doudna JA, Liu DR (2013) High-throughput profiling of off-target DNA cleavage reveals RNA-programmed Cas9 nuclease specificity. Nat Biotechnol 31:839–843

    CAS  Article  PubMed  PubMed Central  Google Scholar 

  56. Pawlowski WP, Somers DA (1998) Transgenic DNA integrated into the oat genome is frequently interspersed by host DNA. Proc Natl Acad Sci 95:12106–12110

    CAS  Article  PubMed  PubMed Central  Google Scholar 

  57. Petolino JF, Davies JP (2013) Designed transcriptional regulators for trait development. Plant Sci 201–202:128–136

    Article  PubMed  Google Scholar 

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

    CAS  Article  PubMed  Google Scholar 

  59. Puchta H (1999) Double-strand break-induced recombination between ectopic homologous sequences in somatic plant cells. Genetics 152:1173–1181

    CAS  PubMed  PubMed Central  Google Scholar 

  60. Puchta H (2016) Using CRISPR/Cas in three dimensions: towards synthetic plant genomes, transcriptomes and epigenomes. Plant J. doi:10.1111/tpj.13100 (epub ahead of print)

    Google Scholar 

  61. Puchta H, Dujon B, Hohn B (1996) Two different but related mechanisms are used in plants for the repair of genomic double-strand breaks by homologous recombination. Proc Natl Acad Sci 93:5055–5060

    CAS  Article  PubMed  PubMed Central  Google Scholar 

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

    CAS  Article  PubMed  PubMed Central  Google Scholar 

  63. Qi Y, Zhang Y, Zhang F, Baller JA, Cleland SC, Ryu Y, Starker CG, Voytas DF (2013b) Increasing frequencies of site-specific mutagenesis and gene targeting in Arabidopsis by manipulating DNA repair pathways. Genome Res 23:547–554

    CAS  Article  PubMed  PubMed Central  Google Scholar 

  64. Ran FA, Hsu PD, Lin C-Y, Gootenberg JS, Konermann S, Trevino AE, Scott DA, Inoue A, Matoba S, Zhang Y et al (2013) Double nicking by RNA-guided CRISPR Cas9 for enhanced genome editing specificity. Cell 154:1380–1389

    CAS  Article  PubMed  PubMed Central  Google Scholar 

  65. Sauer NJ, Narváez-Vásquez J, Mozoruk J, Miller RB, Warburg ZJ, Woodward MJ, Mihiret YA, Lincoln TA, Segami RE, Sanders SL et al (2016) Oligonucleotide-mediated genome editing provides precision and function to engineered nucleases and antibiotics in plants. Plant Physiol 170:1917–1928

    Article  PubMed  PubMed Central  Google Scholar 

  66. 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

    CAS  Article  PubMed  Google Scholar 

  67. Shaked H, Melamed-Bessudo C, Levy AA (2005) High-frequency gene targeting in Arabidopsis plants expressing the yeast RAD54 gene. Proc Natl Acad Sci 102:12265–12269

    CAS  Article  PubMed  PubMed Central  Google Scholar 

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

    CAS  Article  PubMed  Google Scholar 

  69. Slaymaker IM, Gao L, Zetsche B, Scott DA, Yan WX, Zhang F (2016) Rationally engineered Cas9 nucleases with improved specificity. Science 351:84–88

    CAS  Article  PubMed  Google Scholar 

  70. Song J, Yang D, Xu J, Zhu T, Chen YE, Zhang J (2016) RS-1 enhances CRISPR/Cas9- and TALEN-mediated knock-in efficiency. Nat Commun 7:10548

    CAS  Article  PubMed  PubMed Central  Google Scholar 

  71. Steinert J, Schiml S, Fauser F, Puchta H (2015) Highly efficient heritable plant genome engineering using Cas9 orthologues from Streptococcus thermophilus and Staphylococcus aureus. Plant J 84:1295–1305

    CAS  Article  PubMed  Google Scholar 

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

    CAS  Article  PubMed  Google Scholar 

  73. 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  Google Scholar 

  74. Tiwari SB, Belachew A, Ma SF, Young M, Ade J, Shen Y, Marion CM, Holtan HE, Bailey A, Stone JK et al (2012) The EDLL motif: a potent plant transcriptional activation domain from AP2/ERF transcription factors. Plant J 70:855–865

    CAS  Article  PubMed  Google Scholar 

  75. Tsai SQ, Wyvekens N, Khayter C, Foden JA, Thapar V, Reyon D, Goodwin MJ, Aryee MJ, Joung JK (2014) Dimeric CRISPR RNA-guided FokI nucleases for highly specific genome editing. Nat Biotechnol 32:569–576

    CAS  Article  PubMed  PubMed Central  Google Scholar 

  76. Tsai SQ, Zheng Z, Nguyen NT, Liebers M, Topkar VV, Thapar V, Wyvekens N, Khayter C, Iafrate AJ, Le LP et al (2015) GUIDE-seq enables genome-wide profiling of off-target cleavage by CRISPR-Cas nucleases. Nat Biotechnol 33:187–197

    CAS  Article  PubMed  Google Scholar 

  77. Urnov FD, Rebar EJ, Holmes MC, Zhang HS, Gregory PD (2010) Genome editing with engineered zinc finger nucleases. Nat Rev Genet 11:636–646

    CAS  Article  PubMed  Google Scholar 

  78. Wang C, Shen L, Fu Y, Yan C, Wang K (2015a) A simple CRISPR/Cas9 system for multiplex genome editing in rice. J Genet Genomics 42:703–706

    Article  PubMed  Google Scholar 

  79. Wang Z-P, Xing H-L, Dong L, Zhang H-Y, Han C-Y, Wang X-C, Chen Q-J (2015b) Egg cell-specific promoter-controlled CRISPR/Cas9 efficiently generates homozygous mutants for multiple target genes in Arabidopsis in a single generation. Genome Biol 16:1–12

    Article  Google Scholar 

  80. Wiedenheft B, Sternberg SH, Doudna JA (2012) RNA-guided genetic silencing systems in bacteria and archaea. Nature 482:331–338

    CAS  Article  PubMed  Google Scholar 

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

    CAS  Article  PubMed  Google Scholar 

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

    CAS  Article  PubMed  PubMed Central  Google Scholar 

  83. Xing H-L, Dong L, Wang Z-P, Zhang H-Y, Han C-Y, Liu B, Wang X-C, Chen Q-J (2014) A CRISPR/Cas9 toolkit for multiplex genome editing in plants. BMC Plant Biol 14:327

    Article  PubMed  PubMed Central  Google Scholar 

  84. Yang C-F, Chen K-C, Cheng Y-H, Raja JAJ, Huang Y-L, Chien W-C, Yeh S-D (2014) Generation of marker-free transgenic plants concurrently resistant to a DNA geminivirus and a RNA tospovirus. Sci Rep 4:5717

    PubMed  PubMed Central  Google Scholar 

  85. Yin K, Han T, Liu G, Chen T, Wang Y, Yu AYL, Liu Y (2015) A geminivirus-based guide RNA delivery system for CRISPR/Cas9 mediated plant genome editing. Sci Rep 5:14926

    CAS  Article  PubMed  PubMed Central  Google Scholar 

  86. Yu C, Liu Y, Ma T, Liu K, Xu S, Zhang Y, Liu H, La Russa M, Xie M, Ding S et al (2015) Small molecules enhance CRISPR genome editing in pluripotent stem cells. Cell Stem Cell 16:142–147

    CAS  Article  PubMed  PubMed Central  Google Scholar 

  87. Zalatan JG, Lee ME, Almeida R, Gilbert LA, Whitehead EH, La Russa M, Tsai JC, Weissman JS, Dueber JE, Qi LS et al (2015) Engineering complex synthetic transcriptional programs with CRISPR RNA scaffolds. Cell 160:339–350

    CAS  Article  PubMed  Google Scholar 

  88. Zetsche B, Volz SE, Zhang F (2015) A split-Cas9 architecture for inducible genome editing and transcription modulation. Nat Biotechnol 33:139–142

    CAS  Article  PubMed  Google Scholar 

  89. Zhang H, Zhang J, Wei P, Zhang B, Gou F, Feng Z, Mao Y, Yang L, Zhang H, Xu N et al (2014) The CRISPR/Cas9 system produces specific and homozygous targeted gene editing in rice in one generation. Plant Biotechnol J 12:797–807

    CAS  Article  PubMed  Google Scholar 

  90. Zhang Y, Rajan R, Seifert HS, Mondragón A, Sontheimer EJ (2015a) DNase H activity of Neisseria meningitidis Cas9. Mol Cell 60:242–255

    CAS  Article  PubMed  Google Scholar 

  91. Zhang Z, Mao Y, Ha S, Liu W, Botella JR, Zhu JK (2015b) A multiplex CRISPR/Cas9 platform for fast and efficient editing of multiple genes in Arabidopsis. Plant Cell Rep. doi:10.1007/s00299-015-1900-z (epub ahead of print)

    Google Scholar 

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Acknowledgments

Due to limited space, we could not cite the entirety of the current literature that may also be important. We thank A. Malzahn for critical reading of the manuscript and thoughtful advice on its composition and content. This work is supported by startup funds from East Carolina University and a Collaborative Funding Grant (2016-CFG-8003) from North Carolina Biotechnology Center and Syngenta to YQ.

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Correspondence to Yiping Qi.

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Communicated by T. Cardi.

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Paul, J.W., Qi, Y. CRISPR/Cas9 for plant genome editing: accomplishments, problems and prospects. Plant Cell Rep 35, 1417–1427 (2016). https://doi.org/10.1007/s00299-016-1985-z

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Keywords

  • Genome editing
  • Plant biotechnology
  • Transcriptional regulation
  • Gene targeting
  • Synthetic biology
  • CRISPR
  • Cas9