Korean Journal of Agricultural Science (농업과학연구)

Institute of Agricultural Science, CNU (충남대학교 농업과학연구소)
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Overview of CRISPR/Cas9: a chronicle of the CRISPR system and application to ornamental crops

  • Lee, Hyunbae (Department of Horticulture, Chungnam National University) ;
  • Subburaj, Saminathan (Department of Horticulture, Chungnam National University) ;
  • Tu, Luhua (Department of Horticulture, Chungnam National University) ;
  • Lee, Ka-Yeon (Department of Horticulture, Chungnam National University) ;
  • Park, Gwangsu (Department of Horticulture, Chungnam National University) ;
  • Lee, Geung-Joo (Department of Horticulture, Chungnam National University)
  • Received : 2020.09.25
  • Accepted : 2020.10.20
  • Published : 2020.12.01
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Abstract

Since its first demonstration as a practical genome editing tool in the early 2010s, the use of clustered regularly interspaced short palindromic repeat (CRISPR) along with the endonuclease Cas9 (CRISPR/Cas9) has become an essential choice for generating targeted mutations. Due to its relative simplicity and cost-effectiveness compared to other molecular scissors, i.e., zinc finger nuclease (ZFN) and transcription activator-like effector nuclease (TALEN), the CRISPR/Cas9 system has been shown to have a massive influence on genetic studies regardless of the biological kingdom. Although the system is in the process of being established, numerous protocols have already been released for the system and there have been various topics of CRISPR related papers published each year in ever-increasing manner. Here, we will briefly introduce CRISPR/Cas9 system and discuss the variants of the CRISPR system. Also, their applications to crop improvement will be dealt with mainly ornamental crops among horticultural crops other than Arabidopsis as a model plant. Finally, some issues on the barriers restraining the use of CRISPR system on floricultural crops, the prospect of CRISPR system as a DNA-free genome editing tool with efficient facilitators and finally, the future perspectives on the CRISPR system will be described.

Keywords

Acknowledgement

This work was supported by a grant from the Plant Molecular Breeding Center of the Next Generation BioGreen21 Program (No. PJ01319303) and the New Breeding Technologies Development Program (No. PJ01485802), Rural Development Administration, Republic of Korea.

References

  1. Adkins JA, Werner DJ, Ranney TG. 2003. Prospects for genetically modified ornamental plants. Proceedings of The Southern Nursery Association 48:502-504.
  2. Andersson M, Turesson H, Nicolia A, Falt AS, Samuelsson M, Hofvander P. 2017. Efficient targeted multiallelic mutagenesis in tetraploid potato (Solanum tuberosum) by transient CRISPR-Cas9 expression in protoplasts. Plant Cell Reports 36:117-128. https://doi.org/10.1007/s00299-016-2062-3
  3. Anzalone AV, Randolph PB, Davis JR, Sousa AA, Koblan LW, Levy JM, Chen PJ, Wilson C, Newby GA, Raguram A, Liu DR. 2019. Search-and-replace genome editing without double-strand breaks or donor DNA. Nature 576:149-157. https://doi.org/10.1038/s41586-019-1711-4
  4. Babu M, Beloglazova N, Flick R, Graham C, Skarina T, Nocek B, Gagarinova A, Pogoutse O, Brown G, Binkowski A, Phanse S. 2011. A dual function of the CRISPR-Cas system in bacterial antivirus immunity and DNA repair. Molecular Microbiology 79:484-502. https://doi.org/10.1111/j.1365-2958.2010.07465.x
  5. Barrangou R, Fremaux C, Deveau H, Richards M, Boyaval P, Moineau S, Romero DA, Horvath P. 2007. CRISPR provides acquired resistance against viruses in prokaryotes. Science 315:1709-1712. https://doi.org/10.1126/science.1138140
  6. Behe B, Nelson R, Barton S, Hall C, Safley CD, Turner S. 1999. Consumer preferences for geranium flower color, leaf variegation, and price. HortScience 34:740-742. https://doi.org/10.21273/HORTSCI.34.4.740
  7. Belhaj K, Chaparro-Garcia A, Kamoun S, Patron NJ, Nekrasov V. 2015. Editing plant genomes with CRISPR/Cas9. Current Opinion in Biotechnology 32:76-84. https://doi.org/10.1016/j.copbio.2014.11.007
  8. Bortesi L, Fischer R. 2015. The CRISPR/Cas9 system for plant genome editing and beyond. Biotechnology Advances 33:41-52. https://doi.org/10.1016/j.biotechadv.2014.12.006
  9. Braatz J, Harloff HJ, Mascher M, Stein N, Himmelbach A, Jung C. 2017. CRISPR-Cas9 targeted mutagenesis leads to simultaneous modification of different homoeologous gene copies in polyploid oilseed rape (Brassica napus). Plant Physiology 174:935-942. https://doi.org/10.1104/pp.17.00426
  10. Brouns SJ, Jore MM, Lundgren M, Westra ER, Slijkhuis RJ, Snijders AP, Dickman MJ, Makarova KS, Koonin EV, Van Der Oost J. 2008. Small CRISPR RNAs guide antiviral defense in prokaryotes. Science 321:960-964. https://doi.org/10.1126/science.1159689
  11. Burg SP, Burg EA. 1965. Ethylene action and the ripening of fruits: Ethylene influences the growth and development of plants and is the hormone which initiates fruit ripening. Science 148:1190-1196. https://doi.org/10.1126/science.148.3674.1190
  12. Chen K, Liu H, Lou Q, Liu Y. 2017. Ectopic expression of the grape hyacinth (Muscari armeniacum) R2R3-MYB transcription factor gene, MaAN2, induces anthocyanin accumulation in tobacco. Frontiers in Plant Science 8:965. https://doi.org/10.3389/fpls.2017.00965
  13. Chib S, Thangaraj A, Kaul S, Dhar MK, Kaul T. 2020. Development of a system for efficient callus production, somatic embryogenesis and gene editing using CRISPR/Cas9 in Saffron (Crocus sativus L.). Plant Methods 16:1-10. https://doi.org/10.1186/s13007-019-0534-5
  14. Chylinski K, Anaïs LR, Charpentier E. 2013. The tracrRNA and Cas9 families of type II CRISPR-Cas immunity systems. RNA Biology 10:726-737. https://doi.org/10.4161/rna.24321
  15. Clark DG, Loucas H, Shibuya K, Underwood B, Barry K, Jandrew J. 2003. Biotechnology of floriculture crops-scientific questions and real world answers. In Plant Biotechnology 2002 and Beyond. pp. 337-342. Springer, Dordrecht, Netherlands.
  16. Clegg MT, Durbin ML. 2000. Flower color variation: A model for the experimental study of evolution. Proceedings of the National Academy of Sciences 97:7016-7023. https://doi.org/10.1073/pnas.97.13.7016
  17. Deltcheva E, Chylinski K, Sharma CM, Gonzales K, Chao Y, Pirzada ZA, Eckert MR, Vogel J, Charpentier E. 2011. CRISPR RNA maturation by trans-encoded small RNA and host factor RNase III. Nature 471:602-607. https://doi.org/10.1038/nature09886
  18. Friedland AE, Tzur YB, Esvelt KM, Colaiacovo MP, Church GM, Calarco JA. 2013. Heritable genome editing in C. elegans via a CRISPR-Cas9 system. Nature Methods 10:741-743. https://doi.org/10.1038/nmeth.2532
  19. Fromm M, Callis J, Taylor LP, Walbot V. 1987. [21] Electroporation of DNA and RNA into plant protoplasts. In Methods in Enzymology. Vol. 153. pp. 351-366. Academic Press, Cambridge, USA. https://doi.org/10.1016/0076-6879(87)53064-6
  20. Fromm M, Taylor LP, Walbot V. 1985. Expression of genes transferred into monocot and dicot plant cells by electroporation. Proceedings of The National Academy of Sciences 82:5824-5828. https://doi.org/10.1073/pnas.82.17.5824
  21. Fujita T, Fujii H. 2013. Efficient isolation of specific genomic regions and identification of associated proteins by engineered DNA-binding molecule-mediated chromatin immunoprecipitation (enChIP) using CRISPR. Biochemical and Biophysical Research Communications 439:132-136. https://doi.org/10.1016/j.bbrc.2013.08.013
  22. Gaudelli NM, Komor AC, Rees HA, Packer MS, Badran AH, Bryson DI, Liu DR. 2017. Programmable base editing of A• T to G• C in genomic DNA without DNA cleavage. Nature 551:464-471. https://doi.org/10.1038/nature24644
  23. Gilbert LA, Larson MH, Morsut L, Liu Z, Brar GA, Torres SE, Stern-Ginossar N, Brandman O, Whitehead EH, Doudna JA, Lim WA. 2013. CRISPR-mediated modular RNA-guided regulation of transcription in eukaryotes. Cell 154:442-451. https://doi.org/10.1016/j.cell.2013.06.044
  24. Gilles AF, Schinko JB, Averof M. 2015. Efficient CRISPR-mediated gene targeting and transgene replacement in the beetle Tribolium castaneum. Development 142:2832-2839. https://doi.org/10.1242/dev.125054
  25. Guilinger JP, Thompson DB, Liu DR. 2014. Fusion of catalytically inactive Cas9 to FokI nuclease improves the specificity of genome modification. Nature Biotechnology 32:577. https://doi.org/10.1038/nbt.2909
  26. Hale C, Kleppe K, Tern RM, Terns MP. 2008. Prokaryotic silencing (psi) RNAs in Pyrococcus furiosus. Rna 14:2572-2579. https://doi.org/10.1261/rna.1246808
  27. Hale CR, Zhao P, Olson S, Duff MO, Graveley BR, Wells L, Terns RM, Terns MP. 2009. RNA-guided RNA cleavage by a CRISPR RNA-Cas protein complex. Cell 139:945-956. https://doi.org/10.1016/j.cell.2009.07.040
  28. Hara S, Tamano M, Yamashita S, Kato T, Saito T, Sakuma T, Yamamoto T, Inui M, Takada S. 2015. Generation of mutant mice via the CRISPR/Cas9 system using FokI-dCas9. Scientific Reports 5:11221. https://doi.org/10.1038/srep11221
  29. ISAAA (International Service for the Acquisition of Agri-biotech Applications). 2020. South Korea's first genome edited petunia approved in the U.S. Accessed in www.isaaa.org on 16 October 2020.
  30. Jansen R, Embden JDV, Gaastra W, Schouls LM. 2002. Identification of genes that are associated with DNA repeats in prokaryotes. Molecular Microbiology 43:1565-1575. https://doi.org/10.1046/j.1365-2958.2002.02839.x
  31. 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. https://doi.org/10.1126/science.1225829
  32. Junker B, Zimny J, Luhrs R, Lorz H. 1987. Transient expression of chimaeric genes in dividing and non-dividing cereal protoplasts after PEG-induced DNA uptake. Plant Cell Reports 6:329-332. https://doi.org/10.1007/BF00269552
  33. Karkute SG, Singh AK, Gupta OP, Singh PM, Singh B. 2017. CRISPR/Cas9 mediated genome engineering for improvement of horticultural crops. Frontiers in Plant Science 8:1635. https://doi.org/10.3389/fpls.2017.01635
  34. Kim DS, Kim JE, Hur JK, Been KW, Yoon SH, Kim JS. 2016. Genome-wide analysis reveals specificities of Cpf1 endonucleases in human cells. Nature Biotechnology 34:863-868. https://doi.org/10.1038/nbt.3609
  35. Kim R, Song JE, Ga EJ, Min MK, Lee JY, Lim SH, Kim BG. 2019. Current status of CRISPR/Cas9 base editor technologies and their applications in crop precision breeding. Korean Journal of Agricultural Science 46:885-895. [in Korean]
  36. Kishi-Kaboshi M, Aida R, Sasaki K. 2017. Generation of gene-edited Chrysanthemum morifolium using multicopy transgenes as targets and markers. Plant and Cell Physiology 58:216-226.
  37. Kishi-Kaboshi M, Aida R, Sasaki K. 2018. Genome engineering in ornamental plants: Current status and future prospects. Plant Physiology and Biochemistry 131:47-52. https://doi.org/10.1016/j.plaphy.2018.03.015
  38. Kleinstiver BP, Tsai SQ, Prew MS, Nguyen NT, Welch MM, Lopez JM, McCaw ZR, Aryee MJ, Joung JK. 2016. Genomewide specificity profiles of CRISPR-Cas Cpf1 nucleases in human cells. BioRxiv 2016:057802.
  39. 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 533:420-424. https://doi.org/10.1038/nature17946
  40. Kui L, Chen H, Zhang W, He S, Xiong Z, Zhang Y, Yan L, Zhong C, He F, Chen J, Zeng P. 2017. Building a genetic manipulation tool box for orchid biology: Identification of constitutive promoters and application of CRISPR/Cas9 in the orchid, Dendrobium officinale. Frontiers in Plant Science 7:2036.
  41. Landrum MJ, Lee JM, Benson M, Brow G, Chao C, Chitipiralla S, Gu B, Hart J, Hoffman D, Hoover J, Jang W. 2016. ClinVar: Public archive of interpretations of clinically relevant variants. Nucleic Acids Research 44:862-868.
  42. Landrum MJ, Lee JM, Riley GR, Jang W, Rubinstein WS, Church DM, Maglott DR. 2014. ClinVar: Public archive of relationships among sequence variation and human phenotype. Nucleic Acids Research 42:980-985.
  43. Larson MH, Gilbert LA, Wang X, Lim WA, Weissman JS, Qi LS. 2013. CRISPR interference (CRISPRi) for sequencespecific control of gene expression. Nature Protocols 8:2180-2196. https://doi.org/10.1038/nprot.2013.132
  44. Lee M, Kim SW. 2005. Polyethylene glycol-conjugated copolymers for plasmid DNA delivery. Pharmaceutical Research 22:1-10. https://doi.org/10.1007/s11095-004-9003-5
  45. Liang F, Han M, Romanienko PJ, Jasin M. 1998. Homology-directed repair is a major double-strand break repair pathway in mammalian cells. Proceedings of The National Academy of Sciences 95:5172-5177. https://doi.org/10.1073/pnas.95.9.5172
  46. Lieber MR. 2010. The mechanism of double-strand DNA break repair by the non-homologous DNA end-joining pathway. Annual Review of Biochemistry 79:181-211. https://doi.org/10.1146/annurev.biochem.052308.093131
  47. Li H, Beckman KA, Pessino V, Huang B, Weissman JS, Leonetti MD. 2019. Design and specificity of long ssDNA donors for CRISPR-based knock-in. BioRxiv 2019:178905.
  48. Li H, Li J, Chen J, Yan L, Xia L. 2020. Precise modifications of both exogenous and endogenous genes in rice by prime editing. Molecular Plant 13:671-674. https://doi.org/10.1016/j.molp.2020.03.011
  49. 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. Nature Plants 2:1-6.
  50. Lin Q, Zong Y, Xue C, Wang S, Jin S, Zhu Z, Wang Y, Anzalone AV, Raguram A, Doman JL, Liu DR. 2020. Prime genome editing in rice and wheat. Nature Biotechnology 38:582-585. https://doi.org/10.1038/s41587-020-0455-x
  51. Liu F, Hu L, Cai Y, Lin H, Liu J, Yu Y. 2016. Molecular characterization and functional analysis of two petunia PhEILs. Frontiers in Plant Science 7:1606.
  52. Maas C, Werr W. 1989. Mechanism and optimized conditions for PEG mediated DNA transfection into plant protoplasts. Plant Cell Reports 8:148-151. https://doi.org/10.1007/BF00716828
  53. Maeder ML, Linder SJ, Cascio VM, Fu Y, Ho QH, Joung JK. 2013. CRISPR RNA-guided activation of endogenous human genes. Nature Methods 10:977-979. https://doi.org/10.1038/nmeth.2598
  54. Manzoor A, Ahmad T, Bashir MA, Hafiz IA, Silvestri C. 2019. Studies on colchicine induced chromosome doubling for enhancement of quality traits in ornamental plants. Plants 8:194. https://doi.org/10.3390/plants8070194
  55. Marraffini LA, Sontheimer EJ. 2008. CRISPR interference limits horizontal gene transfer in staphylococci by targeting DNA. Science 322:1843-1845. https://doi.org/10.1126/science.1165771
  56. Marzec M, Braszewska-Zalewska A, Hensel G. 2020. Prime editing: A new way for genome editing. Trends in Cell Biology 30:257-259. https://doi.org/10.1016/j.tcb.2020.01.004
  57. Mojica FJ, Diez-Villasenor C, Garcia-Martinez J, Almendros C. 2009. Short motif sequences determine the targets of the prokaryotic CRISPR defence system. Microbiology 155:733-740. https://doi.org/10.1099/mic.0.023960-0
  58. Mojica FJ, Garcia-Martinez J, Soria E. 2005. Intervening sequences of regularly spaced prokaryotic repeats derive from foreign genetic elements. Journal of Molecular Evolution 60:174-182. https://doi.org/10.1007/s00239-004-0046-3
  59. Neuman E. 1982. Gene transfer into mouse lyoma cells by electroporation in high electric field. The European Molecular Biology Organization Journal 1:841-845. https://doi.org/10.1002/j.1460-2075.1982.tb01257.x
  60. Nihongaki Y, Yamamoto S, Kawano F, Suzuki H, Sato M. 2015. CRISPR-Cas9-based photoactivatable transcription system. Chemistry & Biology 22:169-174. https://doi.org/10.1016/j.chembiol.2014.12.011
  61. Nishida K, Arazoe T, Yachie N, Banno S, Kakimoto M, Tabata M, Mochizuki M, Miyabe A, Araki M, Hara KY, Shimatani Z. 2016. Targeted nucleotide editing using hybrid prokaryotic and vertebrate adaptive immune systems. Science 353:aaf8729. https://doi.org/10.1126/science.aaf8729
  62. Nishihara M, Higuchi A, Watanabe A, Tasaki K. 2018. Application of the CRISPR/Cas9 system for modification of flower color in Torenia fournieri. BMC Plant Biology 18:1-9. https://doi.org/10.1186/s12870-017-1213-1
  63. Nishihara M, Hikage T, Yamada E, Nakatsuka T. 2011. A single-base substitution suppresses flower color mutation caused by a novel miniature inverted-repeat transposable element in gentian. Molecular Genetics and Genomics 286:371-382. https://doi.org/10.1007/s00438-011-0652-x
  64. Noman A, Aqeel M, Deng J, Khalid N, Sanaullah T, Shuilin H. 2017. Biotechnological advancements for improving floral attributes in ornamental plants. Frontiers in Plant Science 8:530. https://doi.org/10.3389/fpls.2017.00530
  65. Osakabe Y, Liang Z, Ren C, Nishitani C, Osakabe K, Wada M, Komori S, Malnoy M, Velasco R, Poli M, Jung MH. 2018. CRISPR-Cas9-mediated genome editing in apple and grapevine. Nature Protocols 13:2844-2863. https://doi.org/10.1038/s41596-018-0067-9
  66. 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 Biotechnology Journal 13:578-589. https://doi.org/10.1111/pbi.12284
  67. Picton S, Barton SL, Bouzayen M, Hamilton AJ, Grierson D. 1993. Altered fruit ripening and leaf senescence in tomatoes expressing an antisense ethylene-forming enzyme transgene. The Plant Journal 3:469-481. https://doi.org/10.1111/j.1365-313x.1993.tb00167.x
  68. Potter H, Heller R. 2018. Transfection by electroporation. Current Protocols in Molecular Biology 121:9-3.
  69. Pourcel C, Salvignol G, Vergnaud G. 2005. CRISPR elements in Yersinia pestis acquire new repeats by preferential uptake of bacteriophage DNA and provide additional tools for evolutionary studies. Microbiology 151:653-663. https://doi.org/10.1099/mic.0.27437-0
  70. Qi LS, Larson MH, Gilbert LA, Doudna JA, Weissman JS, Arkin AP, Lim WA. 2013. Repurposing CRISPR as an RNAguided platform for sequence-specific control of gene expression. Cell 152:1173-1183. https://doi.org/10.1016/j.cell.2013.02.022
  71. Ran FA, Hsu PD, Wright J, Agarwala V, Scott DA, Zhang F. 2013. Genome engineering using the CRISPR-Cas9 system. Nature Protocols 8:2281-2308. https://doi.org/10.1038/nprot.2013.143
  72. Rees HA, Liu DR. 2018. Base editing: Precision chemistry on the genome and transcriptome of living cells. Nature Reviews Genetics 19:770-788. https://doi.org/10.1038/s41576-018-0059-1
  73. Rihn AL, Yue C, Hall C, Behe BK. 2014. Consumer preferences for longevity information and guarantees on cut flower arrangements. HortScience 49:769-778. https://doi.org/10.21273/hortsci.49.6.769
  74. Roth TL, Puig-Saus C, Yu R, Shifrut E, Carnevale J, Li PJ, Hiatt J, Saco J, Krystofinski P, Li H, Tobin V. 2018. Reprogramming human T cell function and specificity with non-viral genome targeting. Nature 559:405-409. https://doi.org/10.1038/s41586-018-0326-5
  75. Saint-Oyant LH, Ruttink T, Hamama L, Kirov I, Lakhwani D, Zhou NN, Bourke PM, Daccord N, Leus L, Schulz D, Van de Geest H. 2018. A high-quality genome sequence of Rosa chinensis to elucidate ornamental traits. Nature Plants 4:473-484. https://doi.org/10.1038/s41477-018-0166-1
  76. Schaeffer SM, Nakata PA. 2015. CRISPR/Cas9-mediated genome editing and gene replacement in plants: Transitioning from lab to field. Plant Science 240:130-142. https://doi.org/10.1016/j.plantsci.2015.09.011
  77. Schoen DJ, Schultz ST. 2019. Somatic mutation and evolution in plants. Annual Review of Ecology, Evolution and Systematics 50:49-73. https://doi.org/10.1146/annurev-ecolsys-110218-024955
  78. Shibuya K, Barry KG, Ciardi JA, Loucas HM, Underwood BA, Nourizadeh S, Ecker JR, Klee HJ, Clark DG. 2004. The central role of PhEIN2 in ethylene responses throughout plant development in petunia. Plant Physiology 136:2900-2912. https://doi.org/10.1104/pp.104.046979
  79. Shibuya K, Watanabe K, Ono M. 2018. CRISPR/Cas9-mediated mutagenesis of the EPHEMERAL1 locus that regulates petal senescence in Japanese morning glory. Plant Physiology and Biochemistry 131:53-57. https://doi.org/10.1016/j.plaphy.2018.04.036
  80. Smith I, Greenside PG, Natoli T, Lahr DL, Wadden D, Tirosh I, Narayan R, Root DE, Golub TR, Subramanian A, Doench JG. 2017. Evaluation of RNAi and CRISPR technologies by large-scale gene expression profiling in the Connectivity Map. PLoS Biology 15:e2003213. https://doi.org/10.1371/journal.pbio.2003213
  81. Solano R, Stepanova A, Chao Q, Ecker JR. 1998. Nuclear events in ethylene signaling: A transcriptional cascade mediated by ETHYLENE-INSENSITIVE3 and ETHYLENE-RESPONSE-FACTOR1. Genes & Development 12:3703-3714. https://doi.org/10.1101/gad.12.23.3703
  82. Sparrow AH, Sparrow RC. 1976. Spontaneous somatic mutation frequencies for flower color in several Tradescantia species and hybrids. Environmental and Experimental Botany 16:23-43. https://doi.org/10.1016/0098-8472(76)90030-7
  83. Subburaj S, Chung SJ, Lee CG, Ryu SM, Kim DH, Kim JS, Bae SS, Lee GJ. 2016. Site-directed mutagenesis in Petunia × hybrida protoplast system using direct delivery of purified recombinant Cas9 ribonucleoproteins. Plant Cell Reports 35:1535-1544. https://doi.org/10.1007/s00299-016-1937-7
  84. Sun L, Kao TH. 2018. CRISPR/Cas9-mediated knockout of PiSSK1 reveals essential role of S-locus F-box proteincontaining SCF complexes in recognition of non-self S-RNases during cross-compatible pollination in selfincompatible Petunia inflata. Plant Reproduction 31:129-143. https://doi.org/10.1007/s00497-017-0314-1
  85. Tanaka A, Shikazono N, Hase Y. 2010. Studies on biological effects of ion beams on lethality, molecular nature of mutation, mutation rate, and spectrum of mutation phenotype for mutation breeding in higher plants. Journal of Radiation Research 51:223-233. https://doi.org/10.1269/jrr.09143
  86. Tieleman DP. 2004. The molecular basis of electroporation. BMC Biochemistry 5:10. https://doi.org/10.1186/1471-2091-5-10
  87. Tieman DM, Ciardi JA, Taylor MG, Klee HJ. 2001. Members of the tomato LeEIL (EIN3-like) gene family are functionally redundant and regulate ethylene responses throughout plant development. The Plant Journal 26:47-58. https://doi.org/10.1046/j.1365-313x.2001.01006.x
  88. Tsong TY. 1989. Electroporation of cell membranes. In Electroporation and Electrofusion in Cell Biology. pp. 149-163. Springer, Boston, MA, USA.
  89. Vogel P, Moschref M, Li Q, Merkle T, Selvasaravanan KD, Li JB, Stafforst T. 2018. Efficient and precise editing of endogenous transcripts with SNAP-tagged ADARs. Nature Methods 15:535-538. https://doi.org/10.1038/s41592-018-0017-z
  90. Wagner E, Cotten M, Foisner R, Birnstiel ML. 1991. Transferrin-polycation-DNA complexes: The effect of polycations on the structure of the complex and DNA delivery to cells. Proceedings of the National Academy of Sciences 88:4255-4259. https://doi.org/10.1073/pnas.88.10.4255
  91. Wang B, Zhu L, Zhao B, Zhao Y, Xie Y, Zheng Z, Li Y, Sun J, Wang H. 2019a. Development of a haploid-inducer mediated genome editing system for accelerating maize breeding. Molecular Plant 12:597-602. https://doi.org/10.1016/j.molp.2019.03.006
  92. Wang L, Ji Y, Hu Y, Hu H, Jia X, Jiang M, Zhang X, Zhao L, Zhang Y, Jia Y, Qin C. 2019b. The architecture of intra-organism mutation rate variation in plants. PLoS Biology 17:e3000191. https://doi.org/10.1371/journal.pbio.3000191
  93. Watanabe K, Kobayashi A, Endo M, Sage-Ono K, Toki S, Ono M. 2017. CRISPR/Cas9-mediated mutagenesis of the dihydroflavonol-4-reductase-B (DFR-B) locus in the Japanese morning glory Ipomoea (Pharbitis) nil. Scientific Reports 7:1-9. https://doi.org/10.1038/s41598-016-0028-x
  94. Watanabe K, Oda-Yamamizo C, Sage-Ono K, Ohmiya A, Ono M. 2018. Alteration of flower colour in Ipomoea nil through CRISPR/Cas9-mediated mutagenesis of carotenoid cleavage dioxygenase 4. Transgenic Research 27:25-38. https://doi.org/10.1007/s11248-017-0051-0
  95. Woo JW, Kim JE, Kwon SI, Corvalan C, Cho SW, Kim HR, Kim SG, Kim ST, Choe SH, Kim JS. 2015. DNA-free genome editing in plants with preassembled CRISPR-Cas9 ribonucleoproteins. Nature Biotechnology 33:1162-1164. https://doi.org/10.1038/nbt.3389
  96. Wu Y, Liang D, Wang Y, Bai M, Tang W, Bao S, Yan Z, Li D, Li J. 2013. Correction of a genetic disease in mouse via use of CRISPR-Cas9. Cell Stem Cell 13:659-662. https://doi.org/10.1016/j.stem.2013.10.016
  97. Wyvekens N, Topkar VV, Khayter C, Joung JK, Tsai SQ. 2015. Dimeric CRISPR RNA-guided FokI-dCas9 nucleases directed by truncated gRNAs for highly specific genome editing. Human Gene Therapy 26:425-431. https://doi.org/10.1089/hum.2015.084
  98. Xiong K, Marquart KF, la Cour Karottki KJ, Li S, Shamie I, Lee JS, Gerling S, Yeo NC, Chavez A, Lee GM, Lewis NE. 2019. Reduced apoptosis in Chinese hamster ovary cells via optimized CRISPR interference. Biotechnology and Bioengineering 116:1813-1819. https://doi.org/10.1002/bit.26969
  99. Xu J, Kang BC, Naing AH, Bae SJ, Kim JS, Kim HR, Kim CK. 2020a. CRISPR/Cas9-mediated editing of 1-aminocyclopropane-1-carboxylate oxidase1 enhances Petunia flower longevity. Plant Biotechnology Journal 18:287-297. https://doi.org/10.1111/pbi.13197
  100. Xu Y, Wang F, Chen Z, Wang J, Li WQ, Fan F, Tao Y, Zhao L, Zhong W, Zhu QH, Yang J. 2020b. Intron-targeted gene insertion in rice using CRISPR/Cas9: A case study of the Pi-ta gene. The Crop Journal 8:424-431. https://doi.org/10.1016/j.cj.2019.03.006
  101. Yan R, Wang Z, Ren Y, Li H, Liu N, Sun H. 2019. Establishment of efficient genetic transformation systems and application of CRISPR/Cas9 genome editing technology in Lilium pumilum DC. Fisch. and Lilium longiflorum 'White Heaven'. International Journal of Molecular Sciences 20:2920. https://doi.org/10.3390/ijms20122920
  102. Yu J, Tu L, Subburaj S, Bae S, Lee GJ. 2020. Simultaneous targeting of duplicated genes in Petunia protoplasts for flower color modifcation via CRISPR-Cas9 ribonucleoproteins. Plant Cell Reports (in print). doi.org/10.1007/s00299-020-02593-1
  103. Yu QH, Wang B, Li N, Tang Y, Yang S, Yang T, Xu J, Guo C, Yan P, Wang Q, Asmutola P. 2017. CRISPR/Cas9-induced targeted mutagenesis and gene replacement to generate long-shelf life tomato lines. Scientific Reports 7:1-9. https://doi.org/10.1038/s41598-016-0028-x
  104. Zalipsky S, Harris JM. 1997. In introduction to chemistry and biological applications of poly (ethylene glycol). p. 1-13. ACS publications, Washington D.C., USA.
  105. Zetsche B, Gootenberg JS, Abudayyeh OO, Slaymaker IM, Makarova KS, Essletzbichler P, Volz SE, Joung J, Van Der Oost J, Regev A, Koonin EV. 2015. Cpf1 is a single RNA-guided endonuclease of a class 2 CRISPR-Cas system. Cell 163:759-771. https://doi.org/10.1016/j.cell.2015.09.038
  106. Zetsche B, Heidenreich M, Mohanraju P, Fedorova I, Kneppers J, DeGennaro EM, Winblad N, Choudhury SR, Abudayyeh OO, Gootenberg JS, Wu WY. 2017. Multiplex gene editing by CRISPR-Cpf1 using a single crRNA array. Nature Biotechnology 35:31-34. https://doi.org/10.1038/nbt.3737
  107. Zhang B, Yang X, Yang C, Li M, Guo Y. 2016. Exploiting the CRISPR/Cas9 system for targeted genome mutagenesis in petunia. Scientific Reports 6:20315. https://doi.org/10.1038/srep20315
  108. Zheng Q, Cai X, Tan MH, Schaffert S, Arnold CP, Gong X, Chen CZ, Huang S. 2014. Precise gene deletion and replacement using the CRISPR/Cas9 system in human cells. Biotechniques 57:115-124. https://doi.org/10.2144/000114196
  109. Zhu C, Zheng X, Huang Y, Ye J, Chen P, Zhang C, Zhao F, Xie Z, Zhang S, Wang N, Li H. 2019. Genome sequencing and CRISPR/Cas9 gene editing of an early flowering Mini-Citrus (Fortunella hindsii). Plant Biotechnology Journal 17:2199-2210. https://doi.org/10.1111/pbi.13132