doi:10.48130/vegres-0025-0005

[1]

Li B, Sun C, Li J, Gao C. 2024. Targeted genome-modification tools and their advanced applications in crop breeding. Nature Reviews Genetics 25:603−22

doi: 10.1038/s41576-024-00720-2

[2]

Atia M, Jiang W, Sedeek K, Butt H, Mahfouz M. 2024. Crop bioengineering via gene editing: reshaping the future of agriculture. Plant Cell Reports 43:98

doi: 10.1007/s00299-024-03183-1

[3]

Zhang Y, Malzahn AA, Sretenovic S, Qi Y. 2019. The emerging and uncultivated potential of CRISPR technology in plant science. Nature Plants 5:778−94

doi: 10.1038/s41477-019-0461-5

[4]

Razzaq A, Saleem F, Kanwal M, Mustafa G, Yousaf S, et al. 2019. Modern trends in plant genome editing: an inclusive review of the CRISPR/Cas9 toolbox. International Journal of Molecular Sciences 20:4045

doi: 10.3390/ijms20164045

[5]

Chen K, Wang Y, Zhang R, Zhang H, Gao C. 2019. CRISPR/Cas genome editing and precision plant breeding in agriculture. Annual Review of Plant Biology 70:667−97

doi: 10.1146/annurev-arplant-050718-100049

[6]

Liu Y, Liu Q, Yi C, Liu C, Shi Q, et al. 2025. Past innovations and future possibilities in plant chromosome engineering. Plant Biotechnology Journal 23:695−708

doi: 10.1111/pbi.14530

[7]

Iqbal Z, Iqbal MS, Ahmad A, Memon AG, Ansari MI. 2020. New prospects on the horizon: genome editing to engineer plants for desirable traits. Current Plant Biology 24:100171

doi: 10.1016/j.cpb.2020.100171

[8]

de Lorenzo V, Danchin A. 2008. Synthetic biology: discovering new worlds and new words. EMBO Reports 9:822−27

doi: 10.1038/embor.2008.159

[9]

Tanveer M, Abidin ZU, Alawadi HFN, Shahzad AN, Mahmood A, et al. 2024. Recent advances in genome editing strategies for balancing growth and defence in sugarcane (Saccharum officinarum). Functional Plant Biology 51:FP24036

doi: 10.1071/FP24036

[10]

Ali N, Singh S, Garg R. 2025. Unlocking crops' genetic potential: Advances in genome and epigenome editing of regulatory regions. Current Opinion in Plant Biology 83:102669

doi: 10.1016/j.pbi.2024.102669

[11]

Khan SH. 2019. Genome-editing technologies: concept, pros, and cons of various genome-editing techniques and bioethical concerns for clinical application. Molecular Therapy. Nucleic Acids 16:326−34

doi: 10.1016/j.omtn.2019.02.027

[12]

Jiang C, Li Y, Wang R, Sun X, Zhang Y, et al. 2024. Development and optimization of base editors and its application in crops. Biochemical and Biophysical Research Communications 739:150942

doi: 10.1016/j.bbrc.2024.150942

[13]

Christian M, Cermak T, Doyle EL, Schmidt C, Zhang F, et al. 2010. Targeting DNA double-strand breaks with TAL effector nucleases. Genetics 186:757−61

doi: 10.1534/genetics.110.120717

[14]

Cong L, Ran FA, Cox D, Lin S, Barretto R, et al. 2013. Multiplex genome engineering using CRISPR/Cas systems. Science 339:819−23

doi: 10.1126/science.1231143

[15]

Sovová T, Kerins G, Demnerová K, Ovesná J. 2017. Genome editing with engineered nucleases in economically important animals and plants: state of the art in the research pipeline. Current Issues in Molecular Biology 21:41−62

doi: 10.21775/cimb.021.041

[16]

Puchta H. 1999. Use of I-Sce I to Induce DNA double-strand breaks in Nicotiana. In DNA Repair Protocols, ed. Henderson DS. Vol 113. pp. 447−51. doi: 10.1385/1-59259-675-4:447

[17]

D'Halluin K, Vanderstraeten C, Stals E, Cornelissen M, Ruiter R. 2008. Homologous recombination: a basis for targeted genome optimization in crop species such as maize. Plant Biotechnology Journal 6:93−102

doi: 10.1111/j.1467-7652.2007.00305.x

[18]

Puchta H, Fauser F. 2013. Gene targeting in plants: 25 years later. The International Journal of Developmental Biology 57:629−37

doi: 10.1387/ijdb.130194hp

[19]

Fauser F, Roth N, Pacher M, Ilg G, Sánchez-Fernández R, et al. 2012. In planta gene targeting. Proceedings of the National Academy of Sciences of the United States of America 109:7535−40

doi: 10.1073/pnas.1202191109

[20]

Ochiai H, Yamamoto T. 2017. Construction and evaluation of zinc finger nucleases. In Genome Editing in Animals, ed. Hatada I. Vol 1630. pp. 1−24. doi: 10.1007/978-1-4939-7128-2_1

[21]

Beerli RR, Barbas CF III. 2002. Engineering polydactyl zinc-finger transcription factors. Nature Biotechnology 20:135−41

doi: 10.1038/nbt0202-135

[22]

Kim YG, Cha J, Chandrasegaran S. 1996. Hybrid restriction enzymes: zinc finger fusions to Fok I cleavage domain. Proceedings of the National Academy of Sciences of the United States of America 93:1156−60

doi: 10.1073/pnas.93.3.1156

[23]

Paschon DE, Lussier S, Wangzor T, Xia DF, Li PW, et al. 2019. Diversifying the structure of zinc finger nucleases for high-precision genome editing. Nature Communications 10:1133

doi: 10.1038/s41467-019-08867-x

[24]

Bhuyan SJ, Kumar M, Devde PR, Rai AC, Mishra AK, et al. 2023. Progress in gene editing tools, implications and success in plants: a review. Frontiers in Genome Editing 5:1272678

doi: 10.3389/fgeed.2023.1272678

[25]

Li H, Yang Y, Hong W, Huang M, Wu M, et al. 2020. Applications of genome editing technology in the targeted therapy of human diseases: mechanisms, advances and prospects. Signal Transduction and Targeted Therapy 5:1

doi: 10.1038/s41392-019-0089-y

[26]

Anonymous. 2011. Move over ZFNs. Nature Biotechnology 29:681−84

doi: 10.1038/nbt.1935

[27]

Hui S, Shi Y, Tian J, Wang L, Li Y, et al. 2019. TALE-carrying bacterial pathogens trap host nuclear import receptors for facilitation of infection of rice. Molecular Plant Pathology 20:519−32

doi: 10.1111/mpp.12772

[28]

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

doi: 10.1126/science.1178817

[29]

Bogdanove AJ, Voytas DF. 2011. TAL effectors: customizable proteins for DNA targeting. Science 333:1843−46

doi: 10.1126/science.1204094

[30]

Bhardwaj A, Nain V. 2021. TALENs-an indispensable tool in the era of CRISPR: a mini review. Journal, Genetic Engineering & Biotechnology 19:125

[31]

Hensel G, Kumlehn J. 2019. Genome Engineering Using TALENs. Methods in Molecular Biology 1900:195−15

[32]

Chandrasegaran S, Carroll D. 2016. Origins of Programmable Nucleases for Genome Engineering. Journal of Molecular Biology 428(5 Pt B):963−89

[33]

Makarova KS, Wolf YI, Alkhnbashi OS, Costa F, Shah SA, et al. 2015. An updated evolutionary classification of CRISPR-Cas systems. Nature Reviews Microbiology 13:722−36

doi: 10.1038/nrmicro3569

[34]

Bortesi L, Fischer R. 2015. The CRISPR/Cas9 system for plant genome editing and beyond. Biotechnology Advances 33:41−52

doi: 10.1016/j.biotechadv.2014.12.006

[35]

Sternberg SH, Redding S, Jinek M, Greene EC, Doudna JA. 2014. DNA interrogation by the CRISPR RNA-guided endonuclease Cas9. Nature 507:62−67

doi: 10.1038/nature13011

[36]

Jiang F, Zhou K, Ma L, Gressel S, Doudna JA. 2015. A Cas9-guide RNA complex preorganized for target DNA recognition. Science 348:1477−81

doi: 10.1126/science.aab1452

[37]

Lowder L, Malzahn A, Qi Y. 2016. Rapid evolution of manifold CRISPR systems for plant genome editing. Frontiers in Plant Science 7:1683

doi: 10.3389/fpls.2016.01683

[38]

Carrijo J, Illa-Berenguer E, LaFayette P, Torres N, Aragão FJL, et al. 2021. Two efficient CRISPR/Cas9 systems for gene editing in soybean. Transgenic Research 30:239−49

doi: 10.1007/s11248-021-00246-x

[39]

Gao Y, Zhao Y. 2014. Self-processing of ribozyme-flanked RNAs into guide RNAs in vitro and in vivo for CRISPR-mediated genome editing. Journal of Integrative Plant Biology 56:343−49

doi: 10.1111/jipb.12152

[40]

Do PT, Nguyen CX, Bui HT, Tran LTN, Stacey G, et al. 2019. Demonstration of highly efficient dual gRNA CRISPR/Cas9 editing of the homeologous GmFAD2-1A and GmFAD2-1B genes to yield a high oleic, low linoleic and α-linolenic acid phenotype in soybean. BMC Plant Biology 19:311

doi: 10.1186/s12870-019-1906-8

[41]

González MN, Massa GA, Andersson M, Turesson H, Olsson N, et al. 2019. Reduced enzymatic browning in potato tubers by specific editing of a polyphenol oxidase gene via ribonucleoprotein complexes delivery of the CRISPR/Cas9 system. Frontiers in Plant Science 10:1649

doi: 10.3389/fpls.2019.01649

[42]

Butt H, Jamil M, Wang JY, Al-Babili S, Mahfouz M. 2018. Engineering plant architecture via CRISPR/Cas9-mediated alteration of strigolactone biosynthesis. BMC Plant Biology 18:174

doi: 10.1186/s12870-018-1387-1

[43]

Ortigosa A, Gimenez-Ibanez S, Leonhardt N, Solano R. 2019. Design of a bacterial speck resistant tomato by CRISPR/Cas9-mediated editing of SlJAZ2. Plant Biotechnology Journal 17:665−73

doi: 10.1111/pbi.13006

[44]

Shi J, Gao H, Wang H, Lafitte HR, Archibald RL, et al. 2017. ARGOS8 variants generated by CRISPR-Cas9 improve maize grain yield under field drought stress conditions. Plant Biotechnology Journal 15:207−16

doi: 10.1111/pbi.12603

[45]

Gupta D, Bhattacharjee O, Mandal D, Sen MK, Dey D, et al. 2019. CRISPR-Cas9 system: a new-fangled dawn in gene editing. Life Sciences 232:116636

doi: 10.1016/j.lfs.2019.116636

[46]

Devillars A, Magon G, Pirrello C, Palumbo F, Farinati S, et al. 2024. Not only editing: a Cas-Cade of CRISPR/Cas-based tools for functional genomics in plants and animals. International Journal of Molecular Sciences 25:3271

doi: 10.3390/ijms25063271

[47]

Burstein D, Harrington LB, Strutt SC, Probst AJ, Anantharaman K, et al. 2017. New CRISPR-Cas systems from uncultivated microbes. Nature 542:237−41

doi: 10.1038/nature21059

[48]

Wang Y, Cheng X, Shan Q, Zhang Y, Liu J, et al. 2014. Simultaneous editing of three homoeoalleles in hexaploid bread wheat confers heritable resistance to powdery mildew. Nature Biotechnology 32:947−51

doi: 10.1038/nbt.2969

[49]

Malnoy M, Viola R, Jung MH, Koo OJ, Kim S, et al. 2016. DNA-free genetically edited grapevine and apple protoplast using CRISPR/Cas9 ribonucleoproteins. Frontiers in Plant Science 7:1904

doi: 10.3389/fpls.2016.01904

[50]

Bandyopadhyay A, Kancharla N, Javalkote VS, Dasgupta S, Brutnell TP. 2020. CRISPR-Cas12a (Cpf1): a versatile tool in the plant genome editing tool box for agricultural advancement. Frontiers in Plant Science 11:584151

doi: 10.3389/fpls.2020.584151

[51]

Tang X, Lowder LG, Zhang T, Malzahn AA, Zheng X, et al. 2017. A CRISPR-Cpf1 system for efficient genome editing and transcriptional repression in plants. Nature Plants 3:17103

doi: 10.1038/nplants.2017.103

[52]

Bernabé-Orts JM, Casas-Rodrigo I, Minguet EG, Landolfi V, Garcia-Carpintero V, et al. 2019. Assessment of Cas12a-mediated gene editing efficiency in plants. Plant Biotechnology Journal 17:1971−84

doi: 10.1111/pbi.13113

[53]

Kim H, Kim ST, Ryu J, Kang BC, Kim JS, et al. 2017. CRISPR/Cpf1-mediated DNA-free plant genome editing. Nature Communications 8:14406

doi: 10.1038/ncomms14406

[54]

Li B, Rui H, Li Y, Wang Q, Alariqi M, et al. 2019. Robust CRISPR/Cpf1 (Cas12a)-mediated genome editing in allotetraploid cotton (Gossypium hirsutum). Plant Biotechnology Journal 17:1862−64

doi: 10.1111/pbi.13147

[55]

Jia H, Orbović V, Wang N. 2019. CRISPR-LbCas12a-mediated modification of citrus. Plant Biotechnology Journal 17:1928−37

doi: 10.1111/pbi.13109

[56]

Shimatani Z, Kashojiya S, Takayama M, Terada R, Arazoe T, et al. 2017. Targeted base editing in rice and tomato using a CRISPR-Cas9 cytidine deaminase fusion. Nature Biotechnology 35:441−43

doi: 10.1038/nbt.3833

[57]

Wang M, Mao Y, Lu Y, Tao X, Zhu JK, et al. 2017. Multiplex gene editing in rice using the CRISPR-Cpf1 system. Molecular Plant 10:1011−13

doi: 10.1016/j.molp.2017.03.001

[58]

Pausch P, Soczek KM, Herbst DA, Tsuchida CA, Al-Shayeb B, et al. 2021. DNA interference states of the hypercompact CRISPR-CasΦ effector. Nature Structural & Molecular Biology 28:652−61

doi: 10.1038/s41594-021-00632-3

[59]

Carabias A, Fuglsang A, Temperini P, Pape T, Sofos N, et al. 2021. Structure of the mini-RNA-guided endonuclease CRISPR-Cas12j3. Nature Communications 12:4476

doi: 10.1038/s41467-021-24707-3

[60]

Ma X, Zhang Q, Zhu Q, Liu W, Chen Y, et al. 2015. A robust CRISPR/Cas9 system for convenient, high-efficiency multiplex genome editing in monocot and dicot plants. Molecular Plant 8:1274−84

doi: 10.1016/j.molp.2015.04.007

[61]

Wu Y, Ren Q, Zhong Z, Liu G, Han Y, et al. 2022. Genome-wide analyses of PAM-relaxed Cas9 genome editors reveal substantial off-target effects by ABE8e in rice. Plant Biotechnology Journal 20:1670−82

doi: 10.1111/pbi.13838

[62]

Piatek A, Ali Z, Baazim H, Li L, Abulfaraj A, et al. 2015. RNA-guided transcriptional regulation in planta via synthetic dCas9-based transcription factors. Plant Biotechnology Journal 13:578−89

doi: 10.1111/pbi.12284

[63]

Kleinstiver BP, Prew MS, Tsai SQ, Topkar VV, Nguyen NT, et al. 2015. Engineered CRISPR-Cas9 nucleases with altered PAM specificities. Nature 523:481−85

doi: 10.1038/nature14592

[64]

Hu JH, Miller SM, Geurts MH, Tang W, Chen L, et al. 2018. Evolved Cas9 variants with broad PAM compatibility and high DNA specificity. Nature 556:57−63

doi: 10.1038/nature26155

[65]

Nishimasu H, Shi X, Ishiguro S, Gao L, Hirano S, et al. 2018. Engineered CRISPR-Cas9 nuclease with expanded targeting space. Science 361:1259−62

doi: 10.1126/science.aas9129

[66]

Liang F, Zhang Y, Li L, Yang Y, Fei JF, et al. 2022. SpG and SpRY variants expand the CRISPR toolbox for genome editing in zebrafish. Nature Communications 13:3421

doi: 10.1038/s41467-022-31034-8

[67]

Sretenovic S, Yin D, Levav A, Selengut JD, Mount SM, et al. 2021. Expanding plant genome-editing scope by an engineered iSpyMacCas9 system that targets A-rich PAM sequences. Plant Communications 2:100101

doi: 10.1016/j.xplc.2020.100101

[68]

Kleinstiver BP, Prew MS, Tsai SQ, Nguyen NT, Topkar VV, et al. 2015. Broadening the targeting range of Staphylococcus aureus CRISPR-Cas9 by modifying PAM recognition. Nature Biotechnology 33:1293−98

doi: 10.1038/nbt.3404

[69]

Müller M, Lee CM, Gasiunas G, Davis TH, Cradick TJ, et al. 2016. Streptococcus thermophilus CRISPR-Cas9 systems enable specific editing of the human genome. Molecular Therapy 24:636−44

doi: 10.1038/mt.2015.218

[70]

Karvelis T, Gasiunas G, Young J, Bigelyte G, Silanskas A, et al. 2015. Rapid characterization of CRISPR-Cas9 protospacer adjacent motif sequence elements. Genome Biology 16:253

doi: 10.1186/s13059-015-0818-7

[71]

Jakimo N, Chatterjee P, Nip L, Jacobson JM. 2018. A Cas9 with complete PAM recognition for adenine dinucleotides. bioRxiv 00:429654

doi: 10.1101/429654v1

[72]

Zhong Z, Liu G, Tang Z, Xiang S, Yang L, et al. 2023. Efficient plant genome engineering using a probiotic sourced CRISPR-Cas9 system. Nature Communications 14:6102

doi: 10.1038/s41467-023-41802-9

[73]

Cui Z, Tian R, Huang Z, Jin Z, Li L, et al. 2022. FrCas9 is a CRISPR/Cas9 system with high editing efficiency and fidelity. Nature Communications 13:1425

doi: 10.1038/s41467-022-29089-8

[74]

Zetsche B, Gootenberg JS, Abudayyeh OO, Slaymaker IM, Makarova KS, et al. 2015. Cpf1 is a single RNA-guided endonuclease of a class 2 CRISPR-Cas system. Cell 163:759−71

doi: 10.1016/j.cell.2015.09.038

[75]

Gao L, Cox DBT, Yan WX, Manteiga JC, Schneider MW, et al. 2017. Engineered Cpf1 variants with altered PAM specificities. Nature Biotechnology 35:789−92

doi: 10.1038/nbt.3900

[76]

Kleinstiver BP, Sousa AA, Walton RT, Tak YE, Hsu JY, et al. 2019. Engineered CRISPR–Cas12a variants with increased activities and improved targeting ranges for gene, epigenetic and base editing. Nature Biotechnology 37:276−82

doi: 10.1038/s41587-018-0011-0

[77]

Tóth E, Czene BC, Kulcsár PI, Krausz SL, Tálas A, et al. 2018. Mb- and FnCpf1 nucleases are active in mammalian cells: activities and PAM preferences of four wild-type Cpf1 nucleases and of their altered PAM specificity variants. Nucleic Acids Research 46:10272−85

doi: 10.1093/nar/gky815

[78]

Malzahn A, Lowder L, Qi Y. 2017. Plant genome editing with TALEN and CRISPR. Cell & Bioscience 7:21

doi: 10.1186/s13578-017-0148-4

[79]

Stinson BM, Loparo JJ. 2021. Repair of DNA double-strand breaks by the nonhomologous end joining pathway. Annual Review of Biochemistry 90:137−64

doi: 10.1146/annurev-biochem-080320-110356

[80]

Puchta H. 2005. The repair of double-strand breaks in plants: mechanisms and consequences for genome evolution. Journal of Experimental Botany 56:1−14

doi: 10.1093/jxb/eri025

[81]

Piatek AA, Lenaghan SC, Neal Stewart C Jr. 2018. Advanced editing of the nuclear and plastid genomes in plants. Plant Science 273:42−49

doi: 10.1016/j.plantsci.2018.02.025

[82]

Li H, Beckman KA, Pessino V, Huang B, Weissman JS, et al. 2019. Design and specificity of long ssDNA donors for CRISPR-based knock-in. bioRxiv 00:178905

doi: 10.1101/178905v1

[83]

Huang TK, Puchta H. 2019. CRISPR/Cas-mediated gene targeting in plants: finally a turn for the better for homologous recombination. Plant Cell Reports 38:443−53

doi: 10.1007/s00299-019-02379-0

[84]

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. The Plant Journal 80:1139−50

doi: 10.1111/tpj.12704

[85]

Ghanta KS, Dokshin GA, Mir A, Dokshin GA, Krishnamurthy PM, et al. 2021. 5' Modifications improve potency and efficacy of DNA donors for precision genome editing. Elife 10:e72216

doi: 10.7554/eLife.72216

[86]

Carlson-Stevermer J, Abdeen AA, Kohlenberg L, Goedland M, Molugu K, et al. 2017. Assembly of CRISPR ribonucleoproteins with biotinylated oligonucleotides via an RNA aptamer for precise gene editing. Nature Communications 8:1711

doi: 10.1038/s41467-017-01875-9

[87]

Aird EJ, Lovendahl KN, St. Martin A, Harris RS, Gordon WR. 2018. Increasing Cas9-mediated homology-directed repair efficiency through covalent tethering of DNA repair template. Communications Biology 1:54

doi: 10.1038/s42003-018-0054-2

[88]

Chen X, Janssen JM, Liu J, Maggio I, 'tJong AEJ, et al. 2017. In trans paired nicking triggers seamless genome editing without double-stranded DNA cutting. Nature Communications 8:657

doi: 10.1038/s41467-017-00687-1

[89]

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 533:420−24

doi: 10.1038/nature17946

[90]

Nishida K, Arazoe T, Yachie N, Banno S, Kakimoto M, et al. 2016. Targeted nucleotide editing using hybrid prokaryotic and vertebrate adaptive immune systems. Science 353:aaf8729

doi: 10.1126/science.aaf8729

[91]

Conticello SG. 2008. The AID/APOBEC family of nucleic acid mutators. Genome Biology 9:229

doi: 10.1186/gb-2008-9-6-229

[92]

Komor AC, Zhao KT, Packer MS, Gaudelli NM, Waterbury AL, et al. 2017. Improved base excision repair inhibition and bacteriophage Mu Gam protein yields C: G-to-T: A base editors with higher efficiency and product purity. Science Advances 3:eaao4774

doi: 10.1126/sciadv.aao4774

[93]

Jiang F, Taylor DW, Chen JS, Kornfeld JE, Zhou K, et al. 2016. Structures of a CRISPR-Cas9 R-loop complex primed for DNA cleavage. Science 351:867−71

doi: 10.1126/science.aad8282

[94]

Porto EM, Komor AC, Slaymaker IM, Yeo GW. 2020. Base editing: advances and therapeutic opportunities. Nature Reviews Drug Discovery 19:839−59

doi: 10.1038/s41573-020-0084-6

[95]

Li Y, Liang J, Deng B, Jiang Y, Zhu J, et al. 2023. Applications and prospects of CRISPR/Cas9-mediated base editing in plant breeding. Current Issues in Molecular Biology 45:918−35

doi: 10.3390/cimb45020059

[96]

Azameti MK, Dauda WP. 2021. Base editing in plants: applications, challenges, and future prospects. Frontiers in Plant Science 12:664997

doi: 10.3389/fpls.2021.664997

[97]

Molla KA, Sretenovic S, Bansal KC, Qi Y. 2021. Precise plant genome editing using base editors and prime editors. Nature Plants 7:1166−87

doi: 10.1038/s41477-021-00991-1

[98]

Xie Y, Haq SIU, Jiang X, Zheng D, Feng N, et al. 2022. Plant genome editing: CRISPR, base editing, prime editing, and beyond. Grassland Research 1:234−43

doi: 10.1002/glr2.12034

[99]

Thuronyi BW, Koblan LW, Levy JM, Yeh WH, Zheng C, et al. 2019. Continuous evolution of base editors with expanded target compatibility and improved activity. Nature Biotechnology 37:1070−79

doi: 10.1038/s41587-019-0193-0

[100]

Walton RT, Christie KA, Whittaker MN, Kleinstiver BP. 2020. Unconstrained genome targeting with near-PAMless engineered CRISPR-Cas9 variants. Science 368:290−96

doi: 10.1126/science.aba8853

[101]

Wang M, Wang Z, Mao Y, Lu Y, Yang R, et al. 2019. Optimizing Base Editors for Improved Efficiency and Expanded Editing Scope in Rice. Plant Biotechnology Journal 17:1697−99

doi: 10.1111/pbi.13124

[102]

Zhang C, Wang Y, Wang F, Zhao S, Song J, et al. 2021. Expanding base editing scope to near-PAMless with engineered CRISPR/Cas9 variants in plants. Molecular Plant 14:191−94

doi: 10.1016/j.molp.2020.12.016

[103]

Ren Q, Sretenovic S, Liu S, Tang X, Huang L, et al. 2021. PAM-less plant genome editing using a CRISPR-SpRY toolbox. Nature Plants 7:25−33

doi: 10.1038/s41477-020-00827-4

[104]

Gaudelli NM, Komor AC, Rees HA, Packer MS, Badran AH, et al. 2017. Programmable base editing of A•T to G•C in genomic DNA without DNA cleavage. Nature 551:464−71

doi: 10.1038/nature24644

[105]

Molla KA, Yang Y. 2019. CRISPR/Cas-mediated base editing: technical considerations and practical applications. Trends in Biotechnology 37:1121−42

doi: 10.1016/j.tibtech.2019.03.008

[106]

Hua K, Tao X, Liang W, Zhang Z, Gou R, et al. 2020. Simplified adenine base editors improve adenine base editing efficiency in rice. Plant Biotechnology Journal 18:770−78

doi: 10.1111/pbi.13244

[107]

Qin L, Li J, Wang Q, Xu Z, Sun L, et al. 2020. High-efficient and precise base editing of C•G to T•A in the allotetraploid cotton (Gossypium hirsutum) genome using a modified CRISPR/Cas9 system. Plant Biotechnology Journal 18:45−56

doi: 10.1111/pbi.13168

[108]

Zhang R, Liu J, Chai Z, Chen S, Bai Y, et al. 2019. Generation of herbicide tolerance traits and a new selectable marker in wheat using base editing. Nature Plants 5:480−85

doi: 10.1038/s41477-019-0405-0

[109]

Wu J, Chen C, Xian G, Liu D, Lin L, et al. 2020. Engineering herbicide-resistant oilseed rape by CRISPR/Cas9-mediated cytosine base-editing. Plant Biotechnology Journal 18:1857−59

doi: 10.1111/pbi.13368

[110]

Hillary VE, Ceasar SA. 2024. CRISPR/Cas system-mediated base editing in crops: recent developments and future prospects. Plant Cell Reports 43:271

doi: 10.1007/s00299-024-03346-0

[111]

Zong Y, Liu Y, Xue C, Li B, Li X, et al. 2022. An engineered prime editor with enhanced editing efficiency in plants. Nature Biotechnology 40:1394−402

doi: 10.1038/s41587-022-01254-w

[112]

Ahmad N, Awan MJA, Mansoor S. 2023. Improving editing efficiency of prime editor in plants. Trends in Plant Science 28:1−3

doi: 10.1016/j.tplants.2022.09.001

[113]

Lin Q, Jin S, Zong Y, Yu H, Zhu Z, et al. 2021. High-efficiency prime editing with optimized, paired pegRNAs in plants. Nature Biotechnology 39:923−27

doi: 10.1038/s41587-021-00868-w

[114]

Anzalone AV, Randolph PB, Davis JR, Sousa AA, Koblan LK, et al. 2019. Search-and-replace genome editing without double-strand breaks or donor DNA. Nature 576:149−57

doi: 10.1038/s41586-019-1711-4

[115]

Lin Q, Zong Y, Xue C, Wang S, Jin S, et al. 2020. Prime genome editing in rice and wheat. Nature Biotechnology 38:582−85

doi: 10.1038/s41587-020-0455-x

[116]

Li H, Zhu Z, Li S, Li J, Yan L, et al. 2022. Multiplex precision gene editing by a surrogate prime editor in rice. Molecular Plant 15:1077−80

doi: 10.1016/j.molp.2022.05.009

[117]

Ni P, Zhao Y, Zhou X, Liu Z, Huanget Z, et al. 2023. Efficient and versatile multiplex prime editing in hexaploid wheat. Genome Biology 24:156

doi: 10.1186/s13059-023-02990-1

[118]

Vu TV, Nguyen NT, Kim J, Hong JC, Kim JY. 2024. Prime editing: mechanism insight and recent applications in plants. Plant Biotechnology Journal 22:19−36

doi: 10.1111/pbi.14188

[119]

Woo JW, Kim J, Kwon SI, Corvalán C, Cho SW, et al. 2015. DNA-free genome editing in plants with preassembled CRISPR-Cas9 ribonucleoproteins. Nature Biotechnology 33:1162−64

doi: 10.1038/nbt.3389

[120]

Subburaj S, Chung SJ, Lee C, Ryu SM, Kimet DH, et al. 2016. Site-directed mutagenesis in Petunia × hybrida protoplast system using direct delivery of purified recombinant Cas9 ribonucleoproteins. Plant Cell Reports 35:1535−44

doi: 10.1007/s00299-016-1937-7

[121]

Esvelt KM, Mali P, Braff JL, Moosburner M, Yaung SJ, et al. 2013. Orthogonal Cas9 proteins for RNA-guided gene regulation and editing. Nature Methods 10:1116−21

doi: 10.1038/nmeth.2681

[122]

Čermák T, Baltes NJ, Čegan R, Zhang Y, Voytas DF. 2015. High-frequency, precise modification of the tomato genome. Genome Biology 16:232

doi: 10.1186/s13059-015-0796-9

[123]

Mikami M, Toki S, Endo M. 2017. In planta processing of the SpCas9-gRNA complex. Plant and Cell Physiology 58:1857−67

doi: 10.1093/pcp/pcx154

[124]

Xie K, Minkenberg B, Yang Y. 2015. Boosting CRISPR/Cas9 multiplex editing capability with the endogenous tRNA-processing system. Proceedings of the National Academy of Sciences of the United States of America 112:3570−75

doi: 10.1073/pnas.1420294112

[125]

Wang W, Akhunova A, Chao S, Akhunov E. 2016. Optimizing multiplex CRISPR/Cas9-based genome editing for wheat. bioRxiv 00:51342

doi: 10.1101/051342v3

[126]

Qi W, Zhu T, Tian Z, Li C, Zhang W, et al. 2016. High-efficiency CRISPR/Cas9 multiplex gene editing using the glycine tRNA-processing system-based strategy in maize. BMC Biotechnology 16:58

doi: 10.1186/s12896-016-0289-2

[127]

Tang X, Ren Q, Yang L, Bao Y, Zhong Z, et al. 2019. Single transcript unit CRISPR 2.0 systems for robust Cas9 and Cas12a mediated plant genome editing. Plant Biotechnology Journal 17:1431−45

doi: 10.1111/pbi.13068

[128]

Prado GS, Rocha DC, Dos Santos LN, Contiliani DF, Nobileet PM, et al. 2023. CRISPR technology towards genome editing of the perennial and semi-perennial crops citrus, coffee and sugarcane. Frontiers in Plant Science 14:1331258

doi: 10.3389/fpls.2023.1331258

[129]

Chovatiya A, Rajyaguru R, Tomar RS, Joshi P. 2024. Revolutionizing agriculture: harnessing CRISPR/Cas9 for crop enhancement. Indian Journal of Microbiology 64:59−69

doi: 10.1007/s12088-023-01154-w

[130]

Bravo-Vázquez LA, Méndez-García A, Chamu-García V, Rodríguez AL, Bandyopadhyay A, et al. 2024. The applications of CRISPR/Cas-mediated microRNA and lncRNA editing in plant biology: shaping the future of plant non-coding RNA research. Planta 259:32

doi: 10.1007/s00425-023-04303-z

[131]

Malzahn AA, Tang X, Lee K, Ren Q, Sretenovic S, et al. 2019. Application of CRISPR-Cas12a temperature sensitivity for improved genome editing in rice, maize, and Arabidopsis. BMC Biology 17:9

doi: 10.1186/s12915-019-0629-5

[132]

Shan S, Mavrodiev EV, Li R, Zhang Z, Hauser BA, et al. 2018. Application of CRISPR/Cas9 to Tragopogon (Asteraceae), an evolutionary model for the study of polyploidy. Molecular Ecology Resources 18:1427−43

doi: 10.1111/1755-0998.12935

[133]

Fauser F, Schiml S, Puchta H. 2014. Both CRISPR/Cas-based nucleases and nickases can be used efficiently for genome engineering in Arabidopsis thaliana. The Plant Journal 79:348−59

doi: 10.1111/tpj.12554

[134]

Zhang D, Zhang H, Li T, Chen K, Qiuet JL, et al. 2017. Perfectly matched 20-nucleotide guide RNA sequences enable robust genome editing using high-fidelity SpCas9 nucleases. Genome Biology 18:191

doi: 10.1186/s13059-017-1325-9

[135]

Zhang Q, Xing HL, Wang ZP, Zhang HY, Yang F, et al. 2018. Potential high-frequency off-target mutagenesis induced by CRISPR/Cas9 in Arabidopsis and its prevention. Plant Molecular Biology 96:445−56

doi: 10.1007/s11103-018-0709-x

[136]

Lowe K, Wu E, Wang N, Hoerster G, Hastings C, et al. 2016. Morphogenic regulators Baby boom and Wuschel improve monocot transformation. The Plant Cell 28:1998−2015

doi: 10.1105/tpc.16.00124

[137]

Mookkan M, Nelson-Vasilchik K, Hague J, Zhang ZJ, Kausch AP. 2017. Selectable marker independent transformation of recalcitrant maize inbred B73 and sorghum P898012 mediated by morphogenic regulators BABY BOOM and WUSCHEL2. Plant Cell Reports 36:1477−91

doi: 10.1007/s00299-017-2169-1