[1] Yang H, Cai G, Lu J, Gómez Plaza E. 2021. The production and application of enzymes related to the quality of fruit wine. Critical Reviews in Food Science and Nutrition 61:1605−15 doi: 10.1080/10408398.2020.1763251
[2] Wang Z, Wong DCJ, Wang Y, Xu G, Ren C, et al. 2021. GRAS-domain transcription factor PAT1 regulates jasmonic acid biosynthesis in grape cold stress response. Plant Physiology 186:1660−78 doi: 10.1093/plphys/kiab142
[3] Fennell A. 2004. Freezing tolerance and injury in grapevines. Journal of Crop Improvement 10:201−35 doi: 10.1300/J411v10n01_09
[4] Wang J, Wang S, Liu G, Edwards EJ, Duan W, et al. 2016. The synthesis and accumulation of resveratrol are associated with veraison and abscisic acid concentration in Beihong (Vitis vinifera × Vitis amurensis) berry skin. Frontiers in Plant Science 7:1605 doi: 10.3389/fpls.2016.01605
[5] Wang J, Ma L, Xi H, Wang L, Li S. 2015. Resveratrol synthesis under natural conditions and after UV-C irradiation in berry skin is associated with berry development stages in 'Beihong' (V. vinifera × V. amurensis). Food Chemistry 168:430−38 doi: 10.1016/j.foodchem.2014.07.025
[6] 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 doi: 10.3389/fpls.2017.01635
[7] Meyer RS, Purugganan MD. 2013. Evolution of crop species: genetics of domestication and diversification. Nature Reviews Genetics 14:840−52 doi: 10.1038/nrg3605
[8] 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
[9] Manghwar H, Lindsey K, Zhang X, Jin S. 2019. CRISPR/Cas system: recent advances and future prospects for genome editing. Trends in Plant Science 24:1102−25 doi: 10.1016/j.tplants.2019.09.006
[10] Zhu H, Li C, Gao C. 2020. Applications of CRISPR-Cas in agriculture and plant biotechnology. Nature Reviews Molecular Cell Biology 21:661−77 doi: 10.1038/s41580-020-00288-9
[11] Zhan X, Lu Y, Zhu J, Botella JR. 2021. Genome editing for plant research and crop improvement. Journal of Integrative Plant Biology 63:3−33 doi: 10.1111/jipb.13063
[12] Ren C, Liu X, Zhang Z, Wang Y, Duan W, et al. 2016. CRISPR/Cas9-mediated efficient targeted mutagenesis in Chardonnay (Vitis vinifera L.). Scientific Reports 6:32289 doi: 10.1038/srep32289
[13] 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
[14] Horvath P, Barrangou R. 2010. CRISPR/Cas, the immune system of bacteria and archaea. Science 327:167−70 doi: 10.1126/science.1179555
[15] Makarova KS, Zhang F, Koonin EV. 2017. Snapshot: Class 1 CRISPR-Cas systems. Cell 168:946−946.e1 doi: 10.1016/j.cell.2017.02.018
[16] Makarova KS, Zhang F, Koonin EV. 2017. Snapshot: Class 2 CRISPR-Cas systems. Cell 168:328−328.e1 doi: 10.1016/j.cell.2016.12.038
[17] Chylinski K, Makarova KS, Charpentier E, Koonin EV. 2014. Classification and evolution of type II CRISPR-Cas systems. Nucleic Acids Research 42:6091−105 doi: 10.1093/nar/gku241
[18] Mohanraju P, Makarova KS, Zetsche B, Zhang F, Koonin EV, et al. 2016. Diverse evolutionary roots and mechanistic variations of the CRISPR-Cas systems. Science 353:aad5147 doi: 10.1126/science.aad5147
[19] Nishimasu H, Ran FA, Hsu PD, Konermann S, Shehata SI, et al. 2014. Crystal structure of Cas9 in complex with guide RNA and target DNA. Cell 156:935−49 doi: 10.1016/j.cell.2014.02.001
[20] Jinek M, Jiang F, Taylor DW, Sternberg SH, Kaya E, et al. 2014. Structures of Cas9 endonucleases reveal RNA-mediated conformational activation. Science 343:1247997 doi: 10.1126/science.1247997
[21] Anders C, Niewoehner O, Duerst A, Jinek M. 2014. Structural basis of PAM-dependent target DNA recognition by the Cas9 endonuclease. Nature 513:569−73 doi: 10.1038/nature13579
[22] Chang HHY, Pannunzio NR, Adachi N, Lieber MR. 2017. Non-homologous DNA end joining and alternative pathways to double-strand break repair. Nature Reviews Molecular Cell Biology 18:495−506 doi: 10.1038/nrm.2017.48
[23] Scully R, Panday A, Elango R, Willis NA. 2019. DNA double-strand break repair-pathway choice in somatic mammalian cells. Nature Reviews Molecular Cell Biology 20:698−714 doi: 10.1038/s41580-019-0152-0
[24] Tsai SQ, Joung JK. 2016. Defining and improving the genome-wide specificities of CRISPR-Cas9 nucleases. Nature Reviews Genetics 17:300−12 doi: 10.1038/nrg.2016.28
[25] Feng Z, Zhang B, Ding W, Liu X, Yang D, et al. 2013. Efficient genome editing in plants using a CRISPR/Cas system. Cell Research 23:1229−1232 doi: 10.1038/cr.2013.114
[26] Mao Y, Zhang H, Xu N, Zhang B, Gou F, et al. 2013. Application of the CRISPR-Cas system for efficient genome engineering in plants. Molecular Plant 6:2008−11 doi: 10.1093/mp/sst121
[27] Ran FA, Hsu PD, Lin CY, Gootenberg JS, Konermann S, et al. 2013. Double nicking by RNA-guided CRISPR Cas9 for enhanced genome editing specificity. Cell 154:1380−89 doi: 10.1016/j.cell.2013.08.021
[28] Schiml S, Fauser F, Puchta H. 2014. The CRISPR/Cas9 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
[29] Qi LS, Larson MH, Gilbert LA, Doudna JA, Weissman JS, et al. 2013. Repurposing CRISPR as an RNA-guided platform for sequence-specific control of gene expression. Cell 152:1173−83 doi: 10.1016/j.cell.2013.02.022
[30] Gilbert LA, Larson MH, Morsut L, Liu Z, Brar GA, et al. 2013. CRISPR-mediated modular RNA-guided regulation of transcription in eukaryotes. Cell 154:442−51 doi: 10.1016/j.cell.2013.06.044
[31] Rusk N. 2014. CRISPRs and epigenome editing. Nature Methods 11:28 doi: 10.1038/nmeth.2775
[32] Chen B, Gilbert LA, Cimini BA, Schnitzbauer J, Zhang W, et al. 2013. Dynamic imaging of genomic loci in living human cells by an optimized CRISPR/Cas system. Cell 155:1479−91 doi: 10.1016/j.cell.2013.12.001
[33] Cho SW, Kim S, Kim Y, Kweon J, Kim HS, et al. 2014. Analysis of off-target effects of CRISPR/Cas-derived RNA-guided endonucleases and nickases. Genome Research 24:132−41 doi: 10.1101/gr.162339.113
[34] Pattanayak V, Lin S, Guilinger JP, Ma E, Doudna JA, et al. 2013. High-throughput profiling of off-target DNA cleavage reveals RNA-programmed Cas9 nuclease specificity. Nature Biotechnology 31:839−43 doi: 10.1038/nbt.2673
[35] Fu Y, Foden JA, Khayter C, Maeder ML, Reyon D, et al. 2013. High-frequency off-target mutagenesis induced by CRISPR-Cas nucleases in human cells. Nature Biotechnology 31:822−26 doi: 10.1038/nbt.2623
[36] Kleinstiver BP, Pattanayak V, Prew MS, Tsai SQ, Nguyen NT, et al. 2016. High-fidelity CRISPR-Cas9 nucleases with no detectable genome-wide off-target effects. Nature 529:490−95 doi: 10.1038/nature16526
[37] Slaymaker IM, Gao L, Zetsche B, Scott DA, Yan WX, et al. 2016. Rationally engineered Cas9 nucleases with improved specificity. Science 351:84−88 doi: 10.1126/science.aad5227
[38] Chen JS, Dagdas YS, Kleinstiver BP, Welch MM, Sousa AA, et al. 2017. Enhanced proofreading governs CRISPR-Cas9 targeting accuracy. Nature 550:407−10 doi: 10.1038/nature24268
[39] Lee JK, Jeong E, Lee J, Jung M, Shin E, et al. 2018. Directed evolution of CRISPR-Cas9 to increase its specificity. Nature Communications 9:3048 doi: 10.1038/s41467-018-05477-x
[40] Vakulskas CA, Dever DP, Rettig GR, Turk R, Jacobi AM, et al. 2018. A high-fidelity Cas9 mutant delivered as a ribonucleoprotein complex enables efficient gene editing in human hematopoietic stem and progenitor cells. Nature Medicine 24:1216−24 doi: 10.1038/s41591-018-0137-0
[41] Meng X, Hu X, Liu Q, Song X, Gao C, et al. 2018. Robust genome editing of CRISPR-Cas9 at NAG PAMs in rice. Science China Life Sciences 61:122−25 doi: 10.1007/s11427-017-9247-9
[42] 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
[43] Hu X, Wang C, Fu Y, Liu Q, Jiao X, et al. 2016. Expanding the range of CRISPR/Cas9 genome editing in rice. Molecular Plant 9:943−45 doi: 10.1016/j.molp.2016.03.003
[44] Hua K, Tao X, Han P, Wang R, Zhu JK. 2019. Genome engineering in rice using Cas9 variants that recognize NG PAM sequences. Molecular Plant 12:1003−14 doi: 10.1016/j.molp.2019.03.009
[45] Ren B, Liu L, Li S, Kuang Y, Wang J, et al. 2019. Cas9-NG greatly expands the targeting scope of the genome-editing toolkit by recognizing NG and other atypical PAMs in rice. Molecular Plant 12:1015−26 doi: 10.1016/j.molp.2019.03.010
[46] Zeng D, Li X, Huang J, Li Y, Cai S, et al. 2020. Engineered Cas9 variant tools expand targeting scope of genome and base editing in rice. Plant Biotechnology Journal 18:1348−50 doi: 10.1111/pbi.13293
[47] Wang M, Xu Z, Gosavi G, Ren B, Cao Y, et al. 2020. Targeted base editing in rice with CRISPR/ScCas9 system. Plant Biotechnology Journal 18:1645−47 doi: 10.1111/pbi.13330
[48] Xu Y, Meng X, Wang J, Qin B, Wang K, et al. 2020. ScCas9 recognizes NNG protospacer adjacent motif in genome editing of rice. Science China Life Sciences 63:450−52 doi: 10.1007/s11427-019-1630-2
[49] Qin R, Li J, Li H, Zhang Y, Liu X, et al. 2019. Developing a highly efficient and wildly adaptive CRISPR-SaCas9 toolset for plant genome editing. Plant Biotechnology Journal 17:706−8 doi: 10.1111/pbi.13047
[50] Jia H, Xu J, Orbović V, Zhang Y, Wang N. 2017. Editing citrus genome via SaCas9/sgRNA system. Frontiers in Plant Science 8:2135 doi: 10.3389/fpls.2017.02135
[51] 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
[52] 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
[53] 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
[54] Xu R, Qin R, Li H, Li D, Li L, et al. 2017. Generation of targeted mutant rice using a CRISPR-Cpf1 system. Plant Biotechnology Journal 15:713−17 doi: 10.1111/pbi.12669
[55] 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
[56] 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
[57] 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
[58] Zong Y, Wang Y, Li C, Zhang R, Chen K, et al. 2017. Precise base editing in rice, wheat and maize with a Cas9-cytidine deaminase fusion. Nature Biotechnology 35:438−40 doi: 10.1038/nbt.3811
[59] Zong Y, Song Q, Li C, Jin S, Zhang D, et al. 2018. Efficient C-to-T base editing in plants using a fusion of nCas9 and human APOBEC3A. Nature Biotechnology 36:950−53 doi: 10.1038/nbt.4261
[60] Ren B, Yan F, Kuang Y, Li N, Zhang D, et al. 2018. Improved base editor for efficiently inducing genetic variations in rice with CRISPR/Cas9-guided hyperactive hAID mutant. Molecular Plant 11:623−26 doi: 10.1016/j.molp.2018.01.005
[61] Jin S, Fei H, Zhu Z, Luo Y, Liu J, et al. 2020. Rationally designed APOBEC3B cytosine base editors with improved specificity. Molecular Cell 79:728−740.E6 doi: 10.1016/j.molcel.2020.07.005
[62] 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
[63] Kang BC, Yun JY, Kim ST, Shin Y, Ryu J, et al. 2018. Precision genome engineering through adenine base editing in plants. Nature Plants 4:427−31 doi: 10.1038/s41477-018-0178-x
[64] Li C, Zong Y, Wang Y, Jin S, Zhang D, et al. 2018. Expanded base editing in rice and wheat using a Cas9-adenosine deaminase fusion. Genome Biology 19:59 doi: 10.1186/s13059-018-1443-z
[65] Niu Q, Wu S, Xie H, Wu Q, Liu P, et al. 2021. Efficient A·T to G·C base conversions in dicots using adenine base editors expressed under the tomato EF1α promoter. Plant Biotechnology Journal In Press doi: 10.1111/pbi.13736
[66] Grünewald J, Zhou R, Lareau CA, Garcia SP, Iyer S, et al. 2020. A dual-deaminase CRISPR base editor enables concurrent adenine and cytosine editing. Nature Biotechnology 38:861−64 doi: 10.1038/s41587-020-0535-y
[67] Li C, Zhang R, Meng X, Chen S, Zong Y, et al. 2020. Targeted, random mutagenesis of plant genes with dual cytosine and adenine base editors. Nature Biotechnology 38:875−82 doi: 10.1038/s41587-019-0393-7
[68] Xu R, Kong F, Qin R, Li J, Liu X, et al. 2021. Development of an efficient plant dual cytosine and adenine editor. Journal of Integrative Plant Biology 63:1600−5 doi: 10.1111/jipb.13146
[69] Anzalone AV, Randolph PB, Davis JR, Sousa AA, Koblan LW, 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
[70] 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
[71] 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 13:671−74 doi: 10.1016/j.molp.2020.03.011
[72] 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
[73] Tang X, Sretenovic S, Ren Q, Jia X, Li M, et al. 2020. Plant prime editors enable precise gene editing in rice cells. Molecular Plant 13:667−70 doi: 10.1016/j.molp.2020.03.010
[74] Schmidt C, Pacher M, Puchta H. 2019. Efficient induction of heritable inversions in plant genomes using the CRISPR/Cas system. The Plant Journal 98:577−89 doi: 10.1111/tpj.14322
[75] Beying N, Schmidt C, Pacher M, Houben A, Puchta H. 2020. CRISPR–Cas9-mediated induction of heritable chromosomal translocations in Arabidopsis. Nature Plants 6:638−45 doi: 10.1038/s41477-020-0663-x
[76] Rönspies M, Schindele P, Puchta H. 2021. CRISPR/Cas-mediated chromosome engineering: opening up a new avenue for plant breeding. Journal of Experimental Botany 72:177−83 doi: 10.1093/jxb/eraa463
[77] Zhou Y, Minio A, Massonnet M, Solares E, Lv Y, et al. 2019. The population genetics of structural variants in grapevine domestication. Nature Plants 5:965−79 doi: 10.1038/s41477-019-0507-8
[78] Pelsy F, Dumas V, Bévilacqua L, Hocquigny S, Merdinoglu D. 2015. Chromosome replacement and deletion lead to clonal polymorphism of berry color in grapevine. PLoS Genetics 11:e1005081 doi: 10.1371/journal.pgen.1005081
[79] Carbonell-Bejerano P, Royo C, Torres-Pérez R, Grimplet J, Fernandez L, et al. 2017. Catastrophic unbalanced genome rearrangements cause somatic loss of berry color in grapevine. Plant Physiology 175:786−801 doi: 10.1104/pp.17.00715
[80] Sunitha S, Rock CD. 2020. CRISPR/Cas9-mediated targeted mutagenesis of TAS4 and MYBA7 loci in grapevine rootstock 101-14. Transgenic Research 29:355−67 doi: 10.1007/s11248-020-00196-w
[81] Nakajima I, Ban Y, Azuma A, Onoue N, Moriguchi T, et al. 2017. CRISPR/Cas9-mediated targeted mutagenesis in grape. PLoS One 12:e0177966 doi: 10.1371/journal.pone.0177966
[82] Ren C, Guo Y, Kong J, Lecourieux F, Dai Z, et al. 2020. Knockout of VvCCD8 gene in grapevine affects shoot branching. BMC Plant Biology 20:47 doi: 10.1186/s12870-020-2263-3
[83] Wang X, Tu M, Wang D, Liu J, Li Y, et al. 2018. CRISPR/Cas9-mediated efficient targeted mutagenesis in grape in the first generation. Plant Biotechnology Journal 16:844−55 doi: 10.1111/pbi.12832
[84] Wan D, Guo Y, Cheng Y, Hu Y, Xiao S, et al. 2020. CRISPR/Cas9-mediated mutagenesis of VvMLO3 results in enhanced resistance to powdery mildew in grapevine (Vitis vinifera). Horticulture Research 7:116 doi: 10.1038/s41438-020-0339-8
[85] Li M, Jiao Y, Wang Y, Zhang N, Wang B, et al. 2020. CRISPR/Cas9-mediated VvPR4b editing decreases downy mildew resistance in grapevine (Vitis vinifera L.). Horticulture Research 7:149 doi: 10.1038/s41438-020-00371-4
[86] Li Y, Mansour H, Wang T, Poojari S, Li F. 2019. Naked-eye detection of grapevine red-blotch viral infection using a plasmonic CRISPR Cas12a assay. Analytical Chemistry 91:11510−13 doi: 10.1021/acs.analchem.9b03545
[87] Osakabe Y, Liang Z, Ren C, Nishitani C, Osakabe K, et al. 2018. CRISPR-Cas9-mediated genome editing in apple and grapevine. Nature Protocols 13:2844−63 doi: 10.1038/s41596-018-0067-9
[88] Wang Y, Liu X, Ren C, Zhong G, Yang L, et al. 2016. Identification of genomic sites for CRISPR/Cas9-based genome editing in the Vitis vinifera genome. BMC Plant Biology 16:96 doi: 10.1186/s12870-016-0787-3
[89] Ren F, Ren C, Zhang Z, Duan W, Lecourieux D, et al. 2019. Efficiency optimization of CRISPR/Cas9-mediated targeted mutagenesis in grape. Frontiers in Plant Science 10:612 doi: 10.3389/fpls.2019.00612
[90] Ren C, Liu Y, Guo Y, Duan W, Fan P, et al. 2021. Optimizing the CRISPR/Cas9 system for genome editing in grape by using grape promoters. Horticulture Research 8:52 doi: 10.1038/s41438-021-00489-z
[91] Xing H, Dong L, Wang Z, Zhang H, Han C, et al. 2014. A CRISPR/Cas9 toolkit for multiplex genome editing in plants. BMC Plant Biology 14:327 doi: 10.1186/s12870-014-0327-y
[92] 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
[93] 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
[94] Tang X, Zheng X, Qi Y, Zhang D, Cheng Y, et al. 2016. A single transcript CRISPR-Cas9 system for efficient genome editing in plants. Molecular Plant 9:1088−91 doi: 10.1016/j.molp.2016.05.001
[95] Wang X, Tu M, Wang Y, Yin W, Zhang Y, et al. 2021. Whole-genome sequencing reveals rare off-target mutations in CRISPR/Cas9-edited grapevine. Horticulture Research 8:114 doi: 10.1038/s41438-021-00549-4
[96] Iocco P, Franks T, Thomas MR. 2001. Genetic transformation of major wine grape cultivars of Vitis vinifera L. Transgenic Research 10:105−12 doi: 10.1023/A:1008989610340
[97] Lv Z, Jiang R, Chen J, Chen W. 2020. Nanoparticle-mediated gene transformation strategies for plant genetic engineering. The Plant Journal 104:880−91 doi: 10.1111/tpj.14973
[98] Chen L, Li W, Katin-Grazzini L, Ding J, Gu X, et al. 2018. A method for the production and expedient screening of CRISPR/Cas9-mediated non-transgenic mutant plants. Horticulture Research 5:13 doi: 10.1038/s41438-018-0023-4
[99] Maher MF, Nasti RA, Vollbrecht M, Starker CG, Clark MD, et al. 2020. Plant gene editing through de novo induction of meristems. Nature Biotechnology 38:84−89 doi: 10.1038/s41587-019-0337-2
[100] Ren C, Guo Y, Gathunga EK, Duan W, Li S, et al. 2019. Recovery of the non-functional EGFP-assisted identification of mutants generated by CRISPR/Cas9. Plant Cell Reports 38:1541−49 doi: 10.1007/s00299-019-02465-3