[1]

Pacesa M, Pelea O, Jinek M. 2024. Past, present, and future of CRISPR genome editing technologies. Cell 187:1076−1100

doi: 10.1016/j.cell.2024.01.042
[2]

Grizot S, Epinat JC, Thomas S, Duclert A, Rolland S, et al. 2010. Generation of redesigned homing endonucleases comprising DNA-binding domains derived from two different scaffolds. Nucleic Acids Research 38:2006−2018

doi: 10.1093/nar/gkp1171
[3]

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
[4]

Juillerat A, Dubois G, Valton J, Thomas S, Stella S, et al. 2014. Comprehensive analysis of the specificity of transcription activator-like effector nucleases. Nucleic Acids Research 42:5390−5402

doi: 10.1093/nar/gku155
[5]

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

doi: 10.1126/science.1225829
[6]

Barrangou R, Fremaux C, Deveau H, Richards M, Boyaval P, et al. 2007. CRISPR provides acquired resistance against viruses in prokaryotes. Science 315:1709−1712

doi: 10.1126/science.1138140
[7]

Nussenzweig PM, Marraffini LA. 2020. Molecular mechanisms of CRISPR-Cas immunity in bacteria. Annual Review of Genetics 54:93−120

doi: 10.1146/annurev-genet-022120-112523
[8]

Garneau JE, Dupuis MÈ, Villion M, Romero DA, Barrangou R, et al. 2010. The CRISPR/Cas bacterial immune system cleaves bacteriophage and plasmid DNA. Nature 468:67−71

doi: 10.1038/nature09523
[9]

Sapranauskas R, Gasiunas G, Fremaux C, Barrangou R, Horvath P, et al. 2011. The Streptococcus thermophilus CRISPR/Cas system provides immunity in Escherichia coli. Nucleic Acids Research 39:9275−9282

doi: 10.1093/nar/gkr606
[10]

Haque E, Taniguchi H, Hassan MM, Bhowmik P, Karim MR, et al. 2018. Application of CRISPR/Cas9 genome editing technology for the improvement of crops cultivated in tropical climates: recent progress, prospects, and challenges. Frontiers in Plant Science 9:617

doi: 10.3389/fpls.2018.00617
[11]

Foster AJ, Martin-Urdiroz M, Yan X, Wright HS, Soanes DM, et al. 2018. CRISPR-Cas9 ribonucleoprotein-mediated co-editing and counterselection in the rice blast fungus. Scientific Reports 8:14355

doi: 10.1038/s41598-018-32702-w
[12]

Wang M, Mao Y, Lu Y, Wang Z, Tao X, et al. 2018. Multiplex gene editing in rice with simplified CRISPR-Cpf1 and CRISPR-Cas9 systems. Journal of Integrative Plant Biology 60:626−631

doi: 10.1111/jipb.12667
[13]

Zeng R, Shi Y, Guo L, Fu D, Li M, et al. 2025. A natural variant of COOL1 gene enhances cold tolerance for high-latitude adaptation in maize. Cell 188:1315−1329.e13

doi: 10.1016/j.cell.2024.12.018
[14]

Molla KA, Sretenovic S, Bansal KC, Qi Y. 2021. Precise plant genome editing using base editors and prime editors. Nature Plants 7:1166−1187

doi: 10.1038/s41477-021-00991-1
[15]

Zhao Y, Huang Z, Zhou X, Teng W, Liu Z, et al. 2025. Precise deletion, replacement and inversion of large DNA fragments in plants using dual prime editing. Nature Plants 11:191−205

doi: 10.1038/s41477-024-01898-3
[16]

Khan MA, Herring G, Zhu JY, Oliva M, Fourie E, et al. 2025. CRISPRi-based circuits to control gene expression in plants. Nature Biotechnology 43:416−430

doi: 10.1038/s41587-024-02236-w
[17]

Zhang C, Tang Y, Tang S, Chen L, Li T, et al. 2024. An inducible CRISPR activation tool for accelerating plant regeneration. Plant Communications 5:100823

doi: 10.1016/j.xplc.2024.100823
[18]

Tang Y, Zhang Z, Yang Z, Wu J. 2023. CRISPR/Cas9 and Agrobacterium tumefaciens virulence proteins synergistically increase efficiency of precise genome editing via homology directed repair in plants. Journal of Experimental Botany 74:3518−3530

doi: 10.1093/jxb/erad096
[19]

Tong Y, Charusanti P, Zhang L, Weber T, Lee SY. 2015. CRISPR-Cas9 based engineering of actinomycetal genomes. ACS Synthetic Biology 4:1020−1029

doi: 10.1021/acssynbio.5b00038
[20]

Wang W, Pan Q, He F, Akhunova A, Chao S, et al. 2018. Transgenerational CRISPR-Cas9 activity facilitates multiplex gene editing in allopolyploid wheat. The CRISPR Journal 1:65−74

doi: 10.1089/crispr.2017.0010
[21]

Asmamaw Mengstie M, Teshome Azezew M, Asmamaw Dejenie T, Teshome AA, Tadele Admasu F, et al. 2024. Recent advancements in reducing the off-target effect of CRISPR-Cas9 genome editing. Biologics: Targets and Therapy 18:21−28

doi: 10.2147/btt.s429411
[22]

Zhu M, Xu R, Yuan J, Wang J, Ren X, et al. 2025. Tracking-seq reveals the heterogeneity of off-target effects in CRISPR-Cas9-mediated genome editing. Nature Biotechnology 43:799−810

doi: 10.1038/s41587-024-02307-y
[23]

Withers A, Jenkins ME. 2023. Can gene editing increase ecosystem and species resilience? The Center for Growth and Opportunity at Utah State University (CGO), Logan, UT, USA. www.thecgo.org/research/can-gene-editing-increase-ecosystem-and-species-resilience/
[24]

Li S, Xia L. 2020. Precise gene replacement in plants through CRISPR/Cas genome editing technology: current status and future perspectives. aBIOTECH 1:58−73

doi: 10.1007/s42994-019-00009-7
[25]

Li J, Liu Z, You C, Qi Z, You J, et al. 2024. Convergence and divergence of diploid and tetraploid cotton genomes. Nature Genetics 56:2562−2573

doi: 10.1038/s41588-024-01964-8
[26]

Jiao C, Xie X, Hao C, Chen L, Xie Y, et al. 2025. Pan-genome bridges wheat structural variations with habitat and breeding. Nature 637:384−393

doi: 10.1038/s41586-024-08277-0
[27]

Hanneman RE. 1999. The reproductive biology of the potato and its implication for breeding. Potato Research 42:283−312

doi: 10.1007/BF02357859
[28]

Zhang H, Tang Y, Yue Y, Chen Y. 2024. Advances in the evolution research and genetic breeding of peanut. Gene 916:148425

doi: 10.1016/j.gene.2024.148425
[29]

Shi X, Hernández R, Hoffmann M. 2021. Impact of nitrate and ammonium ratios on flowering and asexual reproduction in the everbearing strawberry cultivar Fragaria × ananassa Albion. Horticulturae 7:571

doi: 10.3390/horticulturae7120571
[30]

Bhattacharjee S, Bhowmick R, Kant L, Paul K. 2023. Strategic transgene-free approaches of CRISPR-based genome editing in plants. Molecular Genetics and Genomics 298:507−520

doi: 10.1007/s00438-023-01998-3
[31]

Gu X, Liu L, Zhang H. 2021. Transgene-free genome editing in plants. Frontiers in Genome Editing 3:805317

doi: 10.3389/fgeed.2021.805317
[32]

Zhang Y, Butelli E, Martin C. 2014. Engineering anthocyanin biosynthesis in plants. Current Opinion in Plant Biology 19:81−90

doi: 10.1016/j.pbi.2014.05.011
[33]

Gao X, Chen J, Dai X, Zhang D, Zhao Y. 2016. An effective strategy for reliably isolating heritable and Cas9-free Arabidopsis mutants generated by CRISPR/Cas9-mediated genome editing. Plant Physiology 171:1794−800

doi: 10.1104/pp.16.00663
[34]

Putterill J, Varkonyi-Gasic E. 2016. FT and florigen long-distance flowering control in plants. Current Opinion in Plant Biology 33:77−82

doi: 10.1016/j.pbi.2016.06.008
[35]

Aliaga-Franco N, Zhang C, Presa S, Srivastava AK, Granell A, et al. 2019. Identification of transgene-free CRISPR-edited plants of rice, tomato, and Arabidopsis by monitoring DsRED fluorescence in dry seeds. Frontiers in Plant Science 10:1150

doi: 10.3389/fpls.2019.01150
[36]

Liu Y, Zeng J, Yuan C, Guo Y, Yu H, et al. 2019. Cas9-PF, an early flowering and visual selection marker system, enhances the frequency of editing event occurrence and expedites the isolation of genome-edited and transgene-free plants. Plant Biotechnology Journal 17:1191−1193

doi: 10.1111/pbi.13118
[37]

He Y, Zhu M, Wang L, Wu J, Wang Q, et al. 2018. Programmed self-elimination of the CRISPR/Cas9 construct greatly accelerates the isolation of edited and transgene-free rice plants. Molecular Plant 11:1210−1213

doi: 10.1016/j.molp.2018.05.005
[38]

Liu JL, Chen MM, Chen WQ, Liu CM, He Y, et al. 2022. A CASE toolkit for easy and efficient multiplex transgene-free gene editing. Plant Physiology 188:1843−1847

doi: 10.1093/plphys/kiab573
[39]

Zhu M, Yan L, Zhan Z, Chen H, Wang D, et al. 2025. Transgene-Killer-CRISPR version 2 (TKC2) eliminates occasional transgene escape by coupling with a RUBY reporter. Plant Biotechnology Journal 23:4621−4632

doi: 10.1111/pbi.70257
[40]

Wu R, Chai Y, Li Y, Chen T, Qi W, et al. 2025. A visual monitoring DNA-free multi-gene editing system excised via LoxP::FRT/FLP in poplar. Plant Biotechnology Journal 23:4017−4029

doi: 10.1111/pbi.70219
[41]

Zhang Y, Liang Z, Zong Y, Wang Y, Liu J, et al. 2016. Efficient and transgene-free genome editing in wheat through transient expression of CRISPR/Cas9 DNA or RNA. Nature Communications 7:12617

doi: 10.1038/ncomms12617
[42]

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
[43]

Huang X, Jia H, Xu J, Wang Y, Wen J, et al. 2023. Transgene-free genome editing of vegetatively propagated and perennial plant species in the T0 generation via a co-editing strategy. Nature Plants 9:1591−1597

doi: 10.1038/s41477-023-01520-y
[44]

Lee E, Kim Y, Kim M, Lee D, Kang BC. 2025. DNA-free base editing in lettuce via in vitro transcribed base editors. Horticulture Research 67:199−201

doi: 10.1111/jipb.13822
[45]

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 33:1162−1164

doi: 10.1038/nbt.3389
[46]

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
[47]

Subburaj S, Chung SJ, Lee C, Ryu SM, Kim DH, et al. 2016. Site-directed mutagenesis in Petunia × hybrida protoplast system using direct delivery of purified recombinant Cas9 ribonucleoproteins. Plant Cell Reports 35:1535−1544

doi: 10.1007/s00299-016-1937-7
[48]

Svitashev S, Schwartz C, Lenderts B, Young JK, Mark Cigan A. 2016. Genome editing in maize directed by CRISPR-Cas9 ribonucleoprotein complexes. Nature Communications 7:13274

doi: 10.1038/ncomms13274
[49]

Liang Z, Chen K, Li T, Zhang Y, Wang Y, et al. 2017. Efficient DNA-free genome editing of bread wheat using CRISPR/Cas9 ribonucleoprotein complexes. Nature Communications 8:14261

doi: 10.1038/ncomms14261
[50]

Liang Z, Chen K, Zhang Y, Liu J, Yin K, et al. 2018. Genome editing of bread wheat using biolistic delivery of CRISPR/Cas9 in vitro transcripts or ribonucleoproteins. Nature Protocols 13:413−430

doi: 10.1038/nprot.2017.145
[51]

Tan Y, Yu X, Zhang Z, Tian J, Feng N, et al. 2023. An efficient CRISPR/Cas9 genome editing system for a Ganoderma lucidum cultivated strain by ribonucleoprotein method. Journal of Fungi 9:1170

doi: 10.3390/jof9121170
[52]

Kuwabara C, Miki R, Maruyama N, Yasui M, Hamada H, et al. 2024. A DNA-free and genotype-independent CRISPR/Cas9 system in soybean. Plant Physiology 196:2320−2329

doi: 10.1093/plphys/kiae491
[53]

Ali Z, Abul-faraj A, Li L, Ghosh N, Piatek M, et al. 2015. Efficient virus-mediated genome editing in plants using the CRISPR/Cas9 system. Molecular Plant 8:1288−1291

doi: 10.1016/j.molp.2015.02.011
[54]

Ali Z, Abul-Faraj A, Piatek M, Mahfouz MM. 2015. Activity and specificity of TRV-mediated gene editing in plants. Plant Signaling & Behavior 10:e1044191

doi: 10.1080/15592324.2015.1044191
[55]

Ellison EE, Nagalakshmi U, Gamo ME, Huang PJ, Dinesh-Kumar S, et al. 2020. Multiplexed heritable gene editing using RNA viruses and mobile single guide RNAs. Nature Plants 6:620−624

doi: 10.1038/s41477-020-0670-y
[56]

Steinberger AR, Voytas DF. 2025. Virus-induced gene editing free from tissue culture. Nature Plants 11:1241−1251

doi: 10.1038/s41477-025-02025-6
[57]

Weiss T, Kamalu M, Shi H, Li Z, Amerasekera J, et al. 2025. Viral delivery of an RNA-guided genome editor for transgene-free germline editing in Arabidopsis. Nature Plants 11:967−976

doi: 10.1038/s41477-025-01989-9
[58]

Yoshida T, Ishikawa M, Toki S, Ishibashi K. 2024. Heritable tissue-culture-free gene editing in Nicotiana benthamiana through viral delivery of SpCas9 and sgRNA. Plant & Cell Physiology 65:1743−1750

doi: 10.1093/pcp/pcae100
[59]

Ma X, Zhang X, Liu H, Li Z. 2020. Highly efficient DNA-free plant genome editing using virally delivered CRISPR-Cas9. Nature Plants 6:773−779

doi: 10.1038/s41477-020-0704-5
[60]

Liu Q, Zhao C, Sun K, Deng Y, Li Z. 2023. Engineered biocontainable RNA virus vectors for non-transgenic genome editing across crop species and genotypes. Molecular Plant 16:616−631

doi: 10.1016/j.molp.2023.02.003
[61]

Li T, Hu J, Sun Y, Li B, Zhang D, et al. 2021. Highly efficient heritable genome editing in wheat using an RNA virus and bypassing tissue culture. Molecular Plant 14:1787−1798

doi: 10.1016/j.molp.2021.07.010
[62]

Budhagatapalli N, Halbach T, Hiekel S, Büchner H, Müller AE, et al. 2020. Site-directed mutagenesis in bread and durum wheat via pollination by cas9/guide RNA-transgenic maize used as haploidy inducer. Plant Biotechnology Journal 18:2376−2378

doi: 10.1111/pbi.13415
[63]

Kelliher T, Starr D, Su X, Tang G, Chen Z, et al. 2019. One-step genome editing of elite crop germplasm during haploid induction. Nature Biotechnology 37:287−292

doi: 10.1038/s41587-019-0038-x
[64]

Wang B, Zhu L, Zhao B, Zhao Y, Xie Y, et al. 2019. Development of a haploid-inducer mediated genome editing system for accelerating maize breeding. Molecular Plant 12:597−602

doi: 10.1016/j.molp.2019.03.006
[65]

Li C, Sang S, Sun M, Yang J, Shi Y, et al. 2021. Direct modification of multiple gene homoeologs in Brassica oleracea and Brassica napus using doubled haploid inducer-mediated genome-editing system. Plant Biotechnology Journal 19:1889−1891

doi: 10.1111/pbi.13632
[66]

Yang L, Machin F, Wang S, Saplaoura E, Kragler F. 2023. Heritable transgene-free genome editing in plants by grafting of wild-type shoots to transgenic donor rootstocks. Nature Biotechnology 41:958−967

doi: 10.1038/s41587-022-01585-8
[67]

Wang Z, Zou Y, Li X, Zhang Q, Chen L, et al. 2006. Cytoplasmic male sterility of rice with boro II cytoplasm is caused by a cytotoxic peptide and is restored by two related PPR motif genes via distinct modes of mRNA silencing. The Plant Cell 18:676−687

doi: 10.1105/tpc.105.038240
[68]

Mariani C, De Beuckeleer M, Truettner J, Leemans J, Goldberg RB. 1990. Induction of male sterility in plants by a chimaeric ribonuclease gene. Nature 347:737−741

doi: 10.1038/347737a0
[69]

Sun JL, Nakagawa H, Karita S, Ohmiya K, Hattori T. 1996. Rice embryo globulins: amino-terminal amino acid sequences, cDNA cloning and expression. Plant & Cell Physiology 37:612−620

doi: 10.1093/oxfordjournals.pcp.a028989
[70]

Abrahamian P, Hammond RW, Hammond J. 2020. Plant virus-derived vectors: applications in agricultural and medical biotechnology. Annual Review of Virology 7:513−535

doi: 10.1146/annurev-virology-010720-054958
[71]

Turnbull C, Lillemo M, Hvoslef-Eide TAK. 2021. Global regulation of genetically modified crops amid the gene edited crop boom − a review. Frontiers in Plant Science 12:630396

doi: 10.3389/fpls.2021.630396
[72]

Reuters. 2024. China approves more GM crops to boost yields, ensure food security. www.reuters.com/markets/commodities/china-approves-more-gm-crops-boost-yields-ensure-food-security-2024-12-31/?utm_source=chatgpt.com
[73]

Chu M. 2024. China approves first gene-edited wheat in step to open up GM tech to food crops. www.reuters.com/markets/commodities/china-approves-first-gene-edited-wheat-step-open-up-gm-tech-food-crops-2024-05-08/?utm_source=chatgpt.com
[74]

Hobson P. 2024. Australian trial of gene-edited wheat aims for 10% bigger yields. www.reuters.com/markets/commodities/australian-trial-gene-edited-wheat-aims-10-bigger-yields-2024-05-23/?utm_source=chatgpt.com
[75]

Jha P, Ochatt SJ, Kumar V. 2020. WUSCHEL: a master regulator in plant growth signaling. Plant Cell Reports 39:431−444

doi: 10.1007/s00299-020-02511-5
[76]

Horstman A, Li M, Heidmann I, Weemen M, Chen B, et al. 2017. The BABY BOOM transcription factor activates the LEC1-ABI3-FUS3-LEC2 network to induce somatic embryogenesis. Plant Physiology 175:848−857

doi: 10.1104/pp.17.00232
[77]

Zhao Y, Cheng P, Liu Y, Liu C, Hu Z, et al. 2025. A highly efficient soybean transformation system using GRF3-GIF1 chimeric protein. Journal of Integrative Plant Biology 67:3−6

doi: 10.1111/jipb.13767
[78]

Naeem M, Zaman W, Saqib S, Shahzad A, Rahman SU, et al. 2024. CRISPR/Cas-mediated genome editing for efficient tomato breeding: past achievements and future directions. South African Journal of Botany 172:277−288

doi: 10.1016/j.sajb.2024.07.038
[79]

Wang J, Kan S, Liao X, Zhou J, Tembrock LR, et al. 2024. Plant organellar genomes: much done, much more to do. Trends in Plant Science 29:754−769

doi: 10.1016/j.tplants.2023.12.014
[80]

Scheben A, Edwards D. 2018. Bottlenecks for genome-edited crops on the road from lab to farm. Genome Biology 19:178

doi: 10.1186/s13059-018-1555-5
[81]

Ahmad A, Munawar N, Khan Z, Qusmani AT, Khan SH, et al. 2021. An outlook on global regulatory landscape for genome-edited crops. International Journal of Molecular Sciences 22:11753

doi: 10.3390/ijms222111753