Journal of Innovative Agriculture | Volume 13 Issue 3 | Pages: 1-11 | Doi : 10.37446/jinagri/ra/13.3.2026.1-11

Review Article

OPEN ACCESS | Published on : 30-Sep-2026

Advances and challenges in plant genome editing: from CRISPR/Cas systems to AI-assisted genome editing

• Mawuli K. Azameti
• Department of Applied Biology, University of Technology and Applied Sciences, Navrongo, Upper East Region, Ghana.

Abstract

The advent of genome editing tools, especially CRISPR/Cas9, has been one of the biggest milestones in the field of plant biology, making precise modifications of crop genomes possible. This review aims to present an overview of opportunities and challenges in plant genome editing. The opportunities include accelerated crop improvement through genetic modification, increased disease resistance via gene editing, and sustainable agriculture through reduced reliance on chemical pesticides and improved climate resilience of crops. However, several technical problems need to be addressed, including unwanted mutations at other sites in the genome (off-target effects), inefficient delivery systems, and recalcitrance during regeneration. Moreover, legislation surrounding the use of genome editing differs significantly from one country to another. While the USA grants exemptions to products derived from genome editing, the EU has formally adopted a new dual-classification regulatory framework for New Genomic Techniques (NGTs), which is now entering a two-year implementation period. These regulations cause obstacles for commercialization, international trade, and scientific collaborations. Recent developments in areas such as prime editing, dual base editing, artificial intelligence-assisted nuclease design, and targeted DNA integration promise improvements in overcoming existing limitations.

Keywords

CRISPR/Cas9, plant genome editing, crop improvement, prime editing, regulatory frameworks, base editing, sustainable agriculture

References

• Achary, V. M. M., Syombua, E. D., Kaur, S., Katamreddy, S. C., Zou, D., Hearne, S. J., & Bandyopadhyay, A. (2026). Advances in the use of morphogenic regulators and peptide regenerating factors for boosting plant transformation and genome editing. Frontiers in Plant Science, 17, 1699984. https://doi.org/10.3389/fpls.2026.1699984

  Ahmar, S., Gill, R. A., Jung, K.-H., Faheem, A., Qasim, M. U., Mubeen, M., & Zhou, W. (2020). Conventional and molecular techniques from simple breeding to speed breeding in crop plants: Recent advances and future outlook. International Journal of Molecular Sciences, 21(7), 2590. https://doi.org/10.3390/ijms21072590

  Alipanahi, R., Safari, L., & Khanteymoori, A. (2025). Advancing CRISPR with deep learning: a comprehensive review of models and databases. Molecular Therapy: Nucleic Acids, 36(4), 102691. https://doi.org/10.1016/j.omtn.2025.102691

  Anzalone, A. V., Randolph, P. B., Davis, J. R., Sousa, A. A., Koblan, L. W., Levy, J. M., ... Liu, D. R. (2019). Search-and-replace genome editing without double-strand breaks or donor DNA. Nature, 576(7785), 149–157. https://doi.org/10.1038/s41586-019-1711-4

  Aslam, M. T., Ghafoor, S., Zia-ul-Haq, M., Noor, M. A., Hassan, M. U., Wu, Z., ... Hashem, M. (2026). ABA-centric signaling networks for drought resilience in cereals: From transcriptional reprogramming to epigenetic memory. Functional Plant Biology, 53, FP25173. https://doi.org/10.1071/FP25173

  Azameti, M. K., & Dauda, W. P. (2021). Base editing in plants: applications, challenges, and future prospects. Frontiers in Plant Science, 12, 664997. https://doi.org/10.3389/fpls.2021.664997

  Barrangou, R. (2020). Finding SECURE ground: USDA edits the biotechnology regulatory framework. The CRISPR Journal, 3(3), 136–137. https://doi.org/10.1089/crispr.2020.29096.rba

  Barrangou, R., Fremaux, C., Deveau, H., Richards, M., Boyaval, P., Moineau, S., ... Horvath, P. (2007). CRISPR provides acquired resistance against viruses in prokaryotes. Science, 315(5819), 1709–1712. https://doi.org/10.1126/science.1138140

  Bhalla, H., Ankita, K., Ahlawat, A., Rode, S. S., Singh, K. H., & Sankaranarayanan, S. (2026). Characterization of self-incompatibility genes in Brassica rapa var. toria and yellow sarson. Frontiers in Plant Science, 17, 1857745. https://doi.org/10.3389/fpls.2026.1857745

  Bickell, E. G. (2023). USDA's SECURE rule to regulate agricultural biotechnology (CRS In Focus IF11573). Congressional Research Service.

  Blumberg, L. C., Bakker, G. M., van Der Kaaij, A., Gariépy, É., van de Geest, H., Slootweg, E. J., ... Wilbers, R. H. (2026). Highly efficient transgene-free ErCas12a RNP-protoplast genome editing and single-cell regeneration in Nicotiana benthamiana for glyco-engineering. Plant Biotechnology Journal, 24(1), 239–255. https://doi.org/10.1111/pbi.70141

  Borg, A. N., Vuts, J., Caulfield, J. C., & Birkett, M. A. (2025). Metabolite-based resistance in wheat varieties to aphid virus vectors: Progress and future opportunities. Pest Management Science, 81(11), 7276–7287. https://doi.org/10.1002/ps.8780

  Borrelli, V., Brambilla, V., Rogowsky, P., Marocco, A., & Lanubile, A. (2018). The enhancement of plant disease resistance using CRISPR/Cas9 technology. Frontiers in Plant Science, 9, 1245.

  Bu, G., Ma, X., Jin, H., & Wang, L. (2025). CRISPR-Cas and RNA sequencing reveal nutrient enhancement pathways in quinoa for plant-based athlete recovery diets and future food security. International Journal of Biological Macromolecules, 318, 144785. https://doi.org/10.1016/j.ijbiomac.2025.144785

  Chen, B., Wang, Y., Zhu, Y., Li, J., Wan, L., Zhu, C., ... El-Sappah, A. H. (2026). Membrane stability under heat stress: Molecular signaling, lipid remodeling, and defense mechanisms in plants. Plant Cell Reports, 45(2), 32. https://doi.org/10.1007/s00299-026-03715-x

  Chen, M., Zhang, Z., Zhu, M., Liu, K., Farag, M. A., Song, L., ... Tao, H. (2025). Biofortification of flavonoids in nuts along the agro-food chain for improved nutritional and health benefits, a comprehensive review and future perspectives. Food Chemistry, 464(Pt. 2), 141754. https://doi.org/10.1016/j.foodchem.2024.141754

  Choi, Y. J., & Ha, S.-H. (2025). Metabolic engineering in rice for functional metabolite production. Rice Science, 32(4), 475–498.

  Council of the European Union. (2025). New genomic techniques: Council agrees negotiating mandate on plants obtained by certain new genomic techniques and their food and feed.

  Das, P., Saha, R., Panda, D., Ghosh, C., Avinash, S. P., Panda, S., ... Molla, K. A. (2026). AI-designed OpenCRISPR-1 performs robust knockout, base editing, and prime editing in rice. New Phytologist. https://doi.org/10.1111/nph.71272

  Decima Oneto, C. A., Massa, G. A., Echarte, L., Rey Burusco, M. F., Gonzalez, M. N., Alfonso, C. S., ... Feingold, S. E. (2025). CRISPR/Cas9 editing of CBP80 enhances drought tolerance in potato (Solanum tuberosum). Frontiers in Plant Science, 16, 1598947. https://doi.org/10.3389/fpls.2025.1598947

  European Commission. (2023). Proposal for a regulation of the European Parliament and of the Council on plants obtained by certain new genomic techniques and their food and feed, and amending Regulation (EU) 2017/625 (COM(2023) 411 final).

  European Parliament Research Service. (2024). New genomic techniques: State of play of the proposed EU regulatory framework.

  Feng, B., Wang, Y., Zhang, X., Mu, T., Zhang, B., Li, Y., ... Li, H. (2025). Targeted mutagenesis and functional marker development of two Bna.TAC1s conferring novel rapeseed germplasm with compact architecture. Theoretical and Applied Genetics, 138(4), 86.

  Fu, L., Zhang, X., Tu, Y., Chen, M., Xu, X., Su, T., ... Zhang, G. (2026). OsNAC10 negatively regulates salt tolerance by repressing OsHKT1;5 expression and reducing shoot-to-root Na⁺ recirculation in rice. Plant Communications, 7(6), 101771. https://doi.org/10.1016/j.xplc.2026.101771

  Gallo, D., Meunier, A.-C., & Périn, C. (2025). A long journey towards genome editing technologies in plants: A technical and critical review of genome editing technologies. Frontiers in Genome Editing, 7, 1663352. https://doi.org/10.3389/fgeed.2025.1663352

  Guzmán, N. M., Esquerra-Ruvira, B., & Mojica, F. J. M. (2021). Digging into the lesser-known aspects of CRISPR biology. International Microbiology, 24(4), 579–589.

  Haider, S., & Mussolino, C. (2025). Fine-tuning homology-directed repair (HDR) for precision genome editing: current strategies and future directions. International Journal of Molecular Sciences, 26(9), 4067.

  Han, X., Li, S., Zeng, Q., Sun, P., Wu, D., Wu, J., ... Li, G. (2025). Genetic engineering, including genome editing, for enhancing broad-spectrum disease resistance in crops. Plant Communications, 6(2), 101195.

  Hu, J., Li, X., Gao, Y., Guo, Y., Liu, Y., Wang, C., ... Wan, J. (2026). Cas9-embedding hyperactive TadA8e confers efficient and highly specific A-to-G base editing in rice. Plant Biotechnology Journal, 24(4), 2576–2591. https://doi.org/10.1111/pbi.70511

  Huang, T. K., & Puchta, H. (2019). CRISPR/Cas-mediated gene targeting in plants: finally a turn for the better for homologous recombination. Plant Cell Reports, 38(4), 443–453.

  Huttunen, K., Artell, J., Heinola, K., Pouta, E., Schulman, A. H., Tienhaara, A., ... Vainio, A. (2026). Is gene editing natural and does it matter? A qualitative analysis of citizen-consumers’ and farmers’ views on the use of new genomic techniques in plants. Agriculture and Human Values, 43(1), 9.

  Iksat, N., Madirov, A., Zhanassova, K., & Masalimov, Z. (2025). Artificial intelligence-assisted CRISPR/Cas systems for targeting plant viruses. Genes, 16(11), 1258. https://doi.org/10.3390/genes16111258

  Iswanto, A. B. B., Kang, H., Park, S., Son, G. H., Pike, S. M., & Kim, S. H. (2025). Recent advances in improving yield and immunity through transcription factor engineering. Journal of Integrative Plant Biology, 67(8), 2005–2027.

  Jin, Y., Kristkova, Z. S., & Wesseler, J. (2025). Welfare impacts of China's regulatory change toward genome-edited crops. Trends in Biotechnology, 43(11), 2681–2683. https://doi.org/10.1016/j.tibtech.2025.04.010

  Jinek, M., Chylinski, K., Fonfara, I., Hauer, M., Doudna, J. A., & Charpentier, E. (2012). A programmable dual-RNA–guided DNA endonuclease in adaptive bacterial immunity. Science, 337(6096), 816–821. https://doi.org/10.1126/science.1225829

  Kamran, M., Zhijun, T., Ullah, A., Alvi, M. H. A., Aqeel, T., Xuejun, C., ... Xu, H. (2026). Integrating genomic technologies with artificial intelligence, CRISPR editing, and high-throughput phenotyping for engineering disease-resistant crops. Plant Stress, 20, 101317. https://doi.org/10.1016/j.stress.2026.101317

  Kim, Y. H., Kim, N., Okafor, I., Choi, S., Min, S., Lee, J., ... Kim, H. H. (2023). Sniper2L is a high-fidelity Cas9 variant with high activity. Nature Chemical Biology, 19(8), 972–980. https://doi.org/10.1038/s41589-023-01279-5

  Lankireddy, S. V., Lekkala, S., Khadgi, A., Sripathi, V. R., & Janga, M. R. (2026). Molecular biology of Cotton Leafroll Dwarf Virus (CLRDV) and potential application of CRISPR-Cas technology for developing virus-resistant cotton. Virology, 614, 110730. https://doi.org/10.1016/j.virol.2025.110730

  Li, J. F., Norville, J. E., Aach, J., McCormack, M., Zhang, D., Bush, J., ... Sheen, J. (2013). Multiplex and homologous recombination-mediated genome editing in Arabidopsis and Nicotiana benthamiana using guide RNA and Cas9. Nature Biotechnology, 31(8), 688–691.

  Li, P., & Xiao, S. (2025). Diverse functions of plant MLO proteins: From mystery to elucidation. Annual Review of Phytopathology, 63(1), 147–173. https://doi.org/10.1146/annurev-phyto-030625-035800

  Liu, P., Panda, K., Edwards, S. A., Swanson, R., Yi, H., Pandesha, P., ... Slotkin, R. K. (2024). Transposase-assisted target-site integration for efficient plant genome engineering. Nature, 631(8021), 593–600. https://doi.org/10.1038/s41586-024-07613-8

  López-Casado, G., Sánchez-Raya, C., Ric-Varas, P. D., Paniagua, C., Blanco-Portales, R., Muñoz-Blanco, J., ... Mercado, J. A. (2023). CRISPR/Cas9 editing of the polygalacturonase FaPG1 gene improves strawberry fruit firmness. Horticulture Research, 10(3), uhad011. https://doi.org/10.1093/hr/uhad011

  Mansoor, S., Karunathilake, E. M. B. M., Tuan, T. T., & Chung, Y. S. (2025). Genomics, phenomics, and machine learning in transforming plant research: Advancements and challenges. Horticultural Plant Journal, 11(2), 486–503. https://doi.org/10.1016/j.hpj.2023.09.005

  McFadden, B. R., Rumble, J. N., Stofer, K. A., & Folta, K. M. (2024). US public opinion about the safety of gene editing in the agriculture and medical fields and the amount of evidence needed to improve opinions. Frontiers in Bioengineering and Biotechnology, 12, 1340398. https://doi.org/10.3389/fbioe.2024.1340398

  Mmbando, G. S. (2025). Exploring the capacity of modern biotechnology to enhance climate smart crop production in Africa. Discover Agriculture, 3(1), 48. https://doi.org/10.1007/s44279-025-00198-4

  Molla, K. A., Shih, J., Wheatley, M. S., & Yang, Y. (2022). Predictable NHEJ insertion and assessment of HDR editing strategies in plants. Frontiers in Genome Editing, 4, 825236. https://doi.org/10.3389/fgeed.2022.825236

  Movahedi, A., Wei, H., Zhou, X., Fountain, J. C., Chen, Z. H., Mu, Z., Sun, W., Zhang, J., Li, D., Guo, B., Varshney, R. K., Yang, L., & Zhuge, Q. (2022). Precise exogenous insertion and sequence replacements in poplar by simultaneous HDR overexpression and NHEJ suppression using CRISPR-Cas9. Horticulture Research, 9, uhac154. https://doi.org/10.1093/hr/uhac154

  Namata, M. J., Xu, J., Habyarimana, E., Palakolanu, S. R., Wang, L., & Li, J. (2025). Genome editing in maize and sorghum: A comprehensive review of CRISPR/Cas9 and emerging technologies. The Plant Genome, 18(2), e70038.

  Nekrasov, V., Wang, C., Win, J., Lanz, C., Weigel, D., & Kamoun, S. (2017). Rapid generation of a transgene-free powdery mildew resistant tomato by genome deletion. Scientific Reports, 7, 482.

  Norfaezah, J., Masani, M. Y. A., Nurfahisza, A. R., Bahariah, B., Fizree, M. P. M. A. A., Shaharuddin, N. A., ... Parveez, G. K. A. (2025). A fast-track system for transgene-free genome editing in oil palm (Elaeis guineensis Jacq.) via biolistic delivery of CRISPR/Cas9 ribonucleoprotein (CRISPR-RNP). 3 Biotech, 15(11), 389. https://doi.org/10.1007/s13205-025-04555-4

  Qi, S., Wei, L., Ding, Z., Zhong, F., Yang, S., Wu, L., ... Su, X. (2026). Targeting transthyretin by one Cas9 variant with superfidelity and broad compatibility. Science Advances, 12(1), eadu6505. https://doi.org/10.1126/sciadv.adu6505

  Ramakrishnan, M., Kaul, R., Sharma, A., Ahmad, Z., Vijayakanth, V., Keerthana, K., ... Wei, Q. (2025). CRISPR RNP-mediated transgene-free genome editing in plants: advances, challenges and future directions for tree species. Plant, Cell & Environment. https://doi.org/10.1111/pce.70176

  Rocha, D. C., Omoregbee, M. O., Luo, W., Fang, H., Ye, Q., Liu, Y., ... Qi, Y. (2026). Transgene-free genome editing in citrus and poplar meristem tissues via biolistic ribonucleoprotein delivery of CRISPR-Cas9. Plant Cell Reports, 45(3), 58. https://doi.org/10.1007/s00299-026-03741-9

  Rönspies, M., Khosravi, S., Helia, O., Valisi, A., Fajkus, J., Fojtová, M., ... Puchta, H. (2025). CRISPR-Cas–mediated heritable chromosome fusions in Arabidopsis. Science, 390(6775), 843–848. https://doi.org/10.1126/science.adz8505

  Ruffolo, J. A., Nayfach, S., Gallagher, J., Bhatnagar, A., Beazer, J., Hussain, R., ... Madani, A. (2025). Design of highly functional genome editors by modelling CRISPR–Cas sequences. Nature, 645(8080), 518–525. https://doi.org/10.1038/s41586-025-09298-z

  Savary, S., Willocquet, L., Pethybridge, S. J., Esker, P., McRoberts, N., & Nelson, A. (2019). The global burden of pathogens and pests on major food crops. Nature Ecology & Evolution, 3(3), 430–439. https://doi.org/10.1038/s41559-018-0793-y

  Shan, Q., Wang, Y., Li, J., Zhang, Y., Chen, K., Liang, Z., ... Gao, C. (2013). Targeted genome modification of crop plants using a CRISPR-Cas system. Nature Biotechnology, 31(8), 686–688.

  Sohail, H., Noor, I., Hussain, H., Zhang, L., Xu, X., Chen, X., & Yang, X. (2026). Genome editing in horticultural crops: Augmenting trait development and stress resilience. Horticultural Plant Journal, 12(1), 1–18. https://doi.org/10.1016/j.hpj.2025.09.001

  Song, L., Niu, K., Yang, Y., Guo, Y., Wu, M., & Liu, T. (2025). The MYB transcription factor MYB48 negatively regulates the resistance to Magnaporthe oryzae by directly enhancing the transcription of HSP71.1 in rice. Plant Science, 360, 112717. https://doi.org/10.1016/j.plantsci.2025.112717

  Srivastava, A. K., Riaz, A., Jiang, J., Li, X., Uzair, M., Mishra, P., Zeb, A., Zhang, J., Luo, L., Chen, S., Yang, S., & Xie, X. (2025). Advancing climate-resilient sorghum: The synergistic role of plant biotechnology and microbial interactions. Rice, 18, 41.

  Sun, C., Lei, Y., Li, B., Gao, Q., Li, Y., Cao, W., ... Gao, C. (2024). Precise integration of large DNA sequences in plant genomes using PrimeRoot editors. Nature Biotechnology, 42(2), 316–327. https://doi.org/10.1038/s41587-023-01769-w

  The Nobel Prize in Chemistry 2020. (2020). NobelPrize.org. Nobel Prize Outreach AB. https://www.nobelprize.org/prizes/chemistry/2020/summary/

  United States Department of Agriculture, Animal and Plant Health Inspection Service. (2025). Revised biotechnology regulations (SECURE rule).

  Vanguri, P. R. (2025). Biofortification-based genetic improvement of rice for nutritional quality enhancement to combat hidden hunger. Journal of Advances in Biology & Biotechnology, 28(12), 1242–1262. https://doi.org/10.9734/jabb/2025/v28i123467

  Wang, Y., & Xiao, S. (2025). Engineering of autoactive NLRs: A big step toward breeding crops with durable and broad-spectrum resistance. Advanced Biotechnology, 3, 24. https://doi.org/10.1007/s44307-025-00079-3

  Wang, Y., Cheng, X., Shan, Q., Zhang, Y., Liu, J., Gao, C., & Qiu, J. L. (2014). Simultaneous editing of three homoeoalleles in hexaploid bread wheat confers heritable resistance to powdery mildew. Nature Biotechnology, 32(9), 947–951. https://doi.org/10.1038/nbt.2969

  World Vegetable Center. (2026, April 30). Triple threat: WorldVeg debuts tomatoes that are insect resilient and attractive to buyers. AgNavigator.com.

  Xu, R., Zhu, J., Wang, H., Wang, H., Zhao, L., Liu, X., ... Li, J. (2026). Development of dual base editors based on ssDNA-targeting SCP1.201 deaminases for the artificial evolution of novel herbicide-tolerant OsEPSPS variants. Plant Communications, 7(3), 101632. https://doi.org/10.1016/j.xplc.2025.101632

  Yıldırım, K., & Kavas, M. (2026). The role of CRISPR in modern plant breeding: Overcoming breeding barriers and legislative challenges through transgene-free genome editing. Genome, 69, 1–17. https://doi.org/10.1139/gen-2025-0063

  Yuan, L., Gai, W., Xuan, X., Ahiakpa, J. K., Li, F., Ge, P., ... Zhang, Y. (2024). Advances in improving tomato fruit quality by gene editing. Horticultural Plant Journal, 11(6). https://doi.org/10.1016/j.hpj.2024.04.008

  Zhan, X., Zhang, F., Li, N., Xu, K., Wang, X., Gao, S., ... Wang, F. (2024). CRISPR/Cas: An emerging toolbox for engineering virus resistance in plants. Plants, 13(23), 3313. https://doi.org/10.3390/plants13233313

  Zhang, R., Guo, R., Zhi, H., Tang, S., Wang, L., Ren, Y., ... Jia, G. (2025). De novo creation of narrowed plant architecture via CRISPR/Cas9-mediated mutagenesis of SiLGs in foxtail millet. Plant Biotechnology Journal, 23(6), 2400. https://doi.org/10.1111/pbi.70037

  Zhang, S., Wu, S., Jia, Z., Zhang, J., Li, Y., Ma, X., ... Wang, W. (2024). Exploring the influence of a single-nucleotide mutation in EIN4 on tomato fruit firmness diversity through fruit pericarp microstructure. Plant Biotechnology Journal, 22(9), 2379–2394.

  Zhang, Y., Aslam, M. N., & Liu, Y. (2025). Rewiring autoactive NLRs into protease-activated switches for broad-spectrum plant immunity. The Crop Journal, 13(6), 1660–1662. https://doi.org/10.1016/j.cj.2025.08.004

  Zhao, Y., Huang, Z., Zhou, X., Teng, W., Liu, Z., Wang, W., ... Zong, Y. (2025). Precise deletion, replacement and inversion of large DNA fragments in plants using dual prime editing. Nature Plants, 11(2), 191–205. https://doi.org/10.1038/s41477-024-01898-3

  Zhou, J., Zou, X., Deng, Z., & Duan, L. (2024). Analysing a group of homologous BAHD enzymes provides insights into the evolutionary transition of rosmarinic acid synthases from hydroxycinnamoyl-CoA/quinate hydroxycinnamoyl transferases. Plants, 13(4), 512.