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CRISPR/Cas System: Recent Advances and Future Prospects for Genome Editing
Open accessAbstract
Genome editing (GE) has revolutionized biological research through the new ability to precisely edit the genomes of living organisms. In recent years, various GE tools have been explored for editing simple and complex genomes. The clustered regularly interspaced short palindromic repeats (CRISPR)/Cas9 system has widely been used in GE due to its high efficiency, ease of use, and accuracy. It can be used to add desirable and remove undesirable alleles simultaneously in a single event. Here, we discuss various applications of CRISPR/Cas9 in a range of important crops, compare it with other GE tools, and review its mechanism, limitations, and future possibilities. Various newly emerging CRISPR/Cas systems, including base editing (BE), xCas9, and Cas12a (Cpf1), are also considered.
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Citations
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“Genome editing entails creating site-specific mutations in the genome, such as insertions, deletions, or base substitutions (Manghwar et al., 2019).”
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Genomic Dynamics and Functional Insights under Salt Stress in Gossypium hirsutum L.
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“In addition to these, there are novel systems that are being introduced such as spCas9-NG, base editing, xCas9, Cpf1, Cas13, and Cas14n [21].”
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Bishnoi, R., Kaur, S., Sandhu, J. S., & Singla, D. (2023) · Functional & Integrative Genomics · doi:10.1007/s10142-023-01133-w · Cited by 25
“Also, there is a need to work on the problem of off-targets, not only to circumvent them but, also to identify them easily and efficiently (Manghwar et al. 2019).”
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Rahimi-Midani, A., Lee, S., & Choi, T. (2021) · Antibiotics · doi:10.3390/antibiotics10121496 · Cited by 21
Schröpfer, S., Lempe, J., Emeriewen, O. F., & Flachowsky, H. (2022) · Frontiers in Plant Science · doi:10.3389/fpls.2022.928292 · Cited by 21
Susceptibility Is New Resistance: Wheat Susceptibility Genes and Exploitation in Resistance Breeding
Li, M., Yang, Z., & Chang, C. (2022) · Agriculture · doi:10.3390/agriculture12091419 · Cited by 21
Wang, X., & Chang, C. (2022) · Frontiers in Plant Science · doi:10.3389/fpls.2022.1064390 · Cited by 21
“As an advanced genome editing (GE) technique, the CRISPRCas9 (clustered regularly interspaced short palindromic repeatsCRISPR associated 9) system has been extensively employed for functional genomics and trait improvement in model and crop plants (Chen et al., 2019; Manghwar et al., 2019; Zhu et al., 2020; Gao, 2021).”
MethodMolecular mechanisms of flowering phenology in trees
Wang, J., & Ding, J. (2023) · Forestry Research · doi:10.48130/fr-2023-0002 · Cited by 21
Shi, L., Li, X., Xue, L., Zhang, J., Huang, B., Sun, Z., Zhang, Z., Dai, X., Han, S., Dong, W., et al. (2023) · Plant Biotechnology Journal · doi:10.1111/pbi.14114 · Cited by 21
Tuo, D., Yao, Y., Yan, P., Chen, X., Qu, F., Xue, W., Liu, J., Kong, H., Guo, J., Cui, H., et al. (2023) · Plant Methods · doi:10.1186/s13007-023-01055-5 · Cited by 21
“In just a decade, clustered regularly interspaced short palindromic repeats (CRISPR)/CRISPR associated (Cas)-mediated genome editing has revolutionized genetic engineering by enabling precise genome modification in cells or organisms [13].”
BackgroundNew Hope for Genome Editing in Cultivated Grasses: CRISPR Variants and Application
Riaz, A., Kanwal, F., Ahmad, I., Ahmad, S., Farooq, A., Madsen, C. K., Brinch‐Pedersen, H., Bekalu, Z. E., Dai, F., Zhang, G., et al. (2022) · Frontiers in Genetics · doi:10.3389/fgene.2022.866121 · Cited by 20
“This was not possible in the traditional C-to-T base editors due to the specific distance requirement in the editing windows (Manghwar et al., 2019).”
BackgroundThe status of the CRISPR/Cas9 research in plant–nematode interactions
Dutta, T. K., Ray, S., & Phani, V. (2023) · Planta · doi:10.1007/s00425-023-04259-0 · Cited by 20
“Interested readers may consult Manghwar et al. (2019) and Molla et al. (2021) for a comprehensive review of these topics.”
BackgroundTargeted A‐to‐T and A‐to‐C base replacement in maize using an optimized adenine base editor
Zhong, D., Pan, H., Li, K., Zhou, Y., Zhao, F., Ye, L., Ruan, S., Deng, Q., Xu, J., & Lu, Y. (2023) · Plant Biotechnology Journal · doi:10.1111/pbi.14256 · Cited by 20
“They enable the generation of single nucleotide variants in plants for research and crop improvement (Li et al ., 2020; Manghwar et al ., 2019; Ren et al ., 2021; Xu et al ., 2021; Zeng et al ., 2022).”
BackgroundAdvancements in genome editing tools for genetic studies and crop improvement
Ahmadikhah, A., Zarabizadeh, H., Nayeri, S., & Abbasi, M. S. (2025) · Frontiers in Plant Science · doi:10.3389/fpls.2024.1370675 · Cited by 21
Yan, C., Zhang, Z., Xu, J., Yu, M., Yan, S., Wei, L., Zou, Q., Zhang, Q., & Cui, F. (2025) · International Journal of Biological Macromolecules · doi:10.1016/j.ijbiomac.2025.142309 · Cited by 21
Menon, A. V., Song, B., Chao, L., Sriram, D., Chansky, P. A., Bakshi, I., Ulianova, J., & Li, W. (2025) · Frontiers in Genome Editing · doi:10.3389/fgeed.2025.1565387 · Cited by 21
“CRISPR technology has revolutionized genome editing by enabling precise modi fi cations to the genome, resulting in insertions, deletions, or base substitutions (Jiang et al., 2020; Manghwar et al., 2019).”
Dashti, M., Sarab, M. M., Shad, F., & Dehnavi, S. (2025) · Stem Cell Research & Therapy · doi:10.1186/s13287-025-04723-6 · Cited by 26
“Gene editing represents a transformative biotechnology that enables precise modifications of genomic sequences, including insertions, deletions, and base substitutions, offering unprecedented control over genetic material [17, 18].”
Shu, X., Zhang, D., Li, X., Zheng, Q., Cai, X., Ding, S., & Yan, Y. (2022) · ACS Synthetic Biology · doi:10.1021/acssynbio.2c00224 · Cited by 19
Gene editing of non-coding regulatory DNA and its application in crop improvement
Chen, Y.-H., Lu, J., Xia, Y., Huang, L., Zhang, C., Liu, Q., & Li, Q. (2023) · Journal of Experimental Botany · doi:10.1093/jxb/erad313 · Cited by 20
Kaur, H., Pandey, D. K., Goutam, U. K., & Kumar, V. (2021) · Scientia Horticulturae · doi:10.1016/j.scienta.2021.110476 · Cited by 18
Mutagenesis of SlNAC4 by CRISPR/Cas9 alters gene expression and softening of ripening tomato fruit
Gao, Y., Zhang, Y., Fan, Z., Yuan, J., Chen, J., Grierson, D. S., Rui, Y., & Fu, D. (2021) · Vegetable Research · doi:10.48130/vr-2021-0008 · Cited by 18
The future of CRISPR gene editing according to plant scientists
de Lange, J., Nalley, L. L., Yang, W., Shew, A. M., & Steur, H. D. (2022) · iScience · doi:10.1016/j.isci.2022.105012 · Cited by 19
“CRISPR allows scientists to delete certain viruses from plants (Jiang and Doudna, 2017; Manghwar et al., 2019; G. Song et al., 2016).”
In vivo and in vitro genome editing to explore GNE functions
Ilouz, N., Harazi, A., Guttman, M., Daya, A., Ruppo, S., Yakovlev, L., & Mitrani‐Rosenbaum, S. (2022) · Frontiers in Genome Editing · doi:10.3389/fgeed.2022.930110 · Cited by 17
High‐efficiency genome editing by Cas12a ribonucleoprotein complex in Euglena gracilis
Nomura, T., Kim, J., Ishikawa, M., Suzuki, K., & Mochida, K. (2024) · Microbial Biotechnology · doi:10.1111/1751-7915.14393 · Cited by 18
“Additionally, Cas12a generates a 5-bp staggered double-stranded break 18–23 bp down-stream of the PAM (Bandyopadhyay et al., 2020; Khan & Sallard, 2023; Manghwar et al., 2019; Zetsche et al., 2015).”
BackgroundMethodZhao, L., Chen, Y., Li, H., Ding, X., & Li, J. (2024) · CNS Neuroscience & Therapeutics · doi:10.1111/cns.14836 · Cited by 18
Duo, H., Yin, M. J., & Wang, R. (2024) · New Crops · doi:10.1016/j.ncrops.2024.100046 · Cited by 18
Engineering cold resilience: implementing gene editing tools for plant cold stress tolerance
Kumari, K., Gusain, S., & Joshi, R. (2024) · Planta · doi:10.1007/s00425-024-04578-w · Cited by 17
“DNA repair mechanisms are required for joining cleaved strands, involving non-homologous end-joining (NHEJ, error-prone) or homology-directed repair (HDR, error-free) (Manghwar et al. 2019).”
Unlocking Wheat Drought Tolerance: The Synergy of Omics Data and Computational Intelligence
le Roux, M.-S. L., Kunert, K. J., Cullis, C. A., & Botha, A. (2024) · Food and Energy Security · doi:10.1002/fes3.70024 · Cited by 20
Mitigating Antibiotic Resistance: The Utilization of CRISPR Technology in Detection
Zhang, X., Huang, Z., Zhang, Y., Wang, W., Ye, Z., Liang, P., Sun, K., Kang, W., Tang, Q., & Yu, X. (2024) · Biosensors · doi:10.3390/bios14120633 · Cited by 17
“It has been rapidly used for genome editing in a variety of various cell types and experimental platforms [100], with some studies suggesting a greater potential for targeting ARGs.”
Wu, T., Zhang, H., Bi, Y., Yu, Y., Liu, H., Yang, H. Y., Yuan, B., Ding, X., & Chu, Z. (2021) · International Journal of Molecular Sciences · doi:10.3390/ijms222413628 · Cited by 17
Fard, G. B., Ahmadi, M. H., Gholamin, M., Amirfakhrian, R., Teimourian, E. S., Karimi, M. A., & Bafghi, M. H. (2023) · Biotechnology and Bioengineering · doi:10.1002/bit.28603 · Cited by 20
Liú, R., Xiāo, X., Gōng, J., Lǐ, J., Yán, H., Gě, Q., Lú, Q., Lǐ, P., Pān, J., Shāng, H., et al. (2023) · Journal of Advanced Research · doi:10.1016/j.jare.2023.12.005 · Cited by 17
“The cotton transformation was conducted following previous descriptions [45], and the resulting putative transgenic plants were removed to a greenhouse with a 16-hour light/8-hour dark cycle at 30 ℃ .”
MethodCRISPR/Cas: An Emerging Toolbox for Engineering Virus Resistance in Plants
Zhan, X., Zhang, F., Li, N., Xu, K., Wang, X., Gao, S., Yin, Y., Yuan, W., Chen, W., Ren, Z., et al. (2024) · Plants · doi:10.3390/plants13233313 · Cited by 19
“As site-directed genome-editing tools, CRISPR–Cas9, Cas12a, and Cas12b have become widely used sequence-specific nucleases in plant genome engineering [16,17].”
CRISPR, animals, and FDA oversight: Building a path to success
Epstein, L. R., Lee, S. S., Miller, M. F., & Lombardi, H. A. (2021) · Proceedings of the National Academy of Sciences · doi:10.1073/pnas.2004831117 · Cited by 17
Zhang, H., Sun, H., Tang, Z., & Wang, G. (2025) · Frontiers in Plant Science · doi:10.3389/fpls.2025.1670445 · Cited by 16
Precision gene editing: The power of CRISPR-Cas in modern genetics
Joo, J. H., Lee, S., & Kim, K. P. (2025) · Molecular Therapy — Nucleic Acids · doi:10.1016/j.omtn.2025.102733 · Cited by 19
Choi, S. H., Lee, M. H., Jin, D. M., Ju, S. J., Ahn, W. S., Jie, E. Y., Lee, J. M., Lee, J., Kim, C. Y., & Kim, S. W. (2021) · International Journal of Molecular Sciences · doi:10.3390/ijms22157817 · Cited by 17
Fine-tuning phosphatidic acid production for optimal plant stress responses
Gong, Q., Yao, S., Wang, X., & Li, G. (2024) · Trends in Biochemical Sciences · doi:10.1016/j.tibs.2024.05.008 · Cited by 16
miRNAs: Primary modulators of plant drought tolerance
Liang, Y., Yang, X., Wang, C., & Wang, Y. (2024) · Journal of Plant Physiology · doi:10.1016/j.jplph.2024.154313 · Cited by 16
Metadata
- Authors
- Manghwar, H., Lindsey, K., Zhang, X., & Jin, S.
- Affiliations
- Huazhong Agricultural University (CN)
- Durham University (GB)
- Corresponding author
- Zhang, Xianlong
- Jin, Shuangxia
- Venue
- Trends in Plant Science
- Publisher
- Elsevier BV
- Published
- 2019-12
- Volume
- 24
- Issue
- 12
- Pages
- 1102-1125
- ISSN
- 1360-1385 (ISSN-L)
- OpenAlex
- W2984281074
- Cited by
- 529
- References
- 140
- Citations by year
- 2026: 49 · 2025: 84 · 2024: 94 · 2023: 91 · 2022: 76 · 2021: 91 · 2020: 43
- FWCI
- 4.65
- Type
- journal article
- Language
- en
- Open access
- hybrid
- doi.org
- Licence
- Locations
- Trends in Plant Science (publishedVersion, cc-by-nc-nd)
- PubMed (publishedVersion)
- Durham Research Online (Durham University) (publishedVersion, other-oa)
- Durham Research Online (Durham University) (acceptedVersion, other-oa)
- Durham Research Online (Durham University) (submittedVersion, cc-by-nc-nd)
- Funders
- Ministry of Science and Technology of the People's Republic of China
- Topics
- Life Sciences › Biochemistry, Genetics and Molecular Biology › Molecular Biology › CRISPR and Genetic Engineering
- Life Sciences › Agricultural and Biological Sciences › Plant Science › Genetically Modified Organisms Research
- Life Sciences › Biochemistry, Genetics and Molecular Biology › Molecular Biology › RNA regulation and disease
- Keywords
- CRISPR/Cas9, genome editing, base editing, genome editing tools
- MeSH terms
- Gene Editing, Crops, Agricultural, Clustered Regularly Interspaced Short Palindromic Repeats, CRISPR-Cas Systems
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