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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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Kandhol, N., Dash, P. K., Singh, V. P., Deshmukh, R. K., Dhankher, O. P., Tran, L. P., White, J. C., & Tripathi, D. K. (2025) · Trends in Plant Science · doi:10.1016/j.tplants.2025.04.012 · Cited by 15
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BackgroundCas14a1-advanced LAMP for ultrasensitive and visual Pathogen diagnostic
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Inhibitors of DNA double-strand break repair at the crossroads of cancer therapy and genome editing
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“CRISPR/Cas9 technology enables accurate and efficient targeting of candidate genes for mutation (Komor et al., 2017b; Manghwar et al., 2019).”
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Electrochemical Biosensors as a Novel Platform in the Identification of Listeriosis Infection
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“The PAM sequences are mainly used to identify targets, and the presence or absence of PAM sequences in target nucleotides is a critical factor in the precise targeting of the CRISPR/Cas9 system (Manghwar et al., 2019).”
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“…of specific traits and the in-depth study of gene functions, providing unprecedented opportunities to develop crops with improved characteristics and to deepen our understanding of plant biology at the genetic level (Bak et al ., 2018; Gaj et al ., 2013; Liu et al ., 2022; Manghwar et al ., 2019).”
Enhancing drought resilience in crops: mechanistic approaches in the face of climate challenge
Parmar, H., Goel, A., Gelaw, T. A., & Reddy, M. K. (2025) · Plant Molecular Biology · doi:10.1007/s11103-025-01616-3 · Cited by 15
“Their integration allows breeders to identify, validate, and utilize specific genomic independently of HDR and NHEJ, thereby minimizing unintended genomic alterations (Manghwar et al. 2019).”
Abdullah, S. N. A., Mayes, S., & Moradpour, M. (2021) · Current Chinese Science · doi:10.2174/2210298101666210709104258 · Cited by 13
CRISPR/Cas9 Mediated Disruption of Seminal Fluid Protein Sfp62 Induces Male Sterility in Bombyx mori
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Research Advances on Swine Acute Diarrhea Syndrome Coronavirus
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Sharma, M., Sidhu, A. K., Samota, M. K., Shah, P., Pandey, M. K., & Gangurde, S. S. (2024) · Discover Agriculture · doi:10.1007/s44279-024-00105-3 · Cited by 13
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“CRISPR/Cas9 [61,155,156] • SpCas9 system is the first CRISPR/Cas system to be used in genome editing and shows robust activity.”
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“CRISPR/Cas9 has revolutionized the pace of plant biology research (Manghwar et al. 2019) and made precise plant genome editing a reality (Zhu et al. 2020).”
Jain, H., Chahal, S., Singh, I., Sain, S. K., & Siwach, P. (2023) · Molecular Biology Reports · doi:10.1007/s11033-023-08266-y · Cited by 12
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“Therefore, the choice of promoter is a crucial factor for gRNA and Cas gene expression in plant cells, thereby affecting the editing efficiencies (Manghwar et al., 2019; Hassan et al., 2021).”
BackgroundTargeted Nanocarrier Delivery of RNA Therapeutics to Control HIV Infection
Agbosu, E., Ledger, S., Kelleher, A. D., Wen, J., & Ahlenstiel, C. (2022) · Pharmaceutics · doi:10.3390/pharmaceutics14071352 · Cited by 13
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“Current methods for targeting lncRNA include small interfering RNA (Alshaer et al., 2021), antisense oligonucleotides (ASOs) (Kim, 2023), and CRISPR technology (Manghwar et al., 2019).”
Phagetherapy updates: New frontiers against antibiotic resistance
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“Class 1, with subtypes I, III, and IV, contains multi-Cas protein complexes, whereas Class 2, containing types II, V, and VI, contains only a single effector protein region [45 – 47].”
InfluentialA visual monitoring DNA‐free multi‐gene editing system excised via LoxP::FRT/FLP in poplar
Wu, R., Chai, Y., Li, Y., Chen, T., Qi, W., Xue, Y., Lu, H., Chen, Z., Guo, B., Li, S., et al. (2025) · Plant Biotechnology Journal · doi:10.1111/pbi.70219 · Cited by 11
“To eliminate the residual elements post-gene editing, the predominant strategies employed involve the transient introduction of Cas9 and gRNA into mutant progeny, as well as outcrossing (Manghwar et al ., 2019).”
Comparative structural and dynamics study of free and gRNA-bound FnCas9 and SpCas9 proteins
Panda, G., & Ray, A. (2022) · Computational and Structural Biotechnology Journal · doi:10.1016/j.csbj.2022.07.041 · Cited by 12
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Sustained release of therapeutic gene by injectable hydrogel for hepatocellular carcinoma
Xu, S., Cai, J., Cheng, H., & Wang, W. (2023) · International Journal of Pharmaceutics X · doi:10.1016/j.ijpx.2023.100195 · Cited by 12
“ising perspective in clinical implementation (Chen et al., 2019; Manghwar et al., 2019).”
Recent progress on the CRISPR/Cas system in optical biosensors
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Targeted editing of CCL5 with CRISPR-Cas9 nanoparticles enhances breast cancer immunotherapy
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“MCF-7 and MDA-MB-231 cells were infected with Lentiviral CRISPR/Cas9 vectors and subsequently screened with 4 µg/ml puromycin (A1113803, Thermo) to establish stable CCL5 knockout cells [ 44].”
CRISPR/Cas genome editing: A frontier for transforming precision cassava breeding
Juma, B. S., Cecilia, M., Ngugi, M. P., & Mbinda, W. M. (2021) · AFRICAN JOURNAL OF BIOTECHNOLOGY · doi:10.5897/ajb2021.17344 · Cited by 11
“The rapid production of the CRISPR/Cas9 genome editing system in plants has been addressed in many reviews (Ma et al., 2016; Liu et al., 2017; Georges and Ray, 2017; Haque et al., 2018; Manghwar et al., 2019).”
BackgroundAdvances in Molecular Marker Technology and their Significance in Plant Improvement Strategies
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“Recently, the development of genome-edited crops using the CRISPR/Cas9 system has attracted attention for reducing the risk associated with genetically modified organisms containing foreign DNA sequences [32, 42].”
BackgroundProbiotic characterization of Bacillus smithii : Research advances, concerns, and prospective trends
Zhao, N., Huang, X., Liu, Z., Gao, Y., Teng, J., Yu, T., & Yan, F. (2024) · Comprehensive Reviews in Food Science and Food Safety · doi:10.1111/1541-4337.13308 · Cited by 14
Precise Gene Knock‐In Tools with Minimized Risk of DSBs: A Trend for Gene Manipulation
Liu, Y. H., Kong, J., Liu, G., Li, Z., & Xiao, Y. (2024) · Advanced Science · doi:10.1002/advs.202401797 · Cited by 10
Li, S., Zhang, P., Gao, R., Li, B., Zheng, Z., Song, X., & Pei, D. (2025) · Horticulture Research · doi:10.1093/hr/uhaf187 · Cited by 9
“This strategy significantly enhances the genome-editing efficiency of the CRISPR/Cas9 system and increases the diversity of mutation types [75].”
Li, X., Mao, Y., Tian, Y., Qiao, J., Zhao, R., Peng, W., Man, S., Gao, Z., & Ma, L. (2025) · Trends in Food Science & Technology · doi:10.1016/j.tifs.2025.105522 · Cited by 9
Genetic transformation and gene delivery strategies in Carica papaya L.
Tuo, D., Ma, C., Yan, P., Kong, H., Zhou, P., Guo, A., Zhao, H., & Shen, W. (2023) · Tropical Plants · doi:10.48130/tp-2023-0005 · Cited by 9
Targeted editing of OsSWEET13, a bacterial leaf blight susceptible gene in rice using CRISPR tool
Ancydiana, P., Shanthinie, A., Arulganesh, T., Kumam, Y., Kumar, K. S., Arul, L., Kokiladevi, E., Varanavasiappan, S., Manonmani, S., & Sudhakar, D. (2022) · Electronic Journal of Plant Breeding · doi:10.37992/2022.1303.139 · Cited by 9
Cheng, Y., Zeng, J., Liu, Y., Yu, H., Tong, Z., Zhang, J.-D., Gao, Q., Wang, Z., Sui, X., Xiao, B., et al. (2024) · Frontiers in Plant Science · doi:10.3389/fpls.2024.1329697 · Cited by 8
Developing a Versatile Arsenal: Novel Antimicrobials as Offensive Tools Against Pathogenic Bacteria
Ma, J., & Lu, Z. (2025) · Microorganisms · doi:10.3390/microorganisms13010172 · Cited by 8
Winiarczyk, D., Khodadadi, H., Leszczyński, P., & Taniguchi, H. (2025) · PLoS ONE · doi:10.1371/journal.pone.0312722 · Cited by 8
Pham, Q. T., Raad, S., Mangahas, C. L., M’Callum, M.-A., Raggi, C. C., & Paganelli, M. (2020) · Cytotherapy · doi:10.1016/j.jcyt.2020.06.008 · Cited by 8
An Episomal CRISPR/Cas12a System for Mediating Efficient Gene Editing
Duan, N., Tang, S., Zeng, B., Hu, Z., Hu, Q., Wu, L., Zhou, M., & Liang, D. (2021) · Life · doi:10.3390/life11111262 · Cited by 8
Current agricultural diversification strategies are already agroecological
Lenné, J. M. (2023) · Outlook on Agriculture · doi:10.1177/00307270231199796 · Cited by 8
“Some have claimed that the genetic base of modern crop varieties is depauperate (McDonald and Stuckenbrock, 2016), however, evidence from studies on their parentage does not support this pessimistic view (Table 1; Witcombe, 1999).”
MethodInfluentialShi, S., Chen, C., Shen, X., Du, S., Liu, K., Gao, Y. S., Qu, L., Yang, J., Tang, M., & Han, X. (2024) · Chemical Engineering Journal · doi:10.1016/j.cej.2024.153152 · Cited by 7
Enhancing tiny millets through genome editing: current status and future prospects
Weldemichael, M. Y., & Gebremedhn, H. M. (2025) · Molecular Genetics and Genomics · doi:10.1007/s00438-025-02231-z · Cited by 7
Advances in locally administered nucleic acid therapeutics
Shen, J., Duan, X., Xie, T., Zhang, X., Cai, Y., Pan, J., Zhang, X., & Sun, X. (2025) · Bioactive Materials · doi:10.1016/j.bioactmat.2025.02.043 · Cited by 8
Concanavalin-A-assisted extraction-free one-pot RPA–CRISPR/Cas12a assay for rapid detection of HPV16
Nie, Y., Li, X., Wen, Y., Fei, S., Wang, Y., Li, Y.-Z., Zhang, K., Kang, J., Cheng, Y. J., Wang, H., et al. (2025) · Microchimica Acta · doi:10.1007/s00604-025-07198-7 · Cited by 7
CRISPR/Cas-Mediated Optimization of Soybean Shoot Architecture for Enhanced Yield
Li, N., Yuan, X., Han, B., Guo, W., & Chen, H. (2025) · International Journal of Molecular Sciences · doi:10.3390/ijms26167925 · Cited by 7
“A single sgRNA directs SpCas9 to its target with precision [69], streamlining edits that once demanded complex protein engineering [70].”
Autopolyploidization affects transcript patterns and gene targeting frequencies in Physcomitrella
Rempfer, C., Wiedemann, G., Schween, G., Kerres, K. L., Lucht, J. M., Horres, R., Decker, E. L., & Reski, R. (2021) · Plant Cell Reports · doi:10.1007/s00299-021-02794-2 · Cited by 8
Li, J., Tang, C., Liang, G., Tian, H., Lai, G., Wu, Y., Liu, S., Zhang, W., Liu, S., & Shao, H. (2023) · Human Gene Therapy · doi:10.1089/hum.2023.115 · Cited by 7
“119 In addition, reducing the size of the effector protein will enable the incorporation of other regulatory elements in the delivery system, which can potentially increase gene editing effi-ciency.”
Detailed Insight into Various Classes of the CRISPR/Cas System to Develop Future Crops
Thakur, N., Lakhani, H., & Tiwari, S. (2024) · Springer eBooks · doi:10.1007/978-981-99-8529-6_9 · Cited by 7
CRISPR technology in human diseases
Feng, Q., Li, Q., Zhou, H., Wang, Z., Lin, C., Jiang, Z., Liu, T., & Wang, D. (2024) · MedComm · doi:10.1002/mco2.672 · Cited by 8
Liao, N., Dong, Z., Zhang, X., Qi, Q., Luo, Y., Huang, L., Chen, P., Lu, C., & Pan, M. (2021) · International Journal of Biological Macromolecules · doi:10.1016/j.ijbiomac.2021.10.125 · Cited by 7
Analysis of the landscape of human enhancer sequences in biological databases
Mulero-Hernández, J., & Fernández‐Breis, J. T. (2022) · Computational and Structural Biotechnology Journal · doi:10.1016/j.csbj.2022.05.045 · Cited by 9
“It also allows other molecules to be incorporated into the Cas9 nuclease, so many technical variants have been developed to activate and silence sequences [139,74,140].”
BackgroundGenetic advancements in obesity management and CRISPR–Cas9-based gene editing system
Jayachandran, M., Fei, Z., & Qu, S. (2022) · Molecular and Cellular Biochemistry · doi:10.1007/s11010-022-04518-w · Cited by 10
“CRISPR/Cas genome editing is a simple, cost-effective, and highly specific technique for introducing genetic variation [12].”
BackgroundLiu, Z., Gong, G., Li, Y., Xu, Q., Akimbekov, N. S., Zha, J., & Wu, X. (2023) · Journal of Agricultural and Food Chemistry · doi:10.1021/acs.jafc.3c00189 · Cited by 7
Strategies to Overcome Antimicrobial Resistance in Nosocomial Infections, A Review and Update
Bakhtiyari, N., Farajnia, S., Ghasemali, S., Farajnia, S., Pormohammad, A., & Saeidvafa, S. (2024) · Infectious Disorders - Drug Targets · doi:10.2174/0118715265276529231214105423 · Cited by 11
Structural basis of negative regulation of CRISPR-Cas7-11 by TPR-CHAT
Tian, H., Luo, Q., Ma, H., Wang, X., Li, X., Shen, C., Pang, J., Wang, Y., Chen, Y., Zhang, C., et al. (2024) · Signal Transduction and Targeted Therapy · doi:10.1038/s41392-024-01821-4 · Cited by 6
“6,7 A CRISPR-Cas system consists of two main components: a Cas protein, which is the catalytic core, and CRISPR loci, which have “ genetic memory ” functions.”
BackgroundAdvances in understanding plant-pathogen interactions: insights from tomato as a model system
Azeez, S. O., & Adeboye, S. E. (2024) · VirusDisease · doi:10.1007/s13337-024-00889-4 · Cited by 6
“Furthermore, biotechnological interventions, such as genome editing and genetic engineering, promise to enhance disease resistance in tomato crops [26–29].”
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Research Progress on Signal Conversion Based on Aptamer Combined CRISPR/Cas System in Biosensors
Wang, Y.-H., Li, H., Luo, S., Zhong, M., Liu, J., & Li, B. (2025) · Molecular Diagnosis & Therapy · doi:10.1007/s40291-025-00785-7 · Cited by 7
“Owing to its high base resolution and remarkable genome editing capabilities, along with isothermal amplification-mediated signal amplification technology, the CRISPR/Cas system has enabled a new era of biosensing applications [7].”
Liu, J., & Gao, Y. (2025) · Biosensors and Bioelectronics · doi:10.1016/j.bios.2025.117865 · Cited by 6
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A Review: CRISPR Cas System and the Mechanism With an Inhibition of Binding of CRISPR Cas‐9
Hosen, A., Nishat, M. N. H., Soaib, M. M. H., Sharkar, O. S., Sahabuddin, M., Sharif, I. H., & Bhajan, S. K. (2024) · Nano Select · doi:10.1002/nano.202400009 · Cited by 7
“Double-strand breaks (DSBs) occur in certain DNA strands in Figure 2 [69].”
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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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