Cited by 529CRISPR and Genetic EngineeringGenetically Modified Organisms ResearchRNA regulation and disease

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CRISPR/Cas System: Recent Advances and Future Prospects for Genome Editing

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Manghwar, Hakim, Lindsey, Keith, Zhang, Xianlong, Jin, Shuangxia·2019·Trends in Plant Science

DOI 10.1016/j.tplants.2019.09.006

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Abstract

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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BackgroundMethodInfluential
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Background
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Method
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BackgroundMethod
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“CRISPR has revolutionized plant biology and CRISPR/Cas9 and associated systems have been used to modify genes to increase crop productivity, enhance grain quality, increase biotic and abiotic stress tolerance (Manghwar et al. 2019).”
Background
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“Currently, the best studied and most frequently applied system is CRISPR/Cas9 belonging to the type II of class 2 system, which consists of two main constituents: a single guide RNA (sgRNA) that recognizes the DNA binding site and Cas9 induces DSBs at the target site (Manghwar et al., 2019).”
Background
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Method
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Background
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“broader PAM compatibility and increased length of gRNA have been used recently (Makarova et al., 2015; Manghwar et al., 2019; Puchta, 2017; Van Eck, 2020).”
Method
Using traditional machine learning and deep learning methods for on- and off-target prediction in CRISPR/Cas9: a review
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“Various Cas proteins have been identified in plants displaying sequence-specific nuclease activity to minimize the impediment and increase the specificity of the CRISPR-Cas system for their effective exploitation [ 50 ].”
BackgroundInfluential
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Background
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“The application of CRISPR/ Cas9-based gene editing technology in plant breeding is an auspicious alternative to the conventional and marker-based breeding due to the ability to precisely and efﬁciently edit genomes of diverse living organism (Fiaz et al ., 2019a; Manghwar et al ., 2019).”
CRISPR-based gene editing technology and its application in microbial engineering
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Background
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Method
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BackgroundMethod
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“2 Plant Communications 2, 100141, March 8 2021 a 2021 The Auth regularly interspaced short palindromic repeats (CRISPR)/ CRISPR-associated protein (Cas) system, have been used to edit nuclear genomes for crop improvement (Chen et al., 2019; Manghwar et al., 2019; Veillet et al., 2020).”
Bacteroides fragilis Toxin Induces Intestinal Epithelial Cell Secretion of Interleukin-8 by the E-Cadherin/β-Catenin/NF-κB Dependent Pathway
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“Once the target sequence is recognized, the endonuclease introduces a double-strand DNA (dsDNA) break (DSB) and induces subsequent activation of the DNA repair pathway (Manghwar et al., 2019).”
Background
Engineering Properties of Sweet Potato Starch for Industrial Applications by Biotechnological Techniques including Genome Editing
Lyu, R., Ahmed, S., Fan, W., Yang, J. M., Wu, X., Zhou, W., Zhang, P., Yuan, L., & Wang, H. (2021) · International Journal of Molecular Sciences · doi:10.3390/ijms22179533 · Cited by 69
A review on emerging technologies and machine learning approaches for sustainable production of biofuel from biomass waste
Sharmila, V. G., Shanmugavel, S. P., & Banu, J. R. (2023) · Biomass and Bioenergy · doi:10.1016/j.biombioe.2023.106997 · Cited by 63
Futuristic avenues of metabolic engineering techniques in bioremediation
Sharma, B., & Shukla, P. (2020) · Biotechnology and Applied Biochemistry · doi:10.1002/bab.2080 · Cited by 60
Bacteriophage strategies for overcoming host antiviral immunity
Gao, Z., & Feng, Y. (2023) · Frontiers in Microbiology · doi:10.3389/fmicb.2023.1211793 · Cited by 67
“First, fundamental research into interactions between phages and bacterial hosts expanded biotechnology tools and helped evolve and screen phages or strains with designated resistance, which have underpinned the development of many fields, including but not limited to gene editing (Adli, 2018; Manghwar et al., 2019),…”
Background
State-of-the-Art in CRISPR Technology and Engineering Drought, Salinity, and Thermo-tolerant crop plants
Chennakesavulu, K., Singh, H., Trivedi, P. K., Jain, M., & Yadav, S. R. (2022) · Plant Cell Reports · doi:10.1007/s00299-021-02681-w · Cited by 60
Combined fluorescent seed selection and multiplex CRISPR/Cas9 assembly for fast generation of multiple Arabidopsis mutants
Ursache, R., Fujita, S., Tendon, V. D., & Geldner, N. (2021) · Plant Methods · doi:10.1186/s13007-021-00811-9 · Cited by 58
“It is a very valuable tool in studying gene function, breaking the redundancy in multigene families and developing new plant traits (Liu and Fan, 2014; Ma et al., 2016; Manghwar et al., 2019; Atkins and Voytas, 2020; Gao, 2021; Sukegawa et al., 2021).”
Method
Functional nucleic acid-based fluorescent probes for metal ion detection
Xu, J., Jiang, R., Feng, Y., Liu, Z., Huang, J. L., Ma, C., & Wang, K. (2022) · Coordination Chemistry Reviews · doi:10.1016/j.ccr.2022.214453 · Cited by 57
Recent Progress and Future Prospect of CRISPR/Cas-Derived Transcription Activation (CRISPRa) System in Plants
Ding, X. L., Yu, L., Chen, L., Li, Y., Zhang, J., Sheng, H., Ren, Z., Li, Y., Yu, X., Jin, S., et al. (2022) · Cells · doi:10.3390/cells11193045 · Cited by 62
Detection of antimicrobial resistance via state-of-the-art technologies versus conventional methods
Elbehiry, A., Marzouk, E., Abalkhail, A., Abdelsalam, M. H., Mostafa, M. E., Alasiri, M., Ibrahem, M. D., Ellethy, A. T., Almuzaini, A. M., Aljarallah, S. N., et al. (2025) · Frontiers in Microbiology · doi:10.3389/fmicb.2025.1549044 · Cited by 69
Strategies to Modulate Specialized Metabolism in Mediterranean Crops: From Molecular Aspects to Field
Balestrini, R., Brunetti, C., Cammareri, M., Caretto, S., Cavallaro, V., Cominelli, E., Palma, M. D., Docimo, T., Giovinazzo, G., Grandillo, S., et al. (2021) · International Journal of Molecular Sciences · doi:10.3390/ijms22062887 · Cited by 62
CRISPR/Cas9-Mediated Targeted Mutagenesis of CYP93E2 Modulates the Triterpene Saponin Biosynthesis in Medicago truncatula
Confalonieri, M., Carelli, M., Gianoglio, S., Moglia, A., Biazzi, E., & Tava, A. (2021) · Frontiers in Plant Science · doi:10.3389/fpls.2021.690231 · Cited by 55
“Of these, the CRISPR (Clustered Regularly Interspaced Short Palindromic Repeats)/Cas9 system due to its high efficiency, simplicity and specificity has become a powerful and effective tool for targeted genome editing and research into gene function in plants (Doudna and Charpentier, 2014; Manghwar et al., 2019).”
Background
Clustered regularly interspaced short palindromic repeats (CRISPR)/CRISPR‐associated genome‐editing toolkit to enhance salt stress tolerance in rice and wheat
Nazir, R., Mandal, S., Mitra, S., Ghorai, M., Das, N., Jha, N. K., Majumder, M., Pandey, D. K., & Dey, A. (2022) · Physiologia Plantarum · doi:10.1111/ppl.13642 · Cited by 60
CRISPR/Cas9-Mediated genetically edited ornamental and aromatic plants: A promising technology in phytoremediation of heavy metals
Nayeri, S., Dehghanian, Z., Lajayer, B. A., Thomson, A., Astatkie, T., & Price, G. W. (2023) · Journal of Cleaner Production · doi:10.1016/j.jclepro.2023.139512 · Cited by 57
A FLASH pipeline for arrayed CRISPR library construction and the gene function discovery of rice receptor-like kinases
Chen, K., Ke, R., Du, M., Yi, Y., Chen, Y., Wang, X., Lu, Y., Liu, H., Hou, X., Xiong, L., et al. (2021) · Molecular Plant · doi:10.1016/j.molp.2021.09.015 · Cited by 54
Intelligent nanotherapeutic strategies for the delivery of CRISPR system
Chen, C., Zhong, W., Du, S., Li, Y., Zeng, Y., Liu, K., Yang, J., Guan, X., & Han, X. (2022) · Acta Pharmaceutica Sinica B · doi:10.1016/j.apsb.2022.12.013 · Cited by 56
Precision Breeding Made Real with CRISPR: Illustration through Genetic Resistance to Pathogens
Veillet, F., Durand, M., Kroj, T., Césari, S., & Gallois, J. (2020) · Plant Communications · doi:10.1016/j.xplc.2020.100102 · Cited by 60
“So far, most genome-editing applications in plants have focused on the production of knockout mutants for single or multiple genes (Manghwar et al., 2019).”
Background
Toward a smart skin: Harnessing cuticle biosynthesis for crop adaptation to drought, salinity, temperature, and ultraviolet stress
Liu, L., Wang, X., & Chang, C. (2022) · Frontiers in Plant Science · doi:10.3389/fpls.2022.961829 · Cited by 54
A CRISPR way for accelerating cereal crop improvement: Progress and challenges
Basu, U., Riaz Ahmed, S., Bhat, B. A., Anwar, Z., Ali, A., Ijaz, A., Gulzar, A., Bibi, A., Tyagi, A., Nebapure, S. M., et al. (2023) · Frontiers in Genetics · doi:10.3389/fgene.2022.866976 · Cited by 51
“The evolution of various GE technologies such as transcription activator-like effector nucleases (TALEN) and zinc finger nuclease (ZFN) have been previously used in the intended modification of human, animal, and plant cell genomes (Shukla et al., 2009; Zhang et al., 2010; Davies et al., 2017; Adli, 2018; Kannan et al…”
Method
Recent advances in the development of Aspergillus for protein production
Li, Q., Lu, J., Zhang, G., Liu, S., Zhou, J., Du, G., & Chen, J. (2022) · Bioresource Technology · doi:10.1016/j.biortech.2022.126768 · Cited by 54
A New Method Based on LAMP-CRISPR–Cas12a-Lateral Flow Immunochromatographic Strip for Detection
Xu, H., Tang, H., Li, R., Xia, Z., Yang, W., Zhu, Y., Liu, Z., Lu, G., Ni, S., & Shen, J. (2022) · Infection and Drug Resistance · doi:10.2147/idr.s348456 · Cited by 51
“The amplified products were trans-cleaved by Cas12a to observe the results.(15)”
Method
CRISPR/Cas9 Based Site-Specific Modification of FAD2 cis-Regulatory Motifs in Peanut (Arachis hypogaea L)
Neelakandan, A. K., Wright, D. A., Traore, S. M., Chen, X., Spalding, M. H., & He, G. (2022) · Frontiers in Genetics · doi:10.3389/fgene.2022.849961 · Cited by 51
“This technology is used to generate gene knockouts when coding regions are targeted, therefore, this approach has been widely used for plant genome editing applications (Manghwar et al., 2019).”
Method
An overview of genome engineering in plants, including its scope, technologies, progress and grand challenges
Sufyan, M., Daraz, U., Hyder, S., Zulfiqar, U., Iqbal, R., Eldin, S. M., Rafiq, F., Mahmood, N., Shahzad, K., Uzair, M., et al. (2023) · Functional & Integrative Genomics · doi:10.1007/s10142-023-01036-w · Cited by 55
CRISPR/Cas9 assisted stem cell therapy in Parkinson's disease
Pinjala, P., Tryphena, K. P., Prasad, R., Khatri, D. K., Sun, W., Singh, S. B., Gugulothu, D. B., Srivastava, S., & Vora, L. K. (2023) · Biomaterials Research · doi:10.1186/s40824-023-00381-y · Cited by 57
“Finally, Cas9 will cleave near the PAM site proximate to the 3′ end of the target region [53].”
Background
CRISPR: History and perspectives to the future
Kozovská, Z., Rajcaniova, S., Munteanu, P., Dzacovska, S., & Demková, L. (2021) · Biomedicine & Pharmacotherapy · doi:10.1016/j.biopha.2021.111917 · Cited by 60
CRISPR/Cas-Mediated Resistance against Viruses in Plants
Khan, Z. A., Kumar, R., & Dasgupta, I. (2022) · International Journal of Molecular Sciences · doi:10.3390/ijms23042303 · Cited by 51
Construction of Host Plant Insect‐Resistance Mutant Library by High‐Throughput CRISPR/Cas9 System and Identification of A Broad‐Spectrum Insect Resistance Gene
Sun, L., Alariqi, M., Wang, Y., Wang, Q., Xu, Z., Zafar, M. N., Yang, G., Jia, R., Hussain, A., Chen, Y., et al. (2023) · Advanced Science · doi:10.1002/advs.202306157 · Cited by 52
Delivery of RNAs to Specific Organs by Lipid Nanoparticles for Gene Therapy
Godbout, K., & Tremblay, J. P. (2022) · Pharmaceutics · doi:10.3390/pharmaceutics14102129 · Cited by 51
Detection of Infectious Viruses Using CRISPR-Cas12-Based Assay
Talwar, C. S., Park, K., Ahn, W., Kim, Y.-S., Kwon, O. S., Yong, D., Kang, T., & Woo, E. (2021) · Biosensors · doi:10.3390/bios11090301 · Cited by 47
Introduction to Artificial Intelligence
Ghosh, M., & Thirugnanam, A. (2021) · Studies in big data · doi:10.1007/978-981-16-0415-7_2 · Cited by 45
Advances in genomics and genome editing for breeding next generation of fruit and nut crops
Savadi, S., Mangalassery, S., & Sandesh, M. S. (2021) · Genomics · doi:10.1016/j.ygeno.2021.09.001 · Cited by 47
Engineering drought-tolerant apple by knocking down six GH3 genes and potential application of transgenic apple as a rootstock
Jiang, L., Shen, W., Liu, C., Tahir, M. M., Li, X., Zhou, S., Ma, F., & Guan, Q. (2022) · Horticulture Research · doi:10.1093/hr/uhac122 · Cited by 45
Large-scale genome editing in plants: approaches, applications, and future perspectives
Liu, T., Zhang, X., Li, K., Yao, Q., Zhong, D., Deng, Q., & Lu, Y. (2023) · Current Opinion in Biotechnology · doi:10.1016/j.copbio.2022.102875 · Cited by 47
Next-generation CRISPR-based diagnostic tools for human diseases
Wang, T., Wang, Z., Bai, L., Zhang, X., Feng, J., Qian, C., Wang, Y., & Wang, R. (2023) · TrAC Trends in Analytical Chemistry · doi:10.1016/j.trac.2023.117328 · Cited by 46
Mitochondria: emerging therapeutic strategies for oocyte rescue
Jiang, Z., & Shen, H. (2021) · Reproductive Sciences · doi:10.1007/s43032-021-00523-4 · Cited by 44
CRISPR/Cas9 and Nanotechnology Pertinence in Agricultural Crop Refinement
Naik, B. J., Shimoga, G. D., Kim, S.-C., Manjulatha, M., Palem, R. R., Palem, R. R., Kumar, M., Kim, S., & Lee, S. (2022) · Frontiers in Plant Science · doi:10.3389/fpls.2022.843575 · Cited by 46
Emerging applications of gene editing technologies for the development of climate-resilient crops
Chavhan, R. L., Jaybhaye, S. G., Hinge, V. R., Deshmukh, A. S., Shaikh, U. S., Jadhav, P. K., Kadam, U. S., & Hong, J. C. (2025) · Frontiers in Genome Editing · doi:10.3389/fgeed.2025.1524767 · Cited by 55
The Critical Role of Small RNAs in Regulating Plant Innate Immunity
Waheed, S., Anwar, M., Saleem, M. A., Wu, J., Tayyab, M., & Hu, Z. (2021) · Biomolecules · doi:10.3390/biom11020184 · Cited by 44
CRISPR-Based Genome Editing and Its Applications in Woody Plants
Min, T., Hwarari, D., Li, D., Movahedi, A., & Yang, L. (2022) · International Journal of Molecular Sciences · doi:10.3390/ijms231710175 · Cited by 49
Identification and Functional Analysis of lncRNA by CRISPR/Cas9 During the Cotton Response to Sap-Sucking Insect Infestation
Zhang, J., Li, J., Saeed, S., Batchelor, W. D., Alariqi, M., Meng, Q., Zhu, F., Zou, J., Xu, Z., Si, H., et al. (2022) · Frontiers in Plant Science · doi:10.3389/fpls.2022.784511 · Cited by 42
Opportunities and challenges with CRISPR-Cas mediated homologous recombination based precise editing in plants and animals
Singh, S., Chaudhary, R., Deshmukh, R. K., & Tiwari, S. (2022) · Plant Molecular Biology · doi:10.1007/s11103-022-01321-5 · Cited by 42
“The enAsCas12a can recognize “TTTV” PAM sequence and showed two-fold higher genome editing activity compared with wild-type AsCas12a with reduced offtarget effects (Kleinstiver et al. 2019; Manghwar et al. 2019).”
Background
Removing the major allergen Bra j I from brown mustard (Brassica juncea) by CRISPR/Cas9
Assou, J., Zhang, D., Roth, K. D. R., Steinke, S., Hust, M., Reinard, T., Winkelmann, T., & Boch, J. (2021) · The Plant Journal · doi:10.1111/tpj.15584 · Cited by 48
“Using programmable nucleases, like CRISPR/Cas9 or TALEN, targeted random mutations and deletions can be induced (Manghwar et al., 2019).”
Method
Advancing cancer research through organoid technology
Zeng, G., Yu, Y., Wang, M., Liu, J., He, G., Yu, S., Yan, H., Yang, L., Li, H., & Peng, X. (2024) · Journal of Translational Medicine · doi:10.1186/s12967-024-05824-1 · Cited by 43
“This mechanism can lead to the mispairing of the designed single-stranded guide RNA (sgRNA) with non-target DNA sequences, resulting in off-target effects and the introduction of unexpected gene mutations [121, 122].”
Background

Authors: Manghwar, H., Lindsey, K., Zhang, X., & Jin, S.
Affiliations: Huazhong Agricultural University (CN)
Durham University (GB)
Corresponding author: Zhang, Xianlong
Jin, Shuangxia
ORCID: Manghwar, Hakim
Lindsey, Keith
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)
DOI: 10.1016/j.tplants.2019.09.006
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: cc-by-nc-nd
www.elsevier.com/tdm/userlicense/1.0/ (tdm)
www.elsevier.com/legal/tdmrep-license (tdm)
creativecommons.org/licenses/by-nc-nd/4.0/ (vor)
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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CRISPR/Cas System: Recent Advances and Future Prospects for Genome Editing

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