Unveiling the Genetic Revolution: A Review of CRISPR-Cas9 in Plant Diseases Management

Authors

  • Muhammad S. Samoo
  • Abdul R. Jamali
  • Imran A. Bhurt
  • Usra Saqib

DOI:

https://doi.org/10.33866/phytopathol.036.02.1122

Keywords:

Keywords, CRISPR Cas9, Viral diseases, Fungal diseases, Bacterial Diseases.

Abstract

The emergence of genome editing tools offers unprecedented opportunities for fortifying crop resilience. From its humble origins in bacterial immune systems to its application in plant pathology, CRISPR/Cas9 has revolutionized our understanding of genetic manipulation and disease control. This review explains the principles of genome editing system and explore its potential applications in augmenting resistance against pathogens in model plants and key crops, with a keen eye on rice, wheat, and other agricultural staples. Among the key roles of the sgRNA/cas9 (single guided RNA) complex in enhancing plant immunity and reducing the burden of disease burden, this review focuses on the role of CRISPR Cas9 in the management of Viral, Bacterial and devastating Fungal plant diseases, bolstering agricultural productivity and ensuring food security. CRISPR/Cas9 is enabling precise genetic edits that enhance plant resilience against specific viruses, fungi, and bacteria, marking a revolutionary shift in sustainable plant pathogen management. The paper provided with some key resistance genes of plant disease resistance.

Author Biography

Muhammad S. Samoo

Govt Muslim Science Degree College Hyderbad, Sindh, Pakistan

References

Abbas, W., S. Rehman, A. Rashid, M. Kamran, M. Atiq and M. E. Haq. 2020. Comparative efficacy of different plant extracts to manage the cotton leaf curl virus disease and its vector (Bemisia tabaci L.). Pakistan Journal of Agricultural Research, 33(1): 22-26.

Ali, Z., A. Abul-Faraj, L. Li, N. Ghosh, M. Piatek, A. Mahjoub, M. Aouida, A. Piatek, N.J. Baltes, D.F. Voytas and S. Dinesh-Kumar. 2015. Efficient virus-mediated genome editing in plants using the CRISPR/Cas9 system. Molecular plant, 8(8): 1288-1291.

Ali, Z., A. Eid, S. Ali and M.M. Mahfouz. 2018. Pea earlybrowning virus-mediated genome editing via the CRISPR/Cas9 system in Nicotiana benthamiana and Arabidopsis. Virus Research, 244: 333–337.

Blicharska, D., I. Szućko-Kociuba, E. Filip and L. Skuza. 2022. CRISPR/Cas as the intelligent immune system of bacteria and archea. Postępy Biochemii, 68(3): 235–245. DOI: https://doi.org/10.18388/pb.2021_453

Brouns, S.J., M.M. Jore, M. Lundgren, E.R. Westra, R.J. Slijkhuis, A.P. Snijders, M.J. Dickman, K.S. Makarova, E.V. Koonin and J. van der Oost. 2008. Small CRISPR RNAs guide antiviral defense in prokaryotes. Science, 321: 960–964. DOI: https:// doi.org/10.1126/science.1159689

Cermak, T., Doyle, E. L., Christian, M., Wang, L., Zhang, Y., Schmidt, C.2011. Efficient design and assembly of custom TALEN and other TAL effector based constructs for DNA targeting. Nucleic Acids Research, 39: e82. doi: 10.1093/nar/ gkr218

Cody, W. B., H.B. Scholthof and T.E. Mirkov. 2017. Multiplexed gene editing and protein overexpression using a tobacco mosaic virus viral vector. Plant Physiology, 175: 23–35

Das A., Sharma N., Prasad M. 2019. CRISPR/Cas9: A novel weapon in the arsenal to combat plant diseases. Frontiers in Plant Science, 9: DOI: https://doi.org/10.3389/ fpls.2018.02008

Doehlemann G., O¨kmen B., Zhu W., Sharon A. 2017. Plant pathogenic fungi. p. 703–726. In: “The Fungal Kingdom (J. Heitman, B. Howlett, P. Crous, E. Stukenbrock, T. James, N. Gow, eds.). Washington, DC: ASM Press.

Dong O.X., and P.C. Ronald. 2019. Genetic engineering for disease resistance in plants: recent progress and future perspectives. Plant Physiology, 180: 26–38. DOI: https://doi.org/10.1104/ pp.18.01224

Dort, E.N., P. Tanguay and R.C. Hamelin. 2020. CRISPR/Cas9 gene editing: an unexplored frontier for forest pathology. Frontiers in Plant Science 11: 1126. DOI: https://doi.org/10.3389/ fpls.2020.01126

Doudna, J.A. and E. Charpentier. 2014. The new frontier of genome engineering with CRISPR-Cas9. Science, 346(6213): 1258096. DOI: https://doi.org/10.1126/science.1258096

Dracatos, P.M., R. Haghdoust, D. Singh and P. Fraser. 2018. Exploring and exploiting the boundaries of host specificity using the cereal rust and mildew models. New Phytologist, 218: 453–462. DOI: https://doi.org/10.1111/nph.15044

Fisher, M.C., D.A. Henk, C.J. Briggs, J.S. Brownstein, L.C. Madoff, S.L. McCraw and S.J. Gurr. 2012. Emerging fungal threats to animal, plant and ecosystem health. Nature, 484: 186–194. DOI: https://doi.org/10.1038/nature10947

Fondong, V.N. 2013. Geminivirus protein structure and function. Molecular Plant Pathology, 14: 635–649. DOI: https:// doi.org/10.1111/mpp.12032

Fones, H. N., D.P. Bebber, T.M. Chaloner, W.T. Kay, G. Steinberg and S.J. Gurr. 2020. Threats to global food security from emerging fungal and oomycete crop pathogens. Nature Food, 1: 332–342. doi: 10.1038/s43016-020-0075-0

Guo, Z., D. Sun, S. Kang, J. Hou, L. Gong, J. Qin, L. Guo, L. Zhu, Y. Bai, L. Luo and Y. Zhang. 2019. CRISPR/Cas9-mediated knockout of both the PxABCC2 and PxABCC3 genes confers high-level resistance to Bacillus thuringiensis Cry1Ac toxin in the diamondback moth, Plutella xylostella (L.). Insect Biochemistry and Molecular Biology, 107: 31–38. DOI: https://doi.org/10.1016/j.ibmb.2019.01.009

Haft, D.H., J. Selengut, E.F. Mongodin and K.E. Nelson. 2005. A guild of 45 CRISPR-associated (Cas) protein families and multiple CRISPR/Cas subtypes exist in prokaryotic genomes. PLOS Computer Biology, 1: e60. DOI: https://doi.org/10.1371/ journal. pcbi.0010060

Hsu, P.D., D.A. Scott and J.A. Weinstein. 2013. DNA targeting specificity of RNA-guided Cas9 nucleases. Nature Biotechnology, 31(9):827–832. DOI: https://doi.org/10.1038/nbt.2647

Ishino, Y., H. Shinagawa, K. Makino, M. Amemura and A. Nakata. 1987. Nucleotide sequence of the iap gene, responsible for alkaline phosphatase isozyme conversion in Escherichia coli, and identification of the gene product. Journal of Bacteriology, 169: 5429–5433. DOI: https://doi.org/10.1128/ jb.169.12.5429-5433.1987

Jansen, R., J.D.V. Embden, W. Gaastra and L.M. Schouls. 2002. Identification of genes that are associated with DNA repeats in prokaryotes. Molecular Microbiology, 43: 1565–1575. doi: 10.1046/j.1365-2958.2002. 02839.x

Ji, X., H. Zhang, Y. Zhang, Y. Wang and C. Gao. 2015. Establishing a CRISPRCas-like immune system conferring DNA virus resistance in plants. Nature Plants, 1:15144. doi: 10.1038/nplants.2015.144

Jiang, N. 2019. Development of beet necrotic yellow vein virus-based vectors for multiple-gene expression and guide RNA delivery in plant genome editing. Plant Biotechnology Journal, 17:1302–1315 (2019). 107.

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

Kamoun, S., O. Furzer, J.D.G. Jones, H.S. Judelson, G.S. Ali and R.J.D. Dalio. 2015. The top 10 oomycete pathogens in molecular plant pathology: top 10 oomycete plant pathogens. Molecular Plant Pathology, 16: 413–434. doi: 10.1111/mpp. 12190

Kerr, A. 2016. Biological control of Crown Gall. Australas. Plant Pathology, 45: 15–18. DOI: https://doi.org/10.1007/s13313- 015-0389-9

Králová, M., V. Bergougnoux and I. Frébort. 2021. CRISPR/Cas9 genome editing in ergot fungus Claviceps purpurea. Journal of Biotechnology, 325: 341–354. doi: 10.1016/j.jbiotec.2020.09.028

Langner, T., S. Kamoun and K. Belhaj. 2018. CRISPR Crops: plant genome editing toward disease resistance. Annual Review of Phytopathology, 56: 479–512. doi: 10.1146/annurev-phyto-080417-050158

Li, M.Y., Y.T. Jiao, Y.T. Wang, N. Zhang, B.B. Wang and R.Q. Liu. 2020. CRISPR/Cas9-mediated VvPR4b editing decreases downy mildew resistance in grapevine (Vitis vinifera L.). Horticultural Research, 7:149. doi: 10.1038/s41438-020-0 0371-4

Lu, W., F. Deng, J. Jia, X. Chen, J. Li and Q. Wen. 2020. The Arabidopsis thaliana gene AtERF019 negatively regulates plant resistance to Phytophthora parasitica by suppressing PAMP-triggered immunity. Molecular Plant Pathology, 21: 1179–1193. doi: 10.1111/mpp.12971

Maikova, A., V. Kreis, A. Boutserin, K. Severinov and O. Soutourina. 2019. Using an endogenous CRISPR-Cas system for genome editing in the human pathogen Clostridium difficile. Applied and Environmental Microbiology, 85 (20): e01416–e01419. DOI: https://doi.org/10.1038/nrmicro3569

Miah, G., M.Y. Rafii, M.R. Ismail, A.B. Puteh, H.A. Rahim, R. Asfaliza and M.A. Latif. 2013. Blast resistance in rice: a review of conventional breeding to molecular approaches. Molecular Biology Reports, 40: 2369– 2388. DOI: https://doi.org/10. 1007/s11033-012-2318-0)

Mojica, F. J. M., C. Díez-Villaseñor, J. García-Martínez and C. Almendros. 2009 Short motif sequences determine the targets of the prokaryotic CRISPR defense system, Microbiology, 155: 733-740, doi: 10.1099/ mic.0.023960-0

Mushtaq, M., A. Ahmad Dar, M. Skalicky, A. Tyagi, N. Bhagat, U. Basu, B.A. Bhat, A. Zaid, S. Ali, T.U. Dar, G.K. Rai, S.H. Wani, M. Habib-Ur-Rahman, V. Hejnak, P. Vachova, M. Brestic, A. Çığ, F. Çığ, M. Erman and A. El Sabagh. 2021. CRISPR- -based genome editing tools: insights into technological breakthroughs and future challenges. Genes (Basel), 12(6): 797. DOI: https://doi.org/10.3390/genes12060797

Naveed, K., M.R. Shafiq and A. Raza. 2023. Citrus tristeza virus: its research status and future prospects in Pakistan. Pakistan Journal of Phytopathology, 35(2): 465-472.

Navet, N. and M. Tian. 2020. Efficient targeted mutagenesis in all tetraploid sweet basil by CRISPR/Cas9. Plant Direct, 4: e00233. doi: 10.1002/pld3.233

Nejat, N., J. Rookes, N.L. Mantri and D.M. Cahill. 2017. Plant- -pathogen interactions: toward development of next-generation disease-resistant plants. Critical Reviews in Biotechnology, 37: 229–237. DOI: https://doi.org/10.3109/0738855 1.2015.1134437

Nekrasov, V. 2017. Rapid generation of a transgene free powdery mildew resistant tomato by genome deletion. Scientific Reports 7: 482

Nekrasov, V., B. Staskawicz, D. Weigel, J.D.G. Jones and S. Kamoun. 2013. Targeted mutagenesis in the model plant Nicotiana benthamiana using Cas9 RNA-guided endonuclease. Nature Biotechnology, 31: 691–693. doi: 10.1038/nbt.2655

Oliva, R. 2019. Broad-spectrum resistance to bacterial blight in rice using genome editing. Nature Biotechnology, 37: 1344–1350.

Pyott, D.E., E. Sheehan and A. Molnar. 2016. Engineering of CRISPR/ Cas9-mediated potyvirus resistance in transgene-free Arabidopsis plants. Molecular Plant Pathology, 17: 1276–1288. DOI: https://doi.org/10.1111/mpp.12417

Roossinck, M.J., D.P. Martin and P. Roumagnac. 2015. Plant virus metagenomics: advances in virus discovery. Phytopathology, 105: 716–727. DOI: https://doi.org/10.1094/PHYTO12-14-0356-RVW

Sánchez-Martín, J. and B. Keller. 2019. Contribution of recent technological advances to future resistance breeding. Theoretical and Applied Genetics, 132: 713–732. doi: 10.1007/s00122-019-03297-1

Schenke, D. and D. Cai. 2020. Applications of CRISPR/Cas to improve crop disease resistance: beyond inactivation of susceptibility factors. Science, 23:101478. doi: 10.1016/j.isci.2020.101478

Stephens, J. and A. Barakate. 2017. “Gene editing technologies – ZFNs, TALENs, and CRISPR/Cas9,” in Encyclopedia of Applied Plant Sciences, 2 eds Cambridge, Academic Press, pp. 157–161. doi: 10.1016/B978-0-12-394807-6.00242-2

Tyagi, S., R. Kumar, V. Kumar, S.Y. Won and P. Shukla. 2021. Engineering disease resistant plants through CRISPR-Cas9 technology. GM Crops Food, 12: 125–144. doi: 10.1080/21645698.2020.1831729

Wang, Y.2014. Simultaneous editing of three homoeoalleles in hexaploid bread wheat confers heritable resistance to powdery mildew. Nature Biotechnology 32: 947–951.

Xu, Z. 2019. Engineering broad-spectrum bacterial blight resistance by simultaneously disrupting variable TALE-binding elements of multiple susceptibility genes in rice. Molecular Plant, 12: 1434–1446. 52.

Yin, K. 2015. A Gemini virus-based guide RNA delivery system for CRISPR/Cas9 mediated plant genome editing. Scientific Reports, 5: 14926.

Yin, K. and J.L. Qiu. 2019. Genome editing for plant disease resistance: applications and perspectives. Philosophical Transactions of the Royal Society B: Biological Sciences, 374:20180322. doi: 10.1098/rstb.2018.0322

Zaidi, S. S., M.M. Mahfouz and S. Mansoo. 2017. CRISPR-Cpf1: a new tool for plant genome editing. Trends in Plant Sciences, 22: 550–553. doi: 10.1016/j.tplants.2017. 05.001

Zaynab, M., Y. Sharif, M. Fatima, M.Z. Afzal, M.M. Aslam and M.F. Raza. 2020. CRISPR/Cas9 to generate plant immunity against pathogen. Microbial Pathogens, 141:103996. doi: 10.1016/j.micpath.2020.103996

Zeng, D. 2020. Quantitative regulation of Waxy expression by CRISPR/Cas9-based promoter and 5’UTR-intron editing improves grain quality in rice. Plant Biotechnology Journal, 1: 1-15. https://doi.org/10.1111/ pbi.13427.

Zhang, Y.2017. Simultaneous modification of three homoeologs of TaEDR1 by genome editing enhances powdery mildew resistance in wheat. Plant Journal, 91: 714–724.

Published

2024-12-04

How to Cite

Samoo, M. S., Jamali, A. R., Bhurt, I. A., & Saqib, U. (2024). Unveiling the Genetic Revolution: A Review of CRISPR-Cas9 in Plant Diseases Management. Pakistan Journal of Phytopathology, 36(2), 513-521. https://doi.org/10.33866/phytopathol.036.02.1122

Issue

Vol. 36 No. 2 (2024): Pak. J. Phytopath.

Section

Review Articles

Submission of a manuscript infers that the work described has not been published before (except in the form of an abstract or as part of a published lecture, or thesis). It is also not under consideration for publication elsewhere.

All works published by Pakistan Journal of Phytopathology is freely available to copy, distribute, transmit and adapt the work provided the original work and source is appropriately cited.