CRISPR-Cas-Based Genome Editing for Crop Improvement: Progress, Challenges and Future Prospects

Authors

  • Godswill Ntsomboh-Ntsefong Department of Plant Biology, Faculty of Science, University of Yaounde I, P. O. Box 812, Yaounde, Cameroon
  • Essubalew Getachew Seyum "Department of Plant Biology, Faculty of Science, University of Yaounde I, P. O. Box 812, Yaounde, Cameroon" & "Jimma University, College of Agriculture and Veterinary Medicine, P. O. Box 307, Jimma, Ethiopia"
  • Tabi Mbi Kingsley Department of Crop Production Technology, College of Technology, University of Bamenda, Cameroon
  • Fentanesh Chekole Kassie "Department of Plant Biology, Faculty of Science, University of Yaounde I, P. O. Box 812, Yaounde, Cameroon" & "Department of Plant Science, College of Agriculture, Wolaita Sodo University, Sodo, P. O. Box 138, Ethiopia"
  • Mahbou Somo Toukam Gabriel Department of Plant Biology, Faculty of Science, University of Yaounde I, P. O. Box 812, Yaounde, Cameroon
  • Mohammad Ali Shariati Kazakh Research Institute of Processing and Food Industry, Semey Branch of the Institute, 238 «G» Gagarin Ave, Almaty, 050060, Republic of Kazakhstan
  • Vesna Karapetkovska Hristova Department of Biotechnology, Faculty of Biotechnical Sciences, "Partizanska"bb, 7000 Bitola, Macedonia
  • Bell Joseph Martin Department of Plant Biology, Faculty of Science, University of Yaounde I, P. O. Box 812, Yaounde, Cameroon
  • Youmbi Emmanuel Department of Plant Biology, Faculty of Science, University of Yaounde I, P. O. Box 812, Yaounde, Cameroon

DOI:

https://doi.org/10.12974/2311-858X.2023.11.3

Keywords:

CRISPR-Cas, Genome editing, Crop improvement, Progress, Challenges, Future prospects

Abstract

The discovery of the CRISPR-Cas genome editing technology has opened up new opportunities for crop improvement through precise genetic modifications. This new technology has shown great promise in improving crop yields, quality, and resilience to biotic and abiotic stresses. This review presents the recent advances in CRISPR-Cas technology, including new tools and techniques for precise genome editing, as well as the challenges associated with off-target effects and unintended consequences. It explores the applications of CRISPR-Cas-based genome editing in different crops, including maize, rice, wheat, and tomato, highlighting the progress achieved in improving important traits such as disease resistance, drought tolerance, and nutrient content. The regulatory concerns around CRISPR-Cas-based genome editing, as well as the ethical considerations associated with this technology are also adressed. Finally, insights into the potential impact of CRISPR-Cas-based genome editing on crop breeding and food security, and the challenges that need to be addressed to fully realize its potential are provided. This review thus highlights the potential of CRISPR-Cas-based genome editing in crop improvement and emphasizes the importance of continued research in this area for sustainable agricultural production.

References

Abdelrahman M, Wei Z, Rohila JS & Zhao K. (2021). Multiplex genome-editing technologies for revolutionizing plant biology and crop improvement. Frontiers in Plant Science, 12, 721203. https://doi.org/10.3389/fpls.2021.721203

Ahmad A, Munawar N, Khan Z, Qusmani AT, Khan SH, Jamil A & Qari SH. (2021). An outlook on global regulatory landscape for genome-edited crops. International journal of molecular sciences, 22(21), 11753. https://doi.org/10.3390/ijms222111753

Ahmad M. (2023). Plant breeding advancements with "CRISPR-Cas" genome editing technologies will assist future food security. Frontiers in Plant Science, 14, 1133036. https://doi.org/10.3389/fpls.2023.1133036

Ahmad S, Tang L, Shahzad R, Mawia AM, Rao GS, Jamil S & Tang S. (2021). CRISPR-based crop improvements: A way forward to achieve zero hunger. Journal of Agricultural and Food Chemistry, 69(30), 8307-8323. https://doi.org/10.1021/acs.jafc.1c02653

Anonymous, 2023. Generating a Knockout Using CRISPR. https://www.addgene.org/guides/crispr/) (Accessed 26/05/2023)

Bahariah B, Masani MYA, Fizree MPMAA, Rasid OA & Parveez GKA. (2023). Multiplex CRISPR/Cas9 gene-editing platform in oil palm targeting mutations in EgFAD2 and EgPAT genes. Journal of Genetic Engineering and Biotechnology, 21(1), 3. https://doi.org/10.1186/s43141-022-00459-5

Barrangou R & Doudna JA. (2016). Applications of CRISPR technologies in research and beyond. Nature biotechnology, 34(9), 933-941. https://doi.org/10.1038/nbt.3659

Biswas S, Zhang D & Shi J. (2021). CRISPR/Cas systems: opportunities and challenges for crop breeding. Plant Cell Reports, 40(6), 979-998. https://doi.org/10.1007/s00299-021-02708-2

Chopy M, Morel P, Rodrigues Bento S & Vandenbussche M. (2019, September). Genome editing by CRISPR-Cas9 technology in Petunia hybrida. In XXVI International Eucarpia Symposium Section Ornamentals: Editing Novelty 1283 (pp. 209-218). https://doi.org/10.17660/ActaHortic.2020.1283.28

Clasen BM, Stoddard TJ, Luo S, Demorest ZL, Li J, Cedrone F & Zhang F. (2016). Improving cold storage and processing traits in potato through targeted gene knockout. Plant biotechnology journal, 14(1), 169-176. https://doi.org/10.1111/pbi.12370

Doudna JA & Charpentier E. (2014). Genome editing. The new frontier of genome engineering with CRISPR-Cas9. Science, 346(6213), 1258096. https://doi.org/10.1126/science.1258096

Eckerstorfer MF, Dolezel M, Heissenberger A, Miklau M, Reichenbecher W, Steinbrecher RA & Waßmann F. (2019). An EU perspective on biosafety considerations for plants developed by genome editing and other new genetic modification techniques (nGMs). Frontiers in bioengineering and biotechnology, 7, 31. https://doi.org/10.3389/fbioe.2019.00031

Haun W, Coffman A, Clasen BM, Demorest ZL, Lowy A, Ray E & Zhang F. (2014). Improved soybean oil quality by targeted mutagenesis of the fatty acid desaturase 2 gene family. Plant biotechnology journal, 12(7), 934-940. https://doi.org/10.1111/pbi.12201

Hsu PD, Lander ES & Zhang F. (2014). Development and applications of CRISPR-Cas9 for genome engineering. Cell, 157(6), 1262-1278. https://doi.org/10.1016/j.cell.2014.05.010

Ito Y, Nishizawa-Yokoi A, Endo M, Mikami M & Toki S. (2015). CRISPR/Cas9-mediated mutagenesis of the RIN locus that regulates tomato fruit ripening. Biochemical and biophysical research communications, 467(1), 76-82. https://doi.org/10.1016/j.bbrc.2015.09.117

Jia H, Orbović V & Wang N. (2019). CRISPR‐LbCas12a‐mediated modification of citrus. Plant biotechnology journal, 17(10), 1928-1937. https://doi.org/10.1111/pbi.13109

Juma BS, Mukami A, Mweu C, Ngugi MP & Mbinda W. (2022). Targeted mutagenesis of the CYP79D1 gene via CRISPR/Cas9-mediated genome editing results in lower levels of cyanide in cassava. Frontiers in Plant Science, 13, 1009860. https://doi.org/10.3389/fpls.2022.1009860

Kumar S, Rymarquis LA, Ezura H & Nekrasov V. (2021). CRISPR-Cas in agriculture: opportunities and challenges. Frontiers in Plant Science, 12, 672329. https://doi.org/10.3389/fpls.2021.672329

Li J, Meng X, Zong Y, Chen K, Zhang H, Liu J & Gao C. (2016). Gene replacements and insertions in rice by intron targeting using CRISPR-Cas9. Nature plants, 2(10), 1-6. https://doi.org/10.1038/nplants.2016.139

Li T, Liu B, Spalding MH, Weeks DP, & Yang B. (2012). High-efficiency TALEN-based gene editing produces disease-resistant rice. Nature biotechnology, 30(5), 390-392. https://doi.org/10.1038/nbt.2199

Li Y, Zhao L, Zhao C, Huang Y, Li Y, Chen Y & Zhang H. (2021). CRISPR/Cas9-mediated targeted mutagenesis of AhFAD2B increases oleic acid content in peanut. PlantCell Reports, 36(1), 109716.

Liu Q, Yang F, Zhang J, Liu H, Rahman S, Islam S & She M. (2021). Application of CRISPR/Cas9 in crop quality improvement. International Journal of Molecular Sciences, 22(8), 4206. https://doi.org/10.3390/ijms22084206

Liu W, Li L, Jiang J, Wu M & Lin P. (2021). Applications and challenges of CRISPR-Cas gene-editing to disease treatment in clinics. Precision Clinical Medicine, 4(3), 179-191. https://doi.org/10.1093/pcmedi/pbab014

Liu Y, Du Z, Lin S, Li H, Lu S, Guo L & Tang S. (2022). CRISPR/Cas9-targeted mutagenesis of BnaFAE1 genes confers low-erucic acid in Brassica napus. Frontiers in plant science, 13, 848723. https://doi.org/10.3389/fpls.2022.848723

Naim F, Dugdale B, Kleidon J, Brinin A, Shand K, Waterhouse P & Dale J. (2018). Gene editing the phytoene desaturase alleles of Cavendish banana using CRISPR/Cas9. Transgenic research, 27, 451-460. https://doi.org/10.1007/s11248-018-0083-0

Nakajima I, Ban Y, Azuma A, Onoue N, Moriguchi T, Yamamoto T & Endo M. (2017). CRISPR/Cas9-mediated targeted mutagenesis in grape. PLoS One, 12(5), e0177966. https://doi.org/10.1371/journal.pone.0177966

Nishihara M, Higuchi A, Watanabe A & Tasaki K. (2018). Application of the CRISPR/Cas9 system for modification of flower color in Torenia fournieri. BMC Plant Biology, 18(1), 1-9. https://doi.org/10.1186/s12870-018-1539-3

Odipio J, Alicai T, Ingelbrecht I, Nusinow DA, Bart R, Taylor NJ & Jones RB. (2020). CRISPR-Cas9-mediated editing of cassava fordisease resistance. Frontiers in plant science, 11, 1061.

Pan C, Li G, Bandyopadhyay A & Qi Y. (2023). Guide RNA library-based CRISPR screens in plants: opportunities and challenges. Current Opinion in Biotechnology, 79, 102883. https://doi.org/10.1016/j.copbio.2022.102883

Peng A, Chen S, Lei T, Xu L, He Y, Wu L & Zou X. (2017). Engineering canker‐resistant plants through CRISPR/Cas9‐targeted editing of the susceptibility gene Cs LOB 1 promoter in citrus. Plant biotechnology journal, 15(12), 1509-1519. https://doi.org/10.1111/pbi.12733

Qaim M. (2020). Role of new plant breeding technologies for food security and sustainable agricultural development. Applied Economic Perspectives and Policy, 42(2), 129-150. https://doi.org/10.1002/aepp.13044

Shan Q, Zhang Y, Chen K, Zhang K & Gao C. (2015). Creation of fragrant rice by targeted knockout of the Os BADH 2 gene using TALEN technology. Plant biotechnology journal, 13(6), 791-800. https://doi.org/10.1111/pbi.12312

Sun B, Zheng A, Jiang M, Xue S, Yuan Q, Jiang L & Tang H. (2018). CRISPR/Cas9-mediated mutagenesis of homologous genes in Chinese kale. Scientific Reports, 8(1), 16786. https://doi.org/10.1038/s41598-018-34884-9

Tasaki K, Yoshida M, Nakajima M, Higuchi A, Watanabe A & Nishihara M. (2020). Molecular characterization of an anthocyanin-related glutathione S-transferase gene in Japanese gentian with the CRISPR/Cas9 system. BMC Plant Biology, 20, 1-14. https://doi.org/10.1186/s12870-020-02565-3

Wang Y, Zafar N, Ali Q, Manghwar H, Wang G, Yu L, Ding X, Ding F, Hong N, Wang G, Jin S. (2022) CRISPR/Cas Genome Editing Technologies for Plant Improvement against Biotic and Abiotic Stresses: Advances, Limitations, and Future Perspectives. Cells. 5; 11(23): 3928. https://doi.org/10.3390/cells11233928

Wang F, Wang C, Liu P, Lei C, Hao W, Gao Y & Zhao K. (2016). Enhanced rice blast resistance by CRISPR/Cas9-targeted mutagenesis of the ERF transcription factor gene OsERF922. PloS one, 11(4), e0154027. https://doi.org/10.1371/journal.pone.0154027

Wang X, Tu M, Wang D, Liu J, Li Y, Li Z & Wang X. (2018). CRISPR/Cas9‐mediated efficient targeted mutagenesis in grape in the first generation. Plant biotechnology journal, 16(4), 844-855.

https://doi.org/10.1111/pbi.12832

Wang Y, Cheng X, Shan Q, Zhang Y, Liu J, Gao C & Qiu JL. (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

Wienert B & Cromer MK. (2022). CRISPR nuclease off-target activity and mitigation strategies. Frontiers in Genome Editing, 4, 1050507. https://doi.org/10.3389/fgeed.2022.1050507

Xu Y & Li Z. (2020). CRISPR-Cas systems: Overview, innovations and applications in human disease research and gene therapy. Computational and Structural Biotechnology Journal, 18, 2401-2415. https://doi.org/10.1016/j.csbj.2020.08.031

Yuan M, Zhu J, Gong L, He L, Lee C, Han S & He G. (2019). Mutagenesis of FAD2 genes in peanut with CRISPR/Cas9 based gene editing. BMC biotechnology, 19(1), 1-7. https://doi.org/10.1186/s12896-019-0516-8

Zafar K, Sedeek KE, Rao GS, Khan MZ, Amin I, Kamel R & Mahfouz MM. (2020). Genome editing technologies for rice improvement: progress, prospects, and safety concerns. Frontiers in Genome Editing, 2, 5. https://doi.org/10.3389/fgeed.2020.00005

Zaidi SSEA, Mahas A, Vanderschuren H & Mahfouz MM. (2020). Engineering crops of the future: CRISPR approaches to develop climate-resilient and disease-resistant plants. Genome biology, 21(1), 1-19. https://doi.org/10.1186/s13059-020-02204-y

Zhang F, LeBlanc C, Irish VF & Jacob Y. (2017). Rapid and efficient CRISPR/Cas9 gene editing in Citrus using the YAO promoter. Plant Cell Reports, 36, 1883-1887. https://doi.org/10.1007/s00299-017-2202-4

Downloads

Published

11-07-2023

How to Cite

Ntsomboh-Ntsefong, G. ., Seyum, E. G., Kingsley, T. M. ., Kassie, F. C. ., Toukam Gabriel, M. S. ., Ali Shariati, M. ., Hristova, V. K. ., Martin, B. J. ., & Emmanuel, Y. . (2023). CRISPR-Cas-Based Genome Editing for Crop Improvement: Progress, Challenges and Future Prospects. Global Journal Of Botanical Science, 11, 28–33. https://doi.org/10.12974/2311-858X.2023.11.3

Issue

Section

Articles