By Gillian Faith Achieng, Joel Onyango, and Eric Magale
Plant diseases remain a threat to global agriculture amidst growing global challenges such as climate change and population growth. In the Biotech field, Clustered Regularly Interspaced Short Palindromic Repeats (CRISPR) gene editing technology stands out as a groundbreaking solution with immense potential for developing disease-resistant crops.
In essence, the CRISPR molecule is made up of short palindromic DNA sequences that are repeated along the molecule and are regularly-spaced. The CRISPR-Cas9 system, which was developed from components of the earliest known bacterial immune system, allows for targeted gene breakage and gene editing in a variety of cells/RNA sequences to guide endonuclease cleavage specificity in the CRISPR-Cas9 system. Editing can be directed to practically any genomic site by altering the guide RNA (gRNA) sequence and delivering it to a target cell along with the Cas9 endonuclease[1]. By utilizing the CRISPR associated protein 9 (Cas9), guided by a custom RNA sequence, researchers can target and edit genes with unprecedented accuracy; offering a precise, efficient, and versatile method for modifying the genetic makeup of organisms, including crops.
Through the CRISPR technology, researchers have been successful in enhancing disease resistance in plants, addressing one of the most significant challenges in agriculture such as crop diseases caused by pathogens[2].Traditional breeding methods to develop disease-resistant crops such as selective breeding are often time-consuming and limited in scope. However, the CRISPR allows for the direct targeting and editing of genes associated with disease susceptibility or resistance, offering a more targeted and rapid approach. This technology not only promises to improve crop yields and reduce losses but also supports the development of more sustainable farming practices by reducing reliance on chemical pesticides. This writing highlights how CRISPR- gene editing has been precisely used to target potential genes and enhance disease resistance in plants. The writing emerges from ongoing “GENTWORK”research between BOKU University, ACTS and Egerton University which aims to modenise breeding programmes in Kenya.
In terms of agricultural advancement, several successful CRISPR applications in creating disease resistant have already been documented in rice[3], soybean[4], wheat[5], sweet orange[6]. The process begins with the identification of target genes associated either with susceptibility or resistance to specific diseases. Researchers design guide RNAs (gRNAs) that match the sequences of these target genes. When introduced into the plant cells, the CRISPR-Cas9 complex locates the precise DNA sequence and makes a specific cut in the DNA sequence[7]. The plant's natural DNA repair mechanisms then either disable the susceptibility gene or incorporate a resistance trait, thus conferring disease resistance. Once the CRISPR-Cas9 complex has successfully edited the target genes, the plant cells undergo a regeneration process to develop into whole plants. This involves cultivating the edited cells in a controlled environment to ensure that they grow and differentiate into full plants. These regenerated plants are then subjected to testing to confirm the desired genetic changes and assess their plants are then subjected to testing to confirm the desired genetic changes and assess their resistance to the targeted diseases.
In 2014, for the first time, the CRISPR/Cas9 system was used successfully in wheat protoplasts to edit the TaMLO gene (Mildew resistance locus O)[8]. The CRISPR TaMLO knockout lines have been successfully established to increase resistance against Blumeria graminis f. sp. Tritici (Btg), the causal organism of powdery mildew disease. In another study, Kim et al., (2018) demonstrated gene editing in wheat protoplasts for dehydration-responsive element-binding protein 2 (TaDREB2) and ethylene-responsive factor 3 (TaERF3) using the wheat U6 snRNA promoter. The CRISPR/Cas9 gene-editing system is capable of editing the complex hexaploid wheat genome (T. aestivum). The availability of whole-genome sequence information for wheat along with the advancements in the CRISPR/Cas9 technique could provide possibilities for the development of a “hypo-immunogenic-wheat variety. This genome editing technology not only improves crop yields contributing to sustainability and food security but also reduces the dependency on chemical treatments and promoting sustainable food crop production.
Figure 1: Ongoing CRISPR research at BOKU University Tulln of gene responsible for DON resistance gene by Dr. Barbara Steiner
Figure 2: A clear indication of fusarium head blight in ongoing study with wheat
As CRISPR genome editing is entering a new era, its future potential is offering unprecedented precision and efficiency in developing disease-resistant crops. This technology's ability to target and modify specific genes associated with disease susceptibility or resistance allows for rapid and accurate enhancements in crop resilience. By reducing reliance on chemical pesticides, CRISPR not only fosters more sustainable agricultural practices but also supports global food security by ensuring higher and more stable crop yields. The successful applications in crops highlight CRISPR's transformative potential. As research advances and regulatory frameworks evolve, CRISPR genome editing is poised to become an integral tool in the ongoing effort to combat plant diseases, identify and characterise the genes responsible for stress responses, contributing to a more resilient and sustainable agricultural future. Moving forward, continued research and refinement of CRISPR technology, along with supportive regulatory frameworks, will be essential in harnessing its full potential.
With CRISPR genome editing, it is possible for Africa to generate crops that are resilient to climate change. It has the potential to increase yields, improve nutrition, reduce inputs like pesticides and fertilizers, and produce crops that can resist changing climates[9]. This may aid in addressing Africa's issues with hunger and food insecurity as already evidenced in East Africa where a disease resistant banana, maize resistant to lethal necrosis, and sorghum resistant to the parasitic plant Striga and enhanced quality, are under development for African farmers[10].
By facilitating capacity building, fostering local and international collaborations, and advocating for supportive regulatory frameworks, ACTS can play a crucial role in harnessing CRISPR gene editing to develop disease-resistant crops in Africa. They can establish training programs to equip African scientists and researchers with the necessary skills in CRISPR technology, and engage in collaborative research with established international institutions to exchange knowledge and resources. Additionally, ACTS can work towards identifying region-specific challenges and target genes for crop improvement, ensuring that the technology addresses local agricultural needs. Through public awareness and dialogue on the ethical and safety aspects of gene editing, and advocating for a conducive regulatory environment, ACTS can help in integrating CRISPR technology into sustainable agricultural practices, thereby enhancing food security and resilience against climate change in Africa.
[1] AHMAD, M. (2023). Plant breeding advancements with “Crispr-cas” genome editing technologies will assist Future Food Security. Frontiers in Plant Science, 14. https://doi.org/10.3389/fpls.2023.1133036
[2]. Min-Yao Jhu, Ellison, E. E., & Sinha, N. (2023). CRISPR gene editing to improve crop resistance to parasitic plants. Frontiers in Genome Editing, 5. https://doi.org/10.3389/fgeed.2023.1289416
[3] Guo M., Zhang X., Liu J., Hou L., Liu H., Zhao X. (2020) OsProDH negatively regulates thermotolerance in rice by modulating proline metabolism and reactive oxygen species scavenging. Rice. 13(1): 1–5. 10.1186/s12284-020-00422-3
[4]Cai Y., Wang L., Chen L., Wu T., Liu L., Sun S., Wu C., Yao W., Jiang B., Yuan S., et al.. (2020) Mutagenesis of GmFT2a and GmFT5a mediated by CRISPR/Cas9 contributes for expanding the regional adaptability of soybean. Plant Biotechnol. J. 18(1): 298–309. 10.1111/pbi.13199
[5] Hayta S., Smedley M.A., Demir S.U., Blundell R., Hinchliffe A., Atkinson N., Harwood W.A. (2019) An efficient and reproducible Agrobacterium-mediated transformation method for hexaploid wheat (Triticum aestivum L.). Plant Meth. 15(1): 1–15. 10.1186/S13007-019-0503-Z
[6] Jia H., Nian W. (2014) Targeted genome editing of sweet orange using Cas9/sgRNA. PLoS One. 9(4): e93806. 10.1371/journal.pone.0093806
[7] Jinek, M., Chylinski, K., Fonfara, I., Hauer, M., Doudna, J. A., & Charpentier, E. (2012). A programmable dual-RNA-guided DNA endonuclease in adaptive bacterial immunity. Science, 337(6096), 816-821. https://doi.org/10.1126/science.1225829
[8] Shan, Q., Wang, Y., Li, J., & Gao, C. (2014). Genome editing in rice and wheat using the CRISPR/Cas system. Nature protocols, 9(10), 2395-2410.
[9] Ndudzo, A., Makuvise, A. S., Moyo, S., & Bobo, E. D. (2024). CRISPR-Cas9 genome editing in crop breeding for climate change resilience: Implications for smallholder farmers in Africa. Journal of Agriculture and Food Research, 16, 101132. https://doi.org/10.1016/j.jafr.2024.101132
[10] Tripathi, L., Dhugga, K. S., Ntui, V. O., Runo, S., Syombua, E. D., Muiruri, S., Wen, Z., & Tripathi, J. N. (2022). Genome editing for sustainable agriculture in Africa. Frontiers in Genome Editing, 4. https://doi.org/10.3389/fgeed.2022.876697.
