CGIAR Initiative on Genome Editing

Permanent URI for this collectionhttps://hdl.handle.net/10568/125130

Part of the CGIAR Action Area on Genetic Innovation

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Now showing 1 - 8 of 8

An Agrobacterium‐mediated base editing approach generates transgene‐free edited banana
(Journal Article, 2025-04-01) Van den Broeck, Senne; Ngapout, Yvan; Panis, Bart; Vanderschuren, Hervé
Genome editing for the development of improved varieties is supported by the possibility of segregating out the editor T-DNA cassette after genome editing in many crop species. Removal of the T-DNA cassette prevents potential continuous editing activity in the transformed plant and furthermore facilitates regulatory approval. While transgene outcrossing of exogenous sequences is possible for many crops, this is not the case for vegetatively propagated and sterile crops, such as Cavendish bananas. Therefore, gene editing techniques leading to transgene-free edited plants are essential to untap the potential of genome editing for those crops. Here, we present a method for transgene-free gene editing in sterile banana (Musa spp.) through a co-editing strategy. A novel Agrobacterium tumefaciens-mediated transgene-free gene editing approach combining embryogenesis and chlorsulfuron selection was established in sterile banana and validated through whole genome sequencing. Editing of the acetolactate synthase (MaALS) genes in banana using a plant base editor allows effective selection of edited plants. Moreover, transgene-free plantlets were regenerated with mutations at two target sites, indicating that the strategy can be used to target multiple genomic sites. The presented method allows for efficient transgene-free gene editing and represents the first report of a co-editing strategy in sterile crop species.
CRISPR-mediated genome editing of wheat for enhancing disease resistance
(Journal Article, 2025-02-25) Waites, Joshua O.; Achary, Mohan Murali; David, Easter S.; Hearne, Sarah; Bandyopadhyay, Anindya
Wheat is cultivated across diverse global environments, and its productivity is significantly impacted by various biotic stresses, most importantly but not limited to rust diseases, Fusarium head blight, wheat blast, and powdery mildew. The genetic diversity of modern cultivars has been eroded by domestication and selection, increasing their vulnerability to biotic stress due to uniformity. The rapid spread of new highly virulent and aggressive pathogen strains has exacerbated this situation. Three strategies can be used for enhancing disease resistance through genome editing: introducing resistance (R) gene-mediated resistance, engineering nucleotide-binding leucine-rich repeat receptors (NLRs), and manipulating susceptibility (S) genes to stop pathogens from exploiting these factors to support infection. Utilizing R gene-mediated resistance is the most common strategy for traditional breeding approaches, but the continuous evolution of pathogen effectors can eventually overcome this resistance. Moreover, modifying S genes can confer pleiotropic effects that hinder their use in agriculture. Enhancing disease resistance is paramount for sustainable wheat production and food security, and new tools and strategies are of great importance to the research community. The application of CRISPR-based genome editing provides promise to improve disease resistance, allowing access to a broader range of solutions beyond random mutagenesis or intraspecific variation, unlocking new ways to improve crops, and speeding up resistance breeding. Here, we first summarize the major disease resistance strategies in the context of important wheat diseases and their limitations. Next, we turn our attention to the powerful applications of genome editing technology in creating new wheat varieties against important wheat diseases.
Molecular characterization workflow of gene-edited rice lines: from development to securing non-transgenic status
(Poster, 2024) Guevarra, Precious; Arcillas, Erwin; Matres, Jerlie Mhay; Enriquez, Blesilda; Kohli, Ajay; Slamet-Loedin, Inez; Trijatmiko, Kurniawan Rudi
Genome editing technology enables precise, cost-effective, and rapid introduction of desirable traits to crops overcoming the limitations posed by conventional plant breeding and transgenesis. Ensuring the presence of desired edits, verifying the editing system's accuracy, and securing non-transgenic status are all crucial in expediting development, Philippine regulatory compliance, and the eventual deployment of plants generated through genome editing. This work outlines a streamlined molecular characterization workflow for gene-edited rice lines, covering the entire development process from construct design to achieving non-transgenic state as a requirement for the certificate of non-coverage from the DOST-DA-DENR-DOH-DILG Joint Department Circular No. 1, Series of 2021 (JDC No.1, s. 2021).
Editing cassava sweet genes for resistance to Xanthomonas. Reporting period: Second Semester 2024
(Report, 2024-10) Sanchez, Francisco J.; Zárate, Carlos A.; Szurek, Boris; Díaz, Paula A.; Chavarriaga, Paul
Cassava (Manihot esculenta Crantz) is considered the third most important crop globally. The mitigation of diseases like cassava bacterial blight (CBB), caused by the phytopathogenic bacterium Xanthomonas phaseoli pv. manihotis (Xpm) is key for the success of the crop. CBB leads to significant yield losses, ranging from 12% to 100%. One of the infection mechanisms employed by Xpm involves TALE-type proteins, which facilitate bacterial proliferation and the onset of disease symptoms. It has been demonstrated that virulence mechanisms activate certain gene families, including the SWEET gene family, which encodes sugar transporters (such as glucose and sucrose) that provide a carbon source for the bacteria to grow a cause infection. The aim of our research is to assess the resistance of cassava lines edited in the MeSweet 10a and 10e genes using CRISPR/Cas9 to confer resistance to CBB in the model variety 60444, susceptible to CBB. The goal is to evaluate the impact of editions in the promoter or coding regions for resistance to Xpm infection. Lines exhibiting the most promising mutations (INDELS) in targeted regions will be identified through molecular assays, whichthen will be established under in vitro and greenhouse conditions to be infected with Xpm strains and evaluatedisease resistance.
Development of a protocol for the regeneration of protoplasts from cassava (Manihot esculenta) isolated from friable embryogenic callus.
(Internal Document, 2024-10) Bueno, Angie M; Sanchez, Francisco J; Buritica, Magdalena; Chavarriaga, Paul
Development of a protocol for the regeneration of protoplasts of cassava (Manihot esculenta) isolated from friable embryogenic callus.
The Gene Editing Platform of the Alliance of Bioversity International and CIAT
(Brochure, 2024-08-01) Sanchez, Francisco; Valdes, Sandra P.; Chavarriaga, Paul
Make gene editing tools like CRISPR an essential component of crop improvement for a more productive, nutritious agriculture, that protects biodiversity and the environment, and guarantees a constant food/feed supply
CGIAR Initiative on Breeding Resources: Plan of Results and Budget 2022-24 (PORB) - Forecast
(Internal Document, 2022-10-13) CGIAR System Organization
CGIAR Research Initiative Proposal Review Report: Accelerating Crop Improvement through Genome Editing
(Report, 2022-07) CGIAR Independent Science for Development Council
Prepared for the 16th meeting of System Council held on July 20, 2022, this report proposes an external review of the “Accelerating Crop Improvement through Genome Editing” CGIAR Initiative proposal. The external review of Initiative proposals is an essential part of good governance and quality assurance, delivering benefits for the researchers, leadership, and System Council. The review presented in this report provide confidence to funders that their investments in One CGIAR research are appropriately targeted with high chances for success. The Initiative reviews occurred in several waves and subsequently the reporting are presented by waves. The first wave report (19 Initiative proposals) was published for the 14th Meeting of the System Council in November 2021 and the second wave (12 Initiative proposals) for the 15th Meeting of the System Council in March 2022.

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