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Develtere W, Decaestecker W, Rombaut D, Anders C, Clicque E, Vuylsteke M, Jacobs TB. Continual improvement of CRISPR-induced multiplex mutagenesis in Arabidopsis. THE PLANT JOURNAL : FOR CELL AND MOLECULAR BIOLOGY 2024; 119:1158-1172. [PMID: 38713824 DOI: 10.1111/tpj.16785] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/22/2024] [Revised: 04/08/2024] [Accepted: 04/16/2024] [Indexed: 05/09/2024]
Abstract
CRISPR/Cas9 is currently the most powerful tool to generate mutations in plant genomes and more efficient tools are needed as the scale of experiments increases. In the model plant Arabidopsis, the choice of the promoter driving Cas9 expression is critical to generate germline mutations. Several optimal promoters have been reported. However, it is unclear which promoter is ideal as they have not been thoroughly tested side by side. Furthermore, most plant vectors still use one of the two Cas9 nuclear localization sequence (NLS) configurations initially reported. We genotyped more than 6000 Arabidopsis T2 plants to test seven promoters and six types of NLSs across 14 targets to systematically improve the generation of single and multiplex inheritable mutations. We found that the RPS5A promoter and bipartite NLS were individually the most efficient components. When combined, 99% of T2 plants contained at least one knockout (KO) mutation and 84% contained 4- to 7-plex KOs, the highest multiplexing KO rate in Arabidopsis to date. These optimizations will be useful to generate higher-order KOs in the germline of Arabidopsis and will likely be applicable to other CRISPR systems as well.
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Affiliation(s)
- Ward Develtere
- Department of Plant Biotechnology and Bioinformatics, Ghent University, Technologiepark 71, 9052, Ghent, Belgium
- VIB Center for Plant Systems Biology, Technologiepark 71, 9052, Ghent, Belgium
| | - Ward Decaestecker
- Department of Plant Biotechnology and Bioinformatics, Ghent University, Technologiepark 71, 9052, Ghent, Belgium
- VIB Center for Plant Systems Biology, Technologiepark 71, 9052, Ghent, Belgium
| | - Debbie Rombaut
- Department of Plant Biotechnology and Bioinformatics, Ghent University, Technologiepark 71, 9052, Ghent, Belgium
- VIB Center for Plant Systems Biology, Technologiepark 71, 9052, Ghent, Belgium
| | - Chantal Anders
- Department of Plant Biotechnology and Bioinformatics, Ghent University, Technologiepark 71, 9052, Ghent, Belgium
- VIB Center for Plant Systems Biology, Technologiepark 71, 9052, Ghent, Belgium
| | - Elke Clicque
- Department of Plant Biotechnology and Bioinformatics, Ghent University, Technologiepark 71, 9052, Ghent, Belgium
- VIB Center for Plant Systems Biology, Technologiepark 71, 9052, Ghent, Belgium
| | | | - Thomas B Jacobs
- Department of Plant Biotechnology and Bioinformatics, Ghent University, Technologiepark 71, 9052, Ghent, Belgium
- VIB Center for Plant Systems Biology, Technologiepark 71, 9052, Ghent, Belgium
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Sahab S, Tibbits J, Spangenberg G, Mason J, Hayden M. Fluorescence-activated protoplast sorting for crop improvement. TRENDS IN PLANT SCIENCE 2024; 29:605-606. [PMID: 38199831 DOI: 10.1016/j.tplants.2023.12.008] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/24/2023] [Revised: 12/07/2023] [Accepted: 12/08/2023] [Indexed: 01/12/2024]
Affiliation(s)
- Sareena Sahab
- Agriculture Victoria, AgriBio, Centre for AgriBioscience, 5 Ring Road, Bundoora, VIC 3083, Australia.
| | - Josquin Tibbits
- Agriculture Victoria, AgriBio, Centre for AgriBioscience, 5 Ring Road, Bundoora, VIC 3083, Australia
| | - German Spangenberg
- School of Applied Systems Biology, La Trobe University, Bundoora, VIC 3083, Australia; Qingdao Agricultural University, Qingdao, Shandong Province, China
| | - John Mason
- School of Applied Systems Biology, La Trobe University, Bundoora, VIC 3083, Australia
| | - Matthew Hayden
- Agriculture Victoria, AgriBio, Centre for AgriBioscience, 5 Ring Road, Bundoora, VIC 3083, Australia; School of Applied Systems Biology, La Trobe University, Bundoora, VIC 3083, Australia
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