CRISPR-finder: A high throughput and cost-effective method to identify successfully edited Arabidopsis thaliana individuals

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Abstract

Genome editing with the CRISPR/Cas (clustered regularly interspaced short palindromic repeats/CRISPR associated protein) system allows mutagenesis of a targeted region of the genome using a Cas endonuclease and an artificial guide RNA. Both because of variable efficiency with which such mutations arise and because the repair process produces a spectrum of mutations, one needs to ascertain the genome sequence at the targeted locus for many individuals that have been subjected to mutagenesis. We provide a complete protocol for the generation of amplicons up until the identification of the exact mutations in the targeted region. CRISPR-finder can be used to process thousands of individuals in a single sequencing run. We successfully identified an ISOCHORISMATE SYNTHASE 1 mutant line in which the production of salicylic acid was impaired compared to the wild type, as expected. These features establish CRISPR-finder as a high-throughput, cost-effective and efficient genotyping method of individuals whose genomes have been targeted using the CRISPR/Cas9 system.

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Symeonidi, E., Regalado, J., Schwab, R., & Weigel, D. (2021). CRISPR-finder: A high throughput and cost-effective method to identify successfully edited Arabidopsis thaliana individuals. Quantitative Plant Biology, 2. https://doi.org/10.1017/qpb.2020.6

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