Comprehensive benchmarking of genome editing quantification methods for plant applications

Abstract

Accurately detecting and quantifying CRISPR edits with high sensitivity is crucial for developing new genome editing applications in plants. This is especially important when analyzing heterogeneous populations from transient expression-based approaches used for technology development as well as evaluating of guide RNA (gRNA) performance in planta. However, current studies employ vastly different techniques to quantify genome editing outcomes, limiting the comparability and repeatability of results. In this study, we systematically evaluated and compared experimental techniques for quantifying plant genome editing across a wide range of efficiencies. We measured genome editing efficiency from 20 transiently expressed Cas9 targets using different techniques, including targeted amplicon sequencing (AmpSeq), PCR-restriction fragment length polymorphism (RFLP) assays, T7 endonuclease 1 (T7E1) assays, Sanger sequencing of amplicon products (deconvoluted and analyzed using three algorithms), PCR-capillary electrophoresis/InDel detection by amplicon analysis (PCR-CE/IDAA), and droplet digital PCR (ddPCR). We assessed methods based on their accuracy, sensitivity, and cost, benchmarked to AmpSeq. Furthermore, we discuss the advantages and drawbacks of each technique, the issues faced during optimization and the solutions we devised. This study will be useful to experienced and new researchers in the field, providing suggestions and guidelines to standardize data output and advice about the most suitable technique/s to quantify genome edits for different plant applications.