Improved selection of zebrafish CRISPR editing by early genotyping and next-generation sequencing. Improved selection of zebrafish CRISPR editing by early genotyping and next-generation sequencing

Despite numerous previous attempts to improve knock-in (KI) efficiency, the introduction of precise base pair substitutions by the CRISPR/Cas9 technique in zebrafish remains challenging. In our efforts to generate KI zebrafish models of human CACNA1c mutations, we have tested the effect of several CRISPR determinants on KI efficiency across two sites in a single gene and developped a novel method for early selection to further improve KI efficiency. We identified optimal KI conditions for Cas9 protein and non-target asymmetric PAM-distal single stranded deoxynucleotide repair templates at both cacna1c sites. An effect of distance to the cut site on the KI efficiency was only observed for a single repair template conformation at one of the two sites. By combining minimally invasive early genotyping with the Zebrafish Embryo Genotyper (ZEG) device and next-generation sequencing, we were able to obtain an over sixteen-fold increase in somatic editing efficiency. The added benefit of the early selection procedure was particularly evident for alleles with lower somatic editing efficiencies. We fully validated our protocol by successfully obtaining germline transmission with the ZEG selection procedure.