Kita crispants for systematic image-based genetic screens of complex traits in zebrafish larvae

Abstract

With thousands of loci identified by genome-wide association studies for complex traits, there is a need for in vivo model systems that can reliably and quickly infer the role of large numbers of candidate genes. CRISPR/Cas9-based functional screens in F0 zebrafish represent such a system. However, negative controls used so far - including scrambled guide RNAs (gRNAs), inactivated Cas9, and sham injections - do not elicit the same cellular and organismal responses as mutagenesis by CRISPR/Cas9, and may fuel biased conclusions. Here, we show that targeting kita facilitates efficient optical pre-screening for successful mutagenesis, higher quality imaging data, and efficient classification of cases and controls. We identified and tested two gRNAs that target kita with similarly high mutagenic efficiency and effects on pigmentation, and are free from off-target effects or major effects on cardiometabolic traits. We propose several approaches that will result in valid, unbiased conclusions.