A second locus contributing to the differential expression of the blue sensitive opsin SWS2A in Lake Malawi cichlids

African cichlids provide an ideal platform for studying genes responsible for mate choice and species divergence. These highly speciose fishes vary in expression of seven distinct cone opsin genes. Each species expresses a subset of these genes, leading to extensive diversity in visual sensitivities. In a genetic cross between two Lake Malawi cichlid species with varying opsin expression, we previously identified two quantitative trait loci responsible for differential expression of the short wavelength sensitive SWS2A opsin gene. We then identified the RX1 gene as contributing the largest effect. Here we aim to identify the second causative factor. We identify MITFA and BHE40 as candidate genes. Several lines of evidence suggest that an intronic insertion at the MITFA locus may be responsible for differential SWS2A expression. We tested the effect of MITFA on SWS2A expression using CRISPR/Cas9 coding sequence knockouts in Astatotilapia burtoni. Although the mutation altered SWS2A expression, its effect contradicted our expectations, with MITFA d10/d10 mutants expressing more SWS2A opsin. This work provides some support for a role for MITFA , but additional work is needed to understand the mechanism by which MITFA acts, and to explore the potential role of other genes, including BHE40.