Mutation of the white gene in Drosophila has widespread phenotypic and transcriptomic effects

The white (w) gene is one of the most widely used genetic markers in Drosophila research, serving as a standard background mutation for transgene insertions and genetic manipulations. While its primary function is in eye pigmentation, w mutations have been associated with diverse phenotypic effects including in metabolism, behavior, and stress responses. However, many studies using w mutants do not account for differences in genetic background, raising concerns about the interpretation of experimental results. Given the potential confounding genetic effects and non-pigment related roles of w, we generated a well-controlled phenotyping dataset. To ensure that the observed phenotypic differences are attributable to white itself, rather than other genetic differences due to background, we established isogenic fly strains through backcrossing that differ only by the presence or absence of the white gene. Given the likely metabolic consequences of white gene dysfunction and its crucial role in neurotransmitter production, we focused our phenotyping assays on behavioral, metabolic and fitness related outcomes and performed transcriptomic analysis on adult fly heads. Our findings reveal widespread changes in adult brain gene expression and behavioral, metabolic and fitness traits, demonstrating that w mutations influence multiple biological processes beyond their established role in pigment transport. These results emphasize the necessity of genetic background control in Drosophila research and suggest that caution is warranted when using w mutants as a baseline for comparative studies. Overall design: RNAseq profiling of heads from 1 week old male and female w+ and w- w1118 Drosophila. Each sample represents 10 pooled heads.