Identifying Genes Related to Retinitis Pigmentosa in <i>Drosophila melanogaster</i> Using Eye Size and Gene Expression Data

The retinal degenerative disease retinitis pigmentosa (RP) is a genetic disease that is the most common cause of blindness in adults. In 2016, Chow et. al. identified over 100 candidate modifier genes for RP through the genome-wide analysis of 173 inbred strains from the Drosophila Genetic Reference Panel (DGRP). However, this type of analysis may miss some modifiers lying in trans to the variation. In this paper, we propose an alternative approach to identify transcripts whose expression is significantly altered in strains demonstrating extreme phenotypes. The differences in the eye size phenotype will, therefore, be associated directly with changes in gene expression rather than indirectly through genetic variation that might then be linked to changes in gene expression. Gene expression data are obtained from the DGRP2 database, where each strain is represented by up to two replicates. The proposed algorithmic approach first chooses the strains’ replicate combination that best represents the relationship between gene expression level and eye size. The extensive correlation analysis identified several genes with known relationships to eye development, along with another set of genes with unknown functions in eye development. The modifiers identified in this analysis can be validated and characterized in biological systems