In simple terms, red or sepia eye color in fruit flies comes from the parents.

Brown and sepia eye color in drosophila is determined by a gene called ‘eye color’. One allele of this gene, the B allele, codes for brown pigment. The b allele codes for no pigment so it appears red after developing. The genome used to store genetic information is double stranded and what we know as DNA. A single strand from each side is referred to as a complementary strand and what we get when we unzip our DNA molecule into two strands which then bind again to form what we call a “double helix.” Thus there exists an A nucleotide and a T nucleotide on one side and G and C nucleotides on the other side that pair up with their counterparts.

This pairing explains how inheritance generally works, but what about drosophila eye color? When fruit flies are bred with white eyes what happens is that the allele cinnabar is expressed over sepia. The cinnabar allele breaks up what would have been homozygous brown/sepia pairs so all offspring have red eyes inherited from their mother.