I am following a great introductory biology course online, MITx: 7.00x on edX.
A question in the course assumes a cross between a pure-breeding male fly and a pure-breeding female fly:
You are studying genetics in a hypothetical fly and you find a fly that has purple eyes. Assume that the purple eye phenotype is due to a mutation at a single locus. Use the notation E and e, where the upper case letter is used for the allele associated with the dominant phenotype and the lower case letter for the allele associated with the recessive phenotype.
You cross a pure-breeding male fly with purple eyes to a pure-breeding female fly with normal eyes. All of the F1 offspring have normal eyes. From this experiment you determine that the purple eye phenotype is ______________ to the normal eye phenotype.
My question is this: how can a male fly be pure-breeding? The reason I wonder is that as far as I understand, pure-breeding implies a homozygote gene, yet the sex chromosome can not be homozygote because the Y chromosome is not homologous to the X chromosome. In other words, does it make sense to speak of homologous sex chromosomes?