Genetics & Bee breeding
At a very basic level female honey bees, both queens and workers, have 32 chromosomes and drones have just 16. This can be useful when breeding bees as we can always say that the drones are carrying forward genetic material from the queen only, although it is just as likely, stastically, to be recessive genes as dominant genes. As an aside if a queen that you value becomes a drone layer dont dispair try and keep the colony going so that you can use her drones to pass on her genes.

The whole of the Apis mellifera genome was sequenced in the USA at the Baylor College of Medicine Human Genome Sequencing Center. It was published in 2006.

The article "Insights into Social Insects from the Genome of the Honey Bee Apis mellifera" published in the publication "Nature" in 2006 is easier reading for non-microbiologists.
Scientific Beekeeping
Explaination of genetics from Glenn Apiaries
Apis mellifera Sub Species
There are believed to be many more CSD (sex) alleles than previously thought. The numbers reported are from 53 to 87 and possibly as many as 146. See the paper by Lechner S et al.

This is important because where two identical CSD genes appear in an apis mellifera gene this results in a diploid drone which is not viable and will be destroyed by the nurse bees. This can be a major limiting factor when selecting breeding stock.
Nucleotide variability at its limit? Insights into the number and evolutionary dynamics of the sex-determining specificities of the honey bee Apis mellifera. Lechner S et al.
Honey Bee Genome Project, BCM-HGSC
Insights into social insects from the genome of the honeybee Apis mellifera

Bee Genetics and Breeding Thomas E Rinderer, 1975
Before we had access to the intricacies of the bee's genome, the only tool we had to to try and differentiate between different subspecies of Apis mellifera was using their established phenotype. The Table below gives some anatomical variations found by Rinderer in his book "Bee Genetics and Breeding".
Origins of Apis mellifera
Non-Apis mellifera Honey Bees