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Honey bee genome

Honey bee genome

Honey Bee Genome

    Smell and taste
    Population genetics

In this age of technological advances in biology, we have much to learn from what the genetic code can tell us.  We hear in the news about research on genes relating to cancer, obesity, and other health related topics.  These same techniques can be used to study insects and other organisms as well.  However, the terminology can get overwhelming at times.  Let’s take a walk through the main factors influencing honey bee genetics, and then we will discuss some of the insights gained from the honey bee genome.

honey bee and DNA
Bee photo by Zachary Huang

Honey bee genetics

Genetics is the study of variable traits of organisms and how they are transmitted from one generation to the next.  Genes are units of DNA that act as a blueprint for these traits.

Even though humans first started keeping honey bees at least 7000 years ago, it was not until the mid-1850s that people started to understand honey bee reproduction and genetics so that they could breed for desirable traits.  Most bees in the hive are female, and the queen is responsible for all reproduction.  Let’s take a look at some of the unique aspects of honey bee genetics and see what the recently sequenced genome can tell us about sociality and bee biology.

In a honey bee colony, the queen is responsible for all reproduction and does all of the egg-laying in the hive.  Female workers do all of the work inside the hive and collect food outside of the hive.  Male drones are fewer in number, and they contribute little to hive function.

Honey bees (and the rest of Hymenoptera: bees, ants, and wasps) have a genetic system that is different than ours and most other insects.  Haplodiploidy is a system where females have two copies of each chromosome, but males have just one copy.  Haplodiploidy increases relatedness between siblings and is related to the social division of labor.  Female honey bees have a full complement of chromosomes (one set from each parent) and are diploid.  Males, however, are formed from unfertilized eggs and are haploid; they contain only one copy of each chromosome. Queens control whether or not they lay a fertilized egg because they are able to store sperm from previous matings.  In this way, the queens manage the sex ratio in the hive.

diagram of chromosomes in honey bees
Bee photos by Zachary Huang

This figure shows only two chromosome sets for purposes of clarity.  Diploid females have 16 pairs, or 32, chromosomes, and haploid males have only 16 single chromosomes.

Honey bee genome

Genomics is the study of DNA at the level of whole chromosomes, large clusters of genes, or the entire genome at once.  A genome is the entire set of genetic material for an individual organism.

To have a complete genome sequence means that we have sequenced all of the genetic code for that particular organism.  Chromosomes are very long strands of DNA that encode a large number of genes in succession.  The ‘alphabet’ for the code contains only four letters: A, T, C, and G.  When we say we ‘sequence’ a genome, it means we determine the whole DNA code for all the chromosomes. 

How it’s done: After the DNA is extracted, it is broken into small pieces, and those small pieces are sequenced.  Then using a computational process, the small pieces of sequence are put back together by matching the overlapping sections.
diagram of how a genome is sequenced

Why was the honey bee selected to have its genome sequenced?  The primary motive was to understand mechanisms underlying social behavior among other aspects of bee biology.  There is no special gene that controls whether a bee grows up to be a queen or a worker; their jobs in the hive are not determined by genetic makeup.  For example, queen bees result from larvae that are fed large amounts of a substance called royal jelly, which leads to development resulting in a queen.  Queens are larger than workers and are responsible for all reproduction in the hive.

Furthermore, there are no specific genes predisposing the workers to the different tasks they do.  Young adult bees perform nursing duties (feeding larvae, for example) inside the hive for about a week, after which there is a transition in behavior to performing foraging (collecting food) duties outside the hive.  Other tasks that may be done for the colony include guarding the hive and removing dead bees from the hive.

There are a little over 10,000 genes in the honey bee genome, but this is likely to be a slight underestimate of the real total.  Of the total predicted genes, 1052 of these are specific to the honey bee and the other insects that had their genomes sequenced at that time: the fruit fly Drosophila melanogaster and the malaria mosquito Anopheles gambiae.

Other insects whose genomes have now been sequenced include Aedes aegypti, the yellow fever mosquito, and Bombyx mori, the silk moth.  Others in progress include the red flour beetle, the human body louse, and the pea aphid.  The number of genome sequencing projects is greatly increasing as the technology becomes ever faster and cheaper.  Comparative genomics is an emerging field that seeks to answer many questions about evolution.

Aedes egypti mosquito
male silkworm
Left: Aedes aegypti mosquito (photo from USDA)
Right: Bombyx mori moth (photo by Kevin Wanner)

Many “families” of genes were examined in the honey bee, and many of these were compared to relatives in the fruit fly and mosquito.  Here are some highlights of what we have learned from the honey bee genome, but it is certainly not an exhaustive list.

Smell and Taste


Believe it or not, insects “smell” with their antennae. Special proteins in the antennae called odorant receptors allow the insect to recognize chemicals in the environment.  The ability to perceive odors is very important in insects; they need to be able to smell possible food sources, locate a mate, and avoid their enemies.

bees use antennae to smell
Insects use antennae to smell.
Photos by Zachary Huang

In comparison to the fruit fly and mosquito, honey bees have over twice as many genes coding for these odorant-sensing proteins.  Indeed, honey bees are able to perceive several pheromones and a variety of floral odors.  They can even recognize their relatives and the queen by smell.


Taste is another method of perceiving chemicals in the environment.  Honey bees have only about 15% of the number of taste receptors compared to fruit flies and malaria mosquitoes.  Possible explanations for the limited number of taste receptors include the fact that larval bees are fed by the adult workers and may not have to rely on taste cues to avoid toxic chemicals.  Furthermore, bees feed on pollen and nectar, which are produced by plants as food for pollinators, and thus rarely contain toxic chemicals.
bee drinking sugar water
A bee tasting sugar water
Photo by Zachary Huang


Insects routinely evolve resistance to plant defense chemicals and even insecticides.  Indeed, some genes responsible for detoxifying plant defense chemicals are involved in insecticide resistance.  Honey bees have fewer genes relating to detoxification than the fruit fly or malaria mosquito, possibly making them more sensitive to insecticides in the environment.  Limiting the use of insecticides in your garden will help protect bees.


Honey bees have fewer genes relating to immunity than the other insects.  This is interesting given the fact that honey bees are exposed to pathogens living in a crowded environment.  It is suggested that perhaps honey bees prevent infection by grooming and other social behaviors.

Population genetics

One use of a genome is to infer the history of the species.  The honey bee genome was scanned for single nucleotide polymorphisms (SNPs): mutations that change one letter of the DNA sequence at a time.  Locations where SNPs occur can be mapped onto chromosomes and used for many purposes.  For example, an analysis of these SNPs showed that honey bees had at least two ancient migrations from Africa and into Europe.  Another use of these SNPs is the study of African ‘killer’ bees, which were introduced to South America in 1954.  These bees have now been hybridizing with bees in Central and South America.

On a final note, just because we have all of the sequence for an organism does not mean we have found all of the information it has to offer yet.  There are many genes with unknown functions, and some genes may not have even been found yet.  There are still many questions to be answered!


Diploid: paired complementary set of chromosomes
Haploid: unpaired, single set of chromosomes
Chromosome: long piece of DNA that contains many genes, genes are transported in these units
Gene: hereditary unit of DNA that codes for a specific protein
DNA: deoxyribonucleic acid.  A double-stranded molecule that encodes proteins.  Code is combination of A, T, C, and G.
Pheromone: a chemical produced by an organism of one species to communicate to a member of the same species
Resistance: a trait where an organism is less affected by something that should be harmful to it.  For example, some insects are resistant to certain insecticides, meaning that those insecticides do not kill resistant insects.