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Honey bee genetics: where’s the miracle?

For a long time, genetics has been the answer to our agricultural problems. I don’t mean modern gene-splicing where you combine genes from different species, but the old-fashioned kind of breeding where you cross hand-selected individuals in order to amplify their best traits. This traditional method has yielded bigger, fatter, disease-resistant, and high-yielding plants and animals that are the backbone of modern agriculture. Over the years, it gave us more milk, bigger cherries, sweeter apples, blight-resistant tomatoes, pink daffodils, and a cajillion breeds of dog.

Inadvertently, we’ve done the same thing with undesirable organisms. Methicillin-resistant Staphylococcus aureus (MRSA) and similar pathogens arose because we killed off most, but not all, of the individuals. Those that survived were the strongest, best adapted, and most able to persist in spite of antibiotics. It’s the same selection principle operating in the opposite direction. Closer to home, we’ve bred Varroa mites that are resistant to nearly everything we throw at them.

Why don’t we breed better bees?

So why don’t we just breed better bees? What’s taking so long?

The answer here is simple: we already have. Breeders have managed all kinds of marvels with honey bees. They can build bees that are gentle, bees that overwinter well, bees with increased honey production, and even bees that cope with Varroa mites. Breeding isn’t the problem.

The problem with honey bees occurs after the queens leave the breeder. The traits bred into honey bee queens in carefully controlled breeding programs soon disappear when the daughters of these queens are allowed to mate with open stock. Within a generation or two, the descendants of these super bees are right back to square one. Why does this keep happening?

Genetic hurdles

The problem has many causes, but four come to mind.

  1. Honey bees in North American have had a restricted gene pool for a long time. This is partly due to the Honey Bee Act of 1922 which prohibited the importation of honey bees into the United States. The idea was to prevent honey bee disease organisms, specifically tracheal mites, from entering the country. But the unintended consequence was to cut off the flow of genes from the honey bee’s native lands.

  2. The honey bee genome is limited in the number of genes that allow for detoxification. Instead of evolving quickly to protect itself from environmental threats, the honey bee uses other mechanisms such as hygienic behavior, propolis, and sacrifice of the individual for the good of the colony. While mosquitoes, cockroaches, and even Varroa mites become resistant seemingly overnight, the honey bee is more genetically stable, less changeable

  3. The honey bee, like all Hymenoptera, is haplodiploid. Haplodiploidy means that some individuals have two sets of chromosomes (diploid) and some have only one set (haploid). If your knowledge of genetics is limited, suffice it to say that haplodiploidy is weird and doesn’t operate like the simple Mendelian genetics you learned in high school. This complexity makes breeding more difficult. In honey bees, males are produced from unfertilized eggs, which means each drone has only one set [1] of chromosomes. Female bees, both workers and queens, have two sets. In most animals, all individuals have two sets of chromosomes.

  4. Honey bee are polyandrous. Polyandry means “many men” and refers to the fact that a queen bee mates many times. Having many mates is not unusual by itself, but a queen bee stores all the sperm in her body for the rest of her egg-laying life. So when she lays her eggs, the eggs are fertilized by an assortment of males. Each of these different couplings represents a different sub-family in the brood nest. Workers of any single sub-family have the same mother and father and are called “super sisters” because they share about 75% of their genes. Workers belonging to different sub-families have the same mother but different fathers. They are known as half-sisters, and share about 25% of their genes. When people ask, “Why are my bees all different colors?” that’s the answer: they represent different sub-families in the same nest.

Successful bee breeders cross queens and drones that exhibit the characteristics they are looking for. Those most successful use instrumental insemination and have a way to control the drone mothers. It is really helpful to have a remote island or vast tracts of land free of other colonies. Successful breeders inundate their area with acceptable drones, and thereby shift the gene pool in their favor. This is especially important in breeding for Varroa resistance and hygienic behavior because all the genes are recessive.

Beekeeping in the real world

But let’s go back to the trouble. In the real world, a carefully bred and inseminated queen will work as advertised. Say for example, you buy a queen bred and mated for hygienic behavior. Her offspring will most likely show the desired trait and the Varroa mites will be dispatched. But at some point, the colony swarms and the queen is lost to the wilds.

If you do not intervene, one of her daughters will become the new queen. She carries the desired trait from both her mother and father, but when she mates, she mates from the local stock of drones. Perhaps some of those fathers have the hygienic gene, especially if some other local beekeepers bought bees from the same breeder. But most of the drones have no such trait.

It’s a numbers game

Imagine that the local bee club in town just purchased 250 packages from a producer in the south. Assume for a moment that they all survived. You would then have, theoretically at least, 250 queens, each laying 1000 eggs per day for the months of April, May, and June. If you assume 15% of those bees are drones, then you have (250 x 1000 x 90) x 15% or 3,375,000 drones in your area during that three-month period. And those are just the drones from the new packages, not those from established and feral colonies. And all of them are eager to mate with the offspring of your hygienic queen.

Sure these are ballpark numbers, but the message is clear: if you bring a Varroa-resistant queen into an area where there are lots of bees but little Varroa resistance, the trait will soon disappear.

Altering the local gene pool takes time

Those beekeepers who are successful at raising treatment-free bees have generally been working in the same area for many years and are at least somewhat protected from outside shipments. These two factors mean they have had a lot of influence on the wild bee populations in their local area. In other words, they have been able to flood their area with “good” genes, so there is a higher probability that their queens will mate with drones who also have Varroa-resistant traits. It is not unusual to hear of treatment-free beekeepers who willingly give away resistant stock to new beekeepers in their area to keep them from importing package bees.

If your new queen mates 16 times, and only one or two of those matings are with a drone with Varroa-resistant genes, you will have, at most, just two subfamilies in your hive exhibiting the trait. Assuming all subfamilies are represented equally, that would be about 1/8 of the bees or 12.5%—perhaps too low to do much good. The more Varroa-resistant drones in the area, the better chance you have of seeing some resistance, which is exactly why we see pockets of Varroa resistance where a lot of breeding has been done. Moving that resistance to another part of the country is not an easy task.


In summary, a persistent beekeeper with a lot of hives can significantly shift the gene pool in his favor. But if the area is constantly bombarded with random bees, it is extremely difficult to get a resistant line of bees going. It will require time, effort, and significant planning.

I’m not saying that you shouldn’t try to breed better bees. But you need to understand why it’s a long row to hoe and why it is so hard to imitate the success of others. It takes a long time to make a difference.

[1] Drones also arise from fertilized eggs that have identical alleles of the sex gene, a common result of inbreeding. Known as diploid drones, these bees are discovered early by the worker bees and consumed by them, leaving obvious holes in the brood pattern.



Erik Brown

I have also read that many of the Varroa-fighting traits are recessive. So VSH genes, for example, are quickly overcome by non-VSH genes from those local packages you mention. Perhaps part of the battle is finding more dominant traits that can stick with the queens across generations.

Thanks for the overview!



It is true that all the hygienic genes, and there are quite a few, are recessive.


Thank you Rusty. So to put it simply, if I’m splitting hives that are healthy, survived winter, etc, before they swarm, their gene pool is being strengthened? I always worried about that. Should I introduce new bees? This spring will be my 4th season. I started with one hive from one nuc. I have only had one hive death, a winter death, smaller cluster they froze in 2014-2015. We had very very single digit weather. It was my first winter not closing in bottom boards. I just wrapped my hives. I have 3 hives. It’s been a very warm mild winter so far here in northeastern Maryland, I didn’t wrap but closed bottoms, now I’m worrying about them being too active and running out of food! But I’m anticipating 3 hives soon to be 6! I also do splits the lazy easy way. I go in take frames of bees with brood, eggs, food put them in a new hive brood box, close it up for 24 hours then open it up and let them make their own queen if they need to. I don’t buy new queens. And that’s it. That’s pretty much my only manipulation. Lol. I’m a hands off beekeeper, just treat for mites or beetles naturally, except for fumagillan in fall.
So should I introduce new bees?
Thanks Robbin



You ask, “if I’m splitting hives that are healthy, survived winter, etc, before they swarm, their gene pool is being strengthened?” The answer is much more complicated than yes or no. Generally, bees that survive your local conditions are adapted to those conditions, so bees you raise yourself seem to do better than those you bring in. Personally, I stopped bringing purchased bees from elsewhere into my apiary years ago, and my success has increased. I still catch swarms which come from who knows where, but other than that, I raise my own bees.

Certainly if your bees show overwintering ability and/or some disease and parasite resistance, it seems prudent not to introduce scores of drones that probably don’t have those characteristics.

Peter Harris

Excellent piece Rusty – we are all very fortunate to have you out there as the Ambassador for our bees ?

Diana A

Fascinating. I love all your posts. I feel like you are far and away the most REAL beek posting out here. Of course I just started doing research about 2 months ago so…


Rusty, I found your footnote interesting about diploid drones and it amazes me that the nurse bees can sniff them out. I followed your link to “DIPLOID DRONES ARE A RESULT OF INBREEDING” posted in 2013 and I’m a bit confused. Even this question is confusing. I assume like in algebra X=X is 0 (canceling each other out) and the organism would die, but how could the egg hatch in the first place then? So if the workers wouldn’t kill them, would they mature and emerge as a drone (except having two alleles)? Would they have the ability to mate with a virgin queen and would the mating be viable? Or would they emerge as some in-conceivable thing like a laying drone? OK strike that last question, getting too abstract.



Apparently the organism perceives two identical alleles in the sex locus as just one allele, so the fertilized egg that normally would have yielded a female, grows into a male. These males (diploid drones) are detected soon after the eggs hatch by some magical bee process, and the workers (little cannibals that they are) eat them.

However, from what I’ve read, you can raise diploid drones into adulthood in a laboratory, but they produce few, if any, sperm cells and are generally weak and unfit.


Very interesting things to ponder. All of my bees are collected from swarms and cutouts from my region, and then splits from those that are doing well or successfully overwinter. Are you suggesting that we should purchase queens and packages from isolated breeders rather than sort out the naturally successful colonies? After all, I have no real idea where my bees originated from.



No, I think the opposite. I think the very best queens are those you raise from your own local stock and that seem to be thriving in your particular environment. No, we don’t know where they originated, but they are generally more fit than those brought in from the outside. What you are doing is perfect. I was trying to point out that you can’t maintain the genetics of breeder queens through future generations in situations where you cannot control mating.


So interesting Rusty! I’m amazed that nurse bees can sniff out diploid drones.


It seems to me that feral hives that survive would tend to carry the mite resistance genes…as those with more of that would survive. I mean no one is doing mite treatments on the feral hives right?

Also, would this mean that it would preferable (say if you have one mite resistant queen In your apiary) to have that hive increase its drone production? Say through allowing them to draw their own comb instead of artificial? (The drone % is higher in those correct?) The idea being that that hive would have more drones and flood the area with better chance of gene expression in the area?



Yes on all counts.

Roger Spaulding


Thanks again for the thoughtful articles. What would be your plan / approach if you lived in a location that had Africanized bees?
(Phoenix, AZ.)

Roger Spaulding



I hear from many beekeepers who keep Africanized bees quite successfully. They are not going to go away any time soon, and they continue to spread further north. I think if I was in their area, I would try to learn how to handle them. Of course, it would depend on how urban the area was, and whether I thought I could do it safely. There is no guarantee that bees we buy from commercial producers are free from Africanized genes, so I think AHB is something we must learn to deal with.



Great article once again, Thank you.

The flow is starting to slow down here in Sydney Australia and before it’s too late I’m hoping to do a spit tomorrow (weather permits) to increase the number of bees I have. The genetic agenda to me is critical and I am trying to maintain a “natural as can be” practice. What concerns me with splits and having only one urban colony, is the high probability of inbreeding when the new queen is out on her mating flight. Not sure if that’s correct or not? To overcome this I have made baby nucs or mating nucs so I can take them away far enough to avoid inbreeding and even hopefully mix with feral bees.

The design of the mating nuc has got me thinking. What I’ve done is made the frames exactly half the length of my existing frames and the same depth. So 2 mating nuc frames side by side is the same length as my standard full deep frames which i run in all my brood boxes & supers. A spacer block goes between the mating nuc frames so no burr comb can be made and a simple 2mm wire u clip at the bottom holds the two together. This twin frame can be placed in any frame location in any box or even super without any modification to the existing hive. Then once its filled with whatever you need, pollen,eggs, larvae etc, its taken out, separated and placed in the mating nuc. Sorry for going off on a tangent, I just thought someone could benefit from this.



Interesting set up on the mating nucs and frames. I love things that work together like that.

As for the queen, don’t worry. Drones from dozens or hundreds of hives get together in the drone congregation areas and wait for a queen to come along. Since there are so many drones, the chance of your queen mating with one of your drones is minuscule. And even if she mates with one, she will mate with a dozen or so others, so don’t worry about that aspect.

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