The Beekeeper’s Companion Since 1861
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The Curious Beekeeper

Honey Bee Genetics: Why Breeding is So Difficult

- August 1, 2018 - Rusty Burlew - (excerpt)

honey bee genetics

Those new to beekeeping frequently ask why we don’t just breed better bees. This is a logical question because breeding has long been the answer to many agricultural problems. When I say “breeding,” I don’t mean modern gene-insertion techniques that allow us to raise glow-in-the-dark cats, 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 higher-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 hairless dogs.

Of course, what you do on purpose, you can also do by accident. Inadvertently, we’ve created a host of undesirable organisms using similar techniques. 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. We selected for the strongest ones by eliminating the weaker ones—the same selection principle operating in reverse. Closer to home, we’ve bred varroa mites that are resistant to nearly everything.

Why Don’t We Breed Better Bees?

So why don’t we just breed better bees? The answer is simple: we already have. Breeders have managed all kinds of marvels with honey bees. They have built 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. The question is, “Why does this keep happening?”

The Road Blocks to Maintaining Better Stocks

There are three main road blocks to maintaining well-bred populations—haplodiploidy, polyandry, and panmixia—plus a few other minor complications. And while those words may sound intimidating, don’t worry, fasten your seat belt, you’ll be an expert on all three in no time. Or at least have enough details to impress your friends at the next dinner party.


Like all other members of the order Hymenoptera—including ants, wasps, and sawflies—honey bees are haplodiploid. Haplodiploidy means that some individuals are diploid, having two sets of chromosomes, while others are haploid, having only one set of chromosomes. If your knowledge of genetics is limited, suffice it to say that haplodiploidy doesn’t operate like the simple Mendelian genetics you learned in high school. I, for one, thought I was a genetic genius after I had the dominant/recessive pea grid worked out, but things in real life are not that simple.

Haplodiploidy makes breeding more challenging, and it has some surprising consequences. In honey bees, drones are produced from unfertilized eggs, which means each drone has only one set of chromosomes, while females—both workers and queens—have two sets. In most animals other than Hymenopterans, all individuals have two complete sets of chromosomes. Also, haplodiploidy results in inexplicable axioms, such as a drone has a grandfather but no father and can have grandsons but no sons.

But it gets even weirder. What they don’t teach you in Beekeeping 101 is that some fertilized eggs become diploid drones—that is, drones with two sets of chromosomes. This happens because the thing that actually determines sex is not the presence or absence of fertilization but the presence or absence of heterozygous alleles at the sex locus. Don’t turn the page yet—you can do this.

A piece of chocolate cake. You see, instead of having an entire chromosome that determines sex, like the X and Y chromosomes in humans, bees have one gene on one chromosome that determines sex. Specific places on chromosomes are called loci (the singular is locus), so the “sex locus” is just the place (think address) on the chromosome where the sex gene is found.

The European honey bee has about 18 different alleles of the sex gene. An allele is just a variation of a gene. All sex alleles do basically the same thing, but the genetic coding is a little different in each one. You can compare it to having 18 different recipes for chocolate cake—the end products are similar but the instructions for getting there vary.

So different bees are running around with different alleles (or instructions) for the sex gene. If an egg is not fertilized, there is only one set of instructions and the bee becomes a drone. If an egg is fertilized and has two different sets of instructions, the bee becomes a female. But—and here’s the kicker—if the egg is fertilized but receives two identical sets of instructions (two identical sex alleles) the bee becomes not a female but a diploid drone. Think of it like this: one set of instructions printed twice is not the same as two different sets of instructions.

The fate of diploid drones. These diploid drones do not survive. In colonies of social insects such as honey bees, the workers eat or destroy the diploid drones soon after the eggs hatch. Because they are destroyed early, having many diploid drones in a colony results in “shot brood” or “scattered brood”—brood combs that have lots of empties or brood of many different ages interspersed. In some solitary bees, the diploid male may die in the cell, or may emerge and mature but be sterile.

The table below shows what would happen when a honey bee queen (with two different alleles of the same gene) mates with five different drones, each with one allele. In this case, two of the drones have the B allele and the rest have different alleles.

Wherever you have homozygous alleles for the sex gene (two of the same alleles), you get a diploid drone. This table shows an extreme example because it has a small number of alleles and a small number of matings, but it illustrates how homozygous alleles happen. In this example, one queen with two different alleles for the sex gene mates with a series of five drones, resulting in only 70% viability of the fertilized offspring.

For the average beekeeper, this property doesn’t make much difference. Since honey bees have about 18 alleles for the sex gene, and a queen may mate twelve or more times, there is little likelihood of diploid males. But for breeders who are trying to control the ….