" Have these genes been identified?"

As far as I know not a single gene in honey bees has been shown to correlate to any phenotype.  Not even the color gene cordovan.  A total honey bee sequence was deposited in gene bank about ten years ago.  The problem is we know that sequence is next to useless due to errors and parts that could not be read.  There are some technical reasons that the honey bee genome is particularly hard to sequence with the technology available until very recently.  These technical issues exist in all animals and plants including humans but not nearly to the extent they exist in honey bees.  The net result is projects like the Saskatraz queens are being run based on doing protein sequencing and abundance rather than looking at DNA.  This is the kind of method that was used trying to learn about human genetics back in the 1980s and met with limited progress in humans.

The technical problem is related to methods like Sanger sequencing being limited to reading roughly 500 base hunks.  The good news is we have new methods that can do much longer hunks.  The record length is now close to one million base hunks.  Just a couple of weeks ago there was an announcement we now actually knew the whole sequence for one human chromosome from end to end.  There is an announcement we now know the human genome about every two or three years since we first claimed we knew the sequence back in 1998.

The net result is practically the only genetic stuff done with honey bees has looked at mitochondiral DNA which does not have the same issues the nuclear DNA has.  But, mitochondrial DNA very seldom is involved in phenotype at all other than when it is a lethal and causes the critter to die.  But, that does not mean we can not know anything about honey bee genetics in a general sense.  Clearly cordovan is a autosomal mutant that impacts the color of the honey bee.  Classic breeding studies show that.  Behavioral stuff is always at least in part genetic in every critter.  My Dad had a registered Holstein dairy cow named King who had a dominant aggression gene.  Most dairy cattle are nearly pets they are so docile.  King was not a pet.  She was sneaky mean.  About half her daughters had this same behavior.  One grand daughter also had this behavior and at that point Dad sold every cow he owned with King's blood.  We never had another cow like her at all.  It had to be genetic.  Pigeons have been selected for homing or to not home.  A decent racing homer will come home from 500 miles the same day of release.  A roller will not come home from one mile away way over 90% of the time.  Clearly homing is genetic, yet we do not know of a single gene in pigeons that results in homing or lack of homing.  There is the same anecdotal evidence that swarming in bees is inherited.  If you select for non swarming you can get far less swarming.  If you propagate from swarm cells long enough you will get bees you can not keep out of the trees.  I have had such bees and know the history on them going back 40 years.  For that whole time they were propagated by catching the owners own swarms and mainly by starting new colonies from swarm cells.  Randy Oliver has commented he found low swarming fairly easy to select in his own bees.

We know of other things in bees that must be genetic based on the same type of information.  Clear back in the early 1930s the U of Minn did experiments on breeding for honey production.  They documented an average colony honey production improvement that was remarkable over a few years simply by killing queens from poor producers and replacing them with queens raised from good producers.  This work was done with a rather small number of colonies.  Only about 35 or 40 as I recall.  No new blood was brought in during the experiment, other than perhaps wandering drones.  This work was reported in Bee  Culture back in the 1940s and in "The ABC" book at least until the early 1970s.  Yet, we still do not know of one single gene that is involved in better honey production.

To make the answer short, if we know some phenotype can be changed by breeding for more or less of that phenotype we know it is genetic.  In honey bees today we do not have a clue if that phenotype change is due to a change in some protein coding gene or a change in the control region for some coding gene or due to duplication of some region in the DNA or the multitude of other changes in the DNA that are known in one or more species to change phenotypes.  My guess is in another 20 or 30 years we will know far more as sequencing methods improve and cost of sequencing drops.  It really is remarkable that we know a lot more about the pigeon genome than we know about honey bees.  After all, pigeons are economically useless while honey bees are economically vital.  We need someone to cough up a few million $ to fund the research.  A lot of what we know about pigeons was done on a shoe string of funding, much of it private from people like me that love the birds.  I recently paid for the total sequence on three pigeons and most of what I donated is still in the bank.  The work in large part is being done by under grads doing it as part of their course work so they are paying their own tuition which supports the lab space they use.  The college provides some funding for reagents and glass ware, but not as much as I donated.  But, it is really slow sledding with such limited funding.

Dick

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