Knowing what traits to breed for is an excuse for poor progress, but is not a reason for poor progress.  In fact knowing what to breed for is usually only going to be helpful if you incorporate a lot of DNA sequencing results in your breeding program.  If you are not incorporating DNA sequencing results (or some DNA surrogate) it is a total waste of time to know what traits you are breeding for a lot more often than not.  You are far better off in the absence of DNA results simply breeding the best performing hives with respect to mite control.  Now, I will admit a few things are so dirt simple genetically that you can use artificial hints.  Hints like brood removal after freeze kill tests to give some hints as to AFB resistance.  But, while freeze kill and subsequent brood removal works for AFB it does not work at all for EFB.  MH queens are well known to be pathetic at dealing with EFB.  Your average feral is likely better at dealing with EFB than MH queens are. The message is if you can find some surrogate test to guide you it is fine to use it in your breeding program.  But, it is very seldom you can find such a test.   And, you can waste years of breeding efforts going down such rabbit holes trying to find a surrogate only to find out first year results were statistical accidents.  You are generally a lot better off simply selecting for the objective by a direct measurement.  In the case of mites why not simply measure how well they are doing at controlling mites?  Or if you want better honey production why not measure honey production of each hive?

Genetics is essentially a brand new science.  We have only really started to have a half decent understanding of the topic in the last 30 years.  And that is actually being generous.  Before that most of what was taught was mainly wishful thinking or worse and yes I learned all that stuff 60 years ago and used to believe it until there was finally some science applied.  Yet a bunch of farmers who likely could not even read have conducted highly successful selective breeding programs for the last several thousand years.  These farmers put together a whole host of traits in our domestic plants and animals that made them highly useful to man simply by selecting for the desired traits for hundreds of years and with a few million offspring to pick from.   The American Indians took teosinte which is a little weedy grass that grows in central America and turned it into the largest grain crop grown in the world.  We call it corn.  Corn looks nothing at all like teosinte. We still today do not know enough genetics to be able to look at a corn plants genome and know if it will be any good at producing corn.  A bunch of Mid Eastern farmers took a critter bigger than a work horse and shrunk it down to useful size starting about 10,000 years ago.  Then they selected some to be excellent meat producers and others to be excellent milk producers that we call cows today.  Neither look very much like their wild ancestor.  We still do not know the genes that make a good meat producer or milk producer.  We have done mapping and do know something about where the most important genes are located on the chomosomes.  So, why would anyone think breeding honey bees should be approached differently than what has been proven over and over to work historically?  The reason is some people today know enough genetics to think they have some expertise and can short cut the process when in fact they would be better off knowing no genetics at all if they are going to under take a breeding program.  The only honey bee breeding program that has actually used science to direct the program did not even use DNA as dealing with honey bee DNA is a technical nightmare.  Instead that program used protein analyses as a surrogate for DNA.  It has worked fairly well actually, althou it suffers greatly from proteins not being very sensitive to DNA controlling genes.  It has resulted in the Saskatraz queens.  You could do this for mites if you have say a million $ a year to spend doing protein analyses.  If you spent that money I suspect you could speed up the breeding program.  Particularly if you also used some single drone II to help.

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