Some of us in the Native bee group have been discussing possible longer term projects. One of the ideas on the table is to try and identify colonies which deal with mites better than others - and selectively breed from these.
Marla Spivak reckons that favourable genes helping to deal with mites are to be found within the population of any race of bee.
The two most obvious beneficial traits are grooming off and biting mites as well as uncapping the cells with a mite infested pupa. The latter behaviour is known as Varroa sensitive hygiene. (VSH)

I see some the main issues as:

-deciding what to record and how to record it
-involving as many beekeepers as possible
-keeping it simple

Anyone got any experience in this area or any bright ideas for what is likely to work or fail?

The cold turkey approach advocated by many of the 'natural' beekeepers is not an option as no-one is going to sign up to a project where the most likely outcome is the loss of most of your bees. (see Ingemar Fries 'Bond' experiment)

The non treatment option was once described by Dan Basterfield as akin to dropping babies off a bridge with regard to selection technique.
Ideally we would be looking for something where progress could be made in incremental steps.
Queens could be grafted and propagated from any promising stock.