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The curious thought that occurred to me is as follows:

How sure are you of the genotype of the mousies you keep and/or breed? I know the question has been posed about whether or not your stock breeds true; appearance can be deceptive.

For instance, some folks think that A^vy always breeds fat meeces with brindling. What happens when you add e and then select for fit and trim meeces? Does that result in weeding out all the A^vy or is there a case to be made that these two genes could work together? A^vy is one of the varieties derived from radiation experiments. Can the brindling be bred out? Will they always be fat?

Things like this keep me from sleeping sometimes....
 

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Avy and Ahvy are both very, very variable in appearance and in how they're inherited. I used to have an epigenetics article about Avy that I will try to find for you when I get home to my own computer. I don't think you can usually tell which allele you are working with, especially in the US, and they're slightly different. That's why I no longer breed them, actually--getting brindles anywhere near standard is very difficult. Because they often (not always) have weight and type issues, you start out three steps backward. Then you move a few more steps backward when you factor in getting the stripes and color just right, which is much more difficult than on any other variety I've ever worked with. :p

I bred brindles for about 2 years and had probably two litters or more a month, fwiw.

With highly inbred varieties like champagne or PEW who are bred for show, they're usually true-breeding and the product of an exceptionally small gene pool (often 2 or 3 original mice who were themselves descended from just 2 or 3). In many cases they have produced consistent mice (in terms of color, type, conformation, size, temperament) for years or even decades, so it's safe to say those lines are pretty well known, although they probably haven't been put under a microscope.

If you think of mice like the BALB/c, which haven't even been bred for as long as some of the older strains of fancy mice have, their genetic material is 100% identical except for sex chromosomes. It stands to reason that a carefully monitored strain of mice which are never outcrossed (like BALB/c or some lines of show mice) would be very uniform, too. The concept of genetic drift dictates that after x number of generations of close inbreeding, the mice will be genetically uniform. Each generation they get closer, and at some point there are at maximum uniformity. Of course if you're breeding for pets and/or outcross ever, you change things up.

So in short, the only way you can be sure (or 99.99% sure) of what your mice carry genetically is persistent, years-long practicing of close inbreeding and only close inbreeding. Many show breeders do just this. It would be fascinating to see what differences were between any two show mice from the same strain as compared to differences (very little or none) between any two BALB/c (or similar inbred strain) mice. I wouldn't be surprised if the level of allelic uniformity was the same in both.
 
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