There's only one way to solve the clean gene pool dilemma and that is to fix it yourself. I have often thought about making that a pet project of mine.

You would have to pair up as many pairs of like animals as possible.

Example: blue x blue, black berkshire x black berkshire etc

Then you would have to keep all the babies back that look like the parents and breed them together.

I have no idea how many generations you would have to do that for in order to call it a clean gene?