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That's something I really respects about Rez' breeding, he doesn't look at the process as a refining of just one trait, but rather the preservation of a strain's many traits.
While strict, selective breeding can yield some excellent results, it also (as Rez said) 'bottlenecks' the genetics, meaning that many of the phenotypes that made a strain tick, are no longer there, and can't be retrieved very easily, or at all.
Rez uses several studs to pollenate with, which means that the strain's natural genetic integrity is much more intact than a strain created with only one stud on one mother.
If the Irish lady next door had 20 kids by 5 different Irish fathers, you'd have a very diverse family, but they'd all be Irish. The family's genetic integrity would be stronger than if there were one Irish lady and one Irish pappa making 20 kids. The 20 kids from the on-on-one pair would all look and act similar, but their genetics are too similar to keep breeding together for long, you'd eventually end up with retardation and 'bottlenecking'.