Various dog breeds were "created" long before genetics was understood. They were also created with a handful of closely kin individuals (usually less that 10) making up the founding population. Whatever faulty genes those individuals had were passed on and concentrated down through the line.

In fact, modern genetic practices are actually improving existing breeds by mapping out their genomes and replacing the defective genes that certain breeds are known to have. Joint problems that are common in some large breeds are being eradicated by germline gene therapy. This is also being done for a whole host of other problems such as blindness, deafness, and skin conditions. Selective breeding takes on a whole new dimension when you have the ability to actually map genes and replace any that cause problems.

We've come a long way since Mendel, and we'll continue to make great leaps in the coming decades. In the not too distant future, we should be able to run computer simulations on designer genomes from conception through the entire life cycle of the organism. Finding and correcting problems before the first individual organism is created.