[Wylie's Mom]

OK, how do pedigrees figure into this?
Remember that it is difficult to spot unaffected carriers. When an affected dog shows up, its pedigree is often examined for likely carriers. For example, PRA is a common problem in many breeds. There are dogs that come down with PRA that have a certain ancestor in common. That ancestor may then be considered a possible carrier and line breeding on him is avoided. This is a simplistic picture, obviously, since it's possible for an unaffected non-carrier of PRA to come from an unaffected carrier that came from an affected dog (therefore the affected dog is in the unaffected dog's pedigree). If a general blood test is ever developed that shows the presence of the recessive in an unaffected dog, then much more accurate breedings may be done; currently this is only possible for Irish Setters.

There is rarely only a single problem a breeder is trying to screen for. Suppose a suspected carrier of PRA is known for producing excellent hips. A breeder might therefore introduce that bloodline into theirs for the hips, and be willing to have the possibility of PRA show up in the line. In screening out one problem you might have to accept the possibility of another appearing.

Examining the pedigrees also lets you know what percent of ancestry the dogs share (since the relationships are often much more complex than simply cousins or aunt/uncle, the degree of common ancestry is often given as a percentage instead) and decide whether or not it's acceptable given your current goals.

What are like-to-like matings and compensatory matings?
Like to like mating implies the best to the best and the worst to the worst where the worst is not used at all. For most breeders, like to like matings are between dogs which resemble each other greatly and so similar type dogs are bred. These dogs may or may not be closely related.

The pups resemble their parents because of the genes in common with them. If those parents resembled each other their progeny would be even more like their parents. This tends to make the population look more uniform, however there is little increase in prepotency from this technique.

Compensatory Mating: This unlike to unlike mating is used by breeders to correct for a defect in an animal by mating it to another animal that might correct for the defect. The system is basically simple but the breeder must identify faults and virtues and it requires breed knowledge. The pedigrees of both dogs should be examined carfully to try to identify the ways in which the dogs differ and what the expected outcomes could be. A correct dog and not one who errs in the opposite direction is required. That is, if you want to improve structure, look for a dog with correct structure and not an overbuilt dog. This technique often results in only one or two pups with the combination desired.

But this is all very vague and complicated!
Yes, it is. There are no easy answers, and there are different things to consider in every breed. This uncertainty with respect to genetic inheritance is exactly the reason that breeding is so difficult to do right. It helps immensely to have a "mentor", someone who is familiar not only with the breeds, but the lines your dog belongs to -- advice from such a knowledgeable person is often extremely valuable.

If we knew everything about genetics, we wouldn't have problems with our dogs any more. We'd eliminate Hip Dysplasia, PRA, heart problems, thyroid problems, seizures, etc. within a few generations if we knew everything. Unfortunately it's an art that few people are actually very good at.