Practical Genetics, Step 1 --
The first order of business for the practical breeder who decides to take steps to reduce the frequency of a particular trait, is to decide whether the trait in question is genetic and heritable.
Those of us who love genetics should repeat NOT EVERY PROBLEM IS GENETIC like a mantra every morning upon awakening (as we do with the dawn, probably, to take care of the pooches). Before you can deal with a genetic problem in your breed, you really have to be pretty sure that it is a genetic problem.
Developmental abnormalities sometimes happen for no special reason (stochastic or random defects). Or birth defects and later-onset illnesses may be caused by environmental factors. An occurrence of a defect or disease in a particular family of dogs is not sufficient to establish genetic causation. Or at least, not sufficient to establish heritable genetic causation. Trisomy and uniparental disomy are genetic problems for the individual, and they're interesting, but they aren't likely to cause problems in a breeding program.
Cleft palates in dogs can be caused by genetic factors and are so listed in Padgett’s Control of Canine Genetic Diseases (mode of inheritance unknown). However, Isabel, in her excellent book Genetics: An Introduction for Dog Breeders, also lists the environmental factors a pregnant bitch could be exposed to that can also cause cleft palates in puppies: a deficiency of riboflavin or vitamin A or zinc; an excess of vitamins A, D or E; exposure to drugs such as corticosteroids, tetracycline, dilantin, or vermiplex; exposure to pesticides such as aldrin and dieldrin; or environmental factors such as dehydration (!). If a breeder routinely worms pregnant bitches with vermiplex, or supplements their diets with additives that manage to exceed allowances for vitamins A, D or E, then a high incidence of cleft palates may be expected. (Both books are briefly reviewed here.)
In the situation above, if the bitches in that kennel are all from one family, it would be very easy to leap to the conclusion that the causation is genetic. However, no solution to this problem can possibly succeed, no matter how carefully the breeder attempts to breed away from the problem, so long as she continues her traditional management practices.
Environmental effects can also be more subtle. How often does inbreeding depression get blamed for a loss of fecundity and general reproductive success? Inbreeding depression can cause these things, of course, but so can environmental factors, as Isobell also notes:
A higher than normal rate of abortion or fetal death can occur if a bitch suffers from niacin, thiamin or vitamin C deficiencies, or is given an excess of vitamin D, or is exposed to vercom paste (a worming agent); low birth weights can result from exposure to aspirin, or to the pesticide fenthion, or from the bitch’s ingestion of pine needles (!); and decreased litter size from exposure to another pesticide, mirex. A beagle breeder I know had a lot of bitches fail to catch and a lot of miscarriages just as West Nile virus was taking off in this region; West Nile is just about harmless to dogs, as it is to people, but I wonder whether contracting the virus for the first time while in whelp might cause problems? This is pure speculation, because he didn't check his dogs for West Nile, but it's the sort of speculation that a breeder ought to be engaged in if a problem seems to be occurring.
If a problem occurs in a line, the breeders first job is to decide whether it is probably genetic or whether it is due to other factors.
You can more safely conclude that a defect is probably genetic in origin if:
1. It occurs at a higher frequency than average for the breed in particular lines of dogs even though the dogs are at multiple kennels that are geographically scattered; or it occurs at a higher frequency in one breed than in other breeds that are roughly similar in anatomical terms.
2. It occurs in a particular line of dogs, but not in other unrelated lines present in the same kennel.
3. The occurrence of the problem follows classic Mendelian inheritance patterns over several generations, given reasonable sample sizes. (This will only be true for simple single-gene or at most two-gene traits and it can be harder to correctly figure Mendelian ratios than you expect, if the breeder has not been properly recording litters in which no affected puppies occurred).
4. The problem is known to be genetic in another breed or another species. You have to be careful with this one, as some problems can be definitely genetic in origin for some animals but might still be caused by an environmental factor for your dogs (like cleft palates). The endpoint may be the same, but not the path by which the animal arrived there. You also need to consider the possibility that the problem is thought to be genetic in another breed, but actually isn’t. If a trait was assumed to be genetic because it occurred in ten dogs in one kennel and they were from an inbred line, this assumption may be wrong. Maybe their breeder went over the top with a particular diet that was not nutritionally balanced and caused the problem herself. Maybe the data were poor or misinterpreted. It’s worth tracking down the source of assumptions. Hutt, in his book, explains why data that seems to show that Collie Eye Anomoly is controlled by a simple recessive mode of inheritance really doesn't show such a clear-cut mode.
If a problem is sporadic and seems to occur at a low frequency all over the place -- in all the lines of a breed, and incidentally in other breeds -- then it is quite possibly not genetic in origin. It is possibly developmental or stochastic or the result of a trisomy or uniparental disomy or caused by a spontaneous mutation that occurs fairly frequently. Such a problem could still be genetic (in the ordinary sense), however, if it came into the breed right at the beginning and got into all the lines. In this case it seems to me much more likely to be a very rare single recessive or else a couple of (perhaps less rare) recessives acting together in a two- or three-gene system. Otherwise it would either show a familial tendency or else it would not be rare. Mitral valve disease is an example of a disease that came in right at the establishment of the breed, probably, and thus is very widely distributed (though almost certainly polygenic).
Once you have decided that a problem is probably genetic – and you don’t need to be absolutely sure; the essence of practical genetics is in making reasonable guesses that give you a good chance of improving your dogs – anyway, once you have concluded that you’re going to treat a problem as genetic in origin, the next step in dealing with it effectively while continuing to move forward with your breeding program is to try to figure out its mode of inheritance.