What happens if the effective population is too small?
One thing that happens is that the inbreeding coefficient increases for every generation. Actually, this happens for ALL populations that are not of unlimited size, but then the natural selection is probably working against more inbred individuals, so that reasonably small increases of the inbreeding are adjusted and status quo is kept. It is also known that a larger number of eggcells get fertilized than the number of offsprings that finally are born in the litters, and one theory is that these early featuses have to "fight" for their place in the uterus, and that the more homozygous featuses are less likely to survive. This theory however not been proven to be true.
What will happen, when the inbreeding coefficient is increased generation by generation? In the beginning, not much at all. It isn't until the degree of homozygosity reaches a certain critical level that the real problems show up, and then it is usually much more difficult to take corrective action. It is much better to start working against these problems before the symptoms show up. The pedagogic problem then of course is that those who begin to breed with too few individuals won't immediately see the problems that it will cause. They think "I have bred in this way for many years, and I have not had any problems". But as we can see, "trial and error" is not a very good approach here! When "error" appears it is a bit late to adjust in an easy way.
Why then is inbreeding so dangerous? One thing - that every educated breeder knows about - is that it means an increased risk of doubling up on harmful or lethal recessive genes. The double set of chromosomes otherwise protects us from this risk, to a great extent in a population that is not too inbred. All individuals carry a few harmful recessive genes. Some people think that the inbreeding clears out the harmful recessives and leads to a healthier breed for the future. But first, the inbreeding doesn't clear out anything in itself, it has to be combined with a strong selection in order to clear out any undesirable genes. Second, you have to inbreed incredibly strongly in order to get all or almost all loci homozygous, so that you can see what the cats are carrying and weed out all the undesirable genes. Mate a female with her full brother, and 25% of all loci are homozygous. Then mate two of these offsprings with eachother, and 37.5% of their loci are homozygous. And then we take two of THOSE offsprings and mate them with each other! Now the inbreeding is so strong that most breeders would back away. But still "only" 50% of the loci are homozygous. So in spite of this drastic inbreeding, we will miss out on exposing other recessive, potentially harmful genes.
But let us assume that we go all the way with this! We breed a line towards 100% homozygosity, selecting strongly against harmful genes all the way. All individuals will then have exactly the same genotype, except for the fact that the males must have a Y chromosome where the females have a second X chromosome.
OK, it took a lot of effort and money to make this so called isogene line, and many cats died on the way. But if we now finally have reached to this point, then we have a line that is 100% healthy from a genetic point of view! Yippeeee!!!
It is possible, this can be done, if you are careful not to let the level of homozygosity increase more quickly than you manage to weed out the bad genes. This has been done with mice that are to be used for scientific tests. It works very well! But... they only manage to get about one line out of twenty to survive. The other 19 lines are dying in the process. Maybe better not to take that chance?
Also, the immune system is not very good in homozygous individuals. The immune system works much better if the loci involved are heterozygous, since this gives the individual the possibility to develop more DIFFERENT kinds of antibodies, not just lots of antibodies of the SAME kind. This is not a major problem in laboratory mice, since their environment is quite protected from (undesired) contagious diseases, and since it isn't exactly considered to be a tragedy, unfortunately, if a laboratory mouse dies. If on the other hand a much loved pet cat and family member dies it is indeed very sad. Hmmm... Perhaps not such a good idea after all?!
On top of that mutations happen spontaniously and would with time destroy our fine genotype. You have to count on one or two new mutations in every individual.
I think we had better change our strategy!