Prepare for a novel guys!
Okay, so just out of my own curiosity I emailed my Genetics professor (he teaches the genetics classes at my college with a pH.D). He's a neutral mind on the subject, since he doesn't know much about horses (dogs is another story) and I thought an unbiased opinion might be nice. I admittedly don't know enough about genetics to get down to the finer points, and we can't ALL be right with our circular discussion - so I went to somebody who could clear things up for me. I've found I was indeed wrong about some things, and correct about others.
I just sent a basic overview of the discussion with the key points from both sides - a few being the 'impossible to genetically improve a breed without inbreeding,' I mentioned genetic testing for problems, and I brought up the Cheetah analogy - It was mentioned back a bunch of pages ago but basically it says that a long time ago, Cheetahs reached a population bottleneck. Because of this, all (Or at least most) cheetahs are closely related, line/inbred. Because of natural selection, the weak were killed off, leaving a population of cheetahs strongly resistant to genetic disease - BUT in return they are extremely susceptible to a spreading illness. The immune system is genetic, and because they are all related and have a similar immune system, if a disease strikes the cheetah population they are all likely to get killed off.
This is his exact response. It does go over basic genetics briefly that most of us know about, but some probably don't, so I won't cut anything out:
"Interesting question / issue. I've found myself having similar discussions many times regarding the pure breed vs. mixed breed dog. The basic genetics is straightforward. Horses, like people, have two versions or alleles of each gene. Those alleles can be either the same or different. Many genetic diseases are recessive - meaning that you or the horse needs two copies of the allele to get the disease. Creatures with one recessive allele will be healthy but are "carriers" of the disease allele. All animals carry disease alleles - but they are typically not in the same genes. Line breeding or inbreeding increases the likelihood that an offspring will inherit disease alleles in the same gene and therefore get the genetic disease. It's not that this breeding makes the alleles worse - it just increases that chance that the parents will be carriers of the same mutant alleles (since the parents are related). The genetic term for having two versions of the same allele is homozygous - and it is incontrovertible that line breeding increases homozygosity. That is, in fact, why breeders do it. They want animals to breed true for desired traits (not that in touch with the horse world - but assume things like conformation, etc). The challenge / question is whether or not it is possible to obtain animals that are homozygous for genes that confer desirable traits - but which do not carry disease genes. The old method that you refer to is to cull (either directly or through natural selection). This can work, but only
for diseases that show up before animals are allowed to breed. Thankfully we now have newer technologies that allow us to test for some
disease genes (I've attached a paper on this). The hope is that breeders will employ such tests prior to breeding and not use animals that carry these mutations. In principal this could ultimately lead to breeds that lack known disease genes and maybe that is what others were referring to when they made the claim that line breeding can enhance a breed? Their are still some problems with this thinking. One is that pathogens change (as you mentioned) - and animal population need
genetic diversity to effectively respond to these changes. Line breeding leads to less
genetic diversity - this should be obvious as it increases homozygosity and diversity refers to the number of different
alleles in a population. Your cheetah analogy is spot on - even with genetic testing line breeding will always lead to populations that are more vulnerable to new diseases.
I hope that this helps."
So, I was wrong that linebreeding will CAUSE genetic problems - whoever mentioned it was right, it can only bring out the worst in a bloodline (whereas breeding out wouldn't bring out those problems). I apologize. What I'm getting out of this is yes, it can indeed do what you're saying it can, but I was right that even with genetic testing we can't be 100% positive we won't get a genetic problem foal as we can only test for known problems, and that by line breeding it decreases the gene pool, and while that means you can 'breed out' KNOWN genetic diseases (didn't know that either, you learn something new every day) it leads to susceptibility of new diseases (like the cheetahs).
Attached is the paper he sent about genetically improving racing thoroughbreds. I'm only partway through it, but it's quite interesting so far. If any of you have any questions you'd like to ask him, as long as I'm talking to him already, I can shoot him another response email, just let me know! http://https://bl2prd0310.outlook.co...61458_39495860