Ok I'll try for a Gina/Cliff's notes on mutations.
A mutation is basically some sort of change in the genome. Various things can happen, such as single base pairs (just one letter on the page) switching to another letter. Or insertions or deletions of extra letters - how many letters can vary.
Mutations are something that happen, not overly frequently, but not extremely rarely either. Sometimes the mutations may be of no consequence at all, such as if they are in an area that does not code for any product, or if the mutation doesn't change the final product. Other times they may have an effect, but not a large one obvious to the naked eye. This is because most traits of interest are controlled by a combination of genes working together, each contributing in their own way. Research now is picking out some of the mutations that have a fairly significant effect. These are known as "major genes" or "quanitative trait loci" and are what tests like the Genestar ones are based upon. (This also brings up the point that, no, not all mutations are "bad". And most times whether it is "good" or "bad" depends on the environment, or our goals, in the case of produciton animals).
But then there are the cases where the mutation is a big deal...these are ones where the proteins produced are not produced at all, or are so different that it changes how they function. And then it also has to be a gene that "matters". To bring in a new example for you guys, the double muscling seen in the Belgian Blue breed is the result of a change in a nucleotide, which creates what's called a "premature stop codon". This means that the assembly of the protein is stopped earlier than it should, making the protein structure totally different and non-functional as a result. In this case, it is the myostatin gene that is affected, which normally works to regulate prenatal muscle production (ie, it says when to stop making muscles).
So then we get to the cases like TH and PHA. These are major mutations obviously, as seem by their drastic effects. They are recessive in nature (ie, the carriers are normal themselves), and they are obviously harmful. Thus, they are what are known as "deleterious recessive mutations". Because you need a defective gene from both dam and sire to be affected, we only see affected animals because of inbreeding. Remember though, it doesn't necessarily have to be close inbreeding, and that's why we see problems now when the mutations originated with bulls popular years ago.
Deleterious recessives are not a new phenomenon. The royal family had this high incidence of hemophelia....... Holsteins had to go through things like mulefoot, which I believe was basically erraticated by not breeding carriers. At the time, the carriers were identified by their having affected calves. The difference is now we have genetic tests available to identify carriers before they are bred.
