First what usually happens in all animals are known genetic mutations that occur that are referred to as non-deleterious or silent mutations, which occur all over the body including in germline cells, ie sperm and egg cells. They are usually harmless to the organism. However sometimes, there are mutations that occur that can have bad results, some of those mutations can be cancer, etc, and some can occur in germline cells that result in diseased offspring due to a dominant mutation, or offspring that has a recessive mutation and appear normal.
What most likely happened in the Miniatures is that some germline cells in some horse many years ago, mare or stallion, most likely a stallion or stallions, since they have high germline mutation rates and since there are different types of dwarfisms, produced sperm that conceived a normal looking foal that had a recessive mutation. This could have happened to more than one horse, mare or stallion, we do not know, and will never know, EVER, the root cause. Anyways, the resulting foal later bred and passed on this recessive mutation to 50% of its offspring, and so on, and so on, until sooner or later related horses were bred together carrying the recessive mutation and 25% of the foals were dwarfs. That is why highly inbred animals quickly display recessive deleterious traits, an inheritance fact well known and documanted in animal breeds. It is well known that severe inbreeding increases genetic abnormalities seen in resulting offspring from recessive traits.
Later those dwarfs were bred because they were very small, which is very likely what was done early on due to the small numbers of miniatures that existed. Perpetuating the gene.
John
