Genetic Basis
Merle is actually a heterozygote of an incompletely dominant gene. If two such dogs are mated, on the average one quarter of the puppies will be "double merles", which is the common term for dogs homozygous for merle, and a high percentage of these double merle puppies could have eye defects and/or be deaf. Knowledgeable breeders who want to produce merle puppies mate a merle with a non-merle dog; roughly half the puppies will be merles without the risk of vision or hearing defects associated with double merle dogs.
In January 2006 scientists at Texas A&M University announced the discovery of a mobile genetic unit called a retrotransposon, responsible for the merle mutation in dogs.
A phantom merle or cryptic merle is one with such small patches of merle—or none at all—that it appears to be a non-merle. This is commonly seen in dogs who are recessive red, clear recessive reds in particular, though patches can still be seen in certain red dogs. In America, a dog with the phantom merle coloring is described as being "cryptic for merle."
Read more about this topic: Merle (dog Coat)
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