MERLES – For those who are not familiar with the merle gene, one fact is indisputable:  In order for a dog to BE a merle, it MUST HAVE one merle parent, either sire or dam.  This gene cannot remain ‘hidden’ for generations, like chocolate or blue, which are recessive colors, thus proving that it has only recently been introduced into our breed.
A merle dog (Mm genetically) contributes one of these genes when bred, either M (merle) or m (non-merle).  If a puppy receives the M (merle) gene, it will be merle. If it receives the m gene, it will not be merle. The M (merle) gene acts on whatever coat color the puppy has. 
MERLE PUPPY 1The problem with allowing the (new) merle color in Chihuahuas, is that we have so many light-colored dogs.  Breeding these light dogs to merle will result in fawn, cream, red, sable, white, etc. merles, which are often NOT recognizable as merles as adults(though when bred to black tris, they will produce blue merles, thus identifying one parent as a hidden merle). When these hidden merles are bred to other merles (accidentally or unknowingly), thus doubling up on the merle (M) gene, the result (if the puppy inherits one M–merle–gene from each parent) will be a puppy with two M genes–a homozygous merle. These puppies will be deaf and/or blind, and some will have other internal health problems as well as possibly being infertile. The fact that they are deaf and/or blind will not be recognized until they are older (around weaning time), hence a decision will have to be made about what to do with them….
At this time, there are already normal (single M) merle Chihuahuas which have been diagnosed by two independent veterinarians with deafness and eye problems that will lead to blindness. Is this really for the betterment of the breed? 
What the Merle Breeders do NOT tell You
Another much more serious and important issue is the higher occurrence of health problems in Merle Chihuahuas. You may wonder how this is so, when merle is only a color pattern? Well, unfortunately, unlike other colors, the merle gene acts on a color and lightens and whitens certain parts of it (creating patches)…the whitening is what causes defects. Often, when a dog’s coat is whitened, the pigment inside of their ear and on their eye, also whitens…making the dog DEAF and BLIND as the nerves endings atrophy and die.
Health Problems Associated with the Merle Allele – Both heterozygous merle (Mm) and homozygous double merle (MM) dogs may exhibit auditory and ophthalmic abnormalities including mild to severe deafness, increased intra ocular pressure, ametropia, microphthalmia and colobomas. The double merle genotype may also be associated with abnormalities of skeletal, cardiac and reproductive systems.”
Definition of Heterozygous-one parent is a merle, the other is a non-merle. Also known as single merles, or Mm.
Definition of Homozygous-both parents are merle. Also known as double merles, or MM.
Based on information about the merle gene in Dachshunds, all merles that are brought into the MERLE PUPPY 2 world have a 36.8% chance of developing some sort of hearing loss, resulting from either slight hardness of hearing to total deafness (Willis). This percent is for puppies that result from one parent that is a merle, and the other that is a non-merle. Other problems such as eye problems were also apparent. While many breeder’s admit that there are problems when breeding two merles together, they do not admit there is also a problem when breeding a merle to a non-merle which is the breeding most breeders do. This is what the Merle Chihuahua breeders DO NOT tell you. You can still get deaf and blind puppies from this type of “safe” breeding.
So please keep in mind, if you are interested in getting a Merle Chihuahua, you may not actually get a healthy puppy. A pup may appear to be healthy, but might actually have impaired hearing or vision. For the reason of health problems and questionable parentage, the presence of the merle pattern in Chihuahuas is being banned in many countries world-wide.
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