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Merle is a pattern in a dog's coat, though is commonly incorrectly referred to as a colour. The merle gene creates mottled patches of color in a solid or piebald coat, blue or odd-colored eyes, and can affect skin pigment as well. Health issues are more typical and more severe when two merles are bred together, so it is recommended that a merle be bred to a dog with a solid coat color only.
Merle can affect all coat colors. The merle forms of brown and black are usually called liver (or red) and blue, respectively. Dogs who are recessive red can still be affected by merle, but the patches are either hardly seen or if the dog is a clear recessive red, it is not visible at all. Combinations such as brindle merle exist, but are not typically accepted in breed standards.
In addition to altering base coat color, merle also modifies eye color and coloring on the nose and paw pads. The merle gene modifies the dark pigment in the eyes, occasionally changing dark eyes to blue, or part of the eye to be colored blue. Since merle causes random modifications, however, both dark-eyed, blue-eyed, and odd-colored eyes are possible. Color on paw pads and nose may be mottled pink and black.
Merle is a distinguishing marking of several breeds, particularly the Australian Shepherd, and appears in others, including the Koolie, German Coolies in Australia, the Shetland Sheepdog, various Collies, the Welsh Corgi (Cardigan), the Pyrenean Shepherd, the Bergamasco Sheepdog, the Old English Sheepdog, and Catahoula Leopard Dog. In Dachshunds the merle marking is known as "dapple". It is also present in the Pomeranian and Chihuahua, but is a disqualification according to the FCI standards. In the Cocker Spaniel breed, it is a recognized pattern, although incorrectly listed as a 'color'. ((American Kennel Club, Cocker Spaniel)) The merle gene also plays a part in producing harlequin Great Danes. In several breeds, such as the Pomeranian and Chihuahua merle is an indicator of cross breeding.
The merle pattern has been incorrectly linked to pure bred the American Pit Bull Terrier (APBT). Historically it was not found in the breed, and is likely the result of southern breeders cross breeding the American Pit Bull Terrier with the Catahoula Leopard Dog. It is considered a genetic flaw and the ADBA and UKC do not accept registration of APBT with the merle pattern.
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.
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."
Certain "modifying genes" work in tandem (co-dominate expressive) with the merle gene to create a completely different look to the pattern.
Often mistaken for a "double merle", a Harlequin Merle (or just Harlequin), is a dog that carries both the merle pattern gene and the co-dominate modifying gene (carried on a different locus) for Harlequin. This causes most or all of the "blue" to be replaced with white, leaving a dog that is mostly white with black patches. All dogs exhibiting the harlequin pattern are also carriers of the merle gene. Common in Great Danes, (and registered as Harlequin) it is less commonly seen in other breeds such as the Catahoula Leopard Dog, Shetland Sheepdog and Collie where the dogs are registered simply as merle. 
Patchwork or Tweed, is a co-dominate modifying gene that turns the gray (in what would be a blue merle) or the liver (in what would be a red merle) into varying shades of brown, gray and tan. This is the color pattern associated with the African Wild Dog and is very uncommon in pet dogs. It has been reported in the Australian Shepherd, Catahoula Leopard Dog and Border Collie. 
Dogs with two copies of the merle gene (homozygous merle or "double merle") have an even higher chance of being born deaf. The UK Kennel Club has acknowledged the health risk associated with homozygous merle and will stop registering puppies produced from merle to merle matings starting from 2013. Merle to merle mating is currently only forbidden in three breeds. Recent research indicates that the majority of health issues occur in dogs carrying both piebald and Merle genes. The piebald gene is indicated by white areas on the dog's coat as seen in the red merle Catahoula pictured below.
The suppression of pigment cells (melanocytes) in the iris and in the stria vascularis of the cochlea (inner ear) leads to blue eyes and deafness. An auditory-pigmentation disorder in humans, Waardenberg syndrome, reflects some of the problems associated with heterozygous and homozygous merle dogs and genetic research in dogs has been undertaken with the goal of better understanding the genetic basis of this human condition.
Dogs who are homozygous for the merle pattern gene often have visual and auditory deficits. These dogs are sometimes referred to as 'double merle' and sometimes incorrectly referred to as 'lethal white.' Ocular defects include micropthalmia, conditions causing increased ocular pressure, and colobomas, among others. Double merle dogs may be deaf or blind or both, and can carry ocular defects in blue or colored eyes. Currently no studies have been done to prove whether or not the merle gene affects the eyes, causing blindness.
One study done by a German researcher showed that out of 38 dachshunds, they found partial hearing loss in 54.6% of double merles, and 36.8% of single merles. 1 out of the 11 (9.1%) double merles was fully deaf while none of the single merles were. Another study done by Texas A&M University found that out of 22 double merles, 8 were completely deaf and two were deaf in one ear. Out of 48 single merles, only one was deaf in one ear, none were completely deaf. Another study done with 70 dogs, 15 of them were Catahoula Curs and 4 of them were deaf, whereas the other 86% of double merles in other breeds were deaf.
Deaf, blind, and deaf and blind dogs can have good lives when properly cared for. There are a variety of internet groups dedicated to supporting carers of such dogs. Deaf dogs can compete successfully in agility and there are many anecdotal reports of deaf/blind dogs earning their Canine Good Citizen certification, working as therapy dogs, and competing in dog sports like tracking or Nosework.
Blue merle Australian Shepherd
Blue merle Smooth Collie
Blue merle Shetland Sheepdog
Blue merle Catahoula Leopard Dog
Blue merle Cardigan Welsh Corgi
Blue merle Mudi
Blue merle (silver dapple) Miniature Dachshund
Blue merle Pomeranian
Blue merle Chihuahua
Blue merle Koolie.
Red merle Australian Shepherd
Red merle Catahoula Leopard Dogs
Red merle (chocolate dapple) Dachshund
Black merle Bergamasco Shepherd
Red merle American Cocker Spaniel.
From right to left, black, red, and chocolate merle mixed breed puppies. You can tell the red is merle due to the faint mottling on her black sable tipped ears, but as she grew the only sign of merling was her blue eye.
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