Merle coloration in dogs

Merle coloration in dogs

Merle gene examination  performs our partner laboratory. For more information, please contact us.

The merle coloration in dogs is often connected with health risks, which should be known to each breeder. The breeder should consider properly the risks prior to breeding and decide to which extent he/she wants to follow the modern trends and requirements of people interested in puppies.

The Merle gene has been identified on canine chromosome 10 (CFA 10). This coat colour is combination of patches of diluted base colour and areas with full pigmentation - irregular grey and/or beige patches occur in the base colour (e.g. black, brown, red or even light). In comparison with other types of coat colour, the diluted merle colour is spread irregularly over the dog body.

Merle colour appears in many dog breeds, however only some of them are accepted in the FCI standard. The breeds with recognised merle colour are as follows:

  • Shetland Sheepdogs
  • Collie
  • Border Collie
  • Australian Shepherds
  • Dachshund
  • Great Danes
  • Cardigan Welsh Corgi
  • Chihuahua
  • Cocker Spaniel
  • Pit Bull
  • Catahoula Leopard Dog
  • Norwegian Hound
  • Pyrenean Shepherd
  • Pomeranian
  • Beauceron Sheepdog

Merle gene has two alleles:

  • M - a Merle allele responsible for merle colouring of the coat - dominant
  • m - an allele responsible for normal coat pigmentation - recessive

An individual with normal pigmentation pattern all over its body is always a homozygote of mm- genotype.

A Merle individual can be either a homozygote of  MM-genotype or a heterozygote of Mm-genotype

Examples of merle coat color:

smooth collie






Australian Sheperd - blue merle



Australian Sheperd - red merle



Cryptic merle

Cryptic merle („phantom" merle) are dogs that show only very slight merle coloration and in some cases it is not visible at all. The dog can have only small patches of merle, for example, at the end of tail or ear or the merle coloration can be concealed by white markings.

These dogs carry the shorter version of the merle gene, sometimes one copy and sometimes two copies. Unlike regular merle dogs, in the cryptic merle dogs no serious health problems connected with the regular (not shortened) merle allele have been described.  They apparently have no eye or hearing problems. Dogs with two copies of cryptic merle gene (Mc/Mc genotype) or dogs with one cryptic merle copy and one regular merle copy (M/Mc genotype) have no health problems. The correct description of cryptic merle is a problem when registering the dog. These dogs appear like normal coloured and are incorrectly registered as non-merle dogs.

Frequent mistakes: Excessive white markings in puppies from a tri-to-merle cross are not an indication that the puppy is a cryptic merle. The genetics of excessive white markings is completely different and have nothing to do with merle gene.

In breeding, a cryptic merle can be mated only with non-merle dogs (like dogs with regular merle allele). When crossed, the cryptic allele may expand again to regular non-shortened merle allele.  When mating a cryptic merle (Mc/N) with a non-merle (N/N) you can find puppies with the following genotypes: Cryptic merle/non-merle (Mc/N), Merle/ non-merle (M/N), non-merle/non-merle (N/N).


Hidden merle

Hidden merles are merle dogs who do not exhibit the merle pattern because their coat colour does not show the pattern (Merling is not normally shown in red, gold, fawn and cream coat colours).  The hidden merle can be distinguished only by a genetic test.



Genetic testing for merle gene is highly recommended in order to avoid severe health problems that may occur when merle, cryptic merle and hidden merle dogs are crossed incorrectly or in case of risky breeding. The genetic test reveals the merle, the hidden merle and the cryptic merle variants.

The breeders of breeds with sufficiently described merle colour should be more careful.  All puppies that appear as "non-merle" at first sight have to be properly checked for any less visible merle patches.  If such patch is found, it is not a non-merle, but a cryptic merle. In particular, the small merle patch can disappear in long hair and such a dog will be identified as a non-merle in your pedigree. Later, such dog can be mated with another cryptic/hidden merle dog. So the breeders run unintentionally the risks of producing double merle dogs, which are connected with severe health problems.


Possible results of genetic testing:


  • non merle dog


  • merle heterozygote (visible merle pattern without health problems)
  • rare hidden merle heterozygote (INVISIBLE merle colour, without health problems) - high risky for breeding, if the genotype is not known


  • merle homozygote (visible merle pattern, severe health problems)


  • cryptic merle heterozygote with shorter gene variant (slight merle patterns can be visible, without health problems) - very risky for breeding, if the merle colour is visibly indistinguishable, the genotype is determined by genetic testing


  • cryptic merle homozygote with two shorter variants of merle gene (slight merle pattern can be visibly distinguished, without health problems) - very risky for breeding, if the merle colour is visibly indistinguishable, the genotype is determined by genetic testing


  • merle / cryptic merle dog (visible merle pattern, without health problems) - high risky for breeding, if the genotype is not known.


Health complications related to merle allele

Both heterozygous merle (Mm) and homozygous merle (MM) may exhibit eye and ear abnormalities incl. mild to severe deafness, increased intraocular pressure, ametropia (bad  refraction ability) and colobomas. Individuals of MM-genotype may also be associated with abnormalities of skeletal, cardiac and reproductive systems.

These dogs often have heterochromia iridis (difference in iris coloration); the individuals often have blue eyes or only one blue eye. Dogs with merle colour have visibly less pigmented eye ground, which may affect their eyesight.

The ear abnormalities are also caused by absence of pigment in hairs of auditory passage. The sound waves (longitudinal oscillation of air molecules) cannot propagate into the middle and internal ear, which results in partial or complete deafness.

Homozygous merle dogs (MM) are very pale, sometimes white and the colour of their mucous membranes is also lighter to pinkish and the eye pigmentation is mostly blue.


Possible genotype combinations

Parent 1

Parent 2




50 % merle dogs of MM-genotype

50 % merle dogs of Mm-genotype → carriers of solid pigmentation



100 % merle dogs of Mm-genotype → carriers of solid pigmentation



25 % merle dogs of MM-genotype

50 % merle dogs of Mm-genotype → carriers of solid pigmentation

25 % dogs with solid pigmentation of mm-genotype



50 % dogs with solid pigmentation of mm-genotype

50 % merle dogs of Mm-genotype → carriers of solid