What is merle at the genetic level?
Merle arises from a mutation in the pigment gene PMEL (we’ll call this mutation “M*” going forward). M* disrupts PMEL expression, leading to mottled or patchy coat pattern. Dogs with the “M*m” genotype are likely to appear merle or phantom merle. This is when the dog is not obviously merle patterned but has a merle allele; dogs with the “M*M*” genotype are likely to appear merle or double merle. Dogs with the “mm” genotype are unlikely to appear merle.
Quick Summary Merle is an incompletely dominant coat color pattern characterized by irregularly shaped patches of diluted pigment and solid color.
Miniature Australian Shepherd puppy with merle pattern.
Phenotype: The merle pattern is characterized by irregularly shaped patches with diluted pigment while other patches on the coat are fully pigmented in color.
Mode of Inheritance: Incomplete dominance
Alleles: N = Non-merle, ### = Merle allele present, size is provided
Breeds appropriate for testing: Many breeds including but not limited to: American Bully, American Pit Bull Terrier, American Staffordshire Terrier, Australian Shepherd, Beauceron, Bergamasco, Border Collie, Cardigan Welsh Corgi, Catahoula Leopard Dog, Chihuahua, Cockapoo, Cocker Spaniel (American), Collie, Dachshund, Dunker, French Bulldog, Great Dane, Koolie, Mudi, Old English Sheepdog, Pomeranian, Pyrenean Shepherd, Shetland Sheepdog, Crossbred
Explanation of Results:
$50 one test per animal $70 two tests for coat color/fur type/bobtail (same animal) $90 three tests for coat color/fur type/bobtail (same animal) + $15 each additional test if ordering more than three coat color/fur type/bobtail tests on the same animal
Merle coat color pattern on a mixed breed dog. credit: Dr. Jennifer Campbell-Smith/Spothound Photography
The merle pattern is characterized by irregularly shaped patches with diluted pigment while other patches on the coat are fully pigmented in color (solid). Merle only dilutes eumelanin (black) pigment; dogs with an MC1R e/e genotype do not produce black pigment and thus do not express merle, but can produce merle offspring depending on the genotype of the mate. Merle is governed by a SINE insertion in the PMEL17 or Silver (SILV) gene. SINEs are defined as short interspersed nuclear elements. These are repetitive DNA sequences that can copy and insert into different locations in the genome. The impact of the insertion depends upon the location: they can impact gene expression and function and, if inserted into the germ line cells, can be passed down to future generations.
The presence or absence of the merle SINE insertion determines the possibility of observing the merle phenotype while the length of the end of the SINE insert sequence, which is composed of the nucleotide A (poly-A tail), correlates to the extent of the merle pattern observed. Only one copy of the merle associated variant is necessary to see the effects but the length of the tail directly influences the phenotype.
The length of the poly-A tail can vary by as much as 80 nucleotides. When originally identified, range of sizes were grouped into three categories with 4 results: no SINE insertion= N, short poly-A tail= Mc (cryptic merle aka phantom or ghost and merle phenotype may or not be observed), longer poly-A tail = M (the merle pattern always observed), and an undefined region between long and short where merle pattern prediction was inconsistent. Until September 9, 2020 the VGL reported these as N, Mc, or M.
Further investigations by multiple, independent, researchers have refined the phenotypic correlation with the poly-A tail length. The following figure shows the allelic ranges and nomenclature defined by each research study. The nomenclature differs by study. Many variables likely contributed to the varied ranges and nomenclature some of which is dependent on sample sizes, breeds used, ascertainment bias, etc.
Given the variation that exists in the scientific literature for allele nomenclature the VGL now reports merle alleles based on size instead of by allele designation (please see Figure 1). This allows animal owners to utilize these numbers with the naming scheme they prefer.
Figure 1: Merle Allele Nomenclature Defined by Multiple Scientific Studies. The VGL reports merle as the size of the detected allele. The figure demonstrates the different proposed nomenclature based on the reported allele size.
Dogs with cryptic merle (also called phantom or ghost merle) typically display little to no merle pattern and some may be misclassified as non-merles. The cryptic merle alleles occur in the lower end of the range (typically from 200-255, however, this range and designation varies by study). As the length of the poly-A tail increases, the degree of eumelanin dilution increases to produce the merle pattern with the highest end of the range producing a phenotype that can be completely white (around 280 bp). In dogs with merle, this has been referred to harlequin or merlequin. It is important to note that the merle derived “harlequin” is distinct and caused by a different genetic mechanism from Great Dane Harlequin (H).
The merle poly-A tail is genetically unstable and, although uncommon, parents and offspring may have different sizes and thus different genotypes. Despite claims to the contrary, exhaustive sampling and testing at the VGL has identified heritable expansion and contraction of the merle insert in offspring where parentage testing has been confirmed. Also, in rare cases, the poly-A tail may expand in some cells leading to the appearance of three alleles in one animal. The distribution throughout the body of cells with differing allele sizes depends upon the timing of the origin of the expansion or retraction of the poly-A during development. If early in development, two distinct populations of cells may be present throughout the dog. If later, the appearance of two populations of cells may be restricted to specific tissues.
A double merle (M/M) Australian Shepherd with visual and auditory defects
Blue and partially blue eyes are typically seen with merle, and merle dogs may possess a wide range of auditory and ophthalmologic defects. Dogs with two copies of any of the size variants consistent with merle (alleles other than N) are called double merles and often can have an all white coat accompanied by multiple abnormalities of skeletal, cardiac, and reproductive systems, therefore breeding two merle dogs is discouraged to avoid producing double merle offspring. However, it is important to consider that many double merle dogs with ophthalmic and auditory defects often have a white spotting component and double merles in a breed with low piebald spotting allele frequency such as Catahoula leopard dogs, have fewer noted auditory and ophthalmologic defects.
Because of the complexities of merle inheritance and potential health concerns, DNA testing is recommended to establish the genetic makeup of dogs for the merle gene for those breeds where this color dilution pattern is present. Type of Sample
What Does the Merle Coat Pattern Look Like in Dogs?
The merle gene dilutes random patches of a dog’s coat to a lighter color. These patches are distributed all over the body. They vary in size, shape, and color. Merle affects the eyes, resulting in dark-eyed, odd-eyed, or blue-eyed dogs. The paw pads and nose are sometimes mottled pink and black because the gene targets the skin as well.
The merle pattern is labeled “red” or “blue.” The merle forms of brown (or liver) are called “red” although red and brown are genetically different. Merle forms of black are called “blue.” Blue merle dogs can be distinguished by the marbling of gray, silver and black in their coat with some copper points possible on the face. Red merle dogs are marbled, light cinnamon to dark liver color with copper points on the face and legs. Tricolor dogs may look similar but typically lack the characteristic marbling of merle.
Some cases of the merle coat in dogs are masked by other genes. Recessive red dogs are affected by merle but patches are subtle or not visible at all. In addition, brindle and sable merles exist but are typically rejected by breed standards. Sable merles can be difficult to recognize and accidental double merle breedings can occur as a result. In addition, hidden or cryptic merles can occur. Cryptic merle dogs are genetically merle but do not visually appear to be merle.
Merle is a heterozygote of an incompletely dominant gene, this is a type of genetic formula. Heterozygote refers to the inheritance of two different alleles from both parents. In this case, it refers to the presence of a dominant “M” allele and a negative “m” allele. This is why merle is written as “M/m.” Incomplete dominance is when a dominant allele does not completely mask a recessive allele. This results in a blending of both alleles. It is not the same as co-dominance. Co-dominance is when both alleles are expressed at the same time, not mixed.
When two merle patterns (“M/m”) are bred to each other, 25% of the puppies will be homozygous for merle. Homozygous refers to the inheritance of the same allele from both parents. These homozygous puppies are known as “double merles”, also written as “M/M.”
Some dogs do not look to have a merle pattern but genetically are merle. These merle dogs are called cryptic, phantom, or hidden merles. Merle pattern can be masked by other genes or heavy patching. Each gene has it’s own labeling including the recessive red (“ee”) and clear sable (ay).
Hidden merles appear to be solid-colored or have very faint merle patches that go unnoticed. The recessive red allele (“ee”) hides some merling. This is because recessive red dogs do not produce eumelanin pigment, leaving them a solid red color caused by phaeomelanin. Phaeomelanin is not affected by merle. This means that a recessive red dog with the merle allele appears to have no merle. The only indication of the merle allele in these cases is through blue or partially blue eyes. Recessive red and merle can be a tricky combination to work with when breeding dogs. The risk of breeding double merles by accident is always present.
Clear sable (ay) is another gene that hides merle patterns. Sable is the top dominant gene of the agouti (a locus) series. This means that one sable allele is enough for the gene to be expressed. Clear sables lack dark hairs (eumelanin) in their coats and look very similar to the recessive red (ee). In tests, the cryptic allele is written as “Mc.” This means that a cryptic merle dog still carries a dominant “M” and can technically produce double merles if bred to a merle.
The Truth about the Merle Gene(SINE Insertion) in dogs
A merle coat in dogs is one of the most interesting and beautiful variations to come from breeding. Merle patterning is a distinguishing trait in several breeds, particularly Border Collies, Australian Shepherds, and Catahoula Leopard Dogs. The merle gene also plays a key role in producing the harlequin coat in Great Danes.
Unfortunately, the intriguing dog merle coat is associated with several health problems. Responsible breeding is important to reduce the risk of these problems.