Introduction And History Of Merle

There have been many questions regarding Merle since Dr. LA Clark first idenfied the mutation in 2006.  Since Merle affects so many other breeds I have included this excerpt from my book in order to make this important information more accessible for everyone in all breeds.

 MERLE - a SINE insertion (Short Interspersed Element) on the SILV gene.

Think of a piece of foreign DNA (viral-like) that has "inserted" itself into the chromosomes and has changed the number of base pairs by adding a piece of DNA. This SINE insertion lives off the host much like a parasite and can change the way cells function.

Both SINEs and LINEs (Long Interspersed Element) are common in canines and all mammals, including ourselves. They can be a form of evolution, sometimes destructive and sometimes a useful incorporation into the genome. Most SINE insertions occur in areas of the genome where they cause no damage or change to the host. However, some occasionally insert in regions where they can disrupt and alter expression.

There is some thought that it is these SINE and LINE insertions in canines that have helped to "create" (with our outside influence) our different dog breeds.

In the case of the Merle mutation, a SINE insertion impairs the ability of cells to produce normal pigment - a defective or faulty design.

Another example of a SINE insertion within the canine genome is the mutation for Tan Trim on the A Locus as previously mentioned. SINE insertions can also cause diseases like Narcolepsy in Dobermans and may be responsible for some cancers.

The Merle SINE mutation consists of 3 parts - a head, a body and a tail (poly-A tail). The tail contains a long string of repeating base pairs. Think of the poly-A tail as a section of a lariat-like thread of DNA that "catches and ties" into the dog's DNA, the head then attaches itself - "bites down" - so the whole invader can work its way into the DNA.
This is not very scientific language, but gives a good visual of the process.

The original Merle test only identified the body of the Merle mutation and the assumption was made that any reasonable length of tail produced some kind of Merle pattern; the longer the tail then the more Merle. No distinction was originally made between the tail length (base pairs) and Merle phenotype.

When Merle testing was first available any length of Merle was reported as a full "M" Merle. Numerous Catahoula owners had their dogs tested and were receiving results that their solid looking dog was in fact "M/M".

Leo - Tested as “M/M” through IDEXX:     Tested as “M(c)/M(c)” through Biofocus
Leo - Tested as “M/M” through IDEXX: Tested as “M(c)/M(c)” through Biofocus

How could a solid dog be a double Merle!?
The Merle test results were just not making sense at all and were considered by many people to be "flawed." 

We now understand that these dogs were most likely "M(c)/M(c)" - or even possibly "Ma /M(c)" - having 2 cryptic Merle mutations - a length of Merle so shortened or truncated that it can no longer cause a change to the coat pattern.

Eventually the test results were given using "M(c)", indicating that the mutation was not a full "M" but a shortened one and genotype results seemed to make more sense with the phenotype of the dog.

As the years have passed more Catahoula owners, especially in Europe, were having their Catahoulas tested through a lab in Germany, Biofocus.

During this time Dr. Helena Synková, was the breed advisor for the Catahoula Club EU in the Czech Republic, as well as being a Catahoula owner and breeder herself. By observation alone of litters produced by dogs that appeared at first glance to be non-Merle, Helena suspected that there was more to Merle then just "M" and "M(c)". These non-Merle, solid looking dogs had a certain quality to their coat, some with even very faint Merle patterning that the eye could see, while maybe not visible in photos. These dogs were Merle testing as "M(c)/m" or "M/m", but did not show the typical Merle expression and did not breed as the tests concluded.

Helena approached Biofocus with this information and working closely with Dr. Beatrix Böckmann, they started testing dogs whose phenotype did not match their genotype. By paying special attention to the length of the base pairs (the length of the poly-A tail), the findings concluded that there was also a third length of Merle - a length longer than cryptic Merle "M(c)", but shorter than a true full Merle "M".

Biofocus started reporting this length on lab results but continued to identify this shortened Merle as "M" - a full Merle. Helena noted that there was a very clear phenotype when this shortened Merle was inherited with either "M" or "m".

In 2011, she wrote an article for several dog magazines in Europe and for the Catahoula Club EU in which she gave this shortened Merle length the working name of "Atypical Merle" - "M(a)".

Helena's translated article can be read on the following page.

PDF file of Helena's article printed in "Svět Psů" Magazine - Jan, 2012

In May 2015, Biofocus officially recognized this shortened Merle as an allele on the M Locus and adopted the working name that Helena had assigned to it in her article - Atypical Merle - "M(a)".


Since that time, 8 more breeds have tested as having the "M(a)" allele - Dachshunds, Great Danes, Chihuahuas, Pugs, French Bulldogs, Koolies, Australian Shepherds  and Border Collies. I have no doubt that there will be more breeds added to this list as more testing is done. Every Merle breed has the potential for M to shorten to Ma.
Dr. Volker Wagner is now the contact for Biofocus - wagner@biofocus.de


Merle testing by Biofocus has now given us 4 separate alleles on the M Locus:

  • Full Merle "M" - a length of 459 - 462 bp
  • Atypical Merle "M(a)" - a length of 443 - 449 bp
  • Cryptic Merle "M(c)" - a length of 400 - 425 bp - at this point the tail has been so shortened that Merle can no longer express.
  • Non-Merle - wild type "m"- no SINE insertion length of 199 - 200 bp

Note - The M, M(a) and M(c) lengths given are a combination of "m" length 200 + the length of the SINE insertion.

Example "M" = length of "m" 200 + SINE length of 259 - 262 = 459 - 462. 

With all 4 alleles identified on the M Locus, breeding results are finally making sense.

This is a prime example of how breeders of all breeds, who are on the frontlines of recognizing the colors and patterns from parent to offspring, have been instrumental in helping labs and researchers to develop new testing.


With the inclusion of the "M(c)" allele, the differences in Hope's Merle test results from 2 different labs are not as noticeably "flawed" as the example of Leo above.

Hope - Tested as "M(c)/M(c)" through Animal Genetics: Tested through Biofocus as "M(a)/M(c)"
Hope - Tested as "M(c)/M(c)" through Animal Genetics: Tested through Biofocus as "M(a)/M(c)"

However, if Hope was bred to an "M/m" male, she would be able to produce "M/M(a)" - Patchwork offspring. This would be confusing to the breeder since she tested as "M(c)/M(c)" at a lab who has not yet included the "M(a)" allele in their test results.

UC Davis - Veterinary Genetics Lab, Paw Print and VetGen are currently looking at introducing the shortened allele of "M(a)" to the M Locus.


The following are the typical phenotypes.
Example photo charts start on page 53
Breeding charts start on page 91

"m/m" - solid/non-Merle

"M(c)/m" - solid/non-Merle

"M(c)/M(c)" - solid/non-Merle

"M(a)/m" - there are several expressions of this combination.

  • Some dogs express no Merle pattern at all and no hint that they may be anything but non-Merle.
  • Some pups are born with a coat appearing solid, which gradually shows faint Merle patterning as the dog ages. This Merle pattern is sometimes no more than a hazy off-coloring or under-shading of the dog's coat. This faint patterning can be difficult to view sometimes in photos only.
  • Other pups appear to be "d/d" - Dilutes in color and may have very faint and small Merle spots showing. Many of these dogs have tested as "D/D" - Non-Dilute, this will be discussed further on page 69.

This combination can create blue or marble/cracked eyes.

"M(a)/M(c)" - same as "M(a)/m"

"M(a)/M(a)" - this Merle pattern is visible at birth. Colors are usually lighter, the Merle areas appearing to be "d/d" - Dilute, but many have tested as "D/D" - Non-Dilute - and the solid coat areas/spots smaller and fewer.
This combination can create blue or marble/cracked eyes.

"M/m" - typical Merle coat pattern.

"M/M(c) - same as "M/m"

"M/M(a)" - responsible for the coat pattern we refer to as "Patchwork." A combination of "Pseudo-Harlequin" (areas of diluted pigment are removed, leaving the background white with full pigment areas remaining) + "Tweed" (Merle patterning appears as random shaded-in areas, usually with two or three distinguishable shades.)
Note - "Patchwork" is not a genetic term, but in the case of "M/M(a)"it is an easy to use descriptive word.

"M/M" - Merle patterning with more prevalent white. Some diluted pigment has been "deleted" to white.

Again, these are the most typical phenotypes, there will always be the exception where Merle is concerned.


Note - Use of the term "Cryptic Merle"
The terms "Cryptic," "Ghost" and "Phantom" Merle have all been used in the past to describe a dog that looked to be "m/m" but then bred as a Merle - "M/m". These terms are common in the Catahoula world and in other Merle breeds as well.
"Cryptic Merle" now genetically refers to "M(c)", an allele on the M Locus that is so shortened/truncated that it no longer expresses a Merle pattern.
Dogs we consider to be "Hidden Merles" - "Ghost" or "Phantom" may actually be "M(a)/m" dogs.
As well we know that red pigment of "e/e" - Clear Red and "A(y)" - Clear Sable can hide Merle very well, so these dogs could be considered to be "Ghost Merles."


The Shortening and Lengthening of Merle

To complicate things further, the Merle SINE is unstable - the number of base pairs in the length of the Poly-A tail can shorten or lengthen from parent to offspring. In one study done in 2006, it was surmised that this can occur in 3 - 4% of cases. It is important to note that this study was done at a time when Merle testing was not yet available so these findings were based strictly on phenotype alone.

Now that "M(a)" has been defined as its own allele on the M Locus, we may find this happens more than first thought.

Note - "M", "M(a)" and "M(c)" cannot shorten to "m". This would require the full removal of the DNA, which does not happen.

Through testing of Catahoulas, we have found several examples of shortening from parent to offspring. 

Full Merle - "M" shortening to Atypical Merle - "M(a)" from parent to offspring seems to be the most common.

No examples have yet been found of "M" shortening to "M(c)".

It is more probable that the changes in the Poly-A tail length are minor as opposed to a major jump. We have also found examples of "M" not shortening completely all the way to "M(a)" but somewhere between the two alleles due to this "minor" shortening.
Examples of Merle shortening start on Page 62.
Note - Every Merle dog of any breed has the potential for the Merle poly-A tail to shorten and therefore the "M(a)" allele.

Merle's poly-A tail can lengthen as well. Through the testing of hundreds of Catahoulas in Europe and following of generations, it is normal to have a slight variance of 1 - 3 base pairs within an allele from parent to offspring but a complete lengthening to another allele has not yet been documented.

I have found two examples of the lengthening of "M(a)" to a length not quite as long as "M".
It is unclear if "M(c)" would be able to lengthen at all given how truncated the tail length is. To date there has not been DNA proof of "M(c)" lengthening.


Further findings of the shortening or lengthening of Merle will be reported on in any further updates done for this book.

Example of Merle lengthening can be seen on Page 67.


Example of a breeding involving M(a)