Description:

The Merle gene (M locus) is responsible for one of the most visually striking coat patterns found in several dog breeds, including Australian Shepherds, Collies, Dachshunds, and, more recently, Poodles. It produces a marbled or mottled effect by diluting areas of the coat and can also affect eye color and, in some cases, skin pigmentation.

However, the Merle gene is genetically complex and can be potentially harmful if mismanaged. It impacts not only coat color but also eye development and auditory function, especially when two Merle alleles are inherited. Some dogs carry cryptic or hidden Merle alleles—meaning they may not display the pattern visually but can still pass it on genetically. When bred to another Merle carrier, this can result in double Merle (homozygous M/M) offspring, who are at significantly higher risk for vision and hearing impairments.

Because of this, it is essential for breeders to understand the full genetic structure of the M locus, including allele base pair lengths and how different variants interact. Responsible Merle breeding requires genetic testing and thoughtful planning to ensure healthy, properly developed puppies.

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What Causes the Merle Pattern?
Merle is caused by an insertion in the PMEL (premelanosome protein) gene at the M locus. The degree to which the Merle pattern is expressed depends on the length of a SINE insertion, measured in base pairs (bp).

The longer the SINE insertion, the more pigment is diluted, in some circles this is called pigment deletion.

Dogs with one copy of a Merle allele (heterozygous) may show the pattern.

Dogs with two copies, (homozygous Merle or “double Merle”) can be at significant risk for serious birth defects if their parents were improperly paired.

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Merle Alleles and Base Pair Ranges:
⚠️ Note: Some labs (e.g., Paw Print Genetics) classify Mc up to 252 bp, which may include unsafe alleles for merle pairings. Always verify exact bp length, not just labels like “cryptic” or “atypical.”

Always use labs that report precise bp lengths, not just "Merle carrier" labels. Use: UC Davis Veterinary Genetics Laboratory (they are currently the most accurate and provide precise bp lengths.)

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Allele:  Common Name:   Base Pair Range:   Visible?:   Breeding Risk:   Notes:
m         Non-Merle           N/A                    No          None               Recessive, safe
Mc       Cryptic Merle       200–230             No          Safe                 Genetically Merle, phenotypically non-Merle
Mc+     Extended Cryptic  231–244             Slight       Risk                  Can affect pigment when paired with M or Mh

            (aka Ma)

Ma       Atypical Merle     245–254             Faint        Unsafe              May show faint patches, unsafe with M
Ma+     Strong Atypical    255–264             Visible      Unsafe              Clear Merle patches, can delete pigment

            Merle

M         Classic Merle       265–268             Yes          High risk            Traditional Merle pattern

                                                                               when doubled

Mh       Harlequin /         269+                   Yes          High risk            Extremely strong pattern; never double

            Mega Merle                                                  when doubled​

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Merle in Poodles and Other Breeds:
Though not historically found in Poodles, the Merle gene was likely introduced through crossbreeding, then fixed back into bloodlines over generations of Poodle X Poodle breedings. As a result, some Merle Poodles now test as 100% Poodle via breed tests while still carrying the Merle allele.

Appearance:

Merle can be expressed in a variety of base colors, including blue, chocolate/brown, sable, and red Merle, and it can also occur alongside other patterns such as Parti, Phantom, and Ghost Tan, all of which influence the dog’s overall appearance.—it’s important to understand that these terms describe the visual appearance of the coat, not the dog’s actual genetic color.

For example, a blue Merle is genetically a black dog whose coat has been altered by the Merle gene, resulting in a mottled or diluted grayish-blue pattern. Similarly, a red Merle may appear "red," but the genetic foundation for that color varies between breeds.

In Australian Shepherds, a "red" dog is typically liver-colored, with the bb genotype at the B locus, which alters eumelanin pigment from black to brown. In contrast, Poodles described as "red" usually carry the ee genotype at the E locus, which blocks eumelanin production entirely and allows only phaeomelanin (red/yellow pigment) to be expressed.

This distinction is critical because the ee genotype masks the expression of the Merle pattern, meaning a dog can carry the Merle gene without showing any visible signs of it. As a result, dogs with the ee genotype may appear solid-colored while still carrying Merle alleles—posing serious risks if bred to another Merle carrier. Without genetic testing, these "hidden" Merles can lead to unintended and potentially harmful double Merle pairings in future generations.

Because different breeds use different terminology to describe coat colors, it's essential to look beyond appearance and understand the underlying genetics to correctly interpret color names and breeding outcomes.

Expression: Suppressed if the dog is ee at the E locus (red/apricot base color).

Health Risks: Same as other breeds—double Merles are at high risk for blindness, deafness, or microphthalmia.

Merle should only be bred by genetically informed, experienced breeders using exact base pair DNA tests.

Safe Merle Breeding Practices
To avoid health issues:

NEVER breed two Merle carriers where either has an allele over 230 bp.

Use labs that report precise bp lengths, not just "Merle carrier" labels. Use: UC Davis Veterinary Genetics Laboratory (they are currently the most accurate and provide precise bp lengths.)

Dogs with Mc (≤230 bp) behave like non-Merles and are safe with M or Mh.

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Understanding the Difference Between Purebred Status and Dog Ancestry:

It’s important to understand that purebred status and dog ancestry are two different concepts, though they are often confused.

Purebred status is a classification used by dog registries (such as the AKC, UKC, or FCI) to indicate that a dog’s lineage has been fully documented from the time the breed was officially accepted into that registry’s breed standard. This means that every dog in the pedigree traces back to other dogs of the same breed, according to the registry’s records.

However, it's worth noting that in some cases—especially when a breed has a very limited gene pool—a registry may temporarily allow approved outcrossing to original or closely related breeds. This is done to improve genetic diversity, revive diminished traits, or boost overall vigor. When this occurs, the resulting dogs may still be considered purebred by the registry, depending on how the program is structured and after how many generations the outcrossed lines are bred back into the primary breed. That said, this type of registry-approved outcrossing is rare in modern times, as most recognized breeds now have large, well-established gene pools.

Dog ancestry, on the other hand, refers to the actual genetic makeup of an individual dog, as revealed through DNA testing. A dog’s ancestry shows which breeds are present in its genome—regardless of what the registry documents say. This distinction becomes especially relevant in cases where a dog’s appearance and DNA suggest one breed, but registry rules do not classify it as purebred due to a known outcross in its background.

A good example of this is the Merle Poodle. While they often look and act like typical Poodles and may test as 100% Poodle on a DNA test—especially after three or more generations of breeding exclusively to Poodles—they may still be disqualified from purebred status by certain registries. That’s because the Merle gene is not naturally found in original Poodle lines and is believed to have been introduced through crossbreeding. Even when DNA testing no longer picks up significant genetic material from the outcrossed breed, the registry may still consider the line ineligible due to its historical origin.

Major canine organizations, such as the American Kennel Club (AKC), do not recognize Merle as a standard color for Poodles. However, it’s important to clarify that the AKC only registers colors in poodles, not patterns—and merle is considered a pattern. Because this pattern likely required crossbreeding to appear in Poodles, it falls outside the AKC’s accepted standards for conformation showing.

In fact, no patterned coats—including merle, phantom, brindle, or parti—are considered acceptable under the AKC breed standard for Poodles. Only solid colors qualify for conformation events. While multicolored Poodles can still be registered, their coat patterns are not officially recognized, and they are ineligible for AKC conformation titles.

That said, not all registries treat patterns the same way. For example, the United Kennel Club (UKC) now allows parti-colored Poodles to compete in conformation shows, recognizing them as part of the breed standard. This reflects a broader acceptance of natural color variation within the breed by some organizations, though patterned dogs like Merles still face restrictions because their origin and how the pattern was introduced.

In the case of Merle Poodles, this lack of recognition is rooted in a desire to preserve the historical purity of the breed standard as it was originally written. Nevertheless, Merle Poodles can still be registered with alternative registries and participate in a wide range of canine activities—from sports like agility and obedience to therapy and service work. Most importantly, they are just as capable of being loving, intelligent, and loyal companions as any other Poodle.

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Visual Appearance vs. Genetic Reality:
Common Term                Likely Genotype             Visible Pattern?                   Risk When Paired with M/Mh
Cryptic Merle                 Mc (≤230 bp)                       No                            ✅ Safe
Minimal Merle                Mc+, Ma (231–254)       Slight/none                      ⚠️ Risk
Hidden/Ghost Merle       Ma, Ma+                        Possibly no                      ⚠️ Risk
Classic Merle                  M (265–268)                       Yes                            ❌ High risk
Harlequin/Mega Merle    Mh (269+)                           Yes                            ❌ Very high risk

❗ Minimal pattern does not mean minimal risk. Some barely-patterned dogs carry dangerous alleles.​

 

🧬 Safe Breeding Table:
Parent 1        Parent 2           Safe?              Notes
m/m             Any                  ✅                No Merle expression
m/Mc           m or Mc            ✅                Breeds like non-Merle
Mc/Mc         m or Mc            ✅                Safe, no visible Merle
m/Mc+         m                     ⚠️                Test base pairs before breeding
Mc+/M         Any                  ❌                Unsafe – pigment deletion risk
M/M            Any                   ❌                Double Merle – high defect risk
Mh/M          Any                   ❌                High risk of sensory defects

 

Ethical Considerations:
The Merle gene does not cause defects on its own—but improper pairings do.

Double Merle puppies (MM or Mh/M) can suffer blindness, deafness, or malformed eyes.

Mc+, Ma, and Ma+ alleles carry unpredictable risks, especially when invisible on the coat.

Breeding should only occur between a known-safe Merle carrier and a confirmed non-Merle with full genetic panel testing.

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Key Takeaways:
✅ Mc (≤230 bp) is the only allele that reliably breeds like non-Merle
⚠️ Minimal or no visible Merle does not equal genetically safe
❌ Never breed two dogs with Merle alleles >230 bp
🔬 Always confirm precise base pair lengths before pairing​

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Recommended Resources:

UC Davis Veterinary Genetics Laboratory -When testing for length UC Davis is currently the most accurate.

🧬 Merle -SINE Insertion from Mc - Mh - Educational Forum -Awesome for understanding merle and getting questions answered.

Mary Langvin's website has great resources: Visit here