Should I Breed My Merle Dog?

Merle carries a risk of deafness and/or blindness of varying levels of severity, with the risk much higher in homozygotes with longer SINE insertions so for many breeds, the answer is not simply yes or no.

The more appropriate question is:

Can these dogs be bred responsibly, and what will health/genetic testing tell us?

What Has Research Taught Us About Merle?

Historically, merle inheritance and breeding advice was largely based on visible coat colour, with the assumption that dogs either had the merle gene or they did not.

However, research over the past two decades has shown that the genetics are considerably more complex.

Merle results from the insertion of a Short Interspersed Nuclear Element (SINE) within the PMEL (previously SILV) gene.

Rather than being a single, fixed mutation, the inserted SINE contains a variable-length poly(A) tail. 

Researchers have demonstrated that the length of this insertion directly influences how the merle gene is expressed, resulting in a spectrum of different merle alleles rather than a single "merle" mutation.

Initial commercial DNA tests recognised only two variants—merle (M) and non-merle (m). However, these classifications could not explain why some apparently non-merle dogs unexpectedly produced merle puppies or why some breeding outcomes did not match predicted inheritance patterns.

Subsequent research identified a series of additional alleles, including cryptic merle (Mc), cryptic merle plus (Mc+), atypical merle (Ma), Ma+, classic merle (M) and harlequin merle (Mh). Each produces different degrees of pigment dilution and carries different implications for breeding decisions.

One particularly important discovery was the existence of cryptic merle dogs. These animals may appear completely solid-coloured because their SINE insertion is shorter and does not produce the typical merle coat pattern. Despite this normal appearance, they still carry merle-associated genetics and can pass these alleles to their offspring. This means that relying solely on a dog's appearance is not sufficient when assessing breeding risk.

Researchers have also described merle ‘mosaicism’, where different cells within the same dog contain different merle alleles. This helps explain why some dogs display unusual or patchy coat patterns and why breeding outcomes can occasionally appear unpredictable. Importantly, even low-frequency merle variants present within mosaic individuals may be inherited by offspring, making comprehensive genetic testing increasingly valuable for breeding decisions.

These discoveries have transformed how responsible breeders approach merle breeding. Breeders can now identify the specific merle allele or alleles present in each proposed parent and assess whether a proposed mating is genetically compatible.

Current commercial laboratories recognise numerous possible allele combinations. One laboratory summarises that 14 combinations result in significant white pigment deletion, while eight combinations are associated with an increased risk of hearing or ocular abnormalities. This highlights an important principle: the welfare risk is determined not simply by the presence of a merle gene, but by the specific combination of merle alleles inherited by the puppies.

Merle Has Also Become a Commercial Trend

The science surrounding merle has become increasingly important because merle is no longer confined to the breeds in which it historically occurred.

Over recent years, merle colouring has become highly desirable in the pet market. In some cases, merle has been deliberately introduced into breeds where it has not traditionally existed through crossbreeding programmes aimed primarily at producing an unusual appearance.

While coat colour itself may not inherently be a welfare problem, breeding decisions driven primarily by novelty or market demand can create additional risks especially when merles are bred without knowledge and genetic testing is not performed - the rise of the ‘fluffy’ French Bulldog, or ‘desirable’ dilute colours show us just how far people will push dogs in order to get ‘cute’ aesthetics.  Commercial demand for unusual aesthetics can encourage breeding decisions that prioritise appearance over health and genetic compatibility.

The growing popularity of merle has therefore reinforced the importance of understanding the underlying genetics rather than relying on appearance or marketing terminology.

For responsible breeders, the question is no longer simply whether a dog is merle.

Instead, it is whether the genetics of both parents have been fully characterised and whether the proposed mating minimises the risk of producing puppies with preventable health problems.

Responsible Breeding

Whether a merle dog should be bred depends not on its appearance alone, but on the breed, and the genetics of both parents and the compatibility of the proposed mating.

Historically, the greatest welfare concern has been high-risk merle-to-merle matings, which can produce puppies with predominantly white coats and a substantially increased risk of congenital deafness, ocular abnormalities and other developmental defects. The severity of this risk varies depending on the specific merle alleles inherited, with dogs homozygous for longer SINE insertions carrying the greatest welfare concern.

Genetic testing has fundamentally changed how these risks can be assessed. Rather than relying on coat colour alone, breeders now identify the precise merle variants carried by each parent and determine whether a proposed mating is considered genetically compatible. This allows breeding decisions to be based on objective genetic information rather than phenotype alone.

The popularity of merle colouring has increased considerably within the commercial pet market. Merle puppies are frequently marketed as "rare", "designer" or "exotic", and the merle gene has been deliberately introduced into some breeds where it was not historically present.

Consequently, responsible merle breeding is no longer simply about avoiding two visibly merle dogs. It requires an understanding of the underlying genetics, appropriate DNA testing, and careful selection of compatible breeding pairs.

Why Did the Innate Health Assessment Cause Controversy?

When the Innate Health Assessment (IHA) was first introduced, visibly merle dogs were unable to achieve a passing score under the merle criterion, but most would still pass overall as the aim is for a minimum of 8 out of 10. The decision reflected the well-established welfare concerns surrounding high-risk merle matings and took a precautionary approach designed to minimise the production of puppies at risk of hearing and ocular disorders.

Many welcomed this decision as a clear animal welfare safeguard.

However, it also generated considerable debate among experienced breeders, geneticists and owners of recognised merle breeds.

The criticism was not that welfare protections were unnecessary, but that the original criterion treated all visible merle dogs equally, essentially saying breeding from merle was always unacceptable, rather than recognising that there are responsible ways to do so with minimal risk, despite growing scientific evidence that the level of risk depends on the specific merle alleles involved, rather than simply the presence of a merle coat pattern.

Many responsible breeders already use testing to select genetically compatible mating pairs and argued that the original IHA criterion did not reflect current scientific understanding of merle genetics.

Following discussions with stakeholders, including the breeding community and the Royal Kennel Club, the IHA announced that the criterion would be amended.

From IHA updates its merle criterion — Innate Health Assessment

Rather than automatically excluding visibly merle dogs, the revised criterion introduces a conditional pass. Breeders who choose to breed a merle dog must undertake appropriate genetic testing and provide a written commitment that any proposed mating partner has been genetically assessed in accordance with the IHA requirements.

The Remaining Debate

Although the amendment has been welcomed by many, discussion continues regarding how the criterion will ultimately be applied.

One area of ongoing debate concerns cryptic merle variants. Some commercial genetic laboratories currently classify variants such as Mc and Mc+ as low-risk alleles that may, following comprehensive genetic testing, be safely paired with certain standard merle dogs. As a result, some breeders have questioned whether the current wording of the IHA criterion may be more restrictive than the available scientific evidence suggests for these particular genetic combinations.

The IHA team had confirmed that further technical guidance, including approved testing methods and explanatory information on merle genetics, was going to accompany the implementation of the revised criterion.

These are found here: Merle Information — Innate Health Assessment 

This guidance essentially summarises that Merle genetic testing identifies the specific PMEL (SILV) gene variant(s) responsible for merle coat colour. Every dog inherits two variants—one from each parent—and test results report both (e.g. m/Mc). Modern testing distinguishes between several merle variants (m, Mc, Mc+, Ma, Ma+, M and Mh), each associated with different levels of visible merle patterning and different breeding risks. Because some dogs carry cryptic merle variants that produce little or no visible merle pattern, appearance alone cannot reliably determine breeding risk. Testing is performed using a simple DNA cheek swab, with results typically available within two to four weeks.

For breeding decisions, the longest merle variant identified is used to assess compatibility, particularly in dogs with merle mosaicism. Under the Innate Health Assessment (IHA), dogs with no merle variant (m) may be bred without restriction. Dogs carrying Mc, Mc+, Ma, Ma+ or M may receive a conditional pass but should only be bred to a genetically tested partner confirmed to be either non-merle (mm) or carrying only a very short cryptic merle (Mc) variant. Dogs carrying the Mh (harlequin/longer merle) variant may also receive a conditional pass, but only if bred to a genetically confirmed non-merle (mm) partner. The IHA recognises a number of laboratories capable of performing advanced merle testing, although testing does not need to be carried out by a Royal Kennel Club-recognised laboratory provided it meets current best-practice standards.

Conclsuion

Ultimately, the question should never simply be "Should I breed my merle dog?"

Instead, it should be:

"Have I fully understood the genetics, undertaken appropriate health testing, and selected a mating that minimises welfare risks for the puppies?"

For responsible breeders, health and genetic testing is an essential part of answering that question. Merle should never be bred because it is 'desirable', 'exotic', or 'rare' without thinking about the implications of doing so.

• Genomia: Testování psů: Lokus M (Merle) 

• The SILV/PMEL17 Gene: Understanding Merle at the Molecular Level | Merle Breeding Safety 

• (PDF) Identification of Cryptic Allele for Merle Patterning in Dogs by Molecular Genetics Methods / Identifikacija Skrivenog Alela Za Mramoriranu Šaru Pasa Pomoću Metoda Molekularne Genetike 

• Merle phenotypes in dogs – SILV SINE insertions from Mc to Mh | PLOS One

• Merle Information — Innate Health Assessment 

• Our updated IHA merle colouration criterion is now live — Innate Health Assessment