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Modifier relationships – it’s complicated


In the most recent post in this series on pigment-type switching, I talked about the fact that both horses and dogs have a wild color that is a combination of red and black pigments: bay in horses, and wolf sable in dogs. Those wild colors involve the interaction of two pigment-type switching genes, Extension and Agouti. Horses and dogs also have a mutation for all-red (located at Extension) and another for all-black (located at Agouti).

One of the most straight-forward ways to explain how this works in horses is to say that the two alleles at Extension determine if black hair is possible, and the alleles at Agouti direct the placement of the black pigment, when it is present. This flow chart might help visualize this.


So far the alleles we have here for dogs line up with those for horses. But dogs have a lot more options at both of these loci, and a look at how those work together is a great way to appreciate the complex nature of pigment-type switching, and why the chart above is only part of the picture.


I mentioned that in dogs one of the alleles at Extension, melanistic mask (EM), directs the placement of black pigment. Those familiar with horse color tend to think that is the role of the Agouti locus, which is why it is so tempting to think of Extension as the primary control, and Agouti as the modifier. However, when it comes to the alleles that control the two basic pigments, the loci themselves do not really have simple primary vs. modifier relationships. It is the individual alleles that act as modifiers, and just which allele plays that role varies with the different colors. In fact, as we’ll see later, in some cases there are multiple layers to these relationships.

So the melanistic mask allele (EM) directs the placement of the black pigment, but like horses, dogs have alleles at Agouti that also do this. In addition to the melanistic mask, the dog in the picture above has the Agouti allele for fawn (Ay), which in some breeds is called sable. Another common allele at this locus is black-and-tan (at). That is the color associated with breeds like the Doberman or Rottweiler. Both the fawn and the black-and-tan alleles direct the placement of black pigment into specific patterns.


These two alleles can work simultaneously with the allele for melanistic mask. Fawn dogs with melanistic masks are common in many breeds. This dog has both the black-and-tan pattern and the melanistic mask, which has partially obscured the tan patches that are so clearly visible on the nose of Doberman above. (This was probably even more striking before age caused the muzzle of this dog to turn gray.)


When present, black-and-tan and melanistic mask are both visible in the final coat. There are also alleles at Extension that modify specific alleles at Agouti, changing the nature of the original color. In Salukis, the color known as grizzle is an allele at Extension (EG) that modifies black-and-tan (at) . A separate allele at Extension (eh) alters black-and-tan in a similar fashion to produce “sable” English Cocker Spaniels. (The linked articles are in German, but they contain numerous images of sable (zobel) Cocker Spaniels.)

Saluki photo by Pleple2000, courtesy of Wikimedia Commons.

As the grizzle Salukis and “sable” Cocker Spaniels show, it is possible for Extension to enable the production of black pigment, direct its distribution and even modify the distribution of black pigment set down by alleles at Agouti. It is, in fact, even more complicated than this, because recent studies suggest that the black-and-tan pattern is itself a modification of a pattern known as saddle tan, which is a separate allele at a completely different locus. So grizzle is probably a modification of a modification, with the “original” pattern of red and black pigment residing at a locus that is neither Extension or Agouti.

This shows that even with dogs, where pigment-type switching has been more extensively studied, we only have a partial picture of the process. However, if we place the pieces of the puzzle that were outlined in this post into our previous flow chart, it gives a broader picture than the small window that the (known) alleles in horses allow. Here is an expanded chart showing the relationships between these alleles. If you hover over the image with your mouse, it will drop out the additional alleles to show the more limited picture provided by those alleles that correspond with the pigment-type switches in horses.

Saluki photo by Pleple2000 and Cocker photo by Louis Mayer, courtesy of Wikimedia Commons.

To make things more complicated, even this expanded flow chart covers only a portion of the pigment-type switches in dogs. While horses have two major sites that are known to control pigment-type (Extension and Agouti), dogs have a third (K Locus). That third locus, which controls dominant black and brindle, is an interesting topic for another day, but I want to take us back to horses, and what this bigger (if incomplete) picture might tell us about some of the mysteries still unsolved in that species.

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Extension in other animals


When talking about horses, the simplest way to explain the interaction between the two common pigment-type switches, Extension and Agouti, is this: Extension determines whether or not there will be black hairs in the coat, and Agouti determines where on the body those black hairs will go. That is a reasonably accurate description of how the distribution of red and black pigment is understood to work. Other animals, however, can be far more complicated.

One difference can be seen in animals—like the agouti Guinea Pigs—that have banded hairs. In horses, the distribution of the black pigment is spatial; black hairs are directed to specific areas of the body. In other species, the distribution of black pigment is about timing; as the individual hairs develop, the two pigments alternate to form bands of red and black. It is also possible to have both kinds of distribution, spatial and timed, on the same animal. The Guinea Pig pictured above has both a timed pattern (banded hairs) and a spatial pattern (tortoiseshell) of black hairs.

Banded hairs are produced when the pigment switches from red to black during the development of the individual hairs

The other difference is that in some species, the distribution of the black hairs is not exclusively controlled by Agouti; other genes, including Extension, can be involved in the arrangement of black pigment. The allele that distributes black in tortoiseshell Guinea Pigs is not at Agouti, which is where most people familiar with horses might guess it to be, but at Extension. Because black pigment is only enabled in portions of the coat, the allele is called “Partial Extension” (ep). It is recessive to the wild-type allele (E), which enables black pigment across the entire coat, but dominant to the allele for the complete restriction of black pigment (e).

ExtenEm ExMask

Dogs are another species where alleles at Extension can determine not just the presence, but the placement of black hairs. An example of this is the black mask seen on some fawn dogs, like the Great Dane and the Belgian Malinois pictured above. Like Partial Extension in Guinea Pigs, the Melanistic Mask (EM) allele was proposed as part of the set of alleles at Extension fairly early (1919). At first it was thought of as a partial extension of black pigment, much like the tortoiseshell pattern in the Guinea Pigs, but later it was seen as a “super-extension” where the black pigment extended more dramatically in specific areas of the coat.

The underlying fawn color, however, is controlled by an allele at Agouti. In common horse color terms, it could be said that the Melanistic Mask allele (EM) modified the Fawn allele (Ay) by adding a black mask and darkening the ears and (usually) the topline. This, of course, is in conflict with the idea that the Agouti locus is a “modifier of Extension“.

The recessive form of Extension (e) produces a clear red dog, just as it produces a red (chestnut) horse

So is the relationship in dogs flipped? Does the canine form of Extension modify Agouti, while the equine form of Agouti modifies Extension? Not really. Dogs have recessive red (e) just as horses do, and their alleles at Agouti still need black pigment enabled to have any effect, just as is true for horses. A recessive red dog like the Golden Retriever above, will hide what he carries at Agouti for the same reason as a chestnut horse; there is no black pigment to distribute. It is just that dogs have many more alleles at both sites. Horses, having far fewer, give an incomplete picture of how the two pigment-type switches interact. The larger picture does not lend itself well to reducing one locus to the “primary” control and the other to its “modifier”. It is accurate to say that some of the alleles at one site modify the effect of an allele at the other, but Extension and Agouti as a whole have a more complex relationship.

The back-and-forth between these two genes is even more obvious when looking at a more recently discovered allele at the canine Extension locus, which is Grizzle (EG). Since that involves another layer of complexity, that will be the subject for the next post in this series. After that, we will look at the third major pigment-type switch in dogs, which—if readers haven’t thrown up their hands and completely given up on the subject by then—will make basic horse colors seem refreshingly simple. (That third switch will also allow us to circle back around to some of the remaining mysteries about horse color, too.)

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