Color Genes: genes that affect the pigment color of hairs.

Pattern Genes: genes that affect the distribution of a particular color.

Different terms are sometimes used for the same genetic colors, depending on breed and sometimes country too. In Border Collies, the dilute brown, is called lilac. A dog that is genetically 'recessive red' ("e/e") is known as yellow in some breeds and red in others. Brown is called chocolate by many and is also referred to as red. This can be confusing.

MELANIN, AGOUTI AND RED:

Melanin is the substance that gives a dog's hair its color.  There are two distinct types of melanin in the dog --- eumelanin and phaeomelanin.

Eumelanin is, in the absence of other modifying genes, black or dark brown.

Phaeomelanin is, in its unmodified form, a yellowish color.

Melanin is produced by cells called melanocytes. These are found in the skin, hair bulbs (from which the hairs grow) and other places.  Melanocytes within the hair follicles cause melanin to be added to the hair as it grows. However, melanin is not added at a constant 'rate'. At the very tip of the hair, eumelanin production is usually most intense, resulting in the darker tip.

A protein called the Agouti protein has a major effect on the amount of melanin injected into the growing hair. The Agouti protein causes a banding effect on the hair: it causes a fairly sudden change from the production of eumelanin (black/brown pigment) to phaeomelanin (red/yellow pigment). An example of this coloration would be like the color of a wild rabbit. The term 'Agouti' actually refers to a South American rodent that exemplifies this type of hair.

The Extension Locus - E
This refers to the extension of eumelanin over the dog's body. The dominant form, "E", is normal extension. The recessive form, "e", is non-extension. When a dog is homozygous for non-extension (e/e), its coat will be entirely red/yellow (phaeomelanin based). All dogs that have a brown (chocolate) coat will have at least one "E" allele, because of the production of eumelanin.

The way to tell the difference between an Agouti red/yellow and an Extension (e/e) red/yellow dog -- is the Agouti red/yellow almost always have some black/brown hair in the coat (usually around the ears and tail) and the Extension (e/e) dog won't. Another way is the Agouti red/yellow must have at least one ("A^y") allele and can carry at most one other agouti allele, the Extension (e/e) can carry any two Agouti alleles (not necessarily "A^y").

DOMINANT BLACK -- "K"
The dominant form of black: completely dominates all formation of phaeomelanin pigment. In the past, dominant black had been placed at the head of the Agouti series (symbol "A^s"). Now, it has been proven to be part of a separate series, the "K" series, and not at the Agouti locus at all.

Dominant black (K) is epistatic to whatever is found at the Agouti locus (simply means that it causes the Agouti allele to act differently from what it normally would), however; "e/e" is dominant to "K" at the E
locus.

When "K" is in the dominant form, "K/K" or "K/k", there would be no expression from the A Locus and the color is dependant on what is at the E Locus.  

When "K" is in the homozygous recessive form "k/k", the coat color will depend on what is located on the "E" and "A" Locus.

Dominant "K" codes for both dominant black and brindle in decreasing order of dominance:

K -- dominant black (does not allow the A Locus alleles to be expressed)
br^k -- brindle (expressed when A Locus alleles are expressed)
k -- normal (allows the A Locus alleles to be expressed)

A dog that is:

"K/K" or "K/k" -- dominant black; dominant black carrying recessive black  
"K^br" -- dominant black, carrying brindle
"br^br" -- brindled
"br^k" -- brindled, carrying recessive black
"k/k" -- 'normal' (recessive black)

Brindling is 'stripes' of eumelanin-based (can be modified by the genes at the B and D Locus, so the color could be black, blue, chocolate or lilac) hairs in areas that are otherwise phaeomelanin based.  In order to produce the brindle color, at least one parent MUST be a brindle.  Brindle is dominant to its absence, so only one copy is needed.  If a person has a brindle colored pup for sale and there are no brindle colors anywhere in the pedigree, then the sire that is reported on the registration papers --- genetically can not be the (true) sire.  There is an exception to this if the dog is "e/e" or "K", he can be a carrier of brindle.  

It is thought that the three loci E, K and A act together as follows:

If the dog is "e/e" at the E locus, and at the K locus, it is "K", "br" or "k", its coat will be entirely red/yellow (phaeomelanin based);

If the dog is E/E or E/e at the E locus, and at the K locus, it is "K", its coat will be entirely dominant black (eumelanin based) [**NOTE: the phenotypic color will depend on what is at the B, D, C and M Locus];

If the dog is E/E or E/e at the E locus, and at the K locus, it is "br^br" or "br^k" it will be brindled with the color of the phaeomelanin part of the brindling affected by the Agouti alleles present;

If the dog is E/E or E/e at the E locus, and at the K locus, it is "k/k" the distribution of eumelanin and phaeomelanin will be determined solely by the Agouti alleles present.

The Agouti Locus - A
Simply, this is how the pigment is distributed on the dog's body and hair shaft.

The Agouti locus controls the formation of the Agouti protein, that in turn is one of the mechanisms that controls the replacement of eumelanin with phaeomelanin in the growing hair. The alleles of the Agouti locus can affect not just whether or not the eumelanin -- phaeomelanin shift occurs, but also where on the dog's body this happens.

Two promoters are generally associated with the "wild type" version of the agouti gene.
 

• Cycling Promoter
   
• Ventral Promoter
   

The Cycling Promoter produces a banded hair with a black tip and yellow middle over the entire body. If only the action of this promoter is disrupted, the hair color on the dog's back will be black and its belly and inside of the legs will be yellow. This produces the black and tan color.

The Ventral Promoter dictates that there will be only yellow color in the hair on the belly.The animal will have black banded hair on the dorsal (back) side andpaler yellow hair on the ventral (belly) side. If only the action of this promoter is disrupted, the hair color on the dog will be banded over its entire body. This is said to be solid agouti color.

If something inactivates the agouti protein, or if both promoters are disrupted, the animal will appear to be solid black.

If a mutation occurs at one of these Promoters, this can cause the yellow to be expressed over most of the body.

NOTE:  In part of a series on Dog Coat Color Genetics by Sheila Schmutz, she states that recent studies show that the agouti signal peptide (ASIP) competes with melanocyte stimulating hormone (MSH), which produces eumelanin pigments, to bind on the melanocortin receptor and must sometimes win. Both the E allele and Em allele are responsive to agouti or melanocortin binding in dogs. However dogs that are ee have a mutation in MC1R and produce only phaeomelanin. The dog's agouti genotype doesn't affect its coat color, which will be some shade of cream, yellow or red.

To further complicate things, agouti has 2 separate and somewhat distant promoters. Roughly, one seems to control ventral or belly color and the other dorsal or back color. The simplest way to "see" this is on a black and tan dog......the back is black from eumelanin pigment being made and the belly is tan or red from phaeomelanin pigment being made.

The agouti gene has been mapped in the dog and DNA studies to determine which patterns are under the control of this gene in the dog are in progress. This gene undoubtedly has several alleles, but how many is still an open question. Some have been identified using DNA studies and tests for agouti phenotypes in some breeds may become available soon. Although several books attempt to state thedominance hierarchy of the agouti alleles, since no breed has all the alleles, it is not possible to know this for sure. Most books suggest that it is aw > ay > at > a. Breeding data and DNA data from our collaborative study with Dr. Greg Barsh's group at Stanford supports this. However the data confirm pairwise dominance/recessive
relationships in different families.......not the entire hierarchy in one family.

Decreasing in order of dominance:  (**sable may be dominant over wolf in some breeders)

~~ "a^w", 'wolf' color - This is like "a^y" but the tan is replaced with a pale gray/cream color and the hairs usually have several bands of light and dark color, not just the black tip of sable. Example would be Keeshond, Siberian and Norwegian Elkhound.

~~ "a^y", 'sable' - also known as 'dominant yellow' or 'golden sable'. This results in an essentially red/yellow phenotype, but the hair tips are black (eumelanin). The extent of the eumelanin tip varies considerably from lighter sables (where just the ear tips are black, called "Clear Sables") to darker sables (where much of the body is dark, called "Shaded Sables").

~~ "a^s", 'saddle' - Eumelanin is restricted to the back and side regions, somewhat like the black/tan ("a^t") allele (below).

~~ "a^t", 'tan points' - This is primarily a solid colored dog with tan (phaeomelanin) "points" above the eyes, muzzle, chest, stomach and lower legs. The hue can range from a pale biscuit to a rich ginger to a golden copper in color. In the Border Collie which has the Irish spotting, along with tan points, this is known as "tri" colored .
 

~~ "a" - last of the Agouti series is recessive black. When a dog is homozygous for recessive black (a/a), there will be no red/yellow (phaeomelanin) in its coat (unless "e/e" is present, which is epistatic to the Agouti series). Examples of breeds that show to be recessive black are German Shepherd and Shetland Sheepdog.

BLACK or BROWN (CHOCOLATE) - B GENE LOCUS: (pigment color)
This gene, when in the homozygous recessive form, has a lightening effect on eumelanin (black-based colors) only. It has no effect on phaeomelanin (red-based colors).

It is believed that the Brown Locus codes for an enzyme, tyrosinase-related protein 1 (TYRP1), which catalyzes the final step in eumelanin production, changing the final intermediate brown pigment (dihydroxyindole) to black pigment.  SO, ALL dogs start as BROWN and after the final step --- this directs the color to be black.

When brown (b/b) is expressed, it means that the final step in eumelanin production has not been completed and the pigment remains brown. The brown color is not a genetic defect.

When the alleles are in the homozygous or heterozygous dominant form of B/B or B/b, the color and pigment (nose, eye rims and lips) remains (or directs the color to be) black.

When the alleles are in the homozygous recessive form (b/b), the color and pigment will be brown. This just means that the final step in eumelanin production of changing brown to black did not occur. Phaemelanin (yellow/red [e/e]) is not affected.  BUT, in the e/e colored dog, if the dog is also b/b; they'll be either red or yellow and will have brown pigment (nose, eye rims and lips). The pigment
granules produced by "bb" are smaller, rounder in shape, and appear lighter than pigment granules in "B" dogs. The iris of the eye is also lightened.

DILUTION - D GENE LOCUS: (dilution of pigment)
This gene has an effect on both eumelanin and phaeomelanin.

When in the dominant form, "D/D" or "D/d", it allows for full color (black or red).

When present in the homozygous recessive form (d/d) it dilutes black (eumelanin) to blue, chocolate to lilac and red to cream.

COMBINATIONS OF B AND D IN EUMELANISTIC COATS:
The effects of these 2 genes, when combined, form a range of 4 eumelanistic ('black-based') colors:

The color of the pup/dog (Eumelanistic Color):
B/B D/D or B/b D/d will be black in color

B/B d/d or B/b d/d will be blue in color

b/b D/D or b/b D/d will be brown/chocolate

b/b d/d will be flat or dull diluted brown/chocolate

WHITE SPOTTING - S GENE:
The "S" series alleles appear to be incompletely dominant. In dogs it is thought there are four alleles that deal with white spotting:

~~ "S" - 'solid/self color'. Most dogs that are homozygous for "S/S" have no white hair at all, or possible a tiny amount, like a white tail tip.

~~ "s^i" - 'irish spotting'. This involves white spotting on most parts of the coat, but not crossing the back beyond the withers.  This color pattern is evident on the Border Collie that have the white collar.  New research has proven that the white undersides of the Border Collie is dictated by a different gene.  

~~ "s^p" - 'piebald'. The white is more extensive than irish spotting, and often crosses the back. It is sometimes confused with the merle pattern. This coloration usually has large colored spots on the body. The white covers approximately 50% of the body.

~~ "s^w" - 'extreme white piebald'. A dog that is homozygous for "s^w" will be almost entirely white. This allelic pair is also responsible for the "color headed" white dogs. Often times, along with a colored head, there will also be a colored spot near the tail.

TICKED - T GENE:
A dominant mutation that causes the presence of color (flecks of color) in areas that have been made white by the effect of alleles in the white spotting (S) series.

Ticked ("T/T") is incompletely dominant to non-ticked ("t/t").  

ALBINO - C GENE: (development of pigment)
The intensity of melanin production in the coat hairs is affected by this gene. The dominant form, "C", is termed 'full color'.

At this locus, almost all dogs are "C/C", or full color.

The lower series alleles, in order of decreasing dominance:

~~ "c^ch" - Chinchilla -- It is an incomplete dominant gene.  Chinchilla lightens most or all of the red/yellow (phaeomelanin) with little or no effect on black/brown (eumelanin). It turns black/tan to black/silver.  In dogs, this gene lightens yellow, tan or reddish phaeomelanin to cream.  Since there is little effect on the dark eumelanin, phaeomelanin is effected more strongly than eumelanin and brown.  
Dilute eumelanin (blue) is effected more strongly than dark (black) eumelanin.  When chinchilla is present, it dilutes brown to milk chocolate, blue to silver and red to a butter cream color.
 

NOTE:   Newer research indicates a chinchilla-like mutation occurs in dogs, although, tyrosinase activity hasn't been shown to be connected. Therefore, some other factor may be involved and the dog chinchilla allele may not belong in this series. Also, there may be more than one form of the chinchilla gene.

~~ "c^e" - is 'extreme dilution'. It causes tan to become almost white. It is thought that the white labrador might be "c^e" with another, lower, "C" series allele. The "c^e" allele may be responsible for producing white hair, while allowing fullexpression of dark nose and eye pigment. West Highland Terriers are thought to be e/e c^e/c^e.

~~ "c^b" - or blue-eyed albino. This is an entirely white coat with a very small amount of residual pigment in the eyes, giving pale blue eyes. It is also called platinum or silver.  This allelic pair could be responsible for the white coated, pink skinned, blue-eyed Doberman's.

~~ "c^c" - true pink-eyed albino. Has not been seen in dogs.

GRAYING - G GENE:
This is a dominant mutant gene that causes the dog to gray with age. The pigmented hairs are progressively replaced with unpigmented hairs.

MERLE - M GENE:

The only way a merle colored pup can be produced is if at least one parent is merle. Some breeders are of the understanding that the merle gene is a recessive gene and is carried from generation to generation. This is not correct. The merle gene is not carried, meaning -- the dog is either a merle or is not a merle. There are no exceptions to this law of genetics (for now, at least, until further research
is conducted).

If someone tells you that they have a litter of merled colored pups and there are no merles for many generations in their bloodlines --- then these merled pups were not sired by the sire the owner thinks there were. In fact, he should look for the hole in the fence!  

The merle gene is an incomplete dominant or a gene with intermediate expression and is another dilution gene. Instead of diluting the whole coat it causes a patchy dilution, with a black coat becoming gray patched with black. Brown becomes dilute brown patched with chocolate, sienna, brick, and various diluted brown colors.  While sable merles can be distinguished from sables, this is sometimes
very difficult because the merle coloration looks like -- to just slightly different from -- the sable color. The merling is clearly visible at birth, but may fade to little more than mottling of the ear tips as an adult. Merling on the tan points of a merle black and tan is not immediately obvious, either, though it does show if the mask factor is present. Eyes of a merle dog are sometimes blue or marbled (brown
and blue segments in the eye).

A "m/m" (homozygous recessive) dog is normal color (no merling). A "M/m" (heterozygous) dog is a merle. A "M/M" (homozygous dominant) dog, known as a double merle (from a merle to merle mating), has much more white than is normal for the breed and may have hearing loss, vision problems including small or missing eyes, and possible infertility. The health effects seem worse if a gene for
white markings is also present. In Border Collies all of which normally have
fairly extensive white markings, the "M/M" white has a strong probability of being deaf or blind. A "M/M", double merle, to "mm", non-merle black in color breeding, is the only one that will produce 100% merles.

Cryptic or phantom (as it's sometimes called) merles are dogs which carry a merle gene but are phenotypically (look like) tri, bi or self colored. These dogs will have some small area of merling somewhere, usually a tiny patch of merle pattern on their ear, tail, top of head, etc. Keep in mind the tiny patch can be only one hair and it can be located anywhere on the body. Cryptic merles are very rare. AGAIN, a cryptic or visible merle can only be produced when one or both parents are merles.

GENOTYPES AND COLORS:
("-" is either the dominant or recessive allele)

B/- D/- E/- K/- = black
b/b D/- E/- K/- = brown (chocolate)
B/- d/d E/- K/- = blue
b/b d/d E/- K/- = lilac

AGOUTI:
at^at B/- D/- E/- k/k = black with tan points
at^at b/b D/- E/- k/k = chocolate with tan points
at^at B/- d/d E/- k/k = blue with dilute tan points
at^at b/b d/d E/- k/k = lilac with dilute tan points

NON-EXTENSION RED (cream):

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