BLACK 

                                E/E  B/B D/D  AND C/C ( LADY )

                                D/d AND C/C

                                d/d AND C/C 

                                d/d AND C/c

                                d/d AND c/c   

BROWN 

                                 E/E  b/b D/D  AND C/C

                                 E/E  b/b D/d AND C/C

                                 E/E  b/b d/d AND C/C 

                                 E/E  b/b d/d AND C/c

                                 E/E  b/b d/d AND c/c  ( PINK POINTS LIGHT EYES )

 RED

                                                                 e / e      B/B  D/D  AND C/C

Canine Coat and Nose Color Testing

C128-Canine Coat and Nose Color Test  Pomeranian DNA TEST Pomeranians  are either black or red  ----  other alleles (genes) act upon each other to create different colors or different shades of colors.  Pomeranians can be tested for the Presence of black, brown and red (cream and orange) coat colors, and black and brown nose (s) .   Brindle - the base color is gold, red, or orange-brindled with strong black cross stripes.  Parti-color - is white with any other color distributed in patches, with a white blaze preferred on the head.on. GENOTYPES Genotype Main Color Nose Color Hidden Color EEBB black black none EeBB black black red/cream/orange EEBb black black brown  EeBb black black red/cream/orange, brown    EEbb brown brown none Eebb brown brown red/cream/orange eeBB red/cream/orange black none eeBb red/cream/orange black brown eebb red/cream/orange brown brown

 

BREED COLORS IT STARTS WITH DNA In sexual reproduction, genetic material from the sire and dam are passed on to their offspring in the form of DNA. The makeup of DNA consists of two strands of genetic material that connect to each other forming what is known as “base pairs”. How these base pairs align with each other, become the genetic blueprint for a particular trait. These aligned base pairs of DNA (one from each parent) are called GENES. Genes are located within chromosomes. A GENE LOCUS is where a gene is located on a chromosome. One published analogy likened a chromosome to a music CD; the genes found on the chromosome, occupy a specific location or “locus” much like music is found on a specific track. This is an important concept to keep in mind, when we talk about the different GENE SERIES OR LOCI later in this guide. PHENOTYPE: Phenotypes are the physical characteristics, created by the combination of genes that can be “observed” about an individual (such as hair or eye color). GENOTYPE: The genetic make up of an individual created by the combination of genes. Not all of the characteristics are visible, such as being a “carrier” of a certain disease or color. ALLELE: Different versions of a gene for the same trait, such as color, which gives rise to different phenotypes, are known as alleles. The individual will have two alleles for each trait as one is inherited from each parent. Alleles may be dominant or recessive. DOMINANT AND RECESSIVE: An allele is dominant if it “show’s itself” and hides the presence of another allele. For example, if a dog has a copy of a black gene and copy of a brown** gene, the dog will be black because black is dominant to brown (recessive). You cannot tell by looking at the dog if they have a copy of the brown gene (genotype). An allele is recessive if its effect is not seen when a more dominant allele is present, as in the brown example above. For the dog to be brown, he must have two copies of the brown gene. ** NOTE: in the United States, the traditional nomenclature for a Border Collie that is brown in color is to call them RED and they are registered as such. However, due to the fact that they are considered “brown” genetically (genetic code “bb”), that is the term that will be used in this guide. HETEROZYGOUS: When the two genes making up an allele are different, such as “Bb” (Black as dominant and brown as recessive), it is referred to as being heterozygous for that gene. HOMOZYGOUS: When the two genes making up the allele are identical, such as “bb” (both genes recessive for brown), it is referred to as being homozygous for that gene. Therefore, when a dog is heterozygous for a specific gene, statistically it will pass the dominant copy to half its offspring and the recessive copy to the other half. When it is homozygous for a particular gene, it will pass this copy to its entire offspring. PUNNETT SQUARE: This is a commonly used diagram to demonstrate genetic combinations that are possible using the concepts of dominant and recessive (expressed in percentage of probability) Here is an example:     SIRE is homozygous black     B B Dam is heterozygous black with brown as recessive B BB BB b Bb Bb When you look at the genetic possibilities, you will see that all the puppies will be Black (phenotype) and two will carry brown color as recessive traits (genotype). If both parents were heterozygous Black, carrying brown recessively, the combinations would look like this:     SIRE     B b Dam B BB Bb b Bb bb This demonstrates that statistically, three dogs would be Black, one would be brown and three would be carriers of brown.   COLORS AND PATTERNS The substance that gives a dog’s hair its color is called MELANIN. There are two types of melanin in the dog:  EUMELANIN: The dark pigments of Black and Brown  PHAEOMELANIN: A yellow or red color  Note: Both of these pigments can be acted upon by other genes, there-by altering these “base” colors (discussed later). Only the dominant version of the color gene results in eumelanin production. If the dog has two copies of the recessive version, he will have no eumelanin, and his hair will contain only the light pigment. His nose leather and eye rims will be red or brown There are also Pattern genes that affect the distribution of a particular color on the dog. Both the color and pattern of a dog is determined by several Loci or gene series. There is no “single” gene that dictates coat color, but rather a combination of genes that are either expressed or carried that determines the color and pattern of the offspring. The following is a very basic discussion that addresses some, but not all, of the Loci and the influence they exert in the total “equation” that makes up colors and patterns. Included in some cases, will be the genetic “coding” used to represent part or all of a dog’s color genotype but it is NOT an all-inclusive list of the genetic possibilities. A (Agouti): This locus is responsible for how pigment is distributed along the dog’s hair shaft and body regions, by inhibiting eumelanin (dark pigment) production. This locus is involved with Sable dogs (both shaded and clear), Saddleback Sable, and “Tan points”.  You will see the following “coding” used to indicate these colors/patterns: A^y Sable  Ay^Ay clear sable  Ay^at shaded sable (sable with dark fur in coat). “a^t” tan points “a^s” saddleback pattern below is another school of thought……. Dominant Black (K) This gene turns the “Agouti” genes on and off and codes are: Black (Agouti genes “off”; not expressed) and Brindle (Agouti genes “on; expressed) code: br^k As well as combinations of the above as “expressed” or “carried” Example: K^br is a black dog carrying brindle. Kk^Ayat is a black dog carrying sable and tricolor Brindle is a pattern of alternating stripes of eumelanin and phaeomelanin pigmentation (yellow/black, or red/black) B Locus (Brown): This gene determines or selects for a black or brown dog. When this gene is in its dominant form (BB or Bb) the dog is black. When this gene is in its homozygous recessive form (bb) it has a lightening effect on the eumelanin only and the dog is brown. BB is homozygous Black (not carrying brown) Bb is heterozygous Black (carrying brown) bb is homozygous Brown. D Locus: This dilution gene acts on both eumelanin and phaeomelanin pigments. It “dilutes” the base color of the dog. If the dog is “D” or dominant, it is fully pigmented. If the dog is “dd”, this recessive gene dilutes the pigment, thereby altering its color. In Border Collies, the d/d gene is associated with skin problems such as Color Dilution Alopecia or hair loss (on the ears is common) which can be seen in the Blue and Lilac dogs.  If the Dilution gene acts on the brown and black coats, you can get the following: black diluted to blue and brown diluted to lilac (see photo to right). Lilac is caused primarily by a “double recessive” condition of bb at the B gene locus and dd at the Dilute gene locus. It is also possible to produce a Lilac color out of pairings of black-to-black, black to brown, brown-to-brown, black to blue and blue to brown IF the genes are paired correctly AND they both carry the recessive forms of the B and the D gene (“b” and “d”) To demonstrate the genetic possibilities as mentioned above, let's make both the sire and the dam genotypes the same as BbDd. These black dogs carry both brown and the dilution gene. BbDd – The Dam can contribute: BD bD Bd bd                         BbDd – The Sire can contribute: BD BBDD BbDD BBDd BbDd     Black Black Black Black               bD BbDD bbDD BbDd bbDd     Black Brown Black Brown               Bd BBDd BbDd BBdd Bbdd     Black Black Blue Blue               bd BbDd bbDd Bbdd bbdd     Black Brown Blue Lilac In this case, Black is dominant (B). If it is acted on by the dilution gene (dd), it will produce a Blue dog. Brown is recessive (bb) and if it is acted on by the dilution gene (dd), it will produce a lilac dog. If the black or the brown dog has Dd, where D indicates the dog is fully pigmented, they retain their base color. If we were to express the above diagram in statistical probability: 56% of the offspring would be black, 19% would be brown, 19% would be blue and 6% would be lilac. Keep in mind that the example above is only showing the B and D gene series affect on the genotype. Other gene series influence and are a part of the total “picture” .  If the Dilution gene acts on the light coat (phaeomelanin) it will dilute a red color to cream (for the description of the red color, see the E locus). E Locus: This gene series either restricts or extends pigments in the hair follicle. If it is in its dominant form (E), it extends the darker pigment (Black or Brown dog). If it is in it’s recessive form (e/e), it allows only the extension of the phaeomelanin, and the dog’s color becomes what is called a TRUE RED, Australian Red or in the United States, “Gold”. This gene is considered a “masking” gene as it will hide a dog’s true color. However, it only affects the hair follicle so you can identify its color by the nose leather and eye rims. For example, a dog that is genetically Brown, will have brown or reddish nose leather /eye rims but has a golden to red coat color. If it also has the dilution gene, the coat will be a creamy color. Its genetic code might look like “b/b, d/d, e/e”. S Locus: The S gene series demonstrates various patterns of white spotting. This includes the traditional white markings seen on black border collies, often called Tuxedo Markings or Irish spotting as well as the piebald spotting pattern and the extreme white spotting pattern. The coding is as follows: s^i tuxedo markings  s^p piebald spotting where there are random spots of color on a white background.  s^w a dog that is almost completely white. Currently, Border Collies that have extreme amounts of white and or white that crosses the flank in lines or patches are referred to as being “white factored.” Having increased white areas is not a problem per se, however from a breeding perspective, there is research-linking deafness to the alleles for piebald spotting or extreme whiteness. T Locus: The T series refers to “ticking” or flecks of color in white areas. Code for Ticked is T^T (and non-ticked is t/t) M locus: The Merle gene is a pattern gene, not a color in of itself. It is also a dilution gene. It causes patchy areas of color dilution, resembling a marble like pattern. This will result in a genetically black dog to show grey patched with black areas and they will have a black nose. If the dog is genetically blue, he will have grey patched with dark blue/grey areas and a grey nose (commonly called a Slate Blue). Both are referred to as BLUE MERLES. A genetically brown dog will show patchy cinnamon/brown/red patches and they will have a liver colored nose (RED MERLE). A genetically SABLE dog would be called a SABLE MERLE, however, with the phaeomelanin dominating the color scheme, they are often difficult to recognize as adults. Only a merle parent can produce a merle puppy…It is not a gene that is “carried”, therefore, the coding would be M for Merle or “m” for non-merle. Breeding a merle to a merle is not recommended as the offspring can have a significant risk of health problems. Summary of the Loci or Gene Series:  A and E Loci control pigment distribution B, D, M Loci modify color by “dilution” S and T Loci control placement of white areas.

 

The color shades can vary anywhere from white, pale yellow, biscuit color, butter cream,  to a burnt red, fox 

red, orange, to a copper penny color. The color depends greatly on the genes at the D and C Locus. This 

coloration is found in the Pomeranian  breed.

Dogs that are (e/e) can range in the colors listed above and if they have a black nose, lips, eye rims, are 

said to be genetically black. 

  This is where Ice White comes in to play

 A TRUE ICE WHITE POMERANIAN has to be genetically 

BLACK 

that is why it is so difficult to produce TRUE ICE WHITE POMERANIANS !

Dogs that are (e/e) and brown (b/b), the color will not change to chocolate. However, the nose, lips, eye rims 

will be brown - readily identifying the dog as being genetically brown. 

Ice Whites can not come from BROWN

Dogs that are (e/e) and blue (d/d), the color will be diluted to yellow (this is the fact *most* of the time, but not 

always -- the dog could be a reddish color).  The nose, lips, eye rims will always be gray - readily identifying 

the dog as being genetically a diluted black (blue).

 Ice Whites can not come from BLUE 

Dogs that are (e/e) and brown (b/b) and blue (d/d), since the brown has no color changing effects, but blue 

does ---- the dog will be diluted to yellow.  

The nose, lips, eye rims will be a rosey-brown.

Ice Whites can not come from this combination

NOTE: if the dog is K/K or K/k --- the tan points can only be carried, not expressed. If the dog is k/k, the tan 

points, even though are expressed, may not be evident on the e/e red or creme  dog, as the tan points are 

usually the same color as the dog's coat. 

 FYI:

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 will be either red or yellow and will 
have brown pigment (nose, eye rims and lips). e 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.

- 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.

Albino - C gene

This gene affects the intensity of melanin production in the coat hairs. The normal or dominant form, C, is what might be termed 'full color'. There are however various incompletely dominant mutant alleles postulated for this locus, with varying effects on color intensity. These mutant forms are temperature sensitive - the higher the temperature, the more effective they are (i.e, the lighter the color).

Almost all dogs are CC at this locus - full color.

The lower series alleles that have been suggested include, in order of decreasing dominance, c_ch, c_e, c_b and c.

The first, c_ch, is chinchilla. This lightens most or all of the phaemelanin with little or no effect on eumelanin. E.g. it turns black+tan to black+silver.

The next allele, c_e, is 'extreme dilution'. Causes tan to become almost white. It is thought that the white labrador might bec_e with another, lower, C series allele. The c_e allele may be responsible for producing white hair in other breeds of dogs, like the West Highland White Terrier, while allowing full expression of dark nose and eye pigment

Moving on down we have c_b, or blue-eyed albino. This is an entirely white coat but with a very small amount of residual pigment in the eyes, giving pale blue eyes. This is known as c_a in cats. Can be called platinum or silver.

Finally we have c, true pink-eyed albino. This doesn't seem to occur in dogs. 

As more research is conducted in the field of  (color) genetics, more information gathered and more of the  'unknowns' are 'known' - Definitions: chromosome: The nuclear structure which houses (contains) the genetic information. Chromosomes exist in  pairs and therefore there are always two copies of a given gene. gene: a unit of inheritance locus (-ci): the position of a gene on a chromosome. Every gene has a specific locus genotype: the genetic make-up of an individual phenotype: that part of the physical appearance of an organism which depends on gene action homozygous: the condition when both alleles of a gene pair are identical heterozygous: the condition when both alleles of a gene pair are different dominant: term describing a gene which can produce a phenotype when present only once; also the  phenotype which results recessive: term describing a gene which must be present twice to produce a phenotype; also refers to the  phenotype which results wild: the "normal" phenotype mutant: the non-normal phenotype; is a relative term (relative to the population from which the organism  originates 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.   for instance,   In Pomeranians , the dilute brown, is called Beaver, Lilac or Lavender or white chocolate   In Dobermans, the dilute brown, is called Isabella.etc   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  ( in the Pomeranian this is called Sable ) 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) k^br -- 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/k^br -- brindled k^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 fawn) 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", 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", "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/K" or "K/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 "k^br/k^br" or "k^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 and paler 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 the dominance 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 breeds such as Pomerannians ) ~~ "a^w", 'wolf SABLE ' 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, Pomeranian,  Siberian  and Norwegian Elkhound. ~~ "a^y", ' NORMAL 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.  Commonly seen in many breeds like Pomeranians,  hounds, Dobermans, Rottweilers and Kelpies.  In breeds that have  the Irish spotting, along with tan points, this is known as "tri" colored (Australian Shepherds and Border Collies).   ~~ "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 will be either red or yellow and will  have brown pigment (nose, eye rims and lips). e 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) Dilute Black   Dilute Brown 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, 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:  ( PARTY COLOR IN POMERANIANS ) 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, Australian Shepherd and other breeds 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, like some Bull  Terriers.  The Australian Cattle Dog, the coloration that is called "Blue" by the ACD breeders/owners, is really the  extreme piebald pattern that is also affected by the ticking gene; giving the coloration a blue appearance.  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.

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 full expression 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 and  Australian Shepherds, 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/- = fawn 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 = fawn with dilute tan points NON-EXTENSION RED (cream): B/B d/d e/e = dilute red to pale cream with gray nose (dog is genetically a  dilute black, but will be a cream color) B/b d/d e/e = dilute red to pale cream with gray nose (dog is genetically a dilute  black, but will be a cream color) b/b d/d e/e = dilute red to pale cream with rosey-brown nose (dog is genetically  dilute brown, but will be cream color) b/b D/d e/e = dilute red to pale cream with brown nose (dog is genetically  brown, but will be cream color) b/b D/D e/e = dilute red to pale cream with brown nose (dog is genetically  brown, but will be cream color) B/B D/D e/e = dilute red to pale cream with black nose (dog is genetically black,  but will be cream color) B/b D/d e/e = dilute red to pale cream with black nose (dog is genetically black,  but will be cream color)

 

Basic Genetics

BY READING THE FOLLOWING  INFORMATION

 ( ESPECIALLY THE INFO HIGHLIGHTED IN YELLOW ) 

 YOU WILL GET A REALLY GOOD UNDERSTANDING  OF BASIC COLOR GENETICS.

Chromosomes in a body cell are arranged in pairs, one from the SIRE  and one from the  DAM. Further, the code for a particular protein is always on the same place on the same chromosome. This place, or location, is called a locus (plural loci.)

There are generally a number of slightly different genes that code for forms of the same protein, and fit into the same locus. Each of these genes is called an allele. 

Each locus, then, will have one allele from the mother and one from the father. How?

When an animal makes an egg or a sperm cell (gametes, collectively) the cells go through a special kind of division process, resulting in a gamete with only one copy of each chromosome. Unless two genes are very close together on the same chromosome, the selection of which allele winds up in a gamete is strictly random. Thus a dog who has one gene for black pigment and one for brown pigment may produce a gamete which has a gene for black pigment OR for brown pigment. If he's a male, 50% of the sperm cells he produces will be B (black) and 50% will be brown (b).

When the sperm cell and an egg cell get together, a new cell is created which once again has two of each chromosome in the nucleus. This implies two alleles at each locus (or, in less technical terms, two copies of each gene, one derived from the mother and one from the father,) in the offspring. The new cell will divide repeatedly and eventually create an animal ready for birth, the offspring of the two parents. How does this combination of alleles affect the offspring?

There are several ways alleles can interact. In the example above, we had two alleles, B for black and b for brown. If the animal has two copies of B, it will be black. If it has one copy of B and one of b, it will be just as black. Finally, if it has two copies of b, it will be brown, like a chocolate Labrador. In this case we refer to B as dominant to b and b as recessive to B.True dominance implies that the dog with one B and one b cannot be distinguished from the dog with two B alleles. Now, what happens when two black dogs are bred together?

We will use a diagram called a Punnett square. For our first few examples, we will stick with the B locus, in which case there are two possibilites for sperm (which we write across the top) and two for eggs (which we write along the left side. Each cell then gets the sum of the alleles in the egg and the sperm. To start out with a very simple case, assume both parents are black not carrying brown, that is, they each have two genes for black. We then have:

	B	B
B	BB (black)	BB (black)
B	BB (black)	BB (black)

All of the puppies are black if both parents are BB (pure for black.

Now suppose the sire is pure for black but the dam carries a recessive gene for brown. In this case she can produce either black or brown gametes, so

	B	B
B	BB (pure for black)	BB (pure for black)
b	Bb (black carrying brown)	Bb (black carrying brown)

This gives appoximately a 50% probability that any given puppy is pure for black, and a 50% probability that it is black carrying brown. All puppies appear black. We can get essentially the same diagram if the sire is black carrying brown and the dam is pure for black. Now suppose both parents are blacks carrying brown:

	B	b
B	BB (pure for black	Bb (black carrying brown)
b	Bb (black carrying brown)	bb (brown)

This time we get 25% probabilty of pure for black, 50% probability of black carrying brown, and - a possible surprise if you don't realize the brown gene is present in both parents - a 25% probability that a pup will be brown. Note that only way to distinguish the pure for blacks from the blacks carrying brown is test breeding or possibly DNA testing - they all look black.

Another possible mating would be pure for black with brown:

	B	B
b	Bb (black carrying brown)	Bb (black carrying brown)
b	Bb (black carrying brown)	Bb (black carrying brown)

In this case, all the puppies will be black carrying brown.

Suppose one parent is black carrying brown and the other is brown:

	B	b
b	Bb (black carrying brown)	bb (brown)
b	Bb (black carrying brown)	bb (brown)

In this case, there is a 50% probability that a puppy will be black carrying brown and a 50% probability that it will be brown.

Finally, look at what happens when brown is bred to brown:

	b	b
b	bb (brown)	bb (brown)
b	bb (brown)	bb (brown)

Recessive to recessive breeds true -

 all of the pups will be brown.

Note that a pure for black can come out of a mating with both parents carrying brown, and that such a pure for black is just as pure for black as one from ten generations of all black parentage. THERE IS NO MIXING OF GENES. They remain intact through their various combinations, and B, for instance, will be the same B no matter how often it has been paired with brown. This, not the dominant-recessive relationship, is the real heart of Mendelian genetics.

This type of dominant-recessive inheritance is common (and at times frustrating if you are trying to breed out a recessive trait, as you can't tell by looking which pups are pure for the dominant and which have one dominant and one recessive gene.) 

Note that dominant to dominant can produce recessive, but recessive to recessive can only produce recessive.

The results of a dominant to recessive breeding depends on whether the dog that looks to be the dominant carries the recessive. A dog that has one parent expressing the recessive gene, or that produces a puppy that shows the recessive gene, has to be a carrier of the recessive gene. Otherwise, you really don't know whether or not you are dealing with a carrier, bar genetic testing  or test breeding.

One more bit of terminology before we move on -

an animal that has matching alleles 

(BB or bb) is called homozygous. 

An animal that has two different alleles at a locus (Bb) is called heterozygous.

A pure dominant-recessive relationship between alleles implies that the heterozygous state cannot be distinguished from the homozygous dominant state. This is by no means the only possibility, and in fact as DNA analysis advances, it may become rare. Even without such analysis, however, there are many loci where three phenotypes (appearances) come from two alleles. An example is merle in the dog. This is often treated as a dominant, but in fact it is a type of inheritance in which there is no clear dominant - recessive relationship. It is sometimes called overdominance, if the heterozyote is the desired state. I prefer incomplete dominance, recognising that in fact neither of the alleles is truly dominant or recessive relative to the other.

As an example, we will consider merle. Merle is a diluting gene, not really a color gene as such. If the major pigment is   eumelanin, a dog with two non-merle genes (mm) is the expected color - black, liver, blue, tan-point, sable, recessive red. If the dog is Mm, it has a mosaic appearance, with random patches of the expected eumelanin pigment in full intensity against a background of diluted eumelanin. Phaeomelanin (tan) shows little visual effect, though there is a possibility that microscopic examination of the tan hair would show some effect of M. Thus a black or black tan-point dog is a blue merle, a brown or brown tan-point dog is red merle, and a sable dog issable merle, though the last color, with phaeomelanin dominating, may be indistinguishable from sable in an adult. (The effect of merle on recessive red is unknown, and I can't think of a breed that has both genes.)What makes this different from the black-brown situation is that an MM dog is far more diluted than is an Mm dog. In those breeds with white markings in the full-color state the MM dog is often almost completely white with a few diluted patches, and has a considerable probablity of being deaf, blind, and/or sterile.

ble on this site, but the gene also occurs in Australian Shepherds, Collies, Border Collies, Cardiganshire Welsh Corgis, Beaucerons(French herding breed), harlequin Great Danes, Catahoula leopard dogs, and Daschunds, at the least.

Note that both of the extremes - normal color and double merle white - breed true when mated to another of the same color, very much like the Punnett squares above for the mating of two browns or two pure for blacks. I will skip those two and go to the more interesting matings involving merles.

First, consider a merle to merle mating. Remember both parents are Mm, so we get:

	M	m
M	MM (sublethal double merle)	Mm (merle)
m	Mm (merle)	mm (non-merle)

Assuming that merle is the desired color, this predicts that each pup has a 25% probability of inheriting the sublethal (and in most cases undesirable by the breed standards) MM combination, only 50% will be the desired merle color, and 25% will be acceptable full-color individuals. (In fact there is some anecdotal evidence that MM puppies make up somewhat less than 25% of the offspring of merle to merle breedings, but we'll discuss that separately.) Merle, being a heterozygous color, cannot breed true.

Merle to double merle would produce 50% double merle and is almost never done intentionally. The Punnet square for this mating is:

	M	M
M	MM (sublethal double merle)	MM (sublethal double merle)
m	Mm (merle)	Mm (merle)

Merle to non-merle is the "safe" breeding, as it produces no MM individuals:

	m	m
M	Mm (merle)	Mm (merle)
m	mm (non-merle)	mm (non-merle)

We get exactly the same probability of merle as in the merle to merle breeding (50%) but all of the remaining pups are acceptable full-colored individuals.

There is one other way to breed merles, which is in fact the only way to get an all-merle litter. This is to breed a double merle (MM) to a non-merle (mm). This breeding does not a use a merle as either parent, but it produces all merle puppies. (The occasional exception will be discussed elsewhere.) In this case,

	M	M
m	Mm (merle)	Mm (merle)
m	Mm (merle)	Mm (merle

The problem with this breeding is that it requires the breeder to maintain a dog for breeding which in most cases cannot be shown and which may be deaf or blind. Further, in order to get that one MM dog who is fertile and of outstanding quality, a number of other MM pups will probably have been destroyed, as an MM dog, without testing for vision and hearing, is a poor prospect for a pet. In Shelties, the fact remains that several double merles have made a definite contribution to the breed. This does not change the fact that the safe breeding for a merle is to a nonmerle.

Thus far, we have concentrated on single locus genes, with two alleles to a locus. Even something as simple as coat color, however, normally involves more than one locus, and it is quite possible to have more than two alleles at a locus. What happens when two or more loci are involved in one coat color?

 

Basic Genetics II: Multiple Loci

Usually more than one gene locus is involved in coat color. We'll take one of the simplest, in which the two loci each have two alleles, with a simple dominant-recessive relationship. The model we will use is the Labrador Retriever. One locus we have already examined: the brown locus. We will now add a second locus, on a different chromosome, called E. An EE or Ee dog will show whatever eumelanin pigment is possible. An ee dog apparently can manufacture only phaeomelanin in the hair, though the skin and eye pigment still includes melanin (of whatever color is allowed by the B series).

A black Lab may be BBEE, BBEe, BbEE or BbEe - any combination that includes at least one B and one E gene.

A chocolate (brown) Lab may be bbEE or bbEe.

A yellow Lab with a black nose may be BBee or Bbee

A yellow Lab with a liver nose is bbee - but since ee dogs tend in many cases to lose nose pigment in winter, this may not be easy to distinguish from BBee or Bbee.

Suppose we mate two BbEe dogs, both blacks carrying brown and yellow:

	BE	Be	bE	be
BE	BBEE (pure for black)	BBEe (black carrying yellow)	BbEE (black carrying brown)	BbEe (black carrying brown and yellow)
Be	BBEe (black carrying yellow)	BBee (pure for yellow, black nose)	BbEe (black carrying brown and yellow)	Bbee (yellow carrying brown)
bE	BbEE (black carrying brown)	BbEe (black carrying brown and yellow)	bbEE (pure for brown)	bbEe (brown carrying yellow)
be	BbEe (black carrying brown and yellow)	Bbee (yellow carrying brown)	bbEe (brown carrying yellow)	bbee (brown-nosed yellow)

Each puppy has one chance in sixteen of having the combination shown in any section of the table above. In this mating between two black dogs both carrying brown and yellow, there is a 9/16 probability that a particular pup will be black, a 3/16 probability that the pup will be brown, a 3/16 probability that the pup will be a black-nosed yellow, and a 1/16 probability of a brown-nosed yellow. Since nose color does not come into registration, the registered colors would be 9 black:3 brown:4 yellow.

What happens if more than two loci are involved? The basic principle is the same - put all of the possible combinations in a sperm cell along the top and all of the possible combinations in an egg cell along the left side. The problem is that the number of possible combinations doubles for each additional locus. For a single locus, we had a 2 x 2 square with 4 cells. For two loci, we had a 4 x 4 square with 16 cells. With three loci, we have an 8 x 8 square with 64 cells. Besides, we've pretty well exhausted the acceptable colors for Labs.

Shetland Sheepdogs might be a good model for our three-locus model. For the moment we'll omit the recessive black, and consider that Sheltie color is determined by three loci.

At the A (agouti) locus, a^y is sable and a^t is tan-point (black and tan = referred to as tricolor if a white spotting gene is present.) An a^ya^t dog is sable, but generally somewhat darker than an a^ya^y dog. The difference is generally of the same order as the difference within a^ya^y or within a^ya^t, so it is not possible to be absolutely sure whether a^t is present by looking at the dog.

At the M locus, Shelties have both M and m, as discussed earlier. Mm produces blue merle in a^ta^t dogs and sable merle on a^ya^t and a^ya^y.

At the S (spotting) locus most correctly marked Shelties have two copies of sⁱ, Irish spotting. A sⁱsⁱ dog generally ranges from white on the chest and feet to high white stockings, white tail tip, and a full shawl collar. The probability of the full collar, as well as white stifles, seems to be somewhat enhanced if the dog is sⁱs^w, so s^w, color headed white, tends to be maintained in the breed as well. (I am keeping it simple by ignoring s^p, piebald, which may also occur in Shelties.) s^ws^w dogs are predominantly white with color on the head and perhaps a few body spots. While healthy, they cannot be shown.

Suppose we mate two white-factored, tri-factored sable merles (not a likely mating, but this is an illustration!) The genetic formula for each parent is a^ya^tMmsⁱs^w. There are eight possible gametes for each sex:

	ayMsi	ayMsw	aymsi	aymsw	atMsi	atMsw	atmsi	atmsw
ayMsi	DMS	DMS	SM	SM	DMS	DMS	StM	StM
ayMsw	DMS	DMS*	SM	WSM	DMS	DMS*	StM	WStM
aymsi	SM	SM	S	S	StM	StM	St	St
aymsw	SM	WSM	S	WS	StM	WStM	St	WSt
atMsi	DMS	DMS	StM	StM	DM	DM	BM	BM
atMsw	DMS	DMS*	StM	WStM	DM	DM*	BM	WBM
atmsi	StM	StM	St	St	BM	BM	T	T
atmsw	StM	WStM	St	WSt	BM	WBM	T	WT

There is no way I could fill in this chart with the detail I used in the 2-loci charts and still have it fit readably into a browser window, so I have used a shorthand to indicate the apparent color:

• S = pure for sable with Irish markings (3)
• St = tri-factored sable with Irish markings (6)
• T = tricolor with Irish markings (3)
• SM = pure for sable merle with Irish markings (6)
• StM = tri-factored sable merle with Irish markings (12)
• BM = blue merle with Irish markings (6)
• WS = white with pure for sable head (1)
• WSt = white with trifactored sable head (2)
• WT = white with tricolor head (1)
• WSM = white with pure for sable merle head (2)
• WStM = white with tri-factored sable merle head (4)
• WBM = white with blue merle head. (2)
• DMS = homozygous merle, dilute sable markings (12)
• DM = normal homozygous merle (4)

I have not distinguished white-factored from Irish dogs, and I have ignored the possibility that the MMs^ws^w pups (starred in chart) might not be viable. In practice such a breeding would probably never be made, as Sheltie breeders tend to avoid breeding merle to merle and white factor to white factor, but it does illustrate the variety that can be obtained with two alleles at each of three loci.

In this case, all three loci are visibly affecting the color. The only exception is the interaction between color-headed white and double merle, and this is frankly an unknown. There are times, however, when a particular gene combination at one locus can block expression of a gene combination at another locus. I will follow Searle on nomenclature and distinguish between a dominant-recessive relationship between alleles at a particular locus and an epistatic-hypostatic relationship between two loci.

The first example is very obvious, but only because the gene action is clear-cut. Consider Cocker Spaniels. They have two alleles at the S locus (S, fully colored, and s^p, piebald.) An SS dog is solid color, an Ss^p dog may have minor white marking (and is often unshowable) and an s^ps^p dog is a parti-color. The second gene is ticking. Ticking works by producing flecks of color in white areas. TT produces ticks of color in any white areas on the dog, tt has clear white areas, and Tt probably produces less ticking than TT, with considerable variation among breeds. s^ps^p and probably Ss^p dogs will show ticking if T is present, since they have white areas that are "available" for ticking, though if the base color is red, tan or cream the ticking may not be obvious. But if the dog is SS, there are no white spots for the ticking to show up on. SS is thus epistatic to ticking.

The final example involves the genes for dominant black, which may or may not (my feeling is probably not, as there are records of dominant black to tricolor producing both sables and tris) be the top dominant in the A series where it is generally placed. I will assume it is at a separate locus K, with K being dominant black, epistatic to anything at the A series, while kk allows the A series to show through. We also have the E series, in which E allows the A series to show through while ee allows only red-yellow pigment in the hair. Functionally we can consider that the A locus determines where eumelanin and phaeomelanin are produced, the K locus allows only eumelanin to be produced if E is at the E locus, but ee at the E locus overrides that to allow only phaeomelanin production. Sounds like a mess? You bet it does! K at the K locus is epistatic to the A locus, but ee (pure recessive at the E locus) is epistatic to both the A and the K locus. But it agrees with what is observed.

Let's look at a breed cross between two "red" dogs. We'll take an accidental breeding I know of between a Belgian Tervuren (a^ya^yEEkk) and a Golden Retriever (??eeKK). Note that ee is epistatic to the A series, so if dominant black is not at the A locus, we do not know what the normal A allele is in the Golden. The gametes are a^yEk for the Terv and ?eK for the Golden. Every puppy inherits a^y?EeKk and is black, as was in fact observed (to the initial astonishment of the owner.) If we mated two of these pups, we would get a 16/64 probability of ee which would be red regardless of what was at other loci. Of the other 48/64 (Ee and EE dogs), 75% would be Kk or KK, and hence black. so there is a 36/64 probability that a particular puppy will be black. The remaining 12/64 will show what is present at the A locus. Of the 12, we expect that 9 will have the a^y gene in at least one dose, and with dominant black moved to the K locus a^y is dominant over all other A alleles. So there is only a 3/64 chance that a given puppy will actually show what A allele is normal in a Golden - if in fact all Goldens have the same allele at A!

Note that in this particular case we can get identical results in the first generation by postulating a top dominant A^s dominant black at the A locus, with A^s- dogs having solid eumelanin pigmentation (unless overridden by ee.) In this case the parent gametes would be A^se and a^yE, giving A^sa^yEe black pups. In the next generation we would again get 4/16 ee red, 9/16 A^s-E- black, and 3/16 a^ya^yE- sables. If we could be absolutely sure that the Terv used was not a^ya^t, the appearance of a tricolor would be good evidence for the first hypothesis.

We still need to discuss penetrance, variable expression, and threshold traits, as well as linkage and crossing over (and their influence on the accuracy of DNA testing), test breeding, andtesting whether a suspected allele is in fact at a particular locus. Some further comments about merle are also in the works.

 

Basic Genetics III: Linkage and Crossing  Over

Up until now we have assumed that all genes were inherited independently. However, we have also said that genes are arranged on chromosomes, which are essentially long strands of DNA residing in the nucleus of the cell. This certainly opens the possibility that two otherwise unrelated genes could reside on the same chromosome. Does independent inheritance hold for these genes?

To start with, we need to consider the rather complex process that forms gametes (egg and sperm cells, each with only one copy of each chromosome) from normal cells with two copies of each chromosome., one derived from each parent. I am not going to go into the details, beyond remarking that at one stage of this process, the maternally-derived chromosome lines up with the corresponding paternally-derived chromosome, and only one of the two goes to a specific gamete. If this were all there were to it dogs, having 39 chromosome pairs, would have only 39 "genes", each of which would code for a wide variety of traits. In fact, things are a little more complicated yet, because while the paternal and maternal chromosomes are lined up, they can and do exchange segments, so that at the time they actually separate, each of the two chromosomes will most likely contain material from both parents.

At this point we need to define a couple of terms. Two genes are linked if they are close together on the same chromosome and thus tend to be inherited together. Linkage in common usage, however, may apply to a single gene having more than one effect. An example which is not linkage in the sense used here is the association between deafness and extreme white spotting. White spotting is due to the melanocytes, the cells which produce pigment, not managing to migrate to all parts of the fetus. Now it turns out that in order for the inner ear to develop properly, it must have melanocytes. If the gene producing white spotting also prevents the precursors of the melanocytes from reaching the inner ear, the result will be deafness in that ear. In other words, the same gene could easily influence both processes. Thus deafness and white spotting are associated, but they are not linked. They are due to what is called pleiotropic (affecting the whole body) effects of a single gene.

In true linkage, there is always the possibility that linked genes can cross over. Imagine each chromosome as a piece of rope, with the genes marked by colored stripes. The matching of the maternal and paternal chromosomes is more or less controlled by the colored stripes, which tend to line up. But the chromosomes are flexible. They bend and twist around each other. They are also self healing, and when both the maternal and paternal chromosomes break, they may heal onto the paired chromosome. This happens often enough that genes far apart on long chromosomes appear to be inherited independently, but if genes are close together, a break is much less likely to form between them than at some other part of the paired chromosomes.

Such breaks, called "crossing over" do occur, and occur often enough that they are used to map where genes genes are located on specific chromosomes. In general, neither linkage nor crossing over is of much importance to the average dog breeder, though one should certainly keep in mind the possibility that the spread of an undesirable gene through a breed is due to the undesirable gene being linked to a gene valued in the breed ring. Crossing over is also important in the use of marker genes for testing whether a dog carries a specific gene, most often a gene producing a health problem.

There are two distinct ways of using DNA testing to identify dogs carrying specific, undesirable genes. The first (and preferable) is actually to sequence the undesirable gene and its normal allele. This allows determination of whether the dog is homozygous normal, a heterozygous carrier, or homozygous affected. Since the genes themselves are being looked at, the results should be unambiguous. (The breeding decisions based on these results are still going to depend on the priorities of the breeders.)

In some tests, however, a marker gene is found that appears to be associated with the trait of interest, but is not actually the gene producing that trait. Such a marker is tightly linked to the gene actually causing that trait. This does not work at all badly providing that the group on which the test was validated is closely related to the group to which the test was applied. Use of this type of test on humans usually requires that the test be validated on close relatives, and applied only to people closely related to the validation group.

It is true that dogs of a given breed tend to be closely related to each other. However, the breed-wide relationship is generally through more distant ancestors than most people can trace in their own genealogy. In Shetland Sheepdogs, for instance, almost all US show stock can be traced to dogs imported from the British Isles between 1929 and 1936, with only a tiny influence of imports after 1950. This means that a crossover appearing on one side of the Atlantic since 1950 (20 or so dog generations) might not show up on the other side. Marker tests that work on U.S. populations might not work at all on British dogs, or on a dog with recent British ancestry.

Even without physical separation here is always the possibility that at some point in the breed history a crossover occurred. Quite a large fraction of the breed may have the original relationship between the marker gene and the problem gene, but if a crossover occurred in an individual who later had a considerable influence on the breed, the breed may also contain individuals in which the marker gene is associated with the opposite form of the problem gene. Since the relationship between individuals of the same breed may go back 30 generations or more, and there is a chance of a crossover occurring in each generation, linked markers need to be used with caution and with constant checking that marker test results correlate with clinical results.

Let's look more closely at this.

Let our marker gene be ma, with ma^a being the gene associated with the healthy gene, and ma^bbeing the marker that seems to be associated with the defective gene, both being true for the test population. For the genes actually producing the problem, we will use H, with H^h being the normal, healthy gene and h^d being the recessive gene which causes the problem. In the original test population, ma^a was always on the same chromosome with H^h, and ma^b was on the same chromosome with h^d. In other words, chromosomes are either ma^aH^h or ma^bh^d, never ma^ah^d or ma^bH^h. If a dog has ma^a on both chromosomes, it is also H^h on both chromosomes, a genetic clear. If it has ma^a on one chromosome and ma^b on the other, it also has one H^h gene and one h^d gene, and is a carrier. If it has ma^b on both chromosomes, it has h^don both chromosomes and is a genetic affected. At least, that is the assumption on which marker tests are based.

Now suppose that at some point a crossover occurred between the ma and H loci. The probability of a crossover may be very small in any individual breeding, but remember that there are a lot of breedings behind any particular dog. We can still assume that most of the chromosomes will still be of the ma^aH^h or ma^bh^d type, or the original validation of the marker test would have failed. But now suppose that a small fraction of the chromosomes are of types ma^ah^d and/or ma^bH^h. We now have four chromosome types, and sixteen possible combinations. Some of these will test the same, since the only difference is in which chromosome comes from the mother and which from the father, but there are still sixteen possible outcomes. In the table below both the marker results (upper) and the true results (lower) are shown for each possible combination:

	maaHh	mabhd	maahd	mabHh
maaHh	clear maamaa	carrier maamab	clear maamaa	carrier maamab
	clear HhHh	carrier Hhhd	carrier Hhhd	clear HhHh
mabhd	carrier maamab	affected mabmab	carrier maamab	affected mabmab
	carrier Hhhd	affected hdhd	affected hdhd	carrier Hhhd
maahd	clear maamaa	carrier maamab	clear maamaa	carrier maamab
	carrier Hhhd	affected hdhd	affected hdhd	carrier Hhhd
mabHh	carrier maamab	affected mabmab	carrier maamab	affected mabmab
	clear HhHh	carrier Hhhd	carrier Hhhd	clear HhHh

Note that in only six of the sixteen possible types is the marker indication of genotype correct. If the crossover genotypes are rare (as would normally be the case if the marker test verified at all) most of the population will be in the upper left quarter of the table, where the marker will correctly predict the true genotype. But if any of the chromosomes trace back to a crossover, a marker test may give a false sense of security (carrier or affected shows clear by marker testing) or result in discarding a healthy dog (carrier or clear shows affected or carrier by marker testing.)

If only three chromosome types are available, the two verifying types plus one crossover, then if the marker gene is associated at times with the healthy allele, (ma^bH^h) the result will include dogs which are affected or carriers by marker analysis which are genetically carriers or clears (false positives.) If the other chromosome type has the undesirable allele not always associated with the marker (ma^ah^d) the results will include dogs clear or carriers by marker analysis that are actually carriers or affected (false negatives.) However, the existance of one crossover chromosome type would make me suspicious that the other might also exist in the breed.

So are marker tests of any use at all?

Yes! In the first place, they demonstrate that the actual gene is on a relatively limited portion of a known chromosome. The marker gene can thus assist in finding and sequencing the gene actually causing the health problem.

In the second place, marker tests are accurate so long as neither parent of an individual has a crossover chromosome. In humans, such tests are most likely to be used when a problem runs in a particular family. The linkage of a marker with the genes actually producing the problem is generally based on studies of how the marker is linked to the genes in that particular family. With dogs, the verification is normally done on a breed basis, and the fact that breeds may actually be split into groups (color, size, country of origin) which interbreed rarely if ever is likely to be ignored. Dogs closely related via close common ancestors to the test population are the best candidates for marker testing. In general, keep up conventional testing side by side with the marker testing. If the marker testing and the conventional testing disagree (e.g, affected dog tests clear or clear dog tests affected) consider the possibility of a crossover, and notify the organization doing the test.

Basic Genetics IV:
the relationship of genes to traits (single locus)

With the exception of the few DNA tests available, we cannot know the genetic makeup of our dogs, only the physical makeup, or phenotype. We tend to break that phenotype up into traits, some breed specific, some more general. For instance, we might know that a Sheltie is 15" tall, a black-nosed sable merle with full white collar, feet and Teletype and a narrow face blaze, OFA good, is missing one premolar, has natural ears, and had double rear decals. All of these "traits" are defined by human beings. Very few of them actually refer to single genes that might be inherited as dominant, recessive, incompletely dominant or co-dominant.

In some cases we can break down a trait into a specific combination of genes. In the case of color, for instance, we know of a considerable number of genes that affect color through specific processes. In some cases, this knowledge has fed back on what we consider to be traits. Thus in the case given, the dog is:

• Sable a^y- (as opposed to black with or without tan-point markings).
• Black (as opposed to brown) B-
• Merle Mm
• Irish-marked sⁱsⁱ or sⁱs^w
• Possibly a face-marking gene

In addition, the dog's color can be affected by minor genes (such as the modifier genes determining how much of the dog is white) by random factors (which probably influence the exact pattern of both white spotting and the location of the dark patches in the merling) and by environmental factors (such as uterine environment, nutrition or excessive exposure to the sun.) The point is that very few of the traits that humans have chosen are in fact due solely to the effect of a single pair of alleles at a single locus. We have looked at some such simple traits as regards color.

However, the height of the dog, the ears, the hip rating, the missing premolar, and the double rear decals are probably not single-gene traits, but rely on the interaction of several pairs of genes, with perhaps some influence from the environment.

In general I am using dominant, recessive, co-dominant or intermediate to refer to genes at the same location on a single pair of chromosomes, i.e., alleles at the same locus. There are cases where genes at one locus can "hide" genes at another locus. An example in dogs is recessive yellow, ee, in which recessive yellow, although a recessive at its own locus, can hide whatever the dog carries at the A locus and the proposed K (dominant black) locus. This type of relationship among different loci is called epistatic. The locus that is hidden is referred to as hypostatic. In some cases (e.g., E at the E locus) an epistatic locus has an allele that allows the hypostatic locus to show its effects.

We will consider a number of types of inheritance. The first group actually refer to single-gene traits. Any of these types of inheritance may also be involved in the inheritance of multiple-gene traits.

Single-locus inheritance

• Dominant-recessive
• Intermediate
• Co-dominant
• Sex-limited
• Sex-linked

More complex inheritance will be covered on the next page, and includes

• Modifier genes
• Polygenic additive
• Threshold traits
• Variable expression
• Incomplete penetrance
• Polygenic recessive or dominant
• Mixed polygenic

Dominant-recessive inheritance

Black and brown provide a clear example of a dominant-recessive relationship among alleles. Every dog has two genes at the black/brown locus. If both genes are for black, or if one is for black and one is for brown, the dog is black, most readily identified by nose color. If both genes are for brown, the dog is brown, again most readily identified by nose color. BB cannot be distinguished from Bb without genetic tests or breeding tests.

Many genetic diseases, especially those that can be traced to an inactive or wrongly active form of a particular protein, are inherited in a simple recessive fashion. van Willebrand's disease (vWD) for instance, is inherited as a simple recessive within the Shetland Sheepdog breed.

Intermediate inheritance

Warning! Although this type of inheritance is common, it has a variety of names (incomplete dominance and overdominance are two common ones) some of which are also used for other things entirely. Here I will use it to refer to the type of inheritance in which the animal carrying two identical alleles shows one phenotype, the animal carrying two different identical alleles shows a different phenotype, and the animal carrying one copy of each of the alleles shows a third phenotype, usually intermediate between the two extremes but clearly distinguishable from either.

In dogs, merle color is a good example of this type of inheritance. If we define M as merle and m as non-merle, we find we have three genotypes:

• mm non-merle, with normal intense color
• Mm merle, with normal color diluted in a rather patchy fashion
• MM homozygous merle, extreme dilution, dog mostly white if a white-spotting gene is also present, and often with anomalies in hearing, vision and/or fertility.

Note that there is really a continuum between dominant-recessive and intermediate inheritance. In Shetland Sheepdogs, for instance, sables carrying one gene for tan-point have on average more dark shading than dogs with two sable genes. However, the darkest shading on dogs pure for sable is probably darker than the lightest shading on dogs carrying a gene for tan-point. In practice, intermediate inheritance is often treated as if it were a special case of dominant-recessive inheritance, as can be seen by the symbols used for merle and non-merle - usually the capital letter refers to a dominant gene and the lower-case letter refers to a recessive gene. I think a separate name is justified because it could be equally well argued that homozygous merle is an undesirable recessive for which the merle color is a marker that the dog carries the merle gene.

Many of the standard color genes normally treated as dominant-recessive do in fact have intermediate inheritance, the heterozygote generally much more similar to one homozygote than the other, between at least some alleles in the series. Coat color gene loci with at least some allele pairs leaning toward intermediate inheritance include A (agouti, patterning of black and tan), C (color, intensity of color), and S (white spotting). I suspect the same is true for T (ticking), G (graying) and even D (dilution) if another diluting gene, such as merle, is present. This may be much more generally true than is recognized.

Co-dominant inheritance

The dividing line between intermediate inheritance and co-dominant inheritance is fuzzy. Co-dominance is more likely to be used when biochemistry is concerned, as in blood types. Co-dominance means that both alleles at a locus are expressed. Co-domininance in X-linked genes is a special case that will be treated under sex-linked inheritance.

Sex-limited autosomal inheritance

Please, don't confuse sex-limited inheritance with sex-linked inheritance. They are two totally different things. Sex-linked inheritance is discussed below. I do include sex-influenced traits under the sex-limited heading, though some genetics texts separate sex-influenced and sex-limited traits.

A classic example of a sex-limited trait in dogs is unilateral or bilateral cryptorchidism, in which one or both testicles cannot be found in their usual position in the scrotum. Since a bitch has no testicles, she cannot be a cryptorchid - but she can carry the gene(s) for cryptorchidism, and pass them to her sons. Likewise, genes affecting milk production are not normally expressed in a male. The main problem with sex-limited inheritance is that it is impossible to know even the phenotypes of the unaffected sex in a pedigree, which makes it difficult to determine the mode of inheritance.

In sex-influenced inheritance, the genes behave differently in the two sexes, probably because the sex hormones provide different cellular environments in males and females. A classic example in people is male early-onset pattern baldness. The gene for baldness behaves as a dominant in males but as a recessive in females. Heterozygous males are bald and will pass the gene to about 50% of their offspring of either sex. However, only the males will normally be bald unless the mother also carries the pattern baldness gene without showing it (female heterozygote.) If the mother is affected with baldness (homozygous) but the father is not, all of the sons will be affected and all of the daughters will be non-affected carriers. A bald man may get pattern baldness from either parent; a bald woman must have received the gene from both parents.

Sex-linked inheritance

In order to understand sex-linked traits, we must first understand the genetic determination of sex. Every mammal has a number of paired chromosomes, that are similar in appearance and line up with each other during gamete production (sperm and eggs). In addition, each mammal has two chromosomes that determine sex. These are generally called X and Y in mammals. Normal pairing of chromosomes during the production of gametes will put one or the other in each sperm or ovum.

In mammals, XY develops testicles which secrete male sex hormones and the fetus develops into a male. An XX fetus develops into a female. Thus sperm can be either X or Y; ova are always X. Sex linked inheritance involves genes located on either the X or the Y chromosome. Females can be homozygous or heterozygous for genes carried on the X chromosome; males can only be hemizygous.

X-linked recessive:

The most common type of sex-linked inheritance involves genes on the X chromosome which behave more or less as recessives. Females, having two X chromosomes, have a good chance of having the normal gene on one of the two. Males, however, have only one copy of the X chromosome - and the Y chromosome does not carry many of the same genes as the X, so there is no normal gene to counter the defective X.

An example of this type of inheritance is color blindness in human beings. Using lower case letters for affecteds, we have

• Affected male: xY Color blind
• Non-affected males XY Normal color vision
• Affected female xx Color blind
• Carrier female xX Normal color vision
• Clear female XX. Normal color vision

Now the possible matings:

xY to xx (both parents affected) xx females and xY males, all offspring affected.

xY to Xx (affected father, carrier mother) half the females will be xX and carriers, half will be xx and affected. Half the males will be XY and clear, half will be xY and affected.

xY to XX (affected father, clear mother) all male offspring XY clear, all daughters Xx carriers.

Note that the daughters of an affected male are obligate carriers or affected. The unaffected sons of an affected male cannot carry the problem.

XY to xx (father clear, mother affected) xY males (affected) and xX daughters (carriers.)

XY to Xx (father clear, mother carrier) half the males affected (xY) and half clear (XY); half females clear (XX) and half carriers (Xx)

XY to XX (father and mother both genetic clears) all offspring clear.

Note that all female offspring of affected males are obligate carriers (if not affected.) Likewise, any female who has an affected son is a carrier. Non-affected sons of affected fathers are genetically clear.

This type of inheritance may be complicated by the sublethal effect of some X-linked genes. Hemophilia A in many mammals (including dogs and people) is a severe bleeding disorder inherited just like the color-blindness above. Many affected individuals will die before breeding, but for those who are kept alive and bred for other outstanding traits, non-affected sons will not have or produce the disease. All daughters, however, will be carriers.

X-linked dominant:

Here I will use X⁺ for the dominant gene on the X chromosome, and X for the gene on the normal X chromosome. The actual possibilities are similar to those for an X-linked recessive, except that X⁺X females are now affected. In X-linked dominant inheritance, more females than males will show the trait. Possible matings are:

Affected to homozygous affected (X⁺Y to X⁺X⁺): All offspring affected.

Affected to heterozygous affected (X⁺Y to X⁺X): All daughters affected; half of sons affected.

Affected to homozygous normal (unaffected female): (X⁺Y to XX): All daughters affected, all sons normal.

Normal to homozygous affected (XY to X⁺X⁺): all offspring affected, but daughters are heterozygous affected.

Normal to heterozygous affected: (XY to X⁺X): Half of offspring affected, regardless of sex. Affected daughters are heterozygous.

Normal to normal (XY to XX) all offspring clear.

X-linked co-dominant:

Mammalian cells, even in females, get along fine with just one X chromosome. In fact, more than one X chromosome within a cell seems to be a problem if both are active. So in female cells, one or the other X chromosome must be inactivated. This occurs more or less at random, so any female mammal has patches of cells with one X chromosome inactivated, and patches with the other not active. If the gene being discussed codes for an enzyme that is spread throughout the body, it may not be obvious that the different patches of cells are behaving differently, and we will get what looks like dominant, recessive, or intermediate inheritance.

However, if the gene is expressed directly within the cell, the mosaic nature of the female may become obvious. The tortoiseshell cat provides an excellent example of this.

In cats, the orange color is on the X chromosome. It is designated as O, and the "wild-type" gene that allows black (eumelanin) to appear in the coat is designated +. Note that a cat homozygous or hemizygous (male) for + may be solid or tabby with the eumelanin pigment showing only in the tabby stripes, ticks and blotches (in extreme cases only on the tips of the hairs) and the "black" may just as well be chocolate or blue. A cat with only O genes will be some shade from cream to deep red., with no black/blue/chocolate pigment in the coat, but usually with tabby markings.

However, a cat with the gene for orange on one X chromosome and the gene for non-orange on the other is neither orange nor non-orange, but has patches of both colors. This color is known as tortoiseshell, and I am going to use the broad definition, including blue/cream or chocolate/yellow tortoiseshells. Most of the time cats with two X chromosomes are female, and since two X-chromosomes are required for tortoiseshell, most tortoiseshell cats are female.

Now and then a cell does not divide properly when it is making a germ cell, and you might, for instance, get an XY sperm cell. This would produce an XXY male, which would look male (he has a Y chromosome) but also have two versions of X and thus could be a tortoiseshell. However, the XXY makeup, corresponding to Klinefelter's syndrome in human beings, is believed to produce sterility. A similar syndrome involving females with only one X chromosome but no Y is called Turner's syndrome in human women, and again appears to produce sterility. We will therefore consider only matings between animals with two sex chromosomes.

Non-orange male to non-orange female (+ to ++): all non-orange offspring.

Non-orange male to tortoiseshell female (+ to +O): Males 50% orange and 50% non-orange; females 50% non-orange and 50% tortoiseshell.

Non-orange male to orange female (+ to OO): all males orange; all females tortoiseshell.

Orange male to non-orange female (O to ++): All males non-orange; all females tortoiseshell.

Orange male to tortoiseshell female (O to O+): males 50% orange and 50% non-orange; females 50% orange and 50% tortoiseshell.

Orange male to orange female (O to OO): All offspring orange.

Y-linked inheritance:

The Y chromosome in most species is very short with very few genes other than those that determine maleness. Y-linked inheritance would show sons the same as their fathers, with no effect from the mother or in daughters. In humans, hairy ears appear to be inherited through the Y chromosome. Padgett does not list any known problem in dogs as being Y-linked.

 

Canine Color Genetics

Dogs have a wide variety of genes that influence color. Further, the same genes may give a very different effect on different types and lengths of coats. While this site is primarily concerned with Shetland Sheepdog colors and a long, working-type (double) coat, I will use comparisons from other breeds and even other species whenever it seems useful. References, including other mammalian color genetics, are on a separate page.

One of the biggest problems people have with genetics is the assumption that a defined trait - size, ear type, color, yappiness - is due to a single gene. In fact, genes code for two types of things. One, which is relatively well understood, is the structure of a particular protein. The normal equivalent of the albino gene, for instance, codes for tyrosinase, an enzyme which breaks up the amino acid tyrosine as a first step in producing melanin, the major pigment in mammalian skin and hair. In an albino, this enzyme cannot be produced, and as a result melanin cannot be produced. A second type of gene controls when and where other genes are turned on or off. These genes are the subject of vigorous ongoing study, and probably have a major impact on such things on the number of vertebrae in the spine or the age at which growth is complete. I've included a page which defines some of the terms used in genetics, as well as explaining dominant, recessive and incompletely dominant genes. Right now, let's look at some of the gene series (loci) known to influence canine color, and try to get a feel for what they do.

Before starting our list, we need to know that mammals have two forms of melanin in their coats. One, eumelanin, is dark, though it can vary somewhat in color due to variations in the protein that forms the framework of the pigment granule. The base form of melanin is black. Melanin can also appear brown (often called liver in dogs) or blue-gray. The second pigment, which varies from pale cream through shades of yellow, tan and red to mahogany (as in the Irish Setter), is called phaeomelanin. There are at least two and possibly as many as four gene series that determine where, on the dog and along the length of the hair, eumelanin and phaeomelanin appear.

The generally recognised color series (loci) in dogs are called A (agouti), B(brown), C (albino series), D (blue dilution) E (extension), G (graying), M(merle), R (roaning), S (white spotting) and T (ticking.) There may be more, unrecognised gene series, and in a given breed modifying factors may drastically affect the actual appearance. Thus one school of thought holds that the round spots on a Dalmation are due to the same gene that produces the roaned areas on a German Shorthair Pointer, but with vastly different modifiers.

A, the agouti series. The standard assumption, based on Little's research, is that this series contains four alleles (different forms of the gene). A fifth allele may exist in Shetland Sheepdogs, and a sixth in certain "saddle-tan" breeds.

• A^s produces black without any tan on the dog. White markings are due to a different gene, and there are other genes that can modify the black to liver (chocolate Lab) or blue dilute (blue Great Dane.) If A^s is present, in most cases the dog will be able to produce only eumelanin pigment (but see the E series). Note that the agouti series is known in a number of mammals, and dominant black is almost always found in a different series, so there is a strong possibility that dominant black is not really in the agouti series.
• a^y in the absense of A^s produces a dog which is predominantly tan (phaeomelanin) sometimes with black tipped hairs or interspersed black hairs. The usual term for this color is "sable." In examining dogs from a^y breeds, I have generally found that even if there is no other black on the coat, the whiskers (the course, stiff vibrissae, not the "beard" seen with some terrier coats) are black if they originate in a pigmented area. Examples of a^y dogs include Collies, fawn Boxers and Great Danes, and some reds (Basenji red is thought to be a^y, for instance.) a^y is recessive to A^s, but incompletely dominant to a^t. That is, an a^ya^t dog is on average darker (more black hairs) than an a^ya^y dog, but the difference is generally within the range of color for a^ya^y within the breed.
• a^t, present in double dose, produces a dog which is predominantly black, with tan markings on the muzzle, over the eyes, on the chest, legs, and under the tail. A Dobermann or Rottweiler is a good example of the classic black and tan pattern. The Bernese Mountain Dog shows the effect of black and tan combined with white markings, often called tricolor.
• a^w is the fourth allele considered by Little. This is the wild "wolf-color" seen in Norwegian Elkhounds and possibly in some salt-and pepper breeds. It differs from sable in two ways. First, the tan is replaced by a pale cream to pale gray color. Second, the hairs are normally banded - not just the scattering of black-tipped hairs sometimes seen in a sable, but several bands of alternating light and black pigment along the length of the hair. Little was unable to determine the dominance relationship of this gene, or even to say with certainty that the banding and the reduction of tan pigment were due to the same gene.

Although Little did not make any distinction between the Dobermann black and tan and the "saddle tan" seen in many terrier breeds (black "saddle" but extensive tan on legs and head), it seems likely that a fifth gene exists in the a series. For the moment I'll call it "saddle tan," a^sa. It seems recessive to a^y sable, but other dominance relationships in the series need more investigation.

Finally, at least two breeds (Shetland Sheepdog and German Shepherd) have a fully recessive black. Since black is the bottom recessive of the A series in many other mammals, it seems logical to assign this color to recessive black, a, and state that recessive black is caused by aa at the agouti locus. There is an alternative theory in Shelties which suggests the existence of a recessive gene that removes tan points from a genetic black and tan or a dominant, widespread gene that forms tan points on all colors but dominant black.

Little's assignment of dominant black in dogs to the A locus (A^s) is totally against experience with this locus in other species, where more yellow is generally dominant to more black. There may be a third locus controlling dominant black, in which case A^y would be the top dominant in the A series.

B, the brown series. This series is relatively simple. B, in single or double dose, allows the production of black pigment. A bb dog produces brown pigment wherever the dog would otherwise have produced black. The gene apparently codes for one of the proteins that makes up the eumelanin pigment granule, so the bb granules are smaller and rounder in shape as well as appearing a lighter color than those of a dog carrying B. This gene is responsible for a number of liver and chocolate colors, especially in the sporting breeds. The same gene produces some "reds" (in Australian Shepherds, Border Collies, and Dobermanns, for example), and probably the bronze Newfoundland. It has some effect on the iris of the eye and on the skin color, including the eye rims and the nose leather. Phaeomelanin (tan) is very little affected, so the color of the tan points on a red Dobermann (a^ta^tbb), for instance, is little affected. I have seen little discussion of the effect of brown on a sable dog, but I would expect a brown nose leather and eye rims, with the coat shaded brown rather than black. Probably the dog would closely resemble a sable, perhaps with an orangey cast and a light nose. Note that some shades of liver, though a eumelanin pigment, overlap some shades of tan, a phaeomelanin pigment. In particular the deadgrass color (bbc^chc^ch) can overlap recessive yellow (ee)

C, the albino series. This again is a fairly complex locus, especially in other mammals. The top dominant, C, allows full color to develop, and is probably the structural gene for tyrosinase. The bottom recessive, c, does not appear to occur in dogs, but in other mammals it completely prevents the formation of any melenin in the coat or the irises of the eyes, giving a pink-eyed or red-eyed white. It is worth pointing out that human albinos from dark-skinned parents often show some yellowish or reddish hair and even skin color, but it seems this is not due to granular melenin. c, therefore, is a form of tyrosinase which cannot act as it is intended to in the formation of melanin. Since c is simply a non-working form, there may be more than one form of c gene (lots of ways to get something not to work), and there is some evidence that when two different forms are mated, colored offspring may result.

There are a number of intermediate genes where the mutation apparently produces a partly active form of tyrosinase. Some C alleles known in other mammals are:

• C full color, allows full expression of whatever pigment is prescribed by other genes. Most dogs are CC.
• c^ch, chinchilla or silver, when present in double dose removes most or all of the phaeomelanin pigment with only a slight effect on black pigment. This is named after a small fur-bearing South American rodent called the chinchilla. Black and silver replacing black and tan, or a wolf-like color without the extra banding (see a^w, above) may also be due to a c^chc^ch genotype. Dogs with very light tan probably are c^chc^ch or something similar. Liver dogs show lightening even of eumelanin pigment, and the "deadgrass" color of the Chesapeake Bay Retriever is thought to be due to a bbc^chc^chgenetic makeup. The possibility of other, rufous modifiers affecting the shade of phaeomelanin pigment needs to be kept in mind, as does the possibility of more than one form of chinchilla in the dog - rabbits are thought to have three.
• c^e, extreme dilution, has also been proposed for the dog. This gene may be part of the makeup of some "white" dog breeds where the white color is due to extreme dilution of tan. The West Highland White Terrier may be c^ec^eee. A cross to a black and tan breed would be interesting from the point of view of color genetics. Eyes may be lightened in some species, but this is doubtful in dogs.
• c^h, Himalyan, is not known to occur in the dog. In homozygous form, it makes the formation of eumelanin dependant on the temperature of the skin. Thus a genetically solid black animal will have reduced black on the extremities (seal brown) and an almost white color on the body. The effect on tan/orange pigment is confusing - the tan in agouti hairs is removed, but that resulting from the orange gene in cats (not in dogs) remains intense on the extremities. There is reason to suspect that this gene, as well as some forms of chinchilla, also affects the organization of the brain, particularly in the neural pathways from the eyes to the brain. There may be a reason for Siamese cats to be cross-eyed. Eyes are normally blue or pink.
• c^p, platinum, is optically similar to albino but retains very slight tysonase activity and in the mouse is described as retaining some luster in the coat as opposed to the pure white seen in albino. Although there is a total absense of proof one way or the other, I would hypothesize that the white Doberman, with pale blue eyes and pink nose, is due to a homologous gene.
• c, albino, is not known to occur in the dog as a regular part of any breed color, though possible candidates for mutations to c have been recorded. As mentioned above, the c gene cannot produce working tyrosinase, and a cc individual cannot produce melanin pigment.

As seen from the above, C is known to have a number of different forms and effects. The usual assumption is that dogs have at least one mutant allele, c^chwhich when homozygous lightens phaeomelanin (yellow) pigment to cream and more weakly affects liver and longhaired black. A second proposed allele, c^e may be responsible for further reduction of cream to white in some breeds, or modifying alleles may be responsible for the further lightening in these cases. While some forms of C modify eye pigment (e.g., blue eyes in Siamese cats) there is little evidence for this in dogs unless "white" Dobermans are indeed due to a C-locus mutation. Although C appears to be fully dominant over any of the other alleles, the dominance relationship between the others generally goes in the direction of more color incompletely dominant over less color, the heterozygote generally resembling but not necessarily identical to the homozygote with more pigment

D, the dilution series. This, again, is a relatively simple series, containing D (dominant, full pigmentation) and d (recessive, dilute pigment). In contrast to C, which has its strongest effect on phaeomelanin, or B, which effects only eumelanin, D affects both eumelanin and phaeomelanin pigment. It is thought to act by causing the clumping of pigment granules in the hair. Like B, it often affects skin and eye color, and in some breeds dd has been associated with skin problems. "Maltese blue" is a term often used to describe dd blacks. If a solid liver dog also is dd, the result is the silvery color seen in Weimararners and known as "fawn" in Dobermans. (In most breeds, fawn refers to a^y yellows.)

While dd acting on black or liver is a part of the genotype of several breeds, dd acting on sable is relatively rare. For one thing, the action of dd on phaeomelanin has been described as a flattening or dulling of color. The cinnamon color in Chows is probably due to an a^ya^ydd genotype, but otherwise the combination of dd with phaeomelanin coat color seems limited to breeds in which color is of little importance (e.g., blue brindle in Whippets.)

Although D is usually described as completely dominant to d, I have seen one blue merle Sheltie bitch who suggested that this may not always be the case. The black merling patches in this bitch were actually an extremely dark blue-gray. Other than this she was an excellently colored blue merle. The owner insisted that she was not a maltese blue, but that she had relatives who were. I suspect that this bitch may have been Dd, with the additional diluting effect of the merle gene allowing the normally hidden effect of a single dose of d to show through.

E, the extension series. This series is probably the least satisfactory of those generally assumed to exist in the dog. In most mammals, the E series includes E^d (dominant black), E (normal extension) and e (recessive red or yellow, and sometimes some intermediate alleles called Japanese brindles. In dogs, this is clearly not the case; breeding experiments have conclusively proven that dominant black and recessive red are not in the same series. This has led to dominant black being thrust into the A series, which as already mentioned conflicts with results in other mammals.

In this summary, I will give the genes as postulated by Little, followed by a brief discussion of other possible explanations and a suggestion for matings that might clarify the situation. Note that the question is not in whether the genes occur, but whether they are in fact alleles in the same gene series. With regard to e and E, recent sequencing of the e and E genes in dogs show definite homology with those in other species.

• E^m, mask factor. This gene replaces phaeomelanin (tan) with eumelanin (black) over part of the dog. There is considerable variation in the area of replacement, probably affected by modifiers but possibly involving more than one form of E^m. At its weakest the mask factor may produce black hair fringing the mouth, or a slightly smutty muzzle. At its strongest (Belgian Tervuren) most of the head is black, and there is considerable blackening of chest and legs. The effect of E^mshows to its fullest extent on clear sable dogs (a^ya^y), but is visible on the tan points of black and tan dogs (a^ta^t) as well. In its strongest version, it can change a black and tan to a pseudo-black, with tan so restricted in its distribution that it may not be immediately apparent that the dog is not black. The occasional "black" puppy produced by two Tervuren parents is probably this type of black, with two a^ya^tE^mE^m parents producing an a^ta^tE^mE^m puppy. A similar but not quite as strong blackening of the head of a genetic black and tan occurs in German Shepherds.
• E^br, brindle. This gene probably got into the E series by mistaken homology with Japanese brindle, which behaves quite differently from brindle in the dog. In Japanese brindle, the patchy color is believed to be due to two alleles of the E series side by side on the same chromosome. Only one can be expressed, and different parts of the animal will show the expression of different genes. The result is a coat made up of random small patches of tan and black pigment, rather like a tortoiseshell cat. If a Japanese brindle animal also has the genes for extensive white spotting, the tan and black pigmented areas tend to become larger and more compact, similar to what one sees in a calico cat (genetically, a tortoiseshell with white markings.) There is a canid which might be Japanese brindle with white spotting, the Cape hunting dog,Lycaon pictus. This animal has a coat which is a rather random patchwork of black, yellow and white. The color has very little similarity to brindle in the dog.
  Brindle in dogs consists of black, vertical stripes on a sable/fawn background, usually rather soft-edged, but much more regular that a typical Japanese brindle, and showing no tendency for the tan and black patches to become more distinct in the presense of white spotting genes. Genes that affect eumelanin will affect the dark stripes, so a bb brindle, for instance, will have brown rather than black stripes. Brindle on a black and tan will show only in the tan areas, while brindle on a black cannot be distinguished at all. If in fact recessive red (ee) is in the same series with brindle, it is not possible for brindle (or mask) to occur on an ee dog as one of the E genes would have to be E^br (or E^m), leaving no room for ee. Little implies that brindle and mask were co-dominant, with masked brindles being E^brE^m, in which case masked brindle could not breed true.
• E, normal extension of black, allows the A-series alleles to show through with no masking or brindling. It is apparently recessive to both E^m and E^br.
• e, recessive red, overrides whatever gene is present at the A locus to produce a dog which shows only phaeomelanin pigment in the coat. Skin and eye color show apparently normal eumelanin, although some ee dogs appear to show reduced pigment on the nose, especially in winter (snow nose.) A number of breeds show recessive red as a normal or even breed-wide characteristic - Irish Setters, Golden Retrievers, yellow Labradors. In a few breeds such as the Cocker Spaniel "reds" may be either a^ya^y or ee, and crossing the two can produce unexpected blacks. I believe there may be a key in the color of the whiskers, which on my observations seem to be black in a^ya^y breeds and straw to cream (dilute red) in ee breeds, always assuming the whisker base sprouts from a pigmented area. Little hypothesized that dogs with both forms of red (a^y-ee) were not viable and would be lost before birth.

The dominance relationships in the Little proposal are not simple. He assumes that E^m and E^br are co-dominant. In an a^ya^y dog, then, brindle without a mask could be E^brE^br, E^brE, or E^bre. A masked dog without brindling would be E^mE^m, E^mE or E^me. A masked brindle would have to have the genotype E^mE^br. This assumption makes some predictions which should be readily testable:

1. Two masked brindles, mated together, should produce appoximately a 1:2:1 ratio of masked fawn to masked brindle to brindle without masking. In other words, masked brindle should not breed true.
2. A masked brindle could not carry E or e. Thus a masked brindle, bred to sable a^ya^yE- would pass either mask or brindle. The expectation would be a litter of brindles without masks and masked sables (fawns) without brindling, but no sables without either mask or brindle and no masked brindles.
3. If a masked brindle is bred to an ee red, the results would depend on the A series genes in the ee red, but there would be neither ee nor a^ya^y reds with neither masking nor brindling. Some blacks might occur, but if the puppy had areas of tan pigment, the tan would be either masked or brindled, but never both and never tan without either mask or brindle.

My impression in talking to breeders of masked brindles is that these predictions are not fulfilled. Possible revisions of the E series include:

1. Remove E^br from the E series, instead recognising that in many ways it is closer to tabby (Ta) in the cat family. This is the gene series responsible for the various stripes, ticking, spots and rosettes seen in both wild and domestic cats. Granted, the pattern is not the same (striped cats normally have stripes ringing the legs), but brindle is also a black striping gene which is visible primarily on an a^y background. This would leave E^m, E and e in the E series, giving a prediction that E^m- bred to ee could produce either 100% masks if the mask is E^mE^m, half masks and half sables without masks if the mask is E^mE, or half masks and half recessive reds if the mask is E^me. The one outcome that would be missing is that a masked to recessive red breeding could produce unmasked sables and unmasked recessive reds in the same litter. Given the difficulty in distinguishing sables from recessive reds, this might prove difficult.
2. Remove E^br from the E series, possibly putting it in the same series with dominant black (currently in the A series.) The new series (here called K - the last letter of black - for convenience) would have three genes, K^ddominant black, K^br producing eumelanin stripes on any phaeomelanin (tan) pigment on the dog. The assumption is that K^d is dominant over K^br which in turn is dominant over k (more black dominant over less black.) The prediction would be that a dominant black (K^d-) bred to a clear sable would produce either all dominant blacks if the black is K^dK^d, a fifty fifty mix of dominant black and brindle if the black is K^dK^br, or a fifty fifty mix of dominant black and clear unmasked sable if the black is K^dk, but never a litter with all three colors. Unpublished studies on racing greyhound litters agree with this prediction.
3. E^m might still be in the E series, but this should be tested. The test breeding would be difficult, because of the difficulty in being sure whether a "red" dog is ee or a^ya^y, but the test is whether a masked dog, bred to another mask or to a recessive red ee, produces both ee red and fully expressed, unmasked tan-point or sable in the same litter. Probably some cross breeding would be required to be sure of the genotypes of parents and offspring.
4. If both removals hold up, this would leave the E series with just two alleles, normal expression of the A series (E -dominant) and recessive red (e - recessive.) It has now been reported in the scientific literature (Newton et al, 2000) that the genetic sequence of canine e/E correponds to the E-locus (specifically recessive red) in several other species (fox, cow, human and mouse.)

G, the graying series. Although only two genes were recognised in this series by Little, this may be a more complex locus, or genes that affect graying may reside at more than one locus. The effect of G, in single or double dose, is the replacement of colored by uncolored hairs as the animal ages, very much like premature graying in human beings. This gene should be suspected in any breed where a dark puppy pales and washes out with age, and the paling is due to interspersed white hairs. The gene is almost certainly present in some Poodles, Old English Sheepdogs, and terriers. The fading may start immediately after birth or after a period of weeks to months has elapsed, and may go as far as it is going to by the first adult coat or may continue through the animal's lifetime. G may or may not be the gene involved in the graying of muzzle and over the eyes in aged dogs, or in the lightening of black to steel blue without interspersed white hairs. This is a series that definitely needs more work.

M, merle. This is another dilution gene, but instead of diluting the whole coat it causes a patchy dilution, with a black coat becoming gray patched with black. Liver becomes dilute red patched with liver, while sable merles can be distinguished from sables with varying amounts of difficulty. The merling is reportedly clearly visible at birth, but may fade to little more than a possible slight mottling of ear tips as an adult. Merling on the tan points of a merled black and tan is not immediately obvious, either, though it does show if mask factor is present, and may be discernable under a microscope. Eyes of an Mm dog are sometimes blue or merled (brown and blue segments in the eye.)

Although merle is generally treated as a dominant gene, it is in fact an incomplete dominant or a gene with intermediate expression. An mm dog is normal color (no merling). A Mm dog is merled. But an MM dog has much more white than is normal for the breed (almost all white in Shelties) and may have hearing loss, vision problems including small or missing eyes, and possible infertility (Little). The health effects seem worse if a gene for white markings is also present. Thus the dachsund, which is normally lacking white markings, has dapples (Mm) and double dapples (MM) the latter often having considerable white, but according to Little other effects are limited to smaller than normal eyes. In Shelties, Collies, Border Collies, and Australian Shepherds, all of which normally have fairly extensive white markings, the MM white has a strong probability of being deaf or blind. The same is probably true with double merle Foxhounds and double merles from Harlequin Great Danes with the desired white chest. A few double merles of good quality have been kept and bred from, as a MM double merle to mm black breeding is the only one that will produce 100% merles.

It is possible that merle is a "fragile" gene, with M having a relatively high probability of mutating back to m. The observed pattern would then be the result of some clones of melanocytes having suffered such a back mutaion to mm while they are migrating to their final site in the skin, producing the black patches, while others remained Mm. This hypothesis also explains why a double merle to black breeding occasionally produces a black puppy, the proposed back mutation in this case occurring in a germ cell. On the other hand, the observed blacks from this ype of breeding may actually be cryptic merles - genetically Mm, but with the random black patches covering virtually all of the coat.

Merle is a part of the pattern of ragged black spots seen in the harlequin Great Dane. There appears to be an additional gene which removes the dilute pigment, leaving the "blue" area clear white. The fact that harlequins continue to produce merles argues that animals pure for this proposed extra factor may not exist, and one possibility is that a homozygote for this whitening factor is an embryonic lethal. Interestingly, there are recent reports of Shelties born with a harlequin pattern, but in this case the "blue" area actually develops color with time, winding up a light silvery blue. These dogs appear to have larger than normal black areas, at the extreme being so-called cryptic merles, that is, no blue is visible without an extensive search. Other shelties born harlequin or "domino" retain the white body color.

Although Danes are usually solid color, the harlequin color description includes a preference for a white neck and front. Since the black patching is as apt to be on neck and front as anywhere else, this requires incorporation of a gene for white spotting (probably irish spotting, sⁱsⁱ). Given that SS double merles seem to fare better than their sⁱ sⁱcounterparts, I would expect that double merles from harlequin Danes with patched fronts and necks might be healthier than from those that fit the standard better. The harlequin description also faults black hairs in the white area. The harlequin - silver blue pattern in Shelties could be an extreme case of black hairs in the white area. Both harlequins and the silver-blue merle Shelties have occasional patches of gray (merle?) as well as black, though this is not considered desirable.

R, roan. This may or may not be a true series. Both Little and Searle suggest that roan may simply be a very fine ticking, with dark hairs growing in an initially white area of the coat. A second type of roan, in which white hairs develop in an initially dark coat, could be due to gray or could be a type of roaning different from the progressive development of dark hair in a light area. In any event, roan (R) appears to be dominant to non-roan (rr). It is not clear whether this is full dominance or incomplete dominance. I will here treat roan as being at the ticking locus.

S, white spotting. This is another somewhat unsatisfactory series, and one in which modifying genes appear to have a very large effect. Certainly there are genes for solid color, for a more regular white spotting, and for basically white with some colored markings. But the variability within each type makes it unclear how many alleles actually occur at this locus. In general dominance is incomplete, with more color being dominant over less color. Heterozygotes commonly resemble the more-pigmented homozygote, but with somewhat more white.

• S, solid color. This is the normal gene in breeds without white markings. An SS dog can completely lack white, but it can also express very minor white markings - white toes, white tail tip, or a star or streak on the chest. SS breeds generally fault these markings.
• sⁱ, irish spotting. Irish spotting is generally confined to the neck, the chest, the underbody, the legs and the tail tip. White does not cross the back between the withers and the tail, though it may appear on the back of the neck. Breeds with "Collie markings" which breed true for the markings are generally sⁱ sⁱ.
• s^p, piebald. This is a more difficult gene to identify. Certainly some breeds, such as parti-color Cockers, seem to breed true for piebald. Crosses of parti-color and solid in Cockers, however, often have minor white marking. Piebald and irish spotting seem to overlap in phenotype in one direction, while piebald and extreme white overlap in the other. In general, it seems a piebald has more than 50% white, white often crosses the back, and the pattern gives the impression of fairly large colored spots on a white ground.
• s^w, extreme white piebald. Extreme white piebalds range from the color-headed whites (Collies, Shelties) which may also have a few colored spots on the body, especially near the tail, through dogs with color confined to the area around the ear or eye (Sealyham, White Bull Terrier, Great Pynenees) to some pure whites (Dalmation ideal). There is some anecdotal evidence that s^ws^w dogs without color on or near the ear have a higher probability of deafness than dogs with color on the ears, but this varies with breed and it is not known whether a separate allele of S might be involved. In Boxers, some whites are produced from show-marked parents. Little believed that the Boxer lacked the gene for sⁱ, the irish-type spotting desired in the show ring being produced by heterozygosity for S and s^w. Since the Boxer club is adamantly opposed to any breeding of whites, even test breeding, this has not been independantly confirmed.

All of the spotting genes are assumed to be affected by the action of modifiers, with + (plus) modifiers being generally understood to increase the amount of pigment (decrease white) while - (minus) modifiers being assumed to decrease the amount of pigment (increase white.) Merle appears to act as a minus modifier, in addition to its effects on coat color.

It is not clear to what extent the S series affects head pigment. Color-headed white shelties, for instance (s^ws^w), can have completely colored heads - not even a forehead star or white nose. On the other hand, relatively conservatively marked dogs can appear with half white or all white heads. There is probably at least one other gene series that affects head markings. It is at least possible that the plus and minus modifiers affect head and body markings simultaneously.

T, ticking. Some dogs develop flecks of color in areas left white by genes in the S series. The clearest and most obvious ticking is seen in Dalmations, where additional modifier genes have enlarged and rounded the ticks. A large number of irish, piebald and extreme white breeds also have variable ticking, though not often as obvious as the Dalmation. The color of the ticking seems to be the color the coat would be in that area if the white spotting genes were not present. Thus a genetically black and tan Dalmation (a fault) will have tan spots where a black and tan would have tan markings. A ticked sable, a^ya^yTT or a^ya^yTt, may not have obvious ticking, becasue there is not much contrast between the tan and the white. Careful examination, however, will often show tan flecks on the legs. Ticking on a long-haired dog is also difficult to discern. The Border Collie on the front page of my site is ticked and probably sⁱs^w, as well as having the gene(?) for half white head. The tick marks in her ruff are not visible in the photo, but they are present (if difficult to find) on the living dog.

The usual dominance relationship given is that T (ticking) is dominant over t (lack of ticking.) Some breed-specific sources suggest that ticking acts as a recessive. I am inclined to suspect incomplete dominance of T. In Border Collies, for instance, a color called blue mottle is in fact a very heavily ticked piebald. The dam of the Border Collie mentioned above was such a blue mottle, presumably TT, while Dot is apparently Tt.

Ticking is also very much affected by genes which modify the size, shape and density of tick marks. In fact roan, which can develop by the gradual growth of pigmented hair in white areas of the coat, may simply be a form of ticking.

 

Size Genetics

The purpose of the following article is to give an explanation about how breeders are able to breed a dog for a certain size.  This article uses the Sheltie breed as an example. This theory is also true for the APBT.

Size as an example of additive inheritance

Sheltie breeders, as a group, tend to be hung up onsize. We have reason to be. The breed was produced by mixing large and small breeds, few if any of which were in the size range we accept as correct today (13" to 16", with preference for 15" and up). Size, however, is not a simple genetic trait. At a minimum, it depends on the genetic codes for growth hormones, the genes that dictate when and how much growth hormone is produced, probably genes that code for receptor proteins that respond to growth hormones, genes that control bone shape and angulation between bones, and other genes affecting various metabolic processes. We don't even know the whole list, or how to determine what makes a particular dog large or small. In some cases the gene for larger size would be dominant, in some cases recessive, in some cases the dog heterozygous at a particular locus would be intermediate is size. It is, however, possible to use a very simple model to explain some of the oddities of Sheltie size. Remember this is a greatly simplified model! The real situation is almost certainly more complicated. We may even have a few genes for correct size hidden in there somewhere!

Suppose we assume we have four loci affecting size. Assume also that each locus has two alleles, one derived from the Collie part of our breed's ancestry, and the other from the original small island Sheltie (remember that at one time 12" was pushed as the maximum height) and toy breeds crossed in late in the 19th Century. We'll call these genes f, i, j, and k. The alleles for large size will be f⁺, i⁺, j⁺ and k⁺; those for small size will be f^-,i^-, j^-, and k^-. The size of the dog will be a base of 15" plus 3/4 times the sum of the "+" genes minus 3/4 times the sum of the "-" genes. A dog with all "+" genes, for instance, would be 21" tall, while a dog with all "-" genes would by 9" tall.

Suppose a breeder, breeding fairly close within her own line and related dogs, winds up with a consistent size genotype of f⁺f⁺i⁺i⁺ j^-j^- k^-k^-. All gametes will be f⁺i⁺j^-k^-. All puppies will have the same size genotype as their parents, and will be 15" tall. But she's had to inbreed quite a bit, and she is looking for an outcross that will give her back what she's lost without sacrificing her predictable size.

She finds another breeder, again breeding fairly closely within her own line, who also gets all 15" Shelties, and whose line is strong for exactly the traits she needs. Breeder A breeds her best bitch to breeder B's best stud dog, and breeder B, who is missing a couple of things A has managed to fix, breeds her own bitch to a stud from breeder A's lines. The puppies arrive, grow up, and all are 15".

Then two of these 15" pups, from litters level in size stemming from strains level in size, are bred to each other. The result could easily be puppies all over the map in size. What happened?

Breeder B had a consistent size genotype of f^-f^-i^-i^- j⁺j⁺ k⁺k⁺, and her dogs consistently produced f^-i^-j⁺k⁺gametes. The uniformly in -size puppies from the strain cross, then, all had the genotype f⁺f^-i⁺i^-j⁺j^-k⁺k^- and could produce any of 16 types of gamete, ranging from f⁺i⁺j⁺k⁺ to f^-i^-j^-k^-. I'm not going to try to draw a 16 x 16 Punnett square, but the expected size distribution in 256 puppies is:

1- 9 inch (all -)
8- 10 1/2 inch (7 -, 1 +)
28- 12 inch (6-, 2+)
56- 13 1/2" (5-, 3+)
70- 15" (4+, 4-)
56- 16 1/2" (5+, 3-)
28- 18" (6+, 2-)
8- 19 1/2" (7+. 1-)
1- 21" (all +)

If we assume some minor size genes as well, so the various categories are smeared out somewhat, the results don't look too unfamiliar. Note that if you breed the 16 1/2" but do not breed the 13 1/2", the result will be a gradual loss of - genes, and an overall upward creep in height. Also, there is no way to look at a 15" dog and determine whether it is fully heterozygous ( f⁺f^-i⁺i^-j⁺j^-k⁺k^-) or homozygous ( f^-f^-i^-i^- j⁺j⁺ k⁺k⁺, for instance) It's not as simple as breeding only from in-size dogs with in-size littermates!

How about genes for correct size? Could we have an additional allele, f, i, j, k at each locus, with ffiijjkk dogs being uniformly 15", and dogs with 7 normal genes and one + gene being 15 3/4"? It would certainly be nice, as then we'd just have to eliminate the + and - genes to have a breed that breeds true for size. It would be a slow process, if only because dogs with the alleles for correct size would so easily be confused with dogs with a balance of + and - genes. Given the background of our breed, though, the source of such genes for correct size is an open question. Most of our breed's ancestors were larger or smaller than 13" to 16". The standard advice on breeding for size, though, is to breed to correct size, which is based on the unstated assumption that the alleles f, i j and k exist.

Other complications undoubtedly occur. The hypothetical small and large genes may differ in their effect - f⁺might contribute more to oversize than j^- does to undersize, for instance. There may be additional loci that have a dominant-recessive effect - NN or Nn might add 2" to the height while nn would allow the fjkl loci to control size. On the other hand, QQ or Qq might allow the fjkl loci to control size while qq would be 2" less than the fjkl size. The important thing to remember is that size is based on more than one gene pair, and as a result can do some very strange things. 

POMERANIAN COLOR GENETICS

This is a very interesting field that is undergoing some changes as the actual genes that affect colour are beginning to be located on the chromosomes. 

DNA specific tests can now be carried out for the presence of most of the colour alleles, particularly where one wants to know if there are unwanted dilution factors hiding within individuals.  While it can look very complicated, try to understand the subject and thus produce the colours you want from matings and not waste litters with incorrect colours.  Knowledge of your proposed breeding pairs’ colour genetics can help maximise desired colour combinations.

 

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General information

Melanocytes are the cells that produce skin and hair colour and they are derived from neural crest cells. These cells arise along the back very early in foetal development and then give rise to a number of cell types, including a large proportion of the peripheral nervous system. If there is a decrease in the number of neural crest cells, other cell types are favoured, leading to a reduction in melanocyte formation (see below). The melanoblasts (immature colour cells) migrate from the dorsal midline over the surface of the body, so the last areas to be reached are the feet, chest and muzzle (ie where you are more likely to see white toes, etc) As you would see in a "Mis-mark " Pomeranian for example. 

Neural crest cells also form part of the nervous system for the inner ear and eye. Animals selected for extreme white spotting (eg. Dalmatians) can have hearing and/or vision problems in other extreme white patterns (merle series).  Dalmatian deafness is thought to be as a result of the absence of melanocytes in the stria vascularis of the inner ear.

Melanoctyes produce melanin by the action of alpha MSH. Large amounts of MSH results in Eumelanin (mainly Tyrosine) which produces black or derivatives of black (blue, chocolate, brown, liver).  Restricted amounts of MSH result in Phaeomelanin (contains varying amounts of cystine and tyrosine) which produces reddish brown or yellowish tan.

#Control of melanoctye function is intricate and many loci(genes) have mutations which affect components of melanogenic control mechanisms.

 

Colour Genes

There are about 10 recognised "loci" of different colour genes. Each locus can have a variable number of alleles that can influence the colour outcome (dilution, pattern, dominant or recessive effects).

 All dogs carry these genes, many of which are in a fixed (homozygous) form eg. Gordon Setters, Elkhounds etc.  In these breeds virtually all loci are fixed and there is very little colour variation across the breed.  In other breeds some loci are fixed, while others have a degree of variation (number of alleles) present at other loci. Not all breeds carry all the possible alleles at each locus.

  
Current research - Many of the colour loci are being extensively studied to precisely locate the position of the various genes on the correct chromosome, and further, which alleles actually occur at that site and how they affect the colour outcomes available.  From this, DNA markers may be developed, and thus allow DNA colour testing in various breeds prior to mating. The DNA research that is being done at this time is going to continue to change our understanding of colour genetics - its a fairly dynamic field - it is certainly not fixed in concrete.

 

Gene / allele designation - The way I write the alleles is to put the loci first as a capital. If only 2 alleles occur (dominant and recessive) then eg. D means the dominant allele, d the recessive allele. Where there are more than 2 alleles for a loci, I find it easier to keep the capital as the indicator for the loci, followed by a smaller letter indicating the allele. (If one has a fancy typewriter/computer, one could do the allele in smaller letters above the series loci letter.) If there are several alleles at a loci, these are usually written in decreasing order of dominance (according to current knowledge).DID YOU KNOW......................a Pomeranian puppy can be born almost black and end up a very light creme color three years later as an adult ? It is fascinating  to see the changes in Pomeranian coat color as they grow from birth to adulthood . Some great examples are documented superbly by     Damascusroad Pomeranins   Click Here     to see how  Damascusroad Pomeranins   puppies change as they grow

There are several coat colors that can be associated with health concerns. 

http://skyway.usask.ca/~schmutz/conditions.html

One such gene is MLPH or the D locus. Several, but not all dogs with a d/d genotype have Color Dilution Alopecia and/or Black Hair Follicular Dysplasia. Although d/d dogs could be blue, grey, pale brown or a dilute red, it is unlikely that the orange or cream of Pomeranians is due to this genotype since blue or grey are not listed as allowed colors and I have not seen photos of such dogs. In addition, there are black-and-cream Pomeranians which have a decrease in phaeomelanin on their undersides to cream but no decrease on their backs which remain black. It is therefore likely that it is the I gene that causes the variation in shade in orange (e/e) dogs.

Another gene that causes major health concerns is AP3 which causes Grey Collie Syndrome. Luckily this has only been identified in Collies since it is lethal to pups.

Yet another gene in the "blue" family that can cause health issues is merle. Merle can not be seen in dogs with an e/e genotype. This e/e genotype occurs commonly in Pomeranians since orange, red and white probably account for the majority of Poms. The problem is that M/M (homozygous merle) dogs are always deaf based on our studies. We recently genotyped 24 mostly white Australian Shepherds and all tested M/M (based on the Clark et al. 2006 PNAS published test) and all were deaf. A proportion of these dogs were also blind in one or both eyes since microphthalmia is another common side effect in M/M dogs. Although in many breeds it is possible to educate breeders to never breed two merle dogs together this advice is not possible to follow in Pomeranians since e/e dogs would not show the merle pattern. It would therefore be necessary instead to advise all persons who breed a merle dog to use only a black or sable mate or to have DNA testing done on their red, orange or white mate prior to breeding to be sure it did not carry merle.

This is a photo of a homozygous merle puppy with microopthalmia (small eyes). Note how small the eyes are compared to those of a normal puppy. One or both eyes can show reduction in size, and one or both eyes can be missing completely (anopthalmia).

 

To determine whether or not a Pomeranian carries the merle gene, a DNA test is now available. This test is only available through GenMark at a cost of $95.00 - see http://www.genmarkag.com/home_companion.php. Because the merle gene can be carried by an apparently normal dog, those that want to avoid this cruel gene will now have to add the expense of merle DNA testing to the other health tests that they already perform. Even those that want to produce merle puppies will have to perform this test to ensure that they are not breeding two merle gene carriers to one another since you cannot always tell by a dog's appearance if it has merle in its genetics

Although albinism is rare in dogs, it does occur. The side effects associated with albinism have not been well documented since the phenotype is so rare and may be caused by different genes in different breeds, each with different side effects. This should not be confused with white dogs that have deeply pigmented nose leather and pads however which do not have health concerns. The occasional white dog with pigmented leather is M/M but usually dogs of this genotype has splashes of mottled color on their body.

 ALBINO 

Sheila Schmutz, Ph.D.

sp piebald or random spotting

 

Sheila Schmutz, Ph.D.

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DID YOU KNOW THAT YOU CAN DO  Color Testing FOR - A Locus ? YOU CAN FIND OUT IF YOU'R POMERANIAN IS REALLY A WOLF SABLE

ASIP, or agouti signalling peptide, is a gene affects pigmentation of coat color in dogs. This protein interacts with the melanocytes to stimulate production of melanin. This gene exists in many forms, or alleles, in dogs. The first of these alleles is generally known asAW, or the wild-type allele. This appears as a "wolf-grey" type of pattern. There is no direct test for this allele, and it is thought that this is the most dominant allele. The second allele, known as AY, is a dominant allele responsible for fawn or sable pigment. A dog only needs 1 copy of the AY allele to be either fawn or sable, depending on the breed. This allele is responsible for the coat color seen in dogs such as Pugs or French Bulldogs. In terms of dominance, it is thought that AW is the most dominant, followed by AY. A third allele is the "tan points" allele, or at. There is no direct test available for this allele at this time, however, it is expressed in dogs that do not carry the AY allele. This phenotype is common in dogs such as Doberman Pinschers or Geman Shepherds. The fourth allele is known as "recessive black," or the a-allele. This variant of the agouti gene causes a dog that does not carry the dominant black gene to be solid black. The recessive black allele is responsible for all-black German Shepherds, for example. The recessive black allele is recessive to all other alleles, meaning that the dog must carry two copies of the "a" allele to express this pattern. The Agouti gene is only visible in dogs that do not carry the dominant black gene. The dog can still carry any of the agouti alleles, however, this effect is hidden by the dominant black gene. A Locus Testing  Animal Genetics currently offers tests for the "AY" and "a" allele. There is no direct test for the "Aw" or "at" alleles, however, these alleles can often be determined based on phenotype and genotype at other alleles. Cost $40.00 US for the AY-allele test. $40.00 US for the a-allele test. $65.00 US combination rate for both tests. Sample Collection Collect sample using buccal swabs provided by Animal Genetics. Ensure that the dog has not eaten within a few hours of sample collection. Any food particles can inhibit the test. Rub each of the swabs along the inside of the dog's mouth for 10-15 seconds, and allow the swabs to dry thoroughly. Label the provided envelope with the dog's name, and place the swab inside it. Download and complete a submission form for each sample and send along with payment to Animal Genetics for testing.   Submission Form  -  Results Results are given using the following symbolic notation: AY-Allele Results: AY/AY The dog carries two copies of the dominant AY allele. The dog will have a fawn or sable colored coat, and will always pass on the "AY" allele to any potential offspring. All offspring will also be fawn or sable dogs. AY/n One copy of the dominant AY allele is present. The dog will have a fawn or sable coat color, and can pass on either allele to potential offspring. n/n The dog does not carry the AY allele, and will not have a fawn or sable coat pattern. a-Allele Results: a/a The dog carries two copies of the recessive black allele. The dog will have a pure black coat, and will always pass on a copy of the allele to future offspring. a/n Only one copy of the recessive black allele is present. The dog will not express the recessive black coat color, however, the dog can still pass on a copy to any offspring. n/n The dog does not carry the recessive black allele. He will not express the recessive black coat color, and cannot pass it on to any offspring.

WANT TO KNOW IF YOU REALLY HAVE A BLUE POMERANIAN

The MLPH gene codes for a protein called melanophilin,  which is responsible for transporting and fixing melanin-containing cells. A mutation in this gene leads to improper distribution of these cells, causing a dilute coat color. This mutation is recessive, so two copies of the mutated gene, or "d" allele, are needed to produce the dilute coat color. This mutation affects both eumelanin and phaeomelanin pigments, so black, brown, and yellow dogs are all affected by the dilution. A dilute black dog is generally known as"blue," though other names do vary for different breeds, such as charcoal or grey. D Locus Testing  Animal Genetics currently offers a test for the D-Locus to determine how many copies of the recessive "d" allele a dog carries. Cost $40.00 US for the D-allele test. Sample Collection Collect sample using buccal swabs provided by Animal Genetics. Ensure that the dog has not eaten within a few hours of sample collection. Any food particles can inhibit the test. Rub each of the swabs along the inside of the dog's mouth for 10-15 seconds, and allow the swabs to dry thoroughly. Label the provided envelope with the dog's name, and place the swab inside it. Download and complete a submission form for each sample and send along with payment to Animal Genetics for testing.   Submission Form  -  Results Results are given using the following symbolic notation: D-Allele Results: D/D The dog carries two copies of the dominant "D" allele. The dog will express a normal, non-dilute coat color, and will always pass on a copy of the "D" allele to all offspring. D/d Both the dominant and recessive alleles detected. The dog will have a normal, non-dilute coat, and is a carrier of the dilute coat color. The dog can pass either allele on to any offspring. d/d The dog has two copies of the recessive "d" allele, and will have a dilute colored coat. He will always pass on a copy of the dilute allele on to any offspring.

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Because TYRP1 is only associated with eumelanin, this mutation only has an effect on dogs that are "EE" or "Ee" at the E-locus. Dogs that are "ee" only produce phaeomelanin in their coats, so a mutation at the B-locus will not have an effect on their coat color. However, eumelanin is still produced in the foot pads and noses of "ee" dogs, so the B-locus still has an effect on these areas. Dogs that are "eebb" will have a brown nose and foot pads, rather than black.

B Locus Testing 
Animal Genetics currently offers a test for the B-Locus to determine how many copies of the recessive "b" allele a dog carries.

Cost
$40.00 US for the B-allele test.

Sample Collection
Collect sample using buccal swabs provided by Animal Genetics. Ensure that the dog has not eaten within a few hours of sample collection. Any food particles can inhibit the test. Rub each of the swabs along the inside of the dog's mouth for 10-15 seconds, and allow the swabs to dry thoroughly. Label the provided envelope with the dog's name, and place the swab inside it. Download and complete a submission form for each sample and send along with payment to Animal Genetics for testing.

 

WANT TO KNOW IF YOU REALLY HAVE A CHOCOLATE OR BEAVER POMERANIAN ?

TYRP1, or tyrosinase-related protein 1, is a protein that plays a role in the synthesis of the pigment eumelanin. In the dominant form of this gene, or the "B" allele, normal eumelanin is produced in the coat, and thedog's coat appears black in color. A mutation in the TYRP1 gene can occur causing a change in function which dilutes the black color pigment to a brown color. This mutated gene is known as the "b" allele. When a dog is homozygous for the mutation, meaning he has 2 copies of the recessive allele, the dog's coat color will be brown in color. This color can also be referred to as liver, chocolate

Results are given using the following symbolic notation:

B/B	The dog carries two copies of the dominant B allele. The dog will have a black-based coat, and will always pass on the "B" allele to any potential offspring. All offspring will also be black-based dogs.
B/b	Both the dominant and recessive copies of the B allele are present. The dog will have black-based coat, but carries the allele responsible for the brown phenotype. The dog can pass on either allele to potential offspring.
b/b	Two copies of the recessive allele are present. The dog has a brown-based coat, as well as a brown nose and foot pads, and will always pass on the recessive allele to all potential offspring.

 

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Coat coloration is controlled by several different genes in dogs. One of these gene is referred to as "Dominant Black." The presence or absence of this gene determines if a dog can express "agouti" color patterns.

The Dominant Black gene consists of three different alleles, or variants. The first allele, which is dominant, is noted as "KB," or dominant black. The Dominant Black allele is actually a mutation that

does not allow the agouti gene to be expressed. Because this mutation is dominant, a dog only needs to have one copy of the mutation to suppress the agouti locus. A dog that has one or two copies of the Dominant Black allele will only express his base coat color, which is determined by the B-Locus and E-Locus. He will not express any colors that occur from the agouti gene, such as "black and tan" or "tricolor."

The second allele is known as the "brindling" allele, and is represented as "Kbr." The Kbr allele is a separate mutation that still allows the agouti gene to be expressed, however, causes brindling of the agouti patterns. The agouti gene represents several different colors, such as fawn/sable, tricolor, tan points, or recessive black.The Kbr allele is recessive to the KB allele, however, it is dominant over a third allele, Ky. Thus, for a dog to express the brindle pattern, he must be either Kbr/Kbr or Kbr/Ky. Dogs that are KB/Kbr will not appear brindle, but can still pass on that allele and potentially produce brindle offspring.

The third allele is represented as "Ky." This allele allows the agouti gene to be expressed without brindling. When a dog is Ky/Ky at the K-locus, the agouti locus determines the dog's coat color. For example, a dog that is Ay/Ay at the agouti locus could be fawn/sable. If that same dog is KB/KB at the K-locus, the agouti locus will be hidden, and his coloration will be determined at the B- and E- loci. However, if that same dog is Ky/Ky at the K-locus, he will then be able to express agouti, and will be fawn/sable.

At this time, there is no direct test for the "Kbr" allele, although it can generally be inferred through testing for the presence of the Dominant Black allele, as well as through phenotypes of the parents and offspring. Testing for the Dominant Black mutation determines if the dog is able to express agouti phenotypes, however, it is limited in that it will not tell you if the dog will be brindled.

DO YOU REALLY HAVE A BRINDLE

Description

Submission Form  -

K Locus Testing 
Animal Genetics currently offers a test for the K-Locus to determine how many copies of the dominant "KB" allele a dog carries.

Cost
$40.00 US for the KB-allele test.

Sample Collection
Collect sample using buccal swabs provided by Animal Genetics. Ensure that the dog has not eaten within a few hours of sample collection. Any food particles can inhibit the test. Rub each of the swabs along the inside of the dog's mouth for 10-15 seconds, and allow the swabs to dry thoroughly. Label the provided envelope with the dog's name, and place the swab inside it. Download and complete a submission form for each sample and send along with payment to Animal Genetics for testing.

 

Results
Results are given using the following symbolic notation:

KB-Allele Results:

KB/KB	The dog carries two copies of the dominant "KB" allele. The dog will be not be brindled or express his agouti phenotype. The dog will always pass on a copy of the "KB" allele to all offspring.
KB/n	One copy of the dominant black allele was detected. The dog will be dominant black, and will not express his agouti phenotype. The dog could pass on this allele, or either the brindle or fawn allele, to any offspring.
n/n	The dog does not carry the dominant black mutation. The dog's coat color will be determined by the agouti gene, and may be brindled or not brindled.

 

Want to know the difference between a RED Pomeranian and an Orange Pomeranian? Canine Color Testing- E Locus

Description MC1R, also known as the extension gene, controls production of pigment in melanocytes. The dominant form of the gene, the "E" allele, allows the dog to produce eumelanin, which is a black pigment. A mutation in the MC1R gene causes the pigment-producing cells to only produce phaeomelanin, which is a yellow pigment. This form of the gene is represented as the "e" allele. The "e" allele is recessive, meaning that a dog must have two copies of the MC1R  mutation to express the solid yellow coat color. A third allele exists in the extension gene, "EM" which is also dominant. This causes the dog to have a black mask on their face, also known as a melanistic mask. This allele acts similarly to the "E" allele, in that it causes a black-based coat. Because it is dominant, a dog only needs one copy of the "EM" allele to express this trait. In solid black dogs with a copy of the "EM" allele, the mask is hidden, however, it can still pass on the melanistic mask to future offspring. The "ee" genotype can vary in expression between different breeds. In some breeds, the difference between a black or brown dog and a yellow dog is obvious, such as in Labrador Retrievers. However, in other breeds, such as Cocker Spaniels, this difference may be more subtle. Other breeds  such as pomeranians express the "ee" phenotype as a red color. It is important to note that the Extension gene is only one of 4 important genes in determining the coat color of a canine. The dogs color can vary greatly with different alleles at other gene. Dogs that are "ee" will always be yellow (base), however, there is a great deal of variation of dogs that are "EE" or "Ee", depending on the B-Locus, A-Locus, and K-Locus. E Locus Testing  The MC1R gene, or E Locus, has three possible forms Black (E), melanistic mask (EM), and Yellow (ee). The E-Allele test determines how many copies of the recessive "e" alleles a dog carries. The EM-Allele test determines how many copies of the Melanistic Mask allele a dog carries. Cost $40.00 US for the E-allele test.  $40.00 US for the EM-allele test. $65.00 US combination rate for both tests. Sample Collection Collect sample using buccal swabs provided by Animal Genetics. Ensure that the dog has not eaten within a few hours of sample collection. Any food particles can inhibit the test. Rub each of the swabs along the inside of the dog's mouth for 10-15 seconds, and allow the swabs to dry thoroughly. Label the provided envelope with the dog's name, and place the swab inside it. Download and complete a submission form for each sample and send along with payment to Animal Genetics for testing.   Submission Form  -  Results Results are given using the following symbolic notation: E-Allele Results: E/E The dog carries two copies of the dominant E allele. The dog will have a black-based coat, and will always pass on the "E" allele to any potential offspring. E/e Both the dominant and recessive copies of the E allele are present. The dog will have a black-based coat, but carries the allele responsible for the yellow phenotype. The dog can pass on either allele to potential offspring. e/e Two copies of the recessive allele are present. The dog has a yellow coat, and will always pass on the recessive allele to all potential offspring. Dogs that are "ee" will always be yellow, however, there is a great deal of variation of dogs that are "EE" or "Ee", depending on the B-Locus, A-Locus, and K-Locus. EM-Allele Results: EM/EM The dog carries two copies of the melanistic mask allele. The dog has a melanistic mask, and will always pass on a copy of the EM allele to potential offspring. All offspring will also have a melanistic mask. EM/n One copy of the melanistic mask allele is present, and the dog will have a black mask. The dog has a 50% chance of passing on this allele to potential offspring. n/n Dog tested negative for the melanistic mask allele. The dog will not have a black mask, and cannot pass a copy on to any offspring. Combination Test Results: EM/EM The dog carries two copies of the melanistic mask allele. The dog has a black-based coat and a melanistic mask, and will always pass on a copy of the EM allele to potential offspring. All offspring will also have a melanistic mask. EM/E One copy of the melanistic mask allele is present. The dog has a black-based coat with a black mask. The dog has a 50% chance of passing on the mask allele to potential offspring. E/E The dog carries two copies of the dominant E allele. The dog will have a black-based coat, and will always pass on the "E" allele to any potential offspring. No masking is present. EM/e The dog has one copy of the melantistic mask allele. The dog's coat is black based, and he will have a mask on his face. There is a 50% chance he will pass on either the yellow allele, or the mask allele on to future offspring. E/e Both the dominant and recessive copies of the E allele are present. The dog will have a black-based coat with no masking, but carries the allele responsible for the yellow phenotype. The dog can pass on either allele to potential offspring. e/e Two copies of the recessive allele are present. The dog has a yellow coat, and will always pass on the recessive allele to all potential offspring. No mask is present.

Melanin, Agouti, and Red

This is quite a complex topic but its understanding is fundamental to understanding the basic color genetics of the dog. Many of the other genes are simple recessives that have easy-to-understand effects.

Melanin is the substance or pigment that gives a dog's hair its color.

There are two distinct types of melanin in the dog - as in many mammals - eumelanin and phaeomelanin. Eumelanin is, in the absence of other modifying genes (see below), 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 in the skin are sensitive to UV radiation and normally produce eumelanin. They are responsible e.g. for tanning in humans, and for darker exposed skin e.g. nose leather in furred mammals.

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, (eu)melanin production is usually most intense, resulting in the darker tip thats frequently seen.

A protein called the Agouti protein has a major effect on the 'injection' of melanin into the growing hair. This is widespread in many mammals, though not in humans. 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). The result is the agouti appearance as typified by the wild rabbit. The term 'Agouti' actually refers to a South American rodent that exemplifies this type of hair.

NOTE: It is worth mentioning at this point that there remain areas of considerable doubt about the exact genes/alleles that affect certain aspects of coat color in dogs. The main ones surround the proposed 'dominant black' (A_s) at the top of the Agouti series, and in the E series there are questionmarks over E_m (black mask) and E_br (brindle).

In the past it was thought that with the A and E series, you had:
Agouti Series (A): A_s, a_y, a_w, a_s, a_t, a
Extension Series (E): E_m, E, E_br, e

But newer research indicates that 'dominant black' A_s may not belong in the Agouti series at all - and this would be consistent with other mammals that also share the Agouti series, none of which has a dominant phaeomelanin suppressor like A_s at the top of the series. Research also indicates that brindle (E_br in the older system) and 'dominant black' form a separate series of at least 3 alleles, which can be called the K series (for blacK); this includes both dominant black and brindle.

We have chosen to adopt this later model.

The Agouti Locus - A

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 whetheror not the eumelanin->phaeomelanin shift occurs, but also where on the dog's body this happens.

The probable alleles at the Agouti locus, in order of decreasing dominance, are: A_y, a_w, a_s, a_t and a.

Dominant Black. Dogs certainly do have a dominant form of black that is indeed very dominant: completely obliterating all formation of phaeomelanin pigment. Traditionally, dominant black has been placed at the head of the Agouti series (symbolA_s). It is now believed to be part of a separate series (the K series - see below) and not at the Agouti locus at all. This is in keeping with the operation of the Agouti locus in all other mammals that have it: increasing dominance of Agouti locus alleles results in increasing production of phaeomelanin without exception. We mention it here simply because it has long been thought, mistakenly, to be part of the Agouti locus.

So at the top of the Agouti series then we have A_y, Sable - also known as 'dominant yellow' or 'golden sable'. This results in an essentially phaeomelanic phenotype, but the hair tips are eumelanin (black). The extent of the eumelanin tip varies considerably from lighter sables (where just the ear tips are black) to darker sables - where much of the body is dark. It is possible that A_y is not completely dominant over the lower Agouti series alleles, with an A_y heterozygote e.g. A_ya_t having a darker body. A_yA_y may be called 'clear red' whereas A_ya_t can be 'sabled red'. Sable is a very common color in many breeds of dog, e.g. German Shepherd.

Next we have 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. Seen in the Keeshond, Siberian and Norwegian Elkhound.

Moving down the series we next come to a_s, 'saddle tan'. This is somewhat like the black+tan allele (below), except that eumelanin is restricted to the back and side regions, hence the name 'saddle'. It is also possible that this is due to another gene interacting with a_t/a_t genotypes.

Allele a_t, 'black+tan' is next. This is a primarily black dog but with tan (phaeomelanin) markings around the eyes, muzzle, chest, stomach and lower legs. Commonly seen in hounds, Doberman's and Rottweilers.

Finally, at the bottom of the Agouti series is recessive black, symbol a. When a dog is homozygous for recessive black (aa), it will have no phaeomelanin in its coat (unless it is also ee, which is epistatic to the Agouti series - see below). Examples of breeds that exhibit recessive black are German Shepherd and Shetland Sheepdog. Whilst some breeders discount the presence of a recessive black at the bottom of the Agouti series is is consistent with the behaviour of this locus in many other mammals.

The existence of all these alleles in the Agouti series is not certain, nor is the precise order of dominance of the intermediate alleles a_w a_s and a_t.

The Extension Locus - E

This refers to the extension of eumelanin over the dog's body. The dominant form, E, is known as normal extension. The recessive form, e, is called non-extension. When a dog is homozygous for non-extension (ee), its coat will be entirely phaeomelanin based - i.e. red/yellow. For this reason this is sometimes termed recessive red or recessive yellow, to distinguish it from the sable reds/yellows generated by the A_y allele at the Agouti locus.

The extension locus is shared by many mammals, e.g. horses, and operates in a very similar way to this description. In the past it had been proposed that there were additional alleles present at the E locus for black mask and brindle, but this is not borne out by breeding data.

The (Dominant) Black Locus - K

This relative newcomer to the traditional models of dog color genetics codes for both dominant black and brindle in decreasing order of dominance: K=dominant blacK, k_br=brindle, k='normal'. So a dog that is KK or Kk_br is dominant black,k_brk_br or k_brk is brindled, and kk is 'normal'.

Brindling is the presence of 'stripes' of eumelanin-based hairs in areas that are otherwise phaeomelanin based. When a dog is brindled the color of the eumelanin stripes may be modified by the normal genes that affect eumelanin (B and D, see below).

Dominant black (K) is epistatic to whatever is found at the Agouti locus, however it in turn is overridden by ee at the Elocus.

Bringing it Together

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

1. If a dog is ee at the E locus, its coat will be entirely phaeomelanin based (red/yellow);
2. Otherwise (it is Ee or EE at the E locus), if it is K- at the K locus its coat will be entirely eumelanin based (dominant black);
3. Otherwise (it is Ee or EE at the E locus), if it is k_brk_br or k_brk at the K locus it will be brindled with the color of the phaeomelanin part of the brindling in turn affected by the Agouti alleles present;
4. Otherwise (it is Ee or EE at the E locus, and it is kk at the K locus), the distribution of eumelanin and phaeomelanin will be determined solely by the Agouti alleles present.

With this topic under our belt we can now move on the describing the genes one by one.

Other Genes

Chocolate - B gene

This gene has a lightening effect on eumelanin only. I.e, it has no effect on red-based colors.

In the dog there are two alleles for this gene, with symbols B and b respectively. When B is present (BB or Bb) the brown/black eumelanin is its normal, unlightened, color. But when a dog is bb the brown is lightened to Chocolate.

Blue Dilution - D gene

This recessive gene has a diluting effect on both eumelanin and phaeomelanin. When present in the homozygous recessive form (dd) it dilutes brown eumelanin to blue, and red to cream.

Combinations of B and D in Eumelanistic Coats

The effects of these 2 genes combine to form a range of 4 eumelanistic ('black-based') colors:

Choc	Dilute	Eumelanistic Color
B-	D-	Black
B-	dd	Blue
bb	D-	Liver/Chocolate
bb	dd	Faded Liver/Chocolate

Albino - C gene

This gene affects the intensity of melanin production in the coat hairs. The normal or dominant form, C, is what might be termed 'full color'. There are however various incompletely dominant mutant alleles postulated for this locus, with varying effects on color intensity. These mutant forms are temperature sensitive - the higher the temperature, the more effective they are (i.e, the lighter the color).

Almost all dogs are CC at this locus - full color.

The lower series alleles that have been suggested include, in order of decreasing dominance, c_ch, c_e, c_b and c.

The first, c_ch, is chinchilla. This lightens most or all of the phaemelanin with little or no effect on eumelanin. E.g. it turns black+tan to black+silver.

The next allele, c_e, is 'extreme dilution'. Causes tan to become almost white. It is thought that the white labrador might bec_e with another, lower, C series allele. The c_e allele may be responsible for producing white hair in other breeds of dogs, like the West Highland White Terrier, while allowing full expression of dark nose and eye pigment

Moving on down we have c_b, or blue-eyed albino. This is an entirely white coat but with a very small amount of residual pigment in the eyes, giving pale blue eyes. This is known as c_a in cats. Can be called platinum or silver.

Finally we have c, true pink-eyed albino. This doesn't seem to occur in dogs.

Graying - G gene

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

Super-Extension - Se

This dominant gene controls the expression of a black mask.

Traditional models of dog color genetics placed black mask in the Extension (E) series. However it seems that a more accurate model is to place it at a separate locus. Alternate literature has used the symbol Ma for this.

Most breeds do not exhibit black mask, and are therefore sese for this locus. Breeds that have black mask (Se-) include the Mastiff, Pug and Belgian sheepdog.

White Spotting - S

The piebalding or 'white spotting' gene is common to many mammals e.g. cats, not just dogs. And, as in cats, it is not really fully understood.

In dogs it is thought there are four alleles, in decreasing order of dominance: S, s_i, s_p and s_w. The S series alleles appear to be incompletely dominant, further complicating matters. E.g. Ss_w will be similar to s_is_i in appearance. The degree of white spotting is also affected by modifiers. E.g when merle (M) is also present, the white spotting has a greater effect (more white).

The most dominant allele, S, means 'solid color'. Most dogs that are homozygous for S (i.e. SS) have no white hair at all, or possible a tiny amount e.g. a white tail tip, though this can be considered a fault in breeds that are normally SS.

The next allele, s_i, mean 'irish spotting'. This involves white spotting on most parts of the coat, but not crossing the back.

Moving on down we next come to s_p, 'piebald'. The white is more extensive than irish spotting, and often crosses the back.

The most recessive allele in the series is s_w, or 'extreme white piebald'. A dog that is homozygous for s_w will be almost entirely white, e.g. the Dalmatian.

Breeds that exhibit white spotting use varying terminology for the differing degrees of white. E.g. in herding dogs the terms 'normal white pattern' (s_is_i), 'white-factored' (s_is_w) and 'color headed' (s_ws_w) are seen. In Boxers there is the term 'flashy white' (Ss_w - s_i is not thought to exist in the Boxer). The term 'Mantle' is applied to a Great Dane that is s_is_w.

Dogs exhibiting extensive white spotting are more likely to suffer from deafness than non-white dogs, e.g. Dalmatians.

Ticked - T

This dominant mutation causes the presence of color in those areas that have been made white by the effect of alleles in the white spotting (S) series. An extreme example of ticking is the Dalmatian.

Merle - M

This is an incomplete dominant that causes 'merling' - patchy dilution e.g. black becoming patched with gray ('blue merled') or sable becoming sable merle. Merling has little or no effect on phaeomelanin. The M allele is not found in all breeds; in fact most don't have it. Examples of breeds that display merling include the Australian Shepherd and Dachshund (where it is called 'dapple'). Merling also affects the eye color.

Most merled dogs are actually the heterozygote, Mm. There is good reason for this; there are serious health problems associated with the homoygote MM, including tiny eyes (microopthalmic) or even entirely missing eyes (anopthamlic). The homozygote is also known as a 'double merle'. They are often predominantly white, hence their alternate name 'defective white'.

When breeding merles, many reputable breeders avoid breeding Mm to Mm; they generally go for Mm X mm and get 50% single merles (Mm) and 50% not.