Equine Color Genetics
Below is a rather lengthy explanation about what the genotypes mean for the coat colors of my horses, to help anyone using my horses for pedigree assignment as well as anyone interested in genetics. Some of the gene interactions are not fully understood, and I will update this if information changes in the future.
Terminology
Allele: an alternative form of a gene; horses have two alleles for every gene, one inherited from each parent
Homozygous: the two alleles are the same
Heterozygous: the two alleles are different
Genotype: designation of alleles (in this case, coat color alleles)
Phenotype: expression of alleles (in this case, horse's coat color)
Dominant allele: this allele will be expressed if present, and "hide" the expression of a recessive allele
Recessive allele: this allele will only be expressed if the dominant allele is not present
Incomplete dominant allele: the dominant allele cannot completely "hide" the expression of the recessive allele, so there is variation in gene expression
Basic coat color
The very basic coat colors of horses are black and red (chestnut). All horses will be one or the other. The gene called "extension" controls the production of pigments called melanins. The alleles are symbolized by the letters "E" and "e." The capital letter represents the dominant allele, and the lower-case letter represents the recessive allele. Black is completely dominant to red, so black is E and red is e. Because horses have two alleles (see above), the following are the potential genotypes for basic coat color:
Here are the offspring possibilities with different combinations of black and chestnut parents:
Solid color modifiers
What about other colors? There are other genes that can modify the expression of the extension gene. The first one is the agouti gene, responsible for the bay color. The alleles are represented by "A" for the dominant agouti and "a" for the recessive non-agouti. Agouti modifies the deposit of black pigment into hairs, such that most of the pigment is limited to hairs on the mane, tail, and points. Non-agouti does nothing, so black pigment is fairly evenly distributed along across the hairs on the body. Agouti is best understood when taken into context with black and red, as described below.
Brown, sometimes called seal brown, is a recently identified color modifier. The phenotype itself has been described for a long time, but not until recently recognized as a genetically distinct coat color from bay. Brown is a mutation in the agouti gene, symbolized as At. This mutation effects the distribution of black pigment. Chestnut-based horses can have the brown agouti allele, but cannot express it because there is no black allele present.
The next color modifer is grey, represented by "G" for grey and "g" for non-grey. Grey "covers up" every other coat color and pattern eventually (other than dominant white). The base color of the horse at foaling, or shortly thereafter depends on the other color alleles present. The genotype possibilities are:
Dun is similarly inherited, and effects the basic coat color, but not grey. Dun is represented by the dominant "D" dun allele, and the recessive "d" non-dun allele. The type of dun (bay dun, grullo, etc.) depends on the other color alleles.
Roan modifies coat color so that white hairs are interspersed with the colored ones on the body, but not on the points. Roan horses therefore tend to have darker looking heads, manes, tails, and legs. The type of roan (bay, strawberry, blue, etc.) depends on the base coat color. Greying horses can appear roan for a time, which is why in Thoroughbreds the color is called grey/roan.
Cream, the most common dilution gene, is represented by "Cr" and is inherited in an incomplete dominant manner. One Cr allele incompletely dilutes coat color (red hairs only), and two Cr alleles completely dilute coat color (red and black hairs).
The combinations of basic coat color, some other modifiers, and cream result in the following coat colors:
Cream's effect on brown is not well known. It may be that brown plus one cream allele looks something like buckskin or smoky black, and brown with two cream alleles like perlino or smoky cream. Because these horses likely resemble other named colors, they are probably labelled buckskin, perlino, etc., and would need genetic testing to distinguish them.
The champagne gene, symbolized by "Ch," is inherited in a simple dominant fashion, so does not have an additive effect like cream. With either one or two genes present, black and red pigments are diluted, black to a brownish color, and red to a goldish color. This dilution also affects eye color.
Color possibilities with champagne and some other solid colors include:
Silver, or silver dapple, is another simple dominant dilution gene. Alleles are represented by the letter "Z." Silver dilutes black pigment to a silvery color, therefore chestnut-based horses carrying silver are not affected.
Pearl (Prl) is a very rare dilution gene found in Iberian breeds and a few other breeds descended from them (like Quarter Horses). Unlike the other dilution genes, pearl is recessive. A horse will only display this dilution if it is homozygous for pearl. It seems to affect mostly red pigmented hairs. Pearl can interact with cream, making heterozygous cream horses appear "double dilute." Genetic testing is the only way to distinguish homozygous cream horses from these pearl-and-cream horses.
Spotted color modifiers
All of the above were relatively solid color modifications. The ones below give the coat different kinds of spotted patterns. They can be present in combination with any of the solid or other spotted modifiers.
Tobiano is one of the more common spotted patterns. A tobiano horse could look mostly base coat color, mostly white or anywhere in between. Their legs are usually all or mostly white. The tobiano allele is represented by "T."
Overo horses tend to have white patches on the sides of their bodies with a lot of white on their faces. They may or may not have white leg markings.
A note on Overo Lethal White Syndrome (OLWS): This a congenital condition in which a foal's enteric (intestinal) nervous system fails to develop properly. The large intestine does not function, and feces cannot be passed, causing affected foals to colic severely. They die within a few days, but are most often euthanized to prevent suffering before that. The foals are born completely white, hence the name of the condition. OLWS is caused by a mutation in a gene that codes for a protein in nerve and melanin-producing cells. It is inherited in a recessive fashion. When the condition was first recognized, it had been associated with overo patterned horses, and so began the long held belief that two overos should not be bred together. The mutation is not associated with the overo gene, so it is possible for two overos that are not carriers of the mutation to be bred together. There are a handful of documented cases from solid-colored parents. To simplify matters, though, for the model Paint Horses here, all of the overo-patterned horses will be considered heterozygous overo (nO), and will not be allowed to produce homozygous overo (OO) foals, even if bred to another overo.
Sabino can resemble overo. The edges of white markings tend to be very lacy or roany. Sometimes, expression of sabino is limited to just high white leg markings! Sb1, which stands for Sabino 1 gene, is found in many breeds of horses.
Arabians and Clydesdales have a pattern called sabino, but it is not linked to Sb1. While some Arabians may be very "white" colored because of sabino, most Clydesdales are not, even if homozygous. Perhaps one day the gene(s) will be identified as Sb2 or Sb3, but for now, the genotypes of the Arabians and Clydesdales listed on this site with sabino coloration will be nSb (heterozygous) or SbSb (homozygous) until more information is known.
Rabicano is a roan-like phenotype, but is distinct from roan. The white hairs are generally distributed on the throat, belly, sides, and tail (giving the appearance of a so-called "skunk tail"). Rabicano and sabino are often expressed together. Whether this is because the genes are very close together on the chromosome (called "linked genes"), or rabicano is a variation of sabino expression has yet to be definitively determined. Therefore, rabicano is not listed as part of the genotype of the rabicano colored horses here.
According to Animal Genetics, Inc., sabino, tobiano, and roan are mutations of the same gene. This means a horse cannot be all three patterns at once, and can at most be heterozygous for any two of those patterns. For instance, a blue roan tobiano cannot also have sabino.
Dominant white is a part of the sabino / tobiano / roan gene. It hides every other color of coat, but is not a very common phenotype. The coat color is, as the name implies, all white, or very nearly so. Dominant white alleles, of which there are at least a dozen, are found in several breeds of horses. White Thoroughbreds have been traced to three alleles (through White Beauty, Puchilingui, and Shirayukihime), Arabians have one (from R Khasper). Only one allele is required to give a foal a dominant white color, but that usually means one of the parents must be dominant white. Many mutations have popped up from non-white parents, but for model pedigree assignment purposes, it is best to have a dominant white parent for a dominant white foal.
The pattern responsible for the spotted appearance of Appaloosas, Knabstruppers, etc. is very complex. According to the Appaloosa Project, there are many genes that work together to produce varnish roan, leopard, and blanket patterns. There could be more! The main one is Leopard Complex, designated "Lp." Lp needs to be present in order for spotted patterns to be expressed, but Lp alone does not result in spots. Lp by itself creates the "varnish roan" pattern, as well as the "characteristics" of mottled skin, white sclera, and hoof stripes. The second gene is called Pattern Type 1, designated here as "P1." This is responsible for the "leopard" pattern, or colored spots all over the body. There are likely pattern modifying genes that effect the extend of the spots (so "blanket" can be variably sized depending on how many modifiers a horse inherited). If Pattern 1 or any pattern modifiers are present, but not Lp, then the horse's coat color will be solid with no characteristics.
A note on congenital stationary night blindness (CSNB): The Lp allele is associated with hereditary night blindness in Appaloosas. Only homozygous "few spot" horses are affected.
Lp is implicated in what is currently called "color shift" in appaloosa colored horses. Genetically black horses appear diluted, some say "bronzed" even, without a known dilution gene present.
All of the above is an amalgam of information from memory, personal experience, UC Davis Genetics Laboratory, Animal Genetics, Inc., Equine Tapestry, and the Appaloosa Project.
Terminology
Allele: an alternative form of a gene; horses have two alleles for every gene, one inherited from each parent
Homozygous: the two alleles are the same
Heterozygous: the two alleles are different
Genotype: designation of alleles (in this case, coat color alleles)
Phenotype: expression of alleles (in this case, horse's coat color)
Dominant allele: this allele will be expressed if present, and "hide" the expression of a recessive allele
Recessive allele: this allele will only be expressed if the dominant allele is not present
Incomplete dominant allele: the dominant allele cannot completely "hide" the expression of the recessive allele, so there is variation in gene expression
Basic coat color
The very basic coat colors of horses are black and red (chestnut). All horses will be one or the other. The gene called "extension" controls the production of pigments called melanins. The alleles are symbolized by the letters "E" and "e." The capital letter represents the dominant allele, and the lower-case letter represents the recessive allele. Black is completely dominant to red, so black is E and red is e. Because horses have two alleles (see above), the following are the potential genotypes for basic coat color:
- EE - The genotype is homozygous dominant, so the horse is black. You may see this on real horse advertisements as "homozygous black."
- Ee - The genotype is heterozygous, as the two alleles are different (one dominant, one recessive). The dominant allele will be expressed, so this horse is black.
- ee - The genotype is homozygous recessive, and the horse is chestnut. There is no dominant black allele to hide the expression of the red alleles, so red (chestnut) is expressed.
Here are the offspring possibilities with different combinations of black and chestnut parents:
- EE (black) x EE (black) - 100% EE (100% black)
- EE (black) x Ee (black) - 50% EE, 50% Ee (100% black)
- EE (black) x ee (chestnut) - 100% Ee (100% black)
- Ee (black) x Ee (black) - 25% EE, 50% Ee, 25% ee (75% black, 25% chestnut)
- Ee (black) x ee (chestnut) - 50% Ee, 50% ee (50% black, 50% chestnut)
- ee (chestnut) x ee (chestnut) - 100% ee (100% chestnut)
Solid color modifiers
What about other colors? There are other genes that can modify the expression of the extension gene. The first one is the agouti gene, responsible for the bay color. The alleles are represented by "A" for the dominant agouti and "a" for the recessive non-agouti. Agouti modifies the deposit of black pigment into hairs, such that most of the pigment is limited to hairs on the mane, tail, and points. Non-agouti does nothing, so black pigment is fairly evenly distributed along across the hairs on the body. Agouti is best understood when taken into context with black and red, as described below.
- EE / aa - Homozygous black, and homozygous non-agouti. Because there is no modifier, the horse is black.
- EE / Aa - This horse is also homozygous black, but heterozygous for agouti. That one A means the black coat will be limited to points, so this horse is bay. This is one way a bay horse can also be homozygous black (the combination below is another).
- EE / AA - Homozygous black and homozygous agouti. The horse is bay.
- Ee / aa - Heterozygous black, and homozygous non-agouti. The horse is black.
- Ee / Aa - This horse is heterozygous for both genes. Its coat color is bay.
- Ee / AA - A bay horse that is homozygous agouti.
- ee / aa - Chestnut horse. No black allele, no agouti allele.
- ee / Aa - This is also a chestnut horse. Because there is no black allele, the A has no effect on coat color.
- ee / AA - This horse is chestnut, but also homozygous agouti.
Brown, sometimes called seal brown, is a recently identified color modifier. The phenotype itself has been described for a long time, but not until recently recognized as a genetically distinct coat color from bay. Brown is a mutation in the agouti gene, symbolized as At. This mutation effects the distribution of black pigment. Chestnut-based horses can have the brown agouti allele, but cannot express it because there is no black allele present.
- EE or Ee / Ata - This horse will be seal brown.
- EE or Ee / AtAt - This horse will be brown, but may be a little lighter than the heterozygous brown horse above.
- EE or Ee / AAt - This horse is bay, because there is one "normal" agouti allele present.
The next color modifer is grey, represented by "G" for grey and "g" for non-grey. Grey "covers up" every other coat color and pattern eventually (other than dominant white). The base color of the horse at foaling, or shortly thereafter depends on the other color alleles present. The genotype possibilities are:
- GG: Homozygous grey
- Gg: Heterozygous grey
- gg: Not grey
Dun is similarly inherited, and effects the basic coat color, but not grey. Dun is represented by the dominant "D" dun allele, and the recessive "d" non-dun allele. The type of dun (bay dun, grullo, etc.) depends on the other color alleles.
- DD - Homozygous dun
- Dd - Heterozygous dun
- dd - Not dun
Roan modifies coat color so that white hairs are interspersed with the colored ones on the body, but not on the points. Roan horses therefore tend to have darker looking heads, manes, tails, and legs. The type of roan (bay, strawberry, blue, etc.) depends on the base coat color. Greying horses can appear roan for a time, which is why in Thoroughbreds the color is called grey/roan.
- RR - Homozygous roan
- Rr - Heterozygous roan
- rr - Not roan
Cream, the most common dilution gene, is represented by "Cr" and is inherited in an incomplete dominant manner. One Cr allele incompletely dilutes coat color (red hairs only), and two Cr alleles completely dilute coat color (red and black hairs).
- CrCr - Homozygous cream
- nCr - Heterozygous cream
The combinations of basic coat color, some other modifiers, and cream result in the following coat colors:
- Black / nCr - Smoky black
- Black / CrCr - Smoky cream
- Black dun / nCr - Smoky grullo
- Black dun / CrCr - Smoky cream grullo
- Bay / nCr - Buckskin
- Bay / CrCr - Perlino
- Bay dun / nCr - Buckskin dun or dunskin
- Bay dun / CrCr - Perlino dun
- Chestnut / nCr - Palomino
- Chestnut / CrCr - Cremello
- Chestnut dun / nCr - Palomino dun or dunalino
- Chestnut dun / CrCr - Cremello dun
Cream's effect on brown is not well known. It may be that brown plus one cream allele looks something like buckskin or smoky black, and brown with two cream alleles like perlino or smoky cream. Because these horses likely resemble other named colors, they are probably labelled buckskin, perlino, etc., and would need genetic testing to distinguish them.
The champagne gene, symbolized by "Ch," is inherited in a simple dominant fashion, so does not have an additive effect like cream. With either one or two genes present, black and red pigments are diluted, black to a brownish color, and red to a goldish color. This dilution also affects eye color.
- ChCh - Homozygous champagne
- nCh - Heterozygous champagne
Color possibilities with champagne and some other solid colors include:
- Black + champagne - classic champagne
- Bay + champagne - amber champagne
- Brown + champagne - sable cream
- Chestnut + champagne - gold champagne
- Smoky black + champagne - classic cream
- Buckskin + champagne - amber cream
- Palomino + champagne - ivory champagne or gold cream
Silver, or silver dapple, is another simple dominant dilution gene. Alleles are represented by the letter "Z." Silver dilutes black pigment to a silvery color, therefore chestnut-based horses carrying silver are not affected.
- ZZ - Homozygous silver
- nZ - Heterozygous silver
Pearl (Prl) is a very rare dilution gene found in Iberian breeds and a few other breeds descended from them (like Quarter Horses). Unlike the other dilution genes, pearl is recessive. A horse will only display this dilution if it is homozygous for pearl. It seems to affect mostly red pigmented hairs. Pearl can interact with cream, making heterozygous cream horses appear "double dilute." Genetic testing is the only way to distinguish homozygous cream horses from these pearl-and-cream horses.
- PrlPrl - horse will have a diluted coat, often an apricot color
- nPrl - horse will not be pearl-diluted, but can pass on the pearl allele to half of its offspring
Spotted color modifiers
All of the above were relatively solid color modifications. The ones below give the coat different kinds of spotted patterns. They can be present in combination with any of the solid or other spotted modifiers.
Tobiano is one of the more common spotted patterns. A tobiano horse could look mostly base coat color, mostly white or anywhere in between. Their legs are usually all or mostly white. The tobiano allele is represented by "T."
- TT - Homozygous tobiano. Sometimes horses that are homozygous tobiano have groups of smaller colored spots in their white areas, called "cat tracks."
- nT - Heterozygous tobiano
Overo horses tend to have white patches on the sides of their bodies with a lot of white on their faces. They may or may not have white leg markings.
- OO - Homozygous overo
- nO - Heterozygous overo
A note on Overo Lethal White Syndrome (OLWS): This a congenital condition in which a foal's enteric (intestinal) nervous system fails to develop properly. The large intestine does not function, and feces cannot be passed, causing affected foals to colic severely. They die within a few days, but are most often euthanized to prevent suffering before that. The foals are born completely white, hence the name of the condition. OLWS is caused by a mutation in a gene that codes for a protein in nerve and melanin-producing cells. It is inherited in a recessive fashion. When the condition was first recognized, it had been associated with overo patterned horses, and so began the long held belief that two overos should not be bred together. The mutation is not associated with the overo gene, so it is possible for two overos that are not carriers of the mutation to be bred together. There are a handful of documented cases from solid-colored parents. To simplify matters, though, for the model Paint Horses here, all of the overo-patterned horses will be considered heterozygous overo (nO), and will not be allowed to produce homozygous overo (OO) foals, even if bred to another overo.
Sabino can resemble overo. The edges of white markings tend to be very lacy or roany. Sometimes, expression of sabino is limited to just high white leg markings! Sb1, which stands for Sabino 1 gene, is found in many breeds of horses.
- Sb1Sb1 - Extreme sabino. The horse may look mostly white.
- nSb1 - Moderate to mild sabino.
Arabians and Clydesdales have a pattern called sabino, but it is not linked to Sb1. While some Arabians may be very "white" colored because of sabino, most Clydesdales are not, even if homozygous. Perhaps one day the gene(s) will be identified as Sb2 or Sb3, but for now, the genotypes of the Arabians and Clydesdales listed on this site with sabino coloration will be nSb (heterozygous) or SbSb (homozygous) until more information is known.
Rabicano is a roan-like phenotype, but is distinct from roan. The white hairs are generally distributed on the throat, belly, sides, and tail (giving the appearance of a so-called "skunk tail"). Rabicano and sabino are often expressed together. Whether this is because the genes are very close together on the chromosome (called "linked genes"), or rabicano is a variation of sabino expression has yet to be definitively determined. Therefore, rabicano is not listed as part of the genotype of the rabicano colored horses here.
According to Animal Genetics, Inc., sabino, tobiano, and roan are mutations of the same gene. This means a horse cannot be all three patterns at once, and can at most be heterozygous for any two of those patterns. For instance, a blue roan tobiano cannot also have sabino.
Dominant white is a part of the sabino / tobiano / roan gene. It hides every other color of coat, but is not a very common phenotype. The coat color is, as the name implies, all white, or very nearly so. Dominant white alleles, of which there are at least a dozen, are found in several breeds of horses. White Thoroughbreds have been traced to three alleles (through White Beauty, Puchilingui, and Shirayukihime), Arabians have one (from R Khasper). Only one allele is required to give a foal a dominant white color, but that usually means one of the parents must be dominant white. Many mutations have popped up from non-white parents, but for model pedigree assignment purposes, it is best to have a dominant white parent for a dominant white foal.
- WW - homozygous white
- Ww - heterozygous white
The pattern responsible for the spotted appearance of Appaloosas, Knabstruppers, etc. is very complex. According to the Appaloosa Project, there are many genes that work together to produce varnish roan, leopard, and blanket patterns. There could be more! The main one is Leopard Complex, designated "Lp." Lp needs to be present in order for spotted patterns to be expressed, but Lp alone does not result in spots. Lp by itself creates the "varnish roan" pattern, as well as the "characteristics" of mottled skin, white sclera, and hoof stripes. The second gene is called Pattern Type 1, designated here as "P1." This is responsible for the "leopard" pattern, or colored spots all over the body. There are likely pattern modifying genes that effect the extend of the spots (so "blanket" can be variably sized depending on how many modifiers a horse inherited). If Pattern 1 or any pattern modifiers are present, but not Lp, then the horse's coat color will be solid with no characteristics.
A note on congenital stationary night blindness (CSNB): The Lp allele is associated with hereditary night blindness in Appaloosas. Only homozygous "few spot" horses are affected.
Lp is implicated in what is currently called "color shift" in appaloosa colored horses. Genetically black horses appear diluted, some say "bronzed" even, without a known dilution gene present.
All of the above is an amalgam of information from memory, personal experience, UC Davis Genetics Laboratory, Animal Genetics, Inc., Equine Tapestry, and the Appaloosa Project.
Copyright 2013-present Elysian Fields Ranch
This is a MODEL HORSE HOBBY site, not to be confused with any real horse facility of the same name.
Any and all references to real horses, living or dead, are for non-profit, educational, and personal entertainment purposes only.
No images or information on this site may be used without permission.
This is a MODEL HORSE HOBBY site, not to be confused with any real horse facility of the same name.
Any and all references to real horses, living or dead, are for non-profit, educational, and personal entertainment purposes only.
No images or information on this site may be used without permission.