Equine Color Genetics
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All horses produce black and/or red pigments in their coats, the distribution and dilution of which are governed by the various genes which affect their coat color. What are typically considered the three most basic of horse colors are black, chestnut, and bay. These are considered the simplest colors because they involve the smallest number of visible gene effects. However, in truth all horses have all color genes present; just not necessarily the version of the gene which makes its effect visible.
Horse coat color genetics is an intricate and fascinating subject and our understanding of it, and the language used to describe it, has vastly improved in the last few decades. Largely this has been due to advances in genetic testing, but a great deal is also owed to breeders, owners, and horse enthusiasts who have come together and pooled resources to better understand this complex subject.
One aspect of these discussions which I personally find particularly beautiful is how it seems to be the case that the more we learn, the more there is which remains unknown.
Zygosity:
Each horse has two copies of each of its genes, one inherited from each parent. However, these two copies are not always the same; most genes involved in coat color inheritance come in at least two versions, called alleles, and discussions of color genetics often focus on only one allele because it has the obvious visible effect. If a horse inherited two copies of the same allele for a particular gene, then it is said to be homozygous for that gene, can only pass on that allele to any of its offspring, and will pass on that allele to each of its offspring. But if it inherited a different allele from each parent, then it is said to be heterozygous for that gene, can pass on either allele to any of its offspring, and will pass on one or the other allele to each of its offspring. So statistically speaking, a homozygous horse reproduces its color 100% of the time, while a heterozygous horse reproduces its color only 50% of the time.
However, no matter its zygosity, each horse can only pass on one allele to each of its offspring, no matter how many alleles there are of any particular gene.
Dominance, Recessiveness, and Incomplete Dominance:
An allele is considered dominant if only one copy of it is necessary for its version of the gene to be expressed, recessive if two copies are needed for a visible effect to be seen, and incompletely dominant if one copy is needed for expression but two copies have a stronger effect. Often only the dominant allele for a particular gene is discussed when talking about horse color genetics because the dominant allele produces a visible effect which makes the horse recognizable as a particular color, while the recessive allele essentially makes the horse plain or "not-color x".
Typically, dominance or recessiveness is represented in shorthand with capitalization; where the dominant allele is presented as a capital letter (X) and the recessive as a lowercase letter (x), and homozygous horses are either XX or xx and heterozygous horses are Xx.
The Basics:
Black and Red:
A gene called extension is the foundation for horse coat color. There are two common alleles of extension which code for the production of either black or red pigment and produce the colors black and chestnut/sorrel (typically referred to as red in genetics discussions). There is a simple dominant relationship between these two alleles, meaning that a horse must be ee to be red but can be either Ee or EE if it is black and there is no difference in the appearance of Ee and EE horses.
A third allele does exist, but it is rare (primarily found in Black Forest Horses) and seems to be functionally no different from the common red allele.
Bay and Brown:
The agouti gene is responsible for bay and brown colors. Dominant forms of agouti work by restricting black hair to the points of the horse (mane, tail, and lower legs) and replacing it with red hair everywhere else; though there is a great deal of individual variation. Because agouti acts on black, it turns horses that are dominant at extension from black to bay and is invisible on horses that are homozygous recessive at extension, since they have no black hair to restrict and are already all red. Because of this, horses must be dominant at both extension and agouti in order to be bay.
Bay horses typically fall within the description of a horse with a red or red-brown body and black mane, tail, and lower legs, possibly with some black shading in the body; though there is much individual variation in the specific body color and the degree of darker shading.
Brown horses typically have more black in their coats than bays and can look anywhere from a dark bay horse with heavy black shading to a black horse with red hairs only in a few areas such as the muzzle, armpits, inner thighs, and underbelly.
Bay (A) is known to be caused by a dominant allele on agouti and its presence in red horses can be proven with genetic testing. Brown horses also test positive for dominant agouti, but brown appears to be inherited strongly enough to imply that it is genetically distinct from bay in some way. However, no reliable genetic test for brown has yet been developed so its exact genetic cause is not yet known. Recessive agouti (a) does not modify black and thus allows for black colors to be expressed normally.
Dilutions:
Dun:
Dun colors are characterized by a diluted body color in combination with a suite of "primitive" markings known a dun factors. Both red and black hairs are diluted and, interestingly, the dilution actually occurs by the arrangement of the pigment towards the core of the hair rather than dilution of the pigment itself. Red hair is typically diluted to a wheat, buff, or tan color while black hair usually becomes some shade of gray. Dun factors always include a dark stripe along the spine, color reduction and/or horizontal stripes on the legs, and dark rims around the ears, but can also include shading/striping across the shoulders, "frosting" in the mane and tail, and a "mask" of dark shading on the face. Bay dun, usually referred to simply as dun, is thought to have been the original coloration of all horses with all other colors being due to later genetic mutations. There are three alleles of dun; dun, non-dun 1, and non-dun 2. Dun (D) is dominant, causes the full suite of dun dilution and markings, and is responsible for the majority of dun horses. Non-dun 1 (nd1) is recessive to D, rare, and puts dun factors on horses, but incuces only a limited, and variable, amount of dilution with some nd1 horses looking like non-duns that someone drew dun markings on. Non-dun 2 (nd2) is recessive to both D and nd1 and allows for all non dun colors to be expressed.
Cream and Pearl:
The cream allele is an incomplete dominant which in heterozygous form typically dilutes only red hair, causing colors such as smokey black (black), palomino (red), and buckskin (bay), and in homozygous form dilutes both red and black hair as well as skin and eye color, causing colors such as smokey cream (black), cremello (red), and perlino (buckskin). In heterozygous horses, red hair is diluted to a golden or yellow color while black hair typically remains unaffected; most smokey blacks look no different than ordinary blacks, though some are diluted to a brownish or not-quite-black color. Heterozygous horses also have normal skin and eye color. Homozygous horses however, are diluted to an overall pale cream color with pink skin and blue eyes. Often, but not always, cremellos have white manes and tails and perlinos have darker points; however, it's not always possible to tell double cream dilutes apart by appearance alone and genetic testing and/or pedigree analysis are often necessary to determine a horse's true color.
In some parts of the world, particularly Australia and the UK, it is common to call buckskin horses "dun" and while the two colors can be similar, they are genetically different.
Pearl is an extremely rare dilution caused by a recessive allele that is thought to be on the same gene as cream. Heterozygous pearl horses look no different than any other horse of their color except that some may have hair, skin, and/or eyes of a slightly lighter shade than normal, while homozygous horses are diluted to a uniformly pale, often slightly metallic, variation on their base color, with dark diluted skin and usually lighter, often green, eyes and are sometimes mistaken for champagne dilutes.
When a horse has both dominant cream and recessive pearl, its color will be nearly identical to that of a double cream dilute of the same base color; though it may have light green eyes instead of blue and may have been darker as a foal than as an adult.
Champagne:
Silver:
Other Modifiers:
Roan:
Rabicano:
Sooty:
White Patterns:
Tobiano:
Frame Overo:
Sabino 1:
Splash White:
White Spotting:
Sabino Phenotype:
Appaloosa:
Leopard Complex:
Pattern 1:
Other pattern genes:
Combination Colors:
Tovero:
Pintaloosa:
All horses produce black and/or red pigments in their coats, the distribution and dilution of which are governed by the various genes which affect their coat color. What are typically considered the three most basic of horse colors are black, chestnut, and bay. These are considered the simplest colors because they involve the smallest number of visible gene effects. However, in truth all horses have all color genes present; just not necessarily the version of the gene which makes its effect visible.
Horse coat color genetics is an intricate and fascinating subject and our understanding of it, and the language used to describe it, has vastly improved in the last few decades. Largely this has been due to advances in genetic testing, but a great deal is also owed to breeders, owners, and horse enthusiasts who have come together and pooled resources to better understand this complex subject.
One aspect of these discussions which I personally find particularly beautiful is how it seems to be the case that the more we learn, the more there is which remains unknown.
Zygosity:
Each horse has two copies of each of its genes, one inherited from each parent. However, these two copies are not always the same; most genes involved in coat color inheritance come in at least two versions, called alleles, and discussions of color genetics often focus on only one allele because it has the obvious visible effect. If a horse inherited two copies of the same allele for a particular gene, then it is said to be homozygous for that gene, can only pass on that allele to any of its offspring, and will pass on that allele to each of its offspring. But if it inherited a different allele from each parent, then it is said to be heterozygous for that gene, can pass on either allele to any of its offspring, and will pass on one or the other allele to each of its offspring. So statistically speaking, a homozygous horse reproduces its color 100% of the time, while a heterozygous horse reproduces its color only 50% of the time.
However, no matter its zygosity, each horse can only pass on one allele to each of its offspring, no matter how many alleles there are of any particular gene.
Dominance, Recessiveness, and Incomplete Dominance:
An allele is considered dominant if only one copy of it is necessary for its version of the gene to be expressed, recessive if two copies are needed for a visible effect to be seen, and incompletely dominant if one copy is needed for expression but two copies have a stronger effect. Often only the dominant allele for a particular gene is discussed when talking about horse color genetics because the dominant allele produces a visible effect which makes the horse recognizable as a particular color, while the recessive allele essentially makes the horse plain or "not-color x".
Typically, dominance or recessiveness is represented in shorthand with capitalization; where the dominant allele is presented as a capital letter (X) and the recessive as a lowercase letter (x), and homozygous horses are either XX or xx and heterozygous horses are Xx.
The Basics:
Black and Red:
A gene called extension is the foundation for horse coat color. There are two common alleles of extension which code for the production of either black or red pigment and produce the colors black and chestnut/sorrel (typically referred to as red in genetics discussions). There is a simple dominant relationship between these two alleles, meaning that a horse must be ee to be red but can be either Ee or EE if it is black and there is no difference in the appearance of Ee and EE horses.
A third allele does exist, but it is rare (primarily found in Black Forest Horses) and seems to be functionally no different from the common red allele.
Bay and Brown:
The agouti gene is responsible for bay and brown colors. Dominant forms of agouti work by restricting black hair to the points of the horse (mane, tail, and lower legs) and replacing it with red hair everywhere else; though there is a great deal of individual variation. Because agouti acts on black, it turns horses that are dominant at extension from black to bay and is invisible on horses that are homozygous recessive at extension, since they have no black hair to restrict and are already all red. Because of this, horses must be dominant at both extension and agouti in order to be bay.
Bay horses typically fall within the description of a horse with a red or red-brown body and black mane, tail, and lower legs, possibly with some black shading in the body; though there is much individual variation in the specific body color and the degree of darker shading.
Brown horses typically have more black in their coats than bays and can look anywhere from a dark bay horse with heavy black shading to a black horse with red hairs only in a few areas such as the muzzle, armpits, inner thighs, and underbelly.
Bay (A) is known to be caused by a dominant allele on agouti and its presence in red horses can be proven with genetic testing. Brown horses also test positive for dominant agouti, but brown appears to be inherited strongly enough to imply that it is genetically distinct from bay in some way. However, no reliable genetic test for brown has yet been developed so its exact genetic cause is not yet known. Recessive agouti (a) does not modify black and thus allows for black colors to be expressed normally.
Dilutions:
Dun:
Dun colors are characterized by a diluted body color in combination with a suite of "primitive" markings known a dun factors. Both red and black hairs are diluted and, interestingly, the dilution actually occurs by the arrangement of the pigment towards the core of the hair rather than dilution of the pigment itself. Red hair is typically diluted to a wheat, buff, or tan color while black hair usually becomes some shade of gray. Dun factors always include a dark stripe along the spine, color reduction and/or horizontal stripes on the legs, and dark rims around the ears, but can also include shading/striping across the shoulders, "frosting" in the mane and tail, and a "mask" of dark shading on the face. Bay dun, usually referred to simply as dun, is thought to have been the original coloration of all horses with all other colors being due to later genetic mutations. There are three alleles of dun; dun, non-dun 1, and non-dun 2. Dun (D) is dominant, causes the full suite of dun dilution and markings, and is responsible for the majority of dun horses. Non-dun 1 (nd1) is recessive to D, rare, and puts dun factors on horses, but incuces only a limited, and variable, amount of dilution with some nd1 horses looking like non-duns that someone drew dun markings on. Non-dun 2 (nd2) is recessive to both D and nd1 and allows for all non dun colors to be expressed.
Cream and Pearl:
The cream allele is an incomplete dominant which in heterozygous form typically dilutes only red hair, causing colors such as smokey black (black), palomino (red), and buckskin (bay), and in homozygous form dilutes both red and black hair as well as skin and eye color, causing colors such as smokey cream (black), cremello (red), and perlino (buckskin). In heterozygous horses, red hair is diluted to a golden or yellow color while black hair typically remains unaffected; most smokey blacks look no different than ordinary blacks, though some are diluted to a brownish or not-quite-black color. Heterozygous horses also have normal skin and eye color. Homozygous horses however, are diluted to an overall pale cream color with pink skin and blue eyes. Often, but not always, cremellos have white manes and tails and perlinos have darker points; however, it's not always possible to tell double cream dilutes apart by appearance alone and genetic testing and/or pedigree analysis are often necessary to determine a horse's true color.
In some parts of the world, particularly Australia and the UK, it is common to call buckskin horses "dun" and while the two colors can be similar, they are genetically different.
Pearl is an extremely rare dilution caused by a recessive allele that is thought to be on the same gene as cream. Heterozygous pearl horses look no different than any other horse of their color except that some may have hair, skin, and/or eyes of a slightly lighter shade than normal, while homozygous horses are diluted to a uniformly pale, often slightly metallic, variation on their base color, with dark diluted skin and usually lighter, often green, eyes and are sometimes mistaken for champagne dilutes.
When a horse has both dominant cream and recessive pearl, its color will be nearly identical to that of a double cream dilute of the same base color; though it may have light green eyes instead of blue and may have been darker as a foal than as an adult.
Champagne:
Silver:
Other Modifiers:
Roan:
Rabicano:
Sooty:
White Patterns:
Tobiano:
Frame Overo:
Sabino 1:
Splash White:
White Spotting:
Sabino Phenotype:
Appaloosa:
Leopard Complex:
Pattern 1:
Other pattern genes:
Combination Colors:
Tovero:
Pintaloosa: