Equine coat color genetics - AbsoluteAstronomy.com

Equine coat color genetics determine a horse

Horse

The horse is one of two extant subspecies of Equus ferus, or the wild horse. It is a single-hooved mammal belonging to the taxonomic family Equidae. The horse has evolved over the past 45 to 55 million years from a small multi-toed creature into the large, single-toed animal of today...

's coat color. There are many different coat colors possible, but all colors are produced by the action of only a few different gene

Gene

A gene is a molecular unit of heredity of a living organism. It is a name given to some stretches of DNA and RNA that code for a type of protein or for an RNA chain that has a function in the organism. Living beings depend on genes, as they specify all proteins and functional RNA chains...

s. The simplest genetic default color of all domesticated horses can be described as either "red" or "non-red", depending on whether a gene known as the "Extension" gene is present . When no other genes are active, a "red" horse is the color popularly known as a chestnut

Chestnut (coat)

Chestnut is a hair coat color of horses consisting of a reddish-to-brown coat with a mane and tail the same or lighter in color than the coat. Genetically and visually, chestnut is characterized by the absolute absence of true black hairs...

. Black

Black (horse)

Black is a hair coat color of horses in which the entire hair coat is black. Black is a relatively uncommon coat color, and novices frequently mistake dark chestnuts or bays for black. However, some breeds of horses, such as the Friesian horse, Murgese and Ariegeois are almost exclusively black...

coat color occurs when the Extension gene is present, but no other genes are acting on coat color.The Agouti gene can be recognized only in "non-red" horses; it determines whether black color is uniform, creating a black

Black (horse)

horse, or limited to the extremities of the body, creating a bay horse.

Chestnut, black, and bay are considered the three "base" colors that all remaining coat color genes act upon. There are a number of dilution gene

Dilution gene

Dilution gene is a popular term for any one of a number of genes that act to create a lighter coat color in living creatures. There are many examples of such genes:-General:...

s that lighten these three colors in a variety of ways, sometimes affecting skin and eyes as well as hair coat. Genes that affect the distribution of white and pigmented coat, skin and eye color create patterns such as roan

Roan (horse)

Roan is a horse coat color pattern characterized by an even mixture of colored and white hairs on the body, while the head and "points"—lower legs, mane and tail—are more solid-colored. The roan pattern is dominantly-inherited, and is found in many horse breeds...

, pinto

Pinto horse

A pinto horse has a coat color that consists of large patches of white and any other color. The distinction between "pinto" and "solid" can be tenuous, as so-called "solid" horses frequently have areas of white hair. Various cultures throughout history appear to have selectively bred for pinto...

, leopard

Leopard complex

The leopard complex is a group of genetically-related coat patterns in horses. These patterns range from progressive increases in interspersed white hair similar to graying or roan to distinctive, Dalmatian-like leopard spots on a white coat. Secondary characteristics associated with the leopard...

, white

White (horse)

White horses are born white and stay white throughout their life. White horses may have brown, blue, or hazel eyes. "True white" horses, especially those that carry one of the dominant white genes, are rare...

, and even white markings

Horse markings

Markings on horses usually are distinctive white areas on an otherwise dark base coat color. Most horses have some markings, and they help to identify the horse as a unique individual. Markings are present at birth and do not change over the course of the horse's life...

. Some of these patterns may be the result of a single gene, others may be influenced by multiple alleles, Finally the gray

Gray (horse)

Gray or grey is a coat color of horses characterized by progressive silvering of the colored hairs of the coat. Most gray horses have black skin and dark eyes; unlike many depigmentation genes, gray does not affect skin or eye color Their adult hair coat is white, dappled, or white intermingled...

gene, which acts differently from other coat color genes, slowly lightens any other hair coat color to white over a period of years, without changing skin or eye color.

Fundamental concepts and terminology

Much of the modern understanding of equine coat color genetics is owed to the work of the late Dr. Ann T. Bowling of the University of California, Davis

University of California, Davis

The University of California, Davis is a public teaching and research university established in 1905 and located in Davis, California, USA. Spanning over , the campus is the largest within the University of California system and third largest by enrollment...

and of Dr. Phillip Sponenberg of Virginia Polytechnic Institute. Modern discussions of horse coat color genetics are based on the distinction between "red" and "non-red" coats, a factor determined by a single gene. More detailed discussions of coat color all refer to the differing effects of separate genes on these "base" coat colors.

Coat color alleles affect melanin

Melanin

Melanin is a pigment that is ubiquitous in nature, being found in most organisms . In animals melanin pigments are derivatives of the amino acid tyrosine. The most common form of biological melanin is eumelanin, a brown-black polymer of dihydroxyindole carboxylic acids, and their reduced forms...

, the pigment or coloring of the coat. There are two chemically distinct types of melanin: phaeomelanin, which is perceived as red to yellow color, and eumelanin, is perceived as brown to black. All coloration genes in mammal

Mammal

Mammals are members of a class of air-breathing vertebrate animals characterised by the possession of endothermy, hair, three middle ear bones, and mammary glands functional in mothers with young...

s affect either the production or distribution of these two chemicals. Alleles affecting melanocyte

Melanocyte

-External links: - "Eye: fovea, RPE" - "Integument: pigmented skin"...

s (pigment cells) do not alter the pigment chemicals themselves but rather by acting on the placement of pigment cells produce distinct patterns of unpigmented pink skin and corresponding white hair.

Heritable characteristics are transmitted, encoded, and used through a substance called DNA

DNA

Deoxyribonucleic acid is a nucleic acid that contains the genetic instructions used in the development and functioning of all known living organisms . The DNA segments that carry this genetic information are called genes, but other DNA sequences have structural purposes, or are involved in...

, which is stored in almost every cell

Cell (biology)

The cell is the basic structural and functional unit of all known living organisms. It is the smallest unit of life that is classified as a living thing, and is often called the building block of life. The Alberts text discusses how the "cellular building blocks" move to shape developing embryos....

in an organism

Organism

In biology, an organism is any contiguous living system . In at least some form, all organisms are capable of response to stimuli, reproduction, growth and development, and maintenance of homoeostasis as a stable whole.An organism may either be unicellular or, as in the case of humans, comprise...

. DNA is organized into storage structures called chromosome

Chromosome

A chromosome is an organized structure of DNA and protein found in cells. It is a single piece of coiled DNA containing many genes, regulatory elements and other nucleotide sequences. Chromosomes also contain DNA-bound proteins, which serve to package the DNA and control its functions.Chromosomes...

s. For the most part, chromosomes come in matched sets, one chromosome from each parent. The location of a gene

Gene

on a chromosome is called its locus. Alternate forms of a gene are called allele

Allele

An allele is one of two or more forms of a gene or a genetic locus . "Allel" is an abbreviation of allelomorph. Sometimes, different alleles can result in different observable phenotypic traits, such as different pigmentation...

s. The terms Alleles and Modifiers are used interchangeably and describe the same concept. An allele identified with a capital letter is a dominant trait, one identified with a lower-case letter is a recessive trait. Because sex cells (sperm and ova) contain only half the usual number of chromosome

Chromosome

s, each parent contributes one allele in each gene set to the ensuing offspring. When an individual's gene set contains two copies of the same allele, it is called homozygous for that gene. When it has two different alleles, it is heterozygous. For a recessive trait to be expressed, it must be homozygous, but a dominant trait will be expressed whether it is heterozygous or homozygous. A horse homozygous for a certain allele will always pass it on to its offspring, while a horse that is heterozygous carries two different alleles and can pass on either one.

Extension

Extension controls whether or not true black pigment (eumelanin) can be formed in the hair. True black pigment may be restricted to the points, as in a bay, or uniformly distributed in a black

Black (horse)

coat. Horses capable of producing eumelanin in the hair may have a genotype of either E/E or E/e. Horses without the ability to produce eumelanin in the hair always have the genotype e/e, and are most often chestnut

Chestnut (coat)

or "red". The e allele is also sometimes called "red factor" and can be identified through DNA testing. Horses homozygous E/E are sometimes called "homozygous black", however depending on the color of the mate, E/E status confers no guarantee of black-coated offspring; only that no offspring will be "red".

The Extension locus

Locus (genetics)

In the fields of genetics and genetic computation, a locus is the specific location of a gene or DNA sequence on a chromosome. A variant of the DNA sequence at a given locus is called an allele. The ordered list of loci known for a particular genome is called a genetic map...

is occupied by the Melanocortin-1-receptor
Melanocortin 1 receptor
The melanocortin 1 receptor , also known as melanocyte-stimulating hormone receptor , melanin-activating peptide receptor, or melanotropin receptor, is a G protein-coupled receptor which binds to a class of pituitary peptide hormones known as the melanocortins, of which include adrenocorticotropic...

(Mc1r) gene, which encodes the eponymous protein

Protein

Proteins are biochemical compounds consisting of one or more polypeptides typically folded into a globular or fibrous form, facilitating a biological function. A polypeptide is a single linear polymer chain of amino acids bonded together by peptide bonds between the carboxyl and amino groups of...

. The MC1R protein straddles the membrane

Cell membrane

The cell membrane or plasma membrane is a biological membrane that separates the interior of all cells from the outside environment. The cell membrane is selectively permeable to ions and organic molecules and controls the movement of substances in and out of cells. It basically protects the cell...

of pigment cells

Melanocyte

-External links: - "Eye: fovea, RPE" - "Integument: pigmented skin"...

(melanocytes). MC1R picks up a chemical called alpha-melanocyte-stimulating hormone

Melanocyte-stimulating hormone

The melanocyte-stimulating hormones are a class of peptide hormones that are produced by cells in the intermediate lobe of the pituitary gland...

(α-MSH), which is produced by the body, from outside the cell. When MC1R comes into contact with α-MSH, a complex reaction is triggered inside the cell, and the melanocyte begins to produce black-brown pigment (eumelanin). Without the stimulation of α-MSH, the melanocyte produces red-yellow pigment (pheomelanin) by default.

Various mutation

Mutation

In molecular biology and genetics, mutations are changes in a genomic sequence: the DNA sequence of a cell's genome or the DNA or RNA sequence of a virus. They can be defined as sudden and spontaneous changes in the cell. Mutations are caused by radiation, viruses, transposons and mutagenic...

s in the human Mc1r gene result in red hair

Red hair

Red hair occurs on approximately 1–2% of the human population. It occurs more frequently in people of northern or western European ancestry, and less frequently in other populations...

, blond hair, fair skin, and susceptibility to sundamaged skin and melanoma

Melanoma

Melanoma is a malignant tumor of melanocytes. Melanocytes are cells that produce the dark pigment, melanin, which is responsible for the color of skin. They predominantly occur in skin, but are also found in other parts of the body, including the bowel and the eye...

. Polymorphisms of Mc1r also lead to light or red coats in mice, cattle, and dogs, among others. The Extension locus was first suggested to have a role in horse coat color determination in 1974 by Stefan Adalsteinsson. Researchers at Uppsala University

Uppsala University

Uppsala University is a research university in Uppsala, Sweden, and is the oldest university in Scandinavia, founded in 1477. It consistently ranks among the best universities in Northern Europe in international rankings and is generally considered one of the most prestigious institutions of...

, Sweden, identified a missense mutation

Missense mutation

In genetics, a missense mutation is a point mutation in which a single nucleotide is changed, resulting in a codon that codes for a different amino acid . This can render the resulting protein nonfunctional...

in the Mc1r gene that resulted in a loss-of-function of the MC1R protein. Without the ability to produce a functional MC1R protein, eumelanin production could not be initiated in the melanocyte, resulting in coats devoid of true black pigment. Since horses with only one copy of the defective gene were normal, the mutation was labeled e or sometimes E^e. A single copy of the wildtype allele, which encodes a fully functional MC1R protein, is protective against the loss-of-function. The normal or wildtype allele is labeled E, or sometimes E⁺ or E^E.

Extension Phenotypes

E/E (+/+, E⁺/E⁺, E^E/E^E) wildtype, homozygous dominant. Visually, such horses are black
Black (horse)
Black is a hair coat color of horses in which the entire hair coat is black. Black is a relatively uncommon coat color, and novices frequently mistake dark chestnuts or bays for black. However, some breeds of horses, such as the Friesian horse, Murgese and Ariegeois are almost exclusively black...

, seal brown
Seal brown (horse)
Seal brown is a hair coat color of horses characterized by a near-black body color; with black points, the mane, tail and legs; but also reddish or tan areas around the eyes, muzzle, behind the elbow and in front of the stifle...

, bay, buckskin, perlino or smoky cream, bay dun
Dun gene
The dun gene is a dilution gene that affects both red and black pigments in the coat color of a horse. The dun gene has the ability to affect the appearance of all black, bay, or chestnut -based horses to some degree by lightening the base body coat and suppressing the underlying base color to the...

or grullo
Grullo
Grullo is a color of horses in the dun family, characterized by tan-gray or mouse-colored hairs on the body, often with shoulder and dorsal stripes and black barring on the lower legs. In this coloration each individual hair is mouse-colored, unlike a roan which is composed of a mixture of dark and...

, silver bay or silver black
Silver dapple gene
The silver dapple gene is a dilution gene that affects the black base coat color. It will typically dilute a black mane and tail to flaxen, and a black body to a shade of brown or chocolate. It is responsible for a group of coat colors in horses called "silver dapple" in the west, or "taffy" in...

. Some horses with genes for gray or white spotting patterns may also have the modifier, but the color may be hidden or overlain by the loss of pigmentation. Horses that are E/E will always pass on a functional copy of the Mc1r gene to its offspring, and will never produce offspring with the e/e genotype.
E/e (+/e, E⁺/E^e, E^E/E^e) wildtype, heterozygous. Visually, the horse may also be any of the colors seen with the E/E genotype. However, they statistically will only pass on the Mc1Lr gene 50% of the time. In addition, a recent study that compared horse genotypes to their coat color phenotypes did find a statistically significant connection that suggested that lighter bay shades were heterozygous for the Extension mutation (E/e) and darker bay shades were homozygous.
e/e (E^e/E^e) homozygous recessive. Visually, the horse may be any color in the "red" family: chestnut
Chestnut (coat)
Chestnut is a hair coat color of horses consisting of a reddish-to-brown coat with a mane and tail the same or lighter in color than the coat. Genetically and visually, chestnut is characterized by the absolute absence of true black hairs...

, palomino
Palomino
Palomino is a coat color in horses, consisting of a gold coat and white mane and tail. Genetically, the palomino color is created by a single allele of a dilution gene called the cream gene working on a "red" base coat...

, cremello, red dun
Dun gene
The dun gene is a dilution gene that affects both red and black pigments in the coat color of a horse. The dun gene has the ability to affect the appearance of all black, bay, or chestnut -based horses to some degree by lightening the base body coat and suppressing the underlying base color to the...

, gold champagne
Champagne gene
The champagne gene is a simple dominant allele responsible for a number of rare horse coat colors. The most distinctive traits of horses with the champagne gene are the hazel eyes and pinkish, freckled skin, which are bright blue and bright pink at birth, respectively...

, gray, and so on. Paired with an e/e mate, such horses will only ever produce red-family coat colors. At birth, the skin may be pink and the eyes blue, but these traits disappear after a few days and the eyes and skin of adult red coated horses are unaffected by this allele. No health defects are associated with the e allele.

Agouti

Agouti controls the restriction of true black pigment (eumelanin) in the coat. Horses with the normal agouti gene have the genotype A/A or A/a. Horses without a normal agouti gene have the genotype a/a, and if they are capable of producing black pigment, it is uniformly distributed throughout the coat. A third option, A^t, restricts black pigment to a black-and-tan pattern called seal brown

Seal brown (horse)

Seal brown is a hair coat color of horses characterized by a near-black body color; with black points, the mane, tail and legs; but also reddish or tan areas around the eyes, muzzle, behind the elbow and in front of the stifle...

. This allele is recessive to A and dominant to a, such that horses with the genotype A/A^t appear bay, while A^t/A^t and A^t/a horses are seal brown in the presence of a dominant Extension allele E.
The Agouti locus is occupied by the Agouti signalling peptide
Agouti signalling peptide
Agouti signalling peptide, a product of the Agouti gene, is a peptide consisting of 131 amino acids. Its discovery was published in 1994 in the scientific journal Nature where its functional properties were described...

(Asip) gene, which encodes the eponymous protein (ASIP). Agouti signalling peptide is a paracrine signaling molecule that competes with alpha-melanocyte stimulating hormone

Melanocyte-stimulating hormone

The melanocyte-stimulating hormones are a class of peptide hormones that are produced by cells in the intermediate lobe of the pituitary gland...

(α-MSH) for melanocortin 1 receptor

Melanocortin 1 receptor

The melanocortin 1 receptor , also known as melanocyte-stimulating hormone receptor , melanin-activating peptide receptor, or melanotropin receptor, is a G protein-coupled receptor which binds to a class of pituitary peptide hormones known as the melanocortins, of which include adrenocorticotropic...

proteins (MC1R). MC1R relies on α-MSH to halt production of red-yellow pheomelanin, and initiate production of black-brown eumelanin in its place.

In many species, successive pulses of ASIP block contact between α-MSH and MC1R, resulting in alternating production of eumelanin and pheomelanin; hairs are banded light and dark as a result. In other species, Asip is regulated such that it only occurs in certain parts of the body. The light undersides of most mammals are due to the carefully controlled action of ASIP. In mice, two mutations on Agouti are responsible for yellow coats and marked obesity, with other health defects. Additionally, the Agouti locus is the site of mutations in several species that result in black-and-tan pigmentations. In normal horses, ASIP restricts the production of eumelanin to the "points": the legs, mane, tail, ear edges, etc. In 2001, researchers discovered a recessive mutation on Asip that, when homozygous, left the horse without any ASIP. As a result, horses capable of producing true black pigment had uniformly black coats. More recently, one coat color testing lab has begun offering a test for A^t. Further research remains to be seen.

Agouti Phenotypes

A/A wildtype, homozygous. Visually, the horse may be bay, buckskin, bay dun
Dun gene
The dun gene is a dilution gene that affects both red and black pigments in the coat color of a horse. The dun gene has the ability to affect the appearance of all black, bay, or chestnut -based horses to some degree by lightening the base body coat and suppressing the underlying base color to the...

, amber champagne
Champagne gene
The champagne gene is a simple dominant allele responsible for a number of rare horse coat colors. The most distinctive traits of horses with the champagne gene are the hazel eyes and pinkish, freckled skin, which are bright blue and bright pink at birth, respectively...

, and so on, or gray
Gray (horse)
Gray or grey is a coat color of horses characterized by progressive silvering of the colored hairs of the coat. Most gray horses have black skin and dark eyes; unlike many depigmentation genes, gray does not affect skin or eye color Their adult hair coat is white, dappled, or white intermingled...

, or any member of the red family. However, such a horse will never be black
Black (horse)
Black is a hair coat color of horses in which the entire hair coat is black. Black is a relatively uncommon coat color, and novices frequently mistake dark chestnuts or bays for black. However, some breeds of horses, such as the Friesian horse, Murgese and Ariegeois are almost exclusively black...

, grullo
Grullo
Grullo is a color of horses in the dun family, characterized by tan-gray or mouse-colored hairs on the body, often with shoulder and dorsal stripes and black barring on the lower legs. In this coloration each individual hair is mouse-colored, unlike a roan which is composed of a mixture of dark and...

, and so on, nor will a homozygous A horse ever produce uniform-black offspring or seal brown offspring.
A/A^t wildtype, heterozygous. Visually indistinguishable from the homozygous A horse, such horses will also never produce a uniform-black foal.
A/a wildtype, heterozygous. Visually indistinguishable from the homozygous A horse. With the right partner, such horses can produce uniform-black foals.
A^t/A^t seal brown or black-and-tan. Visually, the horse may be chestnut or gray, but in the presence of a dominant E allele, the coat will be seal brown
Seal brown (horse)
Seal brown is a hair coat color of horses characterized by a near-black body color; with black points, the mane, tail and legs; but also reddish or tan areas around the eyes, muzzle, behind the elbow and in front of the stifle...

. Variants of seal brown include dark buckskin, perlino, seal brown dun, and sable champagne.
A^t/a indistinguishable from the homozygous seal brown. Such horses may produce uniform-black offspring.
a/a homozygous recessive. Visually, in the presence of a dominant E allele, the horse's coat will be a uniform black, or the related smoky black, smoky cream, grullo, classic champagne, silver black, and so on.

Dun

Dun is one of several genes that control the saturation or intensity of pigment in the coat. Dun is unique in that it is simple dominant, affects eumelanin and pheomelanin equally, and does not affect the eyes or skin. Horses with the dominant D allele (D/D or D/d genotype) exhibit hypomelanism

Dilution gene

Dilution gene is a popular term for any one of a number of genes that act to create a lighter coat color in living creatures. There are many examples of such genes:-General:...

of the body coat, while d/d horses have otherwise intense, saturated coat colors. The mane, tail, head, legs, and primitive markings

Primitive markings

Primitive markings among domestic horses are a group of hair coat markings and qualities associated with primitive breeds, and the dun coat color family in particular. All dun horses possess at least the dorsal stripe but the presence of the other primitive markings varies...

are not diluted. In some breeds, zygosity for Dun can be determined with an indirect DNA test.

While the Dun locus is known to be on equine chromosome 8, its precise location, the gene and protein involved, and exact mutation are not yet known. The molecular cause behind the dun coat colors is similarly not yet understood. The associated coat colors were assigned to the Dun locus in 1974 by Stefan Adalsteinsson, separate from Cream, with the presence of dun dilution indicated by the dominant D allele. The dominant D allele is relatively rare compared to the alternative d allele, and for this reason, the dominant allele is often treated as a mutation. However, the pervasive coat color among wild equids is in fact dun, and researchers from Darwin to modern day consider dun to be the wildtype state.

Dun Phenotypes

D/D (+/+, D⁺/D⁺) wildtype, homozygous dominant. Visually, the horse may be bay dun, grullo, red dun, palomino dun, amber dun, gray, and so on. Such a horse will always pass on the D allele and will therefore always have dun offspring.
D/d (+/d, D⁺/D^d) wildtype, heterozygous. Visually indistinguishable from the homozygous D horse.
d/d (D^d/D^d) non-dun, homozygous recessive. The entire coat, barring the influence of other alleles, is a rich, saturated color. The primitive markings
Primitive markings
Primitive markings among domestic horses are a group of hair coat markings and qualities associated with primitive breeds, and the dun coat color family in particular. All dun horses possess at least the dorsal stripe but the presence of the other primitive markings varies...

are no longer visible. The horse may be chestnut
Chestnut (coat)
Chestnut is a hair coat color of horses consisting of a reddish-to-brown coat with a mane and tail the same or lighter in color than the coat. Genetically and visually, chestnut is characterized by the absolute absence of true black hairs...

, bay, black
Black (horse)
Black is a hair coat color of horses in which the entire hair coat is black. Black is a relatively uncommon coat color, and novices frequently mistake dark chestnuts or bays for black. However, some breeds of horses, such as the Friesian horse, Murgese and Ariegeois are almost exclusively black...

, gray
Gray (horse)
Gray or grey is a coat color of horses characterized by progressive silvering of the colored hairs of the coat. Most gray horses have black skin and dark eyes; unlike many depigmentation genes, gray does not affect skin or eye color Their adult hair coat is white, dappled, or white intermingled...

, palomino
Palomino
Palomino is a coat color in horses, consisting of a gold coat and white mane and tail. Genetically, the palomino color is created by a single allele of a dilution gene called the cream gene working on a "red" base coat...

, and so on.

Cream

Cream is another one of the genes that control the saturation or dilution

Dilution gene

Dilution gene is a popular term for any one of a number of genes that act to create a lighter coat color in living creatures. There are many examples of such genes:-General:...

of pigment in the coat. Cream differs from Dun in that it affects the coat, skin, and eyes, and unlike Dun, is dosage dependent rather than simple dominant. Furthermore, the effects on eumelanin and pheomelanin are not equal. Horses with the homozygous recessive genotype (C/C) are not affected by cream. Heterozygotes (C^Cr/C) have one cream allele and one wildtype non-cream allele. Such horses, sometimes called "single-dilutes", exhibit dilution red pigment in the coat, eyes, and skin to yellow or gold, while eumelanin is largely unaffected. Homozygotes (C^Cr/C^Cr) have two cream alleles, and are sometimes called "double-dilutes." Homozygous creams exhibit strong dilution of both red and black pigment in the coat, eyes, and skin to ivory or cream. The skin is rosy-pink and the eyes are pale blue. Cream is now identifiable by DNA test.
The Cream locus is occupied by the Solute carrier family 45, member 2

SLC45A2

Membrane-associated transporter protein also known as solute carrier family 45 member 2 or melanoma antigen AIM1 is a protein that in humans is encoded by the SLC45A2 gene.-Function:...

(SLC45A2) gene, also called the Membrane associated transport protein or Matp gene. The Matp gene encodes a protein

Protein

illustrated to have roles in melanogenesis in human

Human

Humans are the only living species in the Homo genus...

s, mice

Mouse

A mouse is a small mammal belonging to the order of rodents. The best known mouse species is the common house mouse . It is also a popular pet. In some places, certain kinds of field mice are also common. This rodent is eaten by large birds such as hawks and eagles...

, and medaka, though the specific action is not known.

Mutation

Mutation

s in the human Matp gene result in several distinct forms of Oculocutaneous albinism, Type IV as well as normal variations in skin and hair color. Mice affected by a condition homologous to cream, called underwhite, exhibit irregularly shaped melanosome

Melanosome

In a biological cell, a melanosome is an organelle containing melanin, the most common light-absorbing pigment found in the animal kingdom.Cells that synthesize melanins are called melanocytes, and also the retinal pigment epithelium cells, whereas cells that have merely engulfed the melanosomes...

s, which are the organelles within melanocytes that directly produce pigment. The first descriptions of the dosage-dependent genetic control of the palomino coat color occurred early on in equine coat color inheritance research. However, the distinction between Dun and Cream remained poorly understood until Stefan Adalsteinsson wrote Inheritance of the palomino color in Icelandic horses in 1974. The mutation responsible, a single nucleotide polymorphism

Single nucleotide polymorphism

A single-nucleotide polymorphism is a DNA sequence variation occurring when a single nucleotide — A, T, C or G — in the genome differs between members of a biological species or paired chromosomes in an individual...

in Exon

Exon

An exon is a nucleic acid sequence that is represented in the mature form of an RNA molecule either after portions of a precursor RNA have been removed by cis-splicing or when two or more precursor RNA molecules have been ligated by trans-splicing. The mature RNA molecule can be a messenger RNA...

2 resulting in an aspartic acid

Aspartic acid

Aspartic acid is an α-amino acid with the chemical formula HOOCCHCH2COOH. The carboxylate anion, salt, or ester of aspartic acid is known as aspartate. The L-isomer of aspartate is one of the 20 proteinogenic amino acids, i.e., the building blocks of proteins...

-to-asparagine

Asparagine

Asparagine is one of the 20 most common natural amino acids on Earth. It has carboxamide as the side-chain's functional group. It is not an essential amino acid...

substitution (N153D), was located and described in 2003 by a research team in France.

Cream Phenotypes

C/C homozygous wildtype. Visually, the horse may be any color other than the cream dilute shades of palomino, buckskin, smoky black, cremello, perlino, smoky cream, and so on.
C^Cr/C heterozygous. The colors most commonly associated with this genotype are palomino, buckskin, and smoky black, though the phenotype may vary depending on other factors. Any pheomelanin in the coat is diluted to yellow or gold, and the eyes and skin are often slightly lighter than unaffected horses.
C^Cr/C^Cr homozygous. The colors most commonly associated with this genotype are cremello, perlino, and smoky cream. Regardless, the coat will be cream- or ivory-colored, and the skin a rosy-pink. The eyes are pale blue.

Champagne

Champagne is a gene that controls the saturation or dilution

Dilution gene

Dilution gene is a popular term for any one of a number of genes that act to create a lighter coat color in living creatures. There are many examples of such genes:-General:...

of pigment in the coat. Unlike Cream, Champagne is not strongly dosage-dependent, and affects both types of pigment equally. Champagne differs from Dun in that it affects the color of the coat, skin, and eyes, and in that the unaffected condition is the wildtype. Horses with the dominant CH allele (CH/CH or CH/ch genotype) exhibit hypomelanism of the body coat, such that phaeomelanin is diluted to gold and eumelanin is diluted to tan. Affected horses are born with blue eyes which darken to amber, green, or light brown, and bright pink skin which acquires darker freckling with maturity. The difference in phenotype between the homozygous (CH/CH) and heterozygous (CH/ch) horse may be subtle, in that the coat of the homozygote may be a shade lighter, with less mottling. Horses with the homozygous recessive genotype (ch/ch) are not affected by champagne. Champagne is now identifiable by DNA test.
The Champagne locus is occupied by the Solute carrier family 36, member 1

SLC36A1

Proton-coupled amino acid transporter 1 is a protein that in humans is encoded by the SLC36A1 gene.-Further reading:...

(SLC36A1) gene, which encodes the Proton-coupled amino acid transporter 1 (PAT1) protein. This protein is one of many which is involved in active transport

Active transport

Active transport is the movement of a substance against its concentration gradient . In all cells, this is usually concerned with accumulating high concentrations of molecules that the cell needs, such as ions, glucose, and amino acids. If the process uses chemical energy, such as from adenosine...

. The gene associated with the Cream coat colors is also a solute carrier, and orthologous genes in humans, mice, and other species are also linked to coat color phenotypes. The single nucleotide polymorphism

Single nucleotide polymorphism

responsible for the champagne phenotype is a missense mutation

Missense mutation

in exon

Exon

2, in which a C is replaced with a G, such that a threonine

Threonine

Threonine is an α-amino acid with the chemical formula HO2CCHCHCH3. Its codons are ACU, ACA, ACC, and ACG. This essential amino acid is classified as polar...

is replaced with arginine

Arginine

Arginine is an α-amino acid. The L-form is one of the 20 most common natural amino acids. At the level of molecular genetics, in the structure of the messenger ribonucleic acid mRNA, CGU, CGC, CGA, CGG, AGA, and AGG, are the triplets of nucleotide bases or codons that codify for arginine during...

. This mutation was identified and described by an American research team in 2008.

Champagne Phenotypes

ch/ch (N/N) wildtype, homozygous recessive. Visually, the horse may be any color other than the champagne shades.
CH/ch (CH/N) heterozygous. The colors most commonly associated with this genotype are gold champagne, amber champagne, and classic champagne, though the exact phenotype depends on a variety of factors. At birth, the skin is bright pink and the eyes bright blue, darkening to freckled and light brown or green, respectively, with age. Both red and black pigment in the hair are also diluted.
CH/CH homozygous champagne. Homozygotes, which will never produce non-champagne offspring, are indistinguishable from heterozygotes except that their freckling may be sparser, and their coats a shade lighter.

Alleles and effects

Locus	Alleles	Effect of combined pairs of alleles
Extension (E)	E e	EE or Ee: Horse forms black Black (horse) Black is a hair coat color of horses in which the entire hair coat is black. Black is a relatively uncommon coat color, and novices frequently mistake dark chestnuts or bays for black. However, some breeds of horses, such as the Friesian horse, Murgese and Ariegeois are almost exclusively black... pigment in skin and hair. ee: Horse is chestnut Chestnut (coat) Chestnut is a hair coat color of horses consisting of a reddish-to-brown coat with a mane and tail the same or lighter in color than the coat. Genetically and visually, chestnut is characterized by the absolute absence of true black hairs... , it has black pigment in skin, but red pigment in hair.
Agouti (A)	A a	Agouti: Restricts eumelanin, or black pigment, to "points," allowing red coat color to show on body. No visible effect on red horses, as there is no black pigment to restrict. AA or Aa horse is a Bay, black hair shows only in points pattern (usually mane Mane (horse) The mane is the hair that grows from the top of the neck of a horse or other equine, reaching from the poll to the withers, and includes the forelock or foretop. It is thicker and coarser than the rest of the horse's coat, and naturally grows to roughly cover the neck... , tail, legs, sometimes tips of ears). aa: No agouti gene. If horse has E allele, then horse will be uniformly black.
Cr	Cr C	Cream gene The cream gene Cream gene The cream gene is responsible for a number of horse coat colors. Horses that have the cream gene in addition to a base coat color that is chestnut will become palomino if they are heterozygous, having one copy of the cream gene, or cremello, if they are homozygous. Similarly, horses with a bay... is an incomplete dominant Dominance relationship Dominance in genetics is a relationship between two variant forms of a single gene, in which one allele masks the effect of the other in influencing some trait. In the simplest case, if a gene exists in two allelic forms , three combinations of alleles are possible: AA, AB, and BB... . CC: No dilution factor, horse is fully pigmented. (UC Davis abbreviates as N.) *CCr: Single dilution Dilution gene Dilution gene is a popular term for any one of a number of genes that act to create a lighter coat color in living creatures. There are many examples of such genes:-General:... factor (heterozygous dilute) results in Palomino Palomino Palomino is a coat color in horses, consisting of a gold coat and white mane and tail. Genetically, the palomino color is created by a single allele of a dilution gene called the cream gene working on a "red" base coat... , Buckskin Buckskin Buckskin may refer to:Buckskin , leather made of buck hideBuckskins, an outfit of buckskin leatherBuckskin , a color of horses similar to buckskin leather... or Smoky Black Smoky black Smoky black is a hair coat color of horses in which the coat is either black or a few shades lighter than true black. Smoky black is produced by the action of a heterozygous cream gene on an underlying black coat color... . Red pigment is diluted to gold with cream to white mane and tail; black pigment is not visibly altered on black points or black horses, though genetic testing can reveal "smoky black" coloration. (UC Davis abbreviates as *N/Cr.) CrCr* Cremello or Perlino: Double dilution factor (homozygous dilute). Red pigment is diluted to a pale cream. Black pigment is diluted to a reddish shade. Skin and eye color are also diluted, skin is pink and blue eyes are common with double diluted creams Cream gene The cream gene is responsible for a number of horse coat colors. Horses that have the cream gene in addition to a base coat color that is chestnut will become palomino if they are heterozygous, having one copy of the cream gene, or cremello, if they are homozygous. Similarly, horses with a bay... . (UC Davis abbreviates as Cr.)
D	D d	*DD or Dd*: Dun gene Dun gene The dun gene is a dilution gene that affects both red and black pigments in the coat color of a horse. The dun gene has the ability to affect the appearance of all black, bay, or chestnut -based horses to some degree by lightening the base body coat and suppressing the underlying base color to the... Another dilution gene Dilution gene Dilution gene is a popular term for any one of a number of genes that act to create a lighter coat color in living creatures. There are many examples of such genes:-General:... . Horse shows a diluted body color to pinkish-red, yellow-red, yellow or mouse gray and has dark points including dorsal stripe, shoulder stripe and leg barring. dd: Horse has undiluted coat color.
Ch	Ch ch	Champagne: A rare but dominant dilution gene Dilution gene Dilution gene is a popular term for any one of a number of genes that act to create a lighter coat color in living creatures. There are many examples of such genes:-General:... that creates pumpkin-colored freckled skin, amber, greenish, or blue eyes, and gives a bronze cast to hair. The skin surrounding the eye must be pink with freckles in adulthood. *ChCh* or *Chch: Champagne Champagne gene The champagne gene is a simple dominant allele responsible for a number of rare horse coat colors. The most distinctive traits of horses with the champagne gene are the hazel eyes and pinkish, freckled skin, which are bright blue and bright pink at birth, respectively... dilution evident (See Genetic Formulas Chart below.) chch*: No champagne dilution
Z	Z z	ZZ or Zz: Silver dapple Silver dapple gene The silver dapple gene is a dilution gene that affects the black base coat color. It will typically dilute a black mane and tail to flaxen, and a black body to a shade of brown or chocolate. It is responsible for a group of coat colors in horses called "silver dapple" in the west, or "taffy" in... - Dilutes eumelanin or black pigment. Converts black to brown with white mane and tail or results in silver coloring. zz: No silver dapple.
Prl	Prl prl	Pearl: A new rare recessive Recessive In genetics, the term "recessive gene" refers to an allele that causes a phenotype that is only seen in a homozygous genotype and never in a heterozygous genotype. Every person has two copies of every gene on autosomal chromosomes, one from mother and one from father... dilution gene Dilution gene Dilution gene is a popular term for any one of a number of genes that act to create a lighter coat color in living creatures. There are many examples of such genes:-General:... that looks very much like Champagne. The Pearl gene Pearl gene The Pearl gene, also known as the "Barlink factor," is a dilution gene that somewhat resembles the cream gene and the champagne gene, but is neither. It is a somewhat rare dilution gene found in the American Quarter Horse, American Paint Horse, and Peruvian Paso. The same mutation appears in... is sometimes referred to as the "barlink factor." One dose of the mutation does not change the coat color of black, bay or chestnut horses. Two doses on a chestnut background produce a pale, uniform apricot color of body hair, mane and tail. Skin coloration is also pale. Pearl is known to interact with Cream dilution to produce pseudo-double Cream dilute phenotypes including pale skin and blue/green eyes. *PrlPrl* or *Prlprl: No pearl dilution. prlprl*: Pearl Pearl gene The Pearl gene, also known as the "Barlink factor," is a dilution gene that somewhat resembles the cream gene and the champagne gene, but is neither. It is a somewhat rare dilution gene found in the American Quarter Horse, American Paint Horse, and Peruvian Paso. The same mutation appears in... dilution evident.
TO	TO to	*TOTO* or *TOto: Tobiano Tobiano Tobiano is a spotted color pattern commonly seen in Pinto horses, produced by a dominant gene. The tobiano gene produces white-haired, pink-skinned patches on a base coat color. The coloration is present from birth and does not change throughout the horse's lifetime, unless the horse also carries... , a form of pinto Pinto horse A pinto horse has a coat color that consists of large patches of white and any other color. The distinction between "pinto" and "solid" can be tenuous, as so-called "solid" horses frequently have areas of white hair. Various cultures throughout history appear to have selectively bred for pinto... patterning. Produces regular and distinct ovals or rounded patterns of white and color with a somewhat vertical orientation. White extends across the back, down the legs, but face and tail are usually dark. toto*: No tobiano Tobiano Tobiano is a spotted color pattern commonly seen in Pinto horses, produced by a dominant gene. The tobiano gene produces white-haired, pink-skinned patches on a base coat color. The coloration is present from birth and does not change throughout the horse's lifetime, unless the horse also carries... pattern present.
O Also noted as Fr or FrO	O o	OO or Oo: Overo or Frame Overo pattern - Pinto horse Pinto horse A pinto horse has a coat color that consists of large patches of white and any other color. The distinction between "pinto" and "solid" can be tenuous, as so-called "solid" horses frequently have areas of white hair. Various cultures throughout history appear to have selectively bred for pinto... pattern that forms a solid frame around white spotting. White is usually horizontal in orientation with jagged edges, color crosses the back and legs, face is often white. Overo Overo Overo refers to several genetically unrelated pinto coloration patterns of white-over-dark body markings in horses, and is a term used by the American Paint Horse Association to classify a set of pinto patterns that are not Tobiano... as an allele is different from overo as a registration since the registration also includes the splash overo and sabino Sabino horse Sabino is a group of white spotting patterns in horses that affect the skin and hair. A wide variety of irregular color patterns are accepted as sabino. In the strictest sense, "sabino" refers to the white patterns produced by the Sabino 1 gene, for which there is a DNA test... alleles. Homozygous overo is associated with lethal white syndrome Lethal white syndrome Lethal white syndrome , also called overo lethal white syndrome , lethal white overo , and overo lethal white foal syndrome , is an autosomal genetic disorder most prevalent in the American Paint Horse... , characterized by an incomplete colon Colon (anatomy) The colon is the last part of the digestive system in most vertebrates; it extracts water and salt from solid wastes before they are eliminated from the body, and is the site in which flora-aided fermentation of unabsorbed material occurs. Unlike the small intestine, the colon does not play a... and the inability to defecate, which leads to death or humane euthanization within days of birth. oo: No overo pattern present.
W	W w	WW: Lethal. Embryo reabsorbed or fetus dies en utero. Ww: Horse has pink skin and white hair, brown or dark eyes. Hair coat is white White (horse) White horses are born white and stay white throughout their life. White horses may have brown, blue, or hazel eyes. "True white" horses, especially those that carry one of the dominant white genes, are rare... from birth. ww: Horse is fully pigmented.
G	G g	GG or Gg: gray Gray (horse) Gray or grey is a coat color of horses characterized by progressive silvering of the colored hairs of the coat. Most gray horses have black skin and dark eyes; unlike many depigmentation genes, gray does not affect skin or eye color Their adult hair coat is white, dappled, or white intermingled... gene. Horse shows progressive silvering with age to white or flea-bitten, but is born a non-gray color. Pigment is always present in skin and eyes at all stages of silvering. Gray Gray (horse) Gray or grey is a coat color of horses characterized by progressive silvering of the colored hairs of the coat. Most gray horses have black skin and dark eyes; unlike many depigmentation genes, gray does not affect skin or eye color Their adult hair coat is white, dappled, or white intermingled... horses range from white to dark gray depending on age and the proportion of white hairs in the coat. Horses' coats gray in a manner similar to graying in human hair. gg: Horse does not gray with aging.
Rn	Rn rn	*RnRn* or *Rnrn: roan Roan (horse) Roan is a horse coat color pattern characterized by an even mixture of colored and white hairs on the body, while the head and "points"—lower legs, mane and tail—are more solid-colored. The roan pattern is dominantly-inherited, and is found in many horse breeds... pattern of white hair mixed in with base color. There quite likely is no lethal roan question. rnrn*: No roan pattern.
Sb	Sb sb	Sabino Sabino horse Sabino is a group of white spotting patterns in horses that affect the skin and hair. A wide variety of irregular color patterns are accepted as sabino. In the strictest sense, "sabino" refers to the white patterns produced by the Sabino 1 gene, for which there is a DNA test... - Assorted pinto Pinto horse A pinto horse has a coat color that consists of large patches of white and any other color. The distinction between "pinto" and "solid" can be tenuous, as so-called "solid" horses frequently have areas of white hair. Various cultures throughout history appear to have selectively bred for pinto... or roan-like markings. Sabino Sabino horse Sabino is a group of white spotting patterns in horses that affect the skin and hair. A wide variety of irregular color patterns are accepted as sabino. In the strictest sense, "sabino" refers to the white patterns produced by the Sabino 1 gene, for which there is a DNA test... may be polygenic (a gene-complex rather than a single gene pair), caused by several different genes. Recognized by abundant white on the legs, belly spots or body spots that are can be flecked and roaned, chin spots, or white on the face extending past the eyes. Sabino is registered as overo by some registries, but is not the overo or frame overo allele. No risk of lethal white, though some "Fully expressed" sabinos may be completely white White (horse) White horses are born white and stay white throughout their life. White horses may have brown, blue, or hazel eyes. "True white" horses, especially those that carry one of the dominant white genes, are rare... in coat color. *SbSb* or *Sbsb: Sabino markings. sbsb: No sabino markings. SB1*:The only Sabino gene currently detected by DNA testing, however does not appear to be the gene that creates sabino coloring in Arabians or Clydesdales.
Lp	Lp lp	Appaloosa Appaloosa The Appaloosa is a horse breed best known for its colorful leopard-spotted coat pattern. There is a wide range of body types within the breed, stemming from the influence of multiple breeds of horses throughout its history. Each horse's color pattern is genetically the result of various spotting... or Leopard Leopard (pattern) Leopard is a term used to describe a spotted color pattern, particularly in the hair coat or skin of animals, but also used to describe spotting patterns in plants and fabrics... spotting gene. Produces coat spotting patterns, mottling over otherwise dark skin, striped hooves and white sclera Sclera The sclera , also known as the white or white of the eye, is the opaque , fibrous, protective, outer layer of the eye containing collagen and elastic fiber. In the development of the embryo, the sclera is derived from the neural crest... around the eye.

Genetic formulas and color definitions

Phenotype	Potential Genotype
	Extension	Agouti	Dun	Champagne	Silver	Cream	Pearl
Bay	E/-	A/-	d/d	ch/ch	z/z	cr/cr	prl/prl
Chestnut	e/e	-/-	d/d	ch/ch	-/-	cr/cr	prl/prl
Black	E/-	a/a	d/d	ch/ch	z/z	cr/cr	prl/prl
Bay dun	E/-	A/-	D/-	ch/ch	z/z	cr/cr	prl/prl
Red dun	e/e	-/-	D/-	ch/ch	-/-	cr/cr	prl/prl
Grullo	E/-	a/a	D/-	ch/ch	z/z	cr/cr	prl/prl
Amber champagne	E/-	A/-	d/d	CH/-	z/z	cr/cr	prl/prl
Gold champagne	e/e	-/-	d/d	CH/-	-/-	cr/cr	prl/prl
Classic champagne	E/-	a/a	d/d	CH/-	z/z	cr/cr	prl/prl
Silver bay	E/-	A/-	d/d	ch/ch	Z/-	cr/cr	prl/prl
Silver black	E/-	a/a	d/d	ch/ch	Z/-	cr/cr	prl/prl
Buckskin	E/-	A/-	d/d	ch/ch	z/z	CR/cr	prl/prl
Perlino	E/-	A/-	d/d	ch/ch	z/z	CR/CR	prl/prl
Palomino	e/e	-/-	d/d	ch/ch	z/z	CR/cr	prl/prl
Cremello	e/e	-/-	d/d	ch/ch	z/z	CR/CR	prl/prl
Bay pearl	E/-	A/-	d/d	ch/ch	z/z	cr/cr	PRL/prl
Bay double pearl	E/-	A/-	d/d	ch/ch	z/z	cr/cr	PRL/PRL
Chestnut pearl	e/e	-/-	d/d	ch/ch	z/z	cr/cr	PRL/prl
Apricot	e/e	-/-	d/d	ch/ch	z/z	cr/cr	PRL/PRL
Black pearl	E/-	a/a	d/d	ch/ch	z/z	cr/cr	PRL/prl
Black double pearl	E/-	a/a	d/d	ch/ch	z/z	cr/cr	PRL/PRL

Sources and external links

"Horse coat color tests" from the UC Davis Veterinary Genetics Lab
"Introduction to Coat Color Genetics" from Veterinary Genetics Laboratory, School of Veterinary Medicine, University of California, Davis. Web Site accessed January 12, 2008
"In the Genes." Quarter Horse News, Dec 15, 2004
"Horse Color Calculator" From Animal Genetics Incorporated. This creates the possible coat coloring of the offspring from the imputed color of sire and dam.

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