Equine coat color genetics

thumb|Before domestication, horses are thought to have had these coat colors.

Equine coat color genetics determine a horse's coat color. Many colors are possible, but all variations are produced by changes in only a few genes. Bay is the most common color of horse, Leopard complex patterns also predate domestication, having been found in horse remains from 20,000 years ago. The mutation responsible for black and grullo also predates domestication. Silver and cream dilutions appeared at least 2,600 years ago, and pearl appeared at least 1400 years ago. The gray mutation is also post-domestication but thought to be thousands of years old as well.

Fundamental concepts

Terminology

Heritable characteristics are transmitted, encoded, and used through a substance called DNA, which is stored in almost every cell in an organism. Proteins are molecules that do a variety of different things in organisms. The DNA instructions for how to make a protein are called a gene. A change to the sequence of DNA is called a mutation. Mutations are not inherently bad; genetic diversity itself ultimately comes from mutations. Mutations that happen within a gene create alternate forms of that gene, which are called alleles. Alleles of a gene are simply slightly different versions of the instructions on how to make that gene's protein. The term "allele" is sometimes replaced with the word "modifier", because different alleles tend to modify the horse's appearance in some way. DNA is organized into storage structures called chromosomes. A chromosome is simply a very long piece of DNA, and a gene is a much shorter piece of it. With some rare exceptions, a gene is always found at the same place within a chromosome, which is called its locus. For the most part, chromosomes come in pairs, one chromosome from each parent. When both chromosomes have the same allele for a certain gene, that individual is said to be homozygous for that gene. When the two alleles are different, it is heterozygous. 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. A trait that is only expressed when the gene is homozygous for its allele is called recessive, and a trait that has the same effect no matter whether there is one copy or two is called dominant.

Notation

Often, the dominant allele is represented by an uppercase letter and the recessive allele by a lowercase letter. For instance, in silver dapple, this is Z for the dominant silver trait and z for the recessive non-silver trait. However, sometimes the alleles are distinguished by which is the "normal" or wild type allele and which is a more recent mutation. In our example z (non-silver) would be wild type and Z would be a mutation. Wild type alleles can be represented as + or n, so Zz, Zz+, Z/+, and Z/n are all valid ways to describe a horse heterozygous for silver. Wild type notation is mainly useful when there is no clear dominant/recessive relationship, such as with cream and frame overo, or when there are many alleles on the same gene, such as with MITF, which has four known alleles. Using n is also common in the results of genetic tests, where a negative result usually means none of the known mutations were found, but does not rule out undiscovered mutations.

Melanin

Genes affecting coat color generally do so by changing the process of producing melanin. Melanin is the pigment that colors the hairs and skin of mammals. There are two chemically distinct types of melanin: pheomelanin, which is a red to yellow color, and eumelanin, which is brown to black. Melanin is not a protein and therefore there is no gene that changes its structure directly, but there are many proteins involved in the production of melanin or the formation of melanocytes during embryonic development. Mutations that change the structure of proteins with a role in melanin production can result in slightly different variations of melanin. Some genes do not alter the structure of melanin but instead affect where and whether it is produced.

Extension and agouti

The genes extension and agouti together affect the placement of the two types of pigment, black eumelanin and "red" (coppery brown) pheomelanin.

The extension gene codes for a molecule called the Melanocortin 1 receptor, or MC1R. This receptor straddles the membrane of pigment cells, and when activated it signals the cell to produce black pigment instead of red. A recessive mutation to extension removes this functionality, causing the solid red color of chestnut horses.

The agouti gene codes for a molecule called the agouti-signaling protein, or ASIP. This molecule interacts with MC1R, the receptor coded by extension, to block the signal for black pigment production. The signal for black pigment comes from a melanocyte-stimulating hormone, which is present throughout the horse. ASIP is not present everywhere, which allows some areas to be black while others are red. ASIP can also be limited by the phase of hair growth, allowing the tips of the hairs to be black while the base is red. This can be observed in horses which have their winter coats clipped. When shaved close, the black tip is shorn off leaving the phaeomelanic bottom of the shaft. This produces a dull, orange-gold appearance on the body coat which is lost with the spring shed. This is not usually seen in dark bays, which have little red in the hair shaft. A mutation to agouti removes the ability to block the black signal, resulting in a fully black horse.

Phenotypes

{|class="wikitable sortable"

!Extension!!Agouti!!Image!!Description

| ee

| any

| 150px

| Chestnut, or depending on other genes red dun, palomino, cremello, gold champagne, and others.

| EE or Ee

| aa

| 150px

| Black, or depending on other genes grullo, smoky cream, silver dapple, classic champagne, and others.

| EE or Ee

| AA or Aa

| 150px

| Bay, or depending on other genes bay dun, buckskin, perlino, silver bay, amber champagne, and others.

Extension

Extension is found on equine chromosome 3 as part of a linkage group with roan, tobiano, and the KIT gene. Extension is also sometimes called "red factor" and can be identified through DNA testing.

Mutations that break protein function generally lead to recessively inherited lighter or redder coat colors in various mammals, while mutations that cause MC1R to be constantly active result in dominantly inherited black coats. In horses, both known mutations break the protein and therefore result in red coats.

Various mutations in the human MC1R gene result in red hair, blond hair, fair skin, and susceptibility to sunburnt skin and melanoma. 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, Sweden, identified a missense mutation 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.

Extension alleles

There are three known alleles of extension, the wildtype E, and two recessive alleles e and ea which cause chestnut color.

Agouti

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.

One genetics testing lab began offering a test for another allele At, thought to be responsible for seal brown, but it was later found to be inaccurate and is no longer offered.

Dun

thumb|right|The flat, earthy tone of the coat and vivid dorsal stripe are indicative of the D allele. [[Primitive markings are seldom visible on horses without the dominant, wildtype dun allele (D).]]

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 of the body coat, while d/d horses have otherwise intense, saturated coat colors. The mane, tail, head, legs, and primitive markings are not diluted. Zygosity for Dun can be determined with a DNA test. The molecular cause behind the dun coat colors is not entirely understood, but the dilution effect comes from the placement of pigment in only part of the hair. 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.

An older non-dun mutation was found in 2015 and named non-dun 1. It creates primitive markings but does not dilute the base color, and is co-dominant with the more common non-dun 2 but recessive to dun.

The Cream locus is occupied by the Solute carrier family 45, member 2 (SLC45A2) gene, also called the Membrane associated transport protein or Matp gene. The Matp gene encodes a protein illustrated to have roles in melanogenesis in humans, mice, and medaka, though the specific action is not known. Mice affected by a condition homologous to cream, called underwhite, exhibit irregularly shaped melanosomes, 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 Champagne locus is occupied by the Solute carrier family 36, member 1 (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. 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.

|PMEL or SILV (Silver dapple)

|Z n

|Z/Z or Z/n: Silver dapple - Dilutes eumelanin (black pigment). Converts black to brown with white/silvery mane and tail or results in silver coloring. n/n: No silver.

|MFSD12 (Mushroom)

|Mu mu

|Mu/Mu or Mu/mu: Mushroom - Dilutes red pigment to a sepia shade. mu/mu: No mushroom effect.

|STX17 (Gray)

|G g

|G/G or G/n: gray gene. Horse is born another color and "greys out" as it ages. Pigment in the skin does not change throughout the greying process. Gray The greying process is progressive and unique to the horse. n/n: No grey.

|EDNRB (Frame Overo/Lethal white syndrome)

|OLW or Fr n

|OLW/n: Frame Overo pattern - Pinto horse pattern that forms a solid "frame" around white spotting. White is usually horizontal in orientation with jagged edges, rarely crossing the back, and often has a top-heavy face marking. The Overo "OLW" allele is different from overo as a color pattern classification in those registries which also include the splashed white and sabino genes under the heading "overo." n/n: No frame overo present. OLW/OLW: Homozygous frame overo is lethal white syndrome, characterized by an incomplete colon and the inability to defecate, which leads to death or humane euthanization within days of birth.

|Inversion starting about 100k bp downstream of KIT (Tobiano)

|TO n

|TO/TO or TO/n: Tobiano, a form of 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, and often over the shoulder and crest. A white tail head is also very common. n/n: No tobiano pattern present.

|KIT or CD117 (White, Sabino)

|W1 W2 ... W27 SB1 n

|Complicated. See white and sabino. W/W: Thought to be lethal. Embryo reabsorbed or fetus dies en utero. W/n, W5/W20, W20/W22, or SB1/SB1: Horse has pink skin and white hair, usually with brown or dark eyes. Hair coat is white from birth. There may be some patches of color, which may fade to white as the horse grows older. When this is caused by SB1 it may be referred to as "maximum sabino". SB1/n - Classic sabino has assorted pinto or roan-like markings. Recognized by abundant white on the legs, belly spots or body spots that can be flecked or roaned, chin spots, or white on the face extending past the eyes. Sabino is registered as overo by some registries, but is not frame overo and does not cause overo lethal white syndrome. n/n: No sabino. Note: The above applies when W is one of W1, W2, W3, W4, W9, W10, W11, W13, W14, W17, W23, W24, or W25. See white for a description of the other W alleles.

|Near or at KIT (Roan)

|RN n

|RN/RN or RN/n: roan pattern of white hair mixed in with base color. Head and lower legs remain dark. Inverted "V"s are present just above the knees. It used to be thought that roan was homozygous lethal, but since then living homozygous roan horses have been found. n/n: No roan.

|TRPM1 (Leopard complex)

|LP n

|Appaloosa or Leopard spotting gene. Produces coat spotting patterns, mottling over otherwise dark skin, striped hooves and often white sclera. Can also produce varnish roan. LP/LP: Fewspot or snowcap horse. LP/n: Leopard or blanket horse. n: No leopard complex.

|RFWD3 (Pattern 1)

|PATN1 n

|PATN1/PATN1 or PATN1/n: Combined with the leopard complex, produces a leopard/fewspot or near-leopard/near-fewspot horse. It has no visible effect on n/n (for LP) horses. n/n: Horse is solid or varnish roan, unless it has (an)other (as yet undiscovered) PATN gene(s).

|MITF (Splashed white, macchiato)

|SW1 SW3 macchiato n

|SW1/SW1: Classic splashed white. SW1/n: White markings on head and legs. SW3/SW3: May be embryonic lethal. SW3/n: Splashed white. Macchiato/n: The macchiato allele has been found in a single stallion named Apache, who had a white pattern in similar places as for splashed white, a dilution, deafness, and reduced fertility. It is likely that this mutation will not be passed on. n/n: No splashed white or macchiato.

|PAX3 (Splashed white)

|SW2 SW4 n

|SW2/SW2: Previously thought to be lethal, but SW2/SW2 horses have since been identified. However it often causes short tongue and/or infertility.