English
Horse coat colors are highly diverse and carry historical, cultural, and even functional significance within many horse breeds. The colors and patterns that mark these breeds result from a complex interaction of several genes that geneticists have studied for centuries.
Genetically, equine coat colors are primarily determined by three base colors: chestnut, black, or bay. All other coat colors and patterns are derived form these base colors through various genetic modifications.
Understanding the genetic inheritance of coat colors helps breeders predict the color of their foals, allowing them to make breeding decisions to select for particularly desirable colors or those that meet their breed’s standard. Additionally, applied genetic theory can even help mitigate color-associated diseases such as lethal white overo syndrome.
Read on to learn more about the genetic basis of equine coat colors, how each coat color develops, the possible interactions between different colors and patterns, and health impacts related to color genes.
Horse Coat Color Genetics
Coat colors are governed by a complex interplay of genes located on different chromosomes. These genes determine the base color of a horse’s coat and influence various modifiers that create the wide range of colors and patterns observed on horse coats.
Horses have 64 chromosomes, organized into 32 pairs, that carry the genetic material (DNA) that determines all inherited traits, including coat color. [1] One chromosome in each pair comes from the horse’s dam and one comes from their sire.
Each chromosome has identical gene sites, called loci, consisting of segments of DNA that code for specific proteins or perform different functions. At each gene site, the form of the gene expressed can differ between the two paired chromosomes. [1] These different gene forms are called alleles. [1]
Gene sites that control color in horses are found throughout the horse’s DNA, on many different chromosomes. [1] The horse’s final color depends on the alleles expressed at these different gene sites, and how those different genes interact. [1]
For example, all horses have a base color of chestnut, black, or bay. [1] Some color genes may dilute these colors, resulting in a paler coat color. [1] Other color genes add white, making loud patterns on the horse’s body. [1]
Most horse colors follow a Mendelian inheritance pattern, which means that only one gene site controls production of that color. [1] There are four key concepts in Mendelian inheritance:
- Dominant alleles
- Recessive alleles
- Homozygosity
- Heterozygosity
Dominant Alleles
Every horse has two gene sites for each color pattern, which means that there are two possible alleles. Some alleles are dominant to the opposing allele, meaning if a dominant allele is present, it will always produce the color that allele is associated with. [1]
For example, the allele that produces Dun coloring is dominant, so any horse expressing a Dun allele will have a Dun coat color. [1]
Researchers use capital letters to designate dominant alleles. For example, a horse with a Dun allele on both chromosomes can be written as D/D. [1]
Recessive Alleles
The alleles that dominant alleles override are recessive alleles. The color associated with these alleles only develops if there are no dominant alleles present. In other words, these colors only occur if both chromosomes have the recessive allele.
For example, the Extension gene, which controls chestnut coloring, only produces chestnut if both alleles are recessive. [1]
Lower case letters designate recessive alleles. A chestnut horse would be written as e/e for Extension, since both genes are recessive. [1]
Homozygosity and Heterozygosity
Homozygosity describes having the same allele on both chromosomes for any gene site. Therefore, there are two options for homozygosity: homozygous dominant (two dominant alleles) or homozygous recessive (two recessive alleles). [1]
Horses that have one dominant and one recessive allele are heterozygous. A heterozygous horse expresses the color associated with the dominant gene, even though a recessive allele is present. [1] For example, a horse with heterozygous Dun genes (i.e. D/d) would still be dun, as the dominant D allele would cause dun coloring. [1]
Mendelian Inheritance
Only one of the two chromosomes in each pair passes to developing sperm and eggs. [1] This means that the resulting foal has a 50% chance of receiving each one of their parent’s chromosomes.
Depending on which alleles are present on these chromosomes, the resulting combinations of dominant and recessive alleles can produce new coat colors, including colors that neither parent has themselves. [1]
Geneticists use Punnett squares, a type of table, to calculate the odds of each possible genetic outcome. [1] Each table shows the four possibilities for resulting chromosome pairs, and the probability of that outcome can be determined by adding up the number of instances of that outcome in the table and dividing it by 4. [1]
Examples of four common interactions for genes with Mendelian inheritance are shown below. [1]
Two Homozygous Dominant Horses
In this scenario, there is a 100% chance that the foal will be homozygous dominant like its parents.
Table 1. Punnet square: crossing homozygous dominant parents
| Dam’s Genes → | X | X |
| Sire’s Genes ↓ | Breeding Outcome | |
| X | X/X | X/X |
| X | X/X | X/X |
Two Homozygous Recessive Horses
In this scenario, there is a 100% chance that the foal will be homozygous recessive like its parents.
Table 2. Punnet square: crossing homozygous recessive parents
| Dam’s Genes → | x | x |
| Sire’s Genes ↓ | Breeding Outcome | |
| x | x/x | x/x |
| x | x/x | x/x |
Two Heterozygous Horses
In this scenario, there are three possible outcomes. There is a 25% chance that the foal will receive both dominant alleles, making them homozygous dominant. There is also a 25% chance that the foal receives both recessive alleles. There is a 50% chance that the foal receives one dominant and one recessive allele, making them heterozygous like their parents.
Table 3. Punnet square: crossing heterozygous parents
| Dam’s Genes → | X | x |
| Sire’s Genes ↓ | Breeding Outcome | |
| X | X/X | X/x |
| x | X/x | x/x |
Homozygous Recessive and Homozygous Dominant
In this scenario, there is a 100% chance that the foal will be heterozygous, even though neither of its parents are heterozygous. This is because no matter what scenario occurs, the foal receives one dominant allele from its dam and one from its sire.
Table 4. Punnet square: crossing homozygous parents where one is dominant and the other is recessive
| Dam’s Genes → | X | X |
| Sire’s Genes ↓ | Breeding Outcome | |
| x | X/x | X/x |
| x | X/x | X/x |
Base Colors
All horses have a base coat color of chestnut, bay, or black. [1] When present, other color genes modify these base colors, producing different coat colors. [1] Most horses have a bay or chestnut base color. [1]
Genetic Control
There are two main genes that control base coloring: Extension and Agouti. [1] These genes interact with each other to produce bay, chestnut, and black coloring. [1]
The Extension gene controls the production of eumelanin, the pigment that produces black hair coloring. [1] Horses that do not have a dominant Extension gene (E) cannot produce black hair. [1]
The Agouti gene controls the distribution of black hairs. [1] Horses that have a dominant Agouti gene (A) have a restricted distribution of black hairs, resulting in black points. [1]
Black points include black legs, a black muzzle, black mane and tail, and often black ear tips. [1] Horses that are homozygous recessive for Agouti can produce black hairs anywhere on their body. [1]
Bay
Bay horses have a red-brown body color w