Basics of Horse Color Genetics (Explained with pictures)

Some basics of horse color genetics can help us understand why our horses have the coat color they have.

  • We can know what color to expect in foals when particular mares and stallions are mated. 
  • We can determine how to increase the chances of a particular color.
  • We can be aware of how to avoid colors that are not desirable or even have health risks associated.
horse color genetics

This article is intended for those interested in horse color but have no formal training in genetics. We will learn basic concepts about horse color genetics and inheritance.

Table Of Contents

Genetics can be challenging to understand, and one of the difficulties is related to the terminology used to discuss it. So we will start with some definitions.

Cells

The body of a horse is made up of trillions of cells. These are tiny structures and are the basic unit of living organisms. There exist many types of cells, like bone cells, muscle cells, skin cells, blood cells, nerve cells, and so on.

Basics of horse colour genetics. Equine cells genetics
Equine cells

All the cells have the same set of genes. However, in each cell, different genes are turned on and off. This is what gives each cell a specific function.

So only a small part of the 20,000 genes of the horse are working at any one time in a particular cell.

Nucleus

Each cell has a nucleus. This is where the 64 chromosomes of the horse exist. There are 32 inherited from the sire and 32 inherited from the dam.

horse color genetics. Horse cell nucleous. colour genes
horse cell nucleous

Chromosome

A chromosome is a rod-like body made up of DNA tightly coiled like a noodle. The chromosomes hold the genetic information together, protecting it from getting tangled and damaged. 

Basics of horse colour genetics. Equine chromosome
horse chromosome

DNA

The DNA contains the genetic information. It consists of two long chains of nucleotides coiled into a double helix, similar to a twisted ladder. The sequence of nucleotides is what determines the genetic code. 

horse colour genetics

Basic concepts of equine genetics

Gene

A gene, is a segment of the DNA which contains the information for a specific trait.

A single strand of DNA contains thousands of genes. Some genes are small segments, and others are very long segments, depending on the function it has on the body.

Locus

Each gene has an address, which is a specific location in the chromosome. This address is called locus (loci for plural). Often the locus name is used when referring to a gene. 

Idiogram

Geneticists use diagrams called idiograms as a standard representation for chromosomes. Idiograms show a chromosome’s relative size and its banding pattern. These bands are used to describe the location (locus) of genes on each chromosome.

Basics of horse colour genetics. Iidiogram of equine chromosome
Iidiogram of equine chromosome

Allele

A gene can have different variations which are called alleles

An allele is responsible for the physical traits, whether these traits can be seen or not.

Since chromosomes come in pairs, each horse carries two alleles at a particular locus. One allele is inherited from the male parent and one from the female parent.

Basics of horse colour genetics. Equine genetics inheritance
Equine genetics inheritance. The genes of color

Homozygous

When an organism has two identical alleles (two copies of the same allele), it is said to be homozygous for that gene. 

Let´s consider, for example, the Extension gene, which determines if a horse is black or red. A black horse may be homozygous dominant for the Extension gene (E/E), while a chestnut horse is homozygous recessive for that gene (e/e). 

Basics of horse colour genetics. Homozygous equine chromosome. Colour genes
homozygous equine chromosome. Color genes

Heterozygous

If an organism carries one copy of each allele, it is considered heterozygous.  For example, a phenotypically black horse may be heterozygous (E/e) for the Extension gene.

Basics of horse color genetics. Heterozygous equine chromosome. Color genes
heterozygous equine chromosome. Colour genes

Genotype

A genotype is the genetic makeup of a trait, consisting of a specific combination of alleles. For example, there are three possible genotypes for the Extension gene, and they are E/E, E/e, and e/e

Phenotype

Phenotype is the characteristic of an animal that can be seen or measured, for example, color, height, speed, and so on.

Not every allele that is present is always expressed. Some are masked by other alleles but can still be passed onto offspring. 

Alleles can be expressed in different ways, and we will see three cases: dominant, recessive, and incomplete dominant.

Before we go any further, there is another concept that needs to be introduced, which is the convention that dominant alleles are represented with an uppercase letter and recessive alleles with a lowercase letter.

Dominant allele

Dominant alleles are expressed even if the horse has only one copy of the allele. So heterozygous will look the same as homozygous.

For example, the E allele for the black color is dominant. Horses will be black, whether they have two copies of the “black color” allele (E/E) or only one copy (E/e).

Recessive allele

Recessive alleles are only expressed when the dominant allele is absent. So only when the horse has two copies of the recessive allele.

For example, the allele for red color, e, is recessive, therefore to have a red coat color (chestnut), the horse needs to have two copies of the “red color” allele.

Incomplete dominant allele

Incomplete dominant alleles have a dosage effect, i.e., they will express with more intensity as more copies of the allele are present. So homozygous will be more intensely expressed than heterozygous.

For example, the Cream allele (CR) on a red base coat has the effect of lightening the coat color. 

  • When one copy of the allele is present (heterozygous), it dilutes the red to yellow. 
  • When two copies of the allele are present (homozygous), it will further dilute to cream.

We can explain the incomplete dominance with an example of the Cream gene on the chestnut color. Let’s consider that:

  •  cr represents the non-dilution allele
  •  CR represents the cream dilution allele

We can have three possible genotypes (cr/cr, cr/CR, CR/CR), each one with a different trait, which means we can have three possible phenotypes:

  • If no Cream allele is present, we have the genotype cr/cr, and so the chestnut color will be expressed.
  • If only one Cream allele is present, single dilute, we have the genotype cr/CR so that some dilution will be expressed. The color of the coat will be diluted to a reddish-gold hue. But there is still some visible pigment, and the skin and eyes retain the original color of the chestnut. Therefore we have a mixture of both traits (from cr and CR)
  • If two copies of the cream allele are present, double dilute, we have the genotype CR/CR, and a full dilution will be expressed. The color of the coat lost almost all the pigment. The skin also, which is now pink, and the eyes are blue.
Basics of horse color genetics. Equine cream color gene
equine cream color gene

The Genetic Lottery

Horse genetics explains the transmission of characteristics from sires and dams to their foals. A foal inherits half of its alleles (a variant of a gene) from its dam and the other half from its sire. So it will have a combination of characteristics from both parents.

Punnett Square

Punnett Square is a genetic tool used to predict possible offspring based on the parents’ different genotypes.

We will exemplify how to use the Punnett square with the Extension gene, which determines if a horse is black or red (chestnut).

The dominant allele ‘E’ causes the horse to have black pigment (eumelanin) while the recessive allele, ‘e,’ causes the horse to have only red pigment (pheomelanin).

Scroll through the following Punnett squares to observe possible outcomes from the different combinations.

  • genes inheritance chestnut and black horse
  • genes inheritance chestnut and black horse
  • genes inheritance chestnut and black horse
  • genes inheritance chestnut and black horse
  • The 3 base horse colours. Genes inheritance chestnut and black horse
  • genes inheritance chestnut and black horse

Inheritance Chart

We can also represent the possible outcomes using an inheritance chart:

horse color inheritance chart

As you can see, for any particular gene, a foal has a genotype that may be like that of one or the other parent or like neither of them

In the example above, we can see that two heterozygous black horses could have a foal that is non-black and is instead red.  

On the other hand, two homozygous black horses could only ever have black foals when mated together. 

Breeding together, a heterozygous black and a homozygous black would give only black foals, and breeding two red horses can only give red foals.

Genetic tests

For a long time, horse color genetics has been studied to determine coat color and pattern in horses. As the research in this area progresses, it is getting easier for the interested breeder to forecast the likely color and pattern of foals from breeding specific mares and stallions.

However, the genotype cannot always be determined from the observable color traits (phenotype). For example, a black horse could have either the genotype E/E or E/e.

In these cases, a genetic test can be performed on the sire and dam to provide further insight into the possible offspring coat colors.

Many tests are available and are very simple and cheap. You just need to pull some hairs from the mane or tail of your horse and send them to the laboratory. After the analysis is done, the results will be sent back to you. 

Related Articles