Breeding & Genetic Inheritance

Icon of a book Horse Breeding & Genetic Inheritance

Horse breeds can develop and change overtime. Early horse breeders found that desirable characteristics and traits could be passed on from parents to their offspring. They selected horses with those desirable characteristics and traits to breed with each other.

Early horse breeders practiced horse genetics before they knew about genetic research and science.

Horse Breeding

Many horse breeds are established by a few horses. Therefore, the horses within a breed can be closely related to each other, or inbred. This inbreeding can have positive and negative effects. If a breed’s strengths are passed on to its offspring, more horses within the breed will have these superior abilities. However, there is also a higher chance that genetic disorders will also be passed on from generation to generation. 

Variations between individual horses are influenced by both heredity and the environment.

Heredity is the passing of traits from parents or ancestors to their offspring. It is influenced by genes, which are biochemical structures made of DNA that make up chromosomes. Chromosomes are passed from both parents to their offspring, therefore, passing on genetic material from each parent. Since specific chromosomes are passed on randomly, offspring have a unique set of their own chromosomes and combination of traits.

Variation within a breed and between individual horses is caused by both heredity and environment.

A gene gives only the potential for the development of a trait. The extent to which this potential is achieved depends partly on the interaction of the gene with other genes. However, it is also affected by the environment. 

DO YOU KNOW enough about different breeds of horses? If not, refer back to "Horse Breeds & Heredity" topic. 

Horse Genetics

Horse breeders today apply the principles of horse genetics so they understand how heredity influences the differences and similarities between individual horses within a breed. They breed individual horses with characteristics that are desirable for the breed or for a purpose, such as speed, strength, agility, behaviour or conformation. These characteristics can also include the horse’s physical health and soundness.

A genotype is the actual genetic makeup of an animal.

A phenotype refers to what the animal actually looks like and is determined by the interaction of the animal’s genes with its environmental influences.


Horses are bred to pass on desirable traits to their offspring. Many horses within a breed may be descended from only a few foundational horses, or ancestors, with particular characteristics.

Inbreeding is the reproduction of offspring from the mating of animals that have common ancestors. A horse is called inbred if the same ancestor appears in both the mother’s and father’s pedigree, or family tree.

Line Breeding

Horse breeders also use a form of inbreeding called line breeding. In line breeding, both parent horses have a particular horse more than once in their pedigree. Therefore, line bred horses are more genetically related to that horse than they would be if it appeared with only one of its parents.

Outbreeding and Crossbreeding

When horse breeders mate unrelated horses together, they are outbreeding.

Crossbreeding is the mating of a mare and stallion from different breeds. For example, mating an Arabian mare with a Thoroughbred stallion would produce a crossbred foal. Breeders may also choose breeds that emphasize characteristics such as temperament, height or speed. Some crossbred horses become well known enough to gain their own name, like the Quarab Horse which is a Quarter Horse or Paint crossed with an Arabian.

How Dominant & Recessive Traits Affect Breeding

A foal’s colour is determined based on the genetics passed on from its mother, or dam, and father, or sire. Each parent contributes half of the genes towards the foal. Its coat colour will depend on what is passed on from either parent and whether these traits are dominant or recessive. The dominant or recessive version of each gene is called an allele.

A dominant allele will express itself over a recessive allele. This means that the trait represented by the dominant allele will always be expressed if it is present. A recessive trait will only be expressed if both parents pass on the recessive allele to their offspring. The offspring will now carry two recessive alleles. Upper case or lower case letters stand for different alleles. Upper case letters stand for the dominant, or “on” allele of the gene; lower case stands for the recessive, or “off” allele of the gene.

There are seven main genes that control the colour of a horse. These genes are represented by letters and include:

  • G for grey
  • W for white
  • E for black or red
  • A for the distribution of black hairs
  • C for the degree of pigmentation (the depth of the colour)
  • D for a pattern of pigmented colouration
  • TO for a Tobiano pattern.

There are two expressions for any specific gene – either dominant or recessive. However, there are three possible ways a matched pair of alleles can exist:

  1. Both alleles are in dominant form. For example, a dominant grey gene would be written as GG.
  2. Both alleles are in recessive form. For example, a recessive black gene would be written as ee. This means the horse would be sorrel or chestnut.
  3. One allele is dominant while the other is recessive. For example, a grey gene can be Gg. However, because the dominant gene is present, this horse would be grey.

For example, if two bay horses were bred, their foals would not necessarily all be bays. This is because the parents have both the dominant and recessive black and red alleles in their genetic profile.

The E gene controls the amount of black pigment in hair and skin. If a horse has the dominant allele, which is represented by the letter “E”, it will have some black pigment in its hair. If a horse has two recessive alleles, represented by the letter “e”, it will have red pigment.

The Punnett square below can be used to predict the possible colours in the offspring of these two horses.


Bay Horse

Bay Horse









The genotypes of the offspring of these two horses would be described as 1 EE, 2 Ee and 1 ee. The phenotypes of the offspring would be described as three bay and one sorrel or chestnut.

How do you know what the genetic colour profile of a horse could be? The following steps can help you understand how genetics influences a horse’s colouration.

1. If the horse is grey or white, it will have the G or W gene.

Determine if either G or W is present. If the dominant allele for these two genes is present, then the horse will be grey or white. A grey horse will have the two alleles GG or Gg. A white horse can have the two alleles WW or Ww. The WW allele combination is lethal and causes the foal to die before it is born. The Ww allele combination means that the horse will be white with pink skin. Grey horses usually lighten with age. If the horse is not grey or white, these genes will be in their recessive form. These recessive alleles would be identified as gg and ww.

2. If the horse is not grey or white, it will have the E gene.

If the horse is bay, black, sorrel or chestnut, it will have the E gene. The dominant trait – E – determines that the horse will have black pigment in their hair. The recessive trait – e – allows black pigment in the skin, but not in the hair, which will appear red. If the animal has no black pigmented hair, it will have the gene combination of ee. An ee horse will be some shade of red, ranging from chestnut to sorrel.

3. If the horse is a bay, it will have a dominant A allele.

The gene that controls how a horse’s black hair is distributed on its body is A. If the horse has a dominant A allele and a dominant E allele, it will be a bay. There are various shades of bay, including light, dark, mahogany, blood and copper. A bay horse must have the A allele and the E allele, as well as recessive grey and white traits (gg and ww).

4. If the horse is black, it will have the recessive aa alleles.

If the horse has recessive aa alleles, the distribution of black hair on the body is not controlled. This means that if the horse has the E allele, it will be black. Neither the dominant A or the recessive a affects the distribution of colour in red (ee) horses.

5. If the horse is buckskin, cremello, perlino or albino, it will have the recessive C allele.

The C gene controls the degree of pigmentation. Two dominant alleles – CC – mean that the horse will be fully pigmented, with no colour dilution. The recessive allele – Ccr – causes the pigment in a horse’s hair to be diluted if it is present. For example, a red pigment can be diluted to yellow, flaxen or pale cream. A bay horse can become buckskin. A palomino has the genetic profile of ww, gg, ee, CCcr. If a horse has both recessive alleles – CcrCcr – any coat colour will be diluted to a very pale cream colour. These horses are often called cremello, perlino or albino.

6. If the horse is a dun, it will have the dominant D allele.

The D gene also controls pigmentation, but in a pattern on the horse’s body that affects colouration on its shoulder and legs. This pigment pattern is called dun. If a red horse (ee) has the dominant D allele, it will be called a red dun. If a bay horse (E, A) has the dominant D allele, it will be a buckskin dun. If a black horse (E, aa) has the dominant D allele, it will have grey colouration and be called a mouse dun.

7. If the horse is a Tobiano, it will have the dominant TO allele.

The TO gene controls the Tobiano spotting pattern. If a horse has the dominant TO allele, it will have areas of white hair with underlying pink skin.

Photo Credit: Farell Albert-Puurveen

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