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HORSES COLOR GENETICS


Horse breeding, like all breeding, whether we like it or not, is above all about genetics, even if breeders have always relied on their experience, their "feeling" to choose their crosses, without necessarily translating their choices into genes, chromosomes or other alleles.

Today, science gives breeders access to a tool that can help them considerably reduce the amount of chance and uncertainty: genetic testing.

After the near-complete sequencing of the human genome in 2001, the equine genome was sequenced in 2006, opening the way to genetic testing for horse breeders.

The main interest of these tests is to allow the detection of genetic diseases in breeding stock in order to proceed with reasoned crossbreeding in terms of health. On this subject, we refer you to our article which lists the main genetic diseases in sport horse breeds.

However, it is necessary to have some basic knowledge of genetics to be able to use it with relevance.

This article was largely inspired by the website Robes et génétique des chevaux which is by far the most complete and reliable site on the subject of coat genetics. To go even further, the creator of this site, Caroline Sauvegrain, is also the author of the reference book on the subject, published by Editions de l'IFCE: "Génétique des robes des équidés" and the creator of a reference Facebook group that allows you to learn progressively.


In the meantime, we will try to summarize the essential.


Some basic genetics

DNA/Chromosomes/Genes

Schematically, we can say that the DNA of an individual is composed of several chromosomes, which function in pairs: one chromosome given by the mother + one chromosome given by the father = one pair of chromosomes of the product

The chromosomes are themselves composed of genes that "code" for the characteristics of the product. Each gene of a chromosome pair is composed of two alleles: one allele given by the mother, and one allele given by the father.

Source: www.robesetgenetiquedeschevaux.fr

Each gene has the task of "coding" a characteristic of the individual. A disease, or a colour, for example.


Dominant/semi-dominant or recessive alleles

The challenge is to find out what is the result of the combination of these two alleles that form the gene. The alleles can be classified into 3 categories according to what we might call their "coding power".

  • A dominant allele has a "complete" effect even if it is in one copy (i.e. the other allele of the gene is not the same). One copy is sufficient for it to express its full action.
  • A semi-dominant allele is expressed differently depending on whether it is in one or two copies
  • A recessive allele has no effect if it is in one copy. It needs to be in duplicate to have an effect, i.e. the 2 alleles of the gene are the same.

When a gene is composed of two identical alleles, the animal is said to be homozygous (the Greek word "homoios" means "similar").
When a gene is composed of two different alleles, the animal is said to be heterozygous (the Greek word "heteros" means "similar").


Color genetics in horses

Each horse has a "basic coat color" which could be compared to the background colour of a painting. This base coat, which can be black, chestnut or bay, is coded by two genes: Extension and Agouti. Then, other genes can modify the colour of the base coat, these are the modifier genes.

The basic coat color

This basic coat color can be: Black, Chestnut, or Bay.
To code the basic coat color, the horse has two genes: the Extension gene and the Agouti gene.
 

  • The Extension gene (Black -Chestnut)
    The E allele is the "black" allele, it is a dominant allele
    The e allele is the chestnut allele, it is a recessive allele

    So :
    - an EE horse has a black coat base
    - an Ee horse also has a black coat base (E is dominant to e)
    - a chestnut horse has a chestnut base

  • The Agouti gene (Bay)
    The A allele indicates the presence of Agouti
    The a allele indicates the presence of the Non-Agouti
    How does the Agouti gene work?
    The Agouti gene "transforms" a horse with a black base coat into a bay. It only acts on black coats, not at all on chestnut coats. The Agouti gene is a dominant gene.

    So :
    - a horse with a black base (EE or Ee) + AA will have a bay base coat
    - a horse with a black base (EE or Ee) + Aa will have a bay base coat
    - a basic black horse (EE or Ee) + aa will have a basic black coat

    - a chestnut (ee) + AA or aa or aA will be chestnut

These two genes, Extension and Agouti, therefore code for the basic black, chestnut or bay coat of all horses. But then come the modifier genes...


The most common modifier genes (MATP and grey)

  • The MATP gene

Although there are only 2 "places" on a gene (the 2 alleles), a gene can group together more than 2 alleles. This is the case of the MATP gene which groups 5 alleles:

- 4 mutations: the Cream, the Pearl, the Sunshine, the Snowdrop,
- and the Wild allele, i.e. the non-mutated allele.
Imagine a game of musical chairs where there are 2 chairs (the 2 slots available on the gene for the alleles) and 5 alleles, which rotate around the 2 chairs...

> The most common allele is Cream, which is responsible for isabelle and palomino colours among others.
The CR allele indicates the presence of cream.
The C (or sometimes cr) allele indicates the presence of the so-called "wild" allele, i.e. the non-mutated allele, which is neither Crème, nor Pearl, nor Sunshine, nor Snowdrop: it is "non-colouring".
The Cream allele is semi-dominant. In a single copy it "dilutes" (lightens) the coat, in a double copy it dilutes it even more, and makes the horse's eyes blue.

Let's see for each basic coat (black, chestnut and bay) how the Cream gene works:

- Chestnut base coat
If the horse is CC (homozygous non-cream) it remains chestnut
If the horse is CRC (heterozygous Cream), it is palomino
If the horse is CRCR (homozygous Cream), it is cremello (visually it is almost white, or washed out/creamy beige, and has blue eyes)

- Bay base coat
If the horse is CC (homozygous non-cream) it remains bay
If the horse is CRC (heterozygous Cream), it is isabelle
If the horse is CRCR (homozygous Cream), it is perlino (visually it is almost white, or washed out/creamy beige, and has blue eyes. Theoretically, the manes can have a deeper shade than in cremello, but it is not systematic and not easy to see...)

- Black base coat
The cream allele has little (or no) effect on the black colour (which explains why the manes of a bay horse remain black with a cream allele)
If the horse is CC (homozygous non-cream) it remains black
If the horse is CRC (heterozygous Cream), it is smoky black. Visually it remains black (even if sometimes the coat can tend towards chocolate)
If the horse is CRCR (homozygous Cream), it is smoky cream (visually it is almost white, or faded beige/cream, and it has blue eyes. Theoretically the hair and manes can have a darker / greyer shade than in cremello or perlinos, but it is not systematic and not easy to see...)

> The Pearl allele
The Pearl allele is much less common than the Cream allele. It is highly prized by some enthusiasts as it gives the horse very beautiful green eyes and a slightly golden coat...
The prl allele indicates the presence of the Pearl allele
The C (or sometimes cr) allele indicates the presence of the "wild" allele, i.e. the non-mutated allele

If the horse has only one copy of the Pearl allele (C prl), its colour remains unchanged. It is said to be a Pearl carrier
If the horse has 2 copies of the Pearl allele (prl prl), its colour is diluted, its coat is shiny, but its eyes remain dark. It is said to be double Perle.
Finally, if the horse has a combination of cream and pearl (CR prl), its coat will be "double diluted", with a colour similar to that of double cream horses (cremello, perlinos, or smoky cream) but a little darker and shinier, and the eyes will be green.

The double Pearl is highly sought after by Pearl breeders, as it allows the Pearl gene to be passed on to 100% of the offspring, and to seek to combine it with the Cream to produce Cream Pearl foals with green eyes...

> Snowdrop and Sunshine alleles are still very rare, if you want to know more about them, click here.

  • The grey gene

The Grey gene has the particularity of being an evolutionary gene. The foal is born with a coloured coat, whatever it is, and the Grey gene controls depigmentation: progressively white hairs appear and the horse gradually becomes completely white.

The G allele designates the "Grey" allele, it is a dominant allele
The g allele designates the "not grey" allele, it is a recessive allele
- a GG horse will therefore turn grey
- a Gg horse will therefore also turn grey
- a gg horse will not turn grey.


There are other modifier genes, less common than Cream or Grey: Dun, Silver, Champagne, and Mushroom. We invite you to visit the website Robes et génétique des chevaux if you wish to learn more about this subject.


Piebald, Leopard, and the particulars genes

White spots in horses are the result of many different genes, not just one (that would be too simple). These genes can be almost invisible, or give, for example, small bales or head markings, to large white spots like cows, or spots like appaloosa, or even make horses completely white.
In short, a whole range of white markings governed by a whole series of genes, too numerous to mention here. The piebald or leopard patterns are also not very common (for the moment) among sport horses.
The piebald gene that causes large white spots and is the most frequent among sport horses is certainly Tobiano (To).
To find out more about white markings, go here!

Finally, there are other genes, often still unidentified and untestable, which can, for example, darken the coat and calls (sooty), lighten the manes (flaxen), introduce a kind of stripe/branching (IP, Brindle 1)...


Pathologies linked to colour genes.

We previously published an article on testable genetic conditions here.

Here is an overview of genetic diseases linked to colour genes in horses, to help you reason out your crossbreeding.

  • Grey (G) - This is probably the best known case. Grey is indeed associated with the occurrence of melanoma, benign or malignant. Horses homozygous for grey, or grey with a black base, are thought to be more heavily affected.
  • Overo (noted O or LWO): lethal in the homozygous state. The foal is born non-viable and dies within 48 hours, in great pain, because its digestive tract is not functional.
  • Silver (Z) - The Silver gene is linked to several eye diseases: ASD (Anterior Segment Dysgenesis) and MCOA (Multiple Congenital Ocular Animalies). Homozygous carriers are more severely and more often affected than heterozygous carriers, so great care should be taken when crossing Silver carriers.
  • Leopard (LP) - in the homozygous state, the Leopard gene is associated with a vision disorder: Congenital Stationary Night Blindness (CSNB)
  • Dominant White 19 (DW19) - The DW19 gene, when homozygous, causes a blockage in the growth of the male and female reproductive organs.
    A series of Dominant White genes are lethal in the homozygous state: DW1, DW3, DW4, DW8, DW10, DW21, DW22, and probably also DW5.
    A number of SplashWhite (SW) genes are linked to deafness issues, even in the heterozygous state: SW2, SW5, SW6, and SW7
  • Incontinentia Pigmenti (IP), one of the genes that causes brindle, but is mostly associated with a serious condition ("incontinentia pigmenti") which is a disease affecting the skin, hair, teeth, eyes and central nervous system - No homozygous individuals are known (it is possible that homozygosity is not viable). There are no healthy heterozygous carriers either. Heterozygous males die in utero, females are ill.
    Not to be confused with the Brindle1 gene, which provides colour brindle, but is not associated with any disease.