Basic Colours & Genetics in Welsh Ponies

This is the first of a series of articles attempting to explain the basic mechanism of colour inheritance in horses and the definitions of those colours. It is not designed for the experienced colour genetics enthusiast as many of the definitions are designed to explain rather than to educate.


There are only two base colours in horses, chestnut & non-chestnut (black). All other colours occur as a result of other genes and modifying factors working on those two base colours. Non-chestnut (black) is dominant over chestnut which means that if an animal has a non-chestnut & a chestnut gene it will look non-chestnut. Conversely, if it looks chestnut that means it has no non-chestnut genes, it contains 2 chestnut genes ie is homozygous for chestnut.

All genes occur in pairs. When two animals are mated each pair of genes will contribute 1 gene only to the offspring. Therefore the offspring will contain 1 gene for a characteristic or colour from one parent and another from the second parent.

For example, if you mate two bays (each of which has a hidden chestnut gene) each has a 50% chance of throwing the chestnut gene or the bay gene. This means you have a 25% chance that both will throw the chestnut gene and give you a chestnut foal. If one parent throws bay and the other throws chestnut then the resulting foal will be bay (as bay is dominant over chestnut) 50%. If both parents throw bay then the resulting foal will be homozygous for bay (25%); as these foals do not contain a chestnut gene they can never have a chestnut foal even if mated to chestnut (remember chestnut is recessive and must get a chestnut gene from each parent).
Therefore, in general
Bay (carrying chestnut) x Bay (carrying chestnut) will result in 25% chestnut & 75% bay
Bay (carrying chestnut) x Chestnut will result in 50% bay & 50% chestnut
Homozygous bay (no chestnut gene) x Chestnut will result in 100% bay

Genotype is the composition of the genes in an animal.
Phenotype is the way the animal looks, the genotype can often not be determined by looking at the phenotype eg a bay horse (phenotype bay) may be carrying chestnut so genotype is bay/chestnut.
A dominant gene will mask a recessive gene if both occur in the animal.
Homozygous for a gene means that both copies are the same
Heterozygous for a gene means that both copies are different

These days much of the mystery of colour genetics has been resolved, most colour genes can now be tested for genetically.

For the purpose of these articles we will assume, for the most part, that animals are heterozygous for genes.

The most common colours are bay and chestnut. There is a gene called Agouti which acts to restrict the black pigment to the points, mane & tail. A black horse has no agouti gene whereas a bay has one or two copies of Agouti. As agouti only affects black pigment, a chestnut can carry one or two agouti genes without the colour being affected. Some genes only express themselves on certain colours, on others they remain hidden eg agouti & cream dilution (which will be described in a further article).

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