Introduction – Chromosomes and Genes
Horses have 32 pairs of chromosomes, and these chromosomes are made of DNA (deoxyribonucleic acid)  forming the complex genetic code that controls the shape, size, and colouration of every animal. Each section of DNA that controls the development of a particular feature is called a gene. Chromosomes are always found in matched pairs in normal animal cells, which means that every gene on a chromosome is also paired. During reproduction the pairs of chromosomes are separated (meiosis) to form either an egg with half the normal chromosome compliment in the female,  or a sperm with half the normal chromosome compliment in the male, ie each egg and sperm produced will contain half the genetic information from the mare or the stallion., and therefore only one of each gene pair as well. When conception occurs in the mare, the two sets of chromosomes from sire and dam, are paired up again, like to like, to create the foal with a new genetic profile.
Located somewhere on these chromosomes are the sections of DNA, ie. the genes, that control coat colour; each section of DNA that acts as a gene is referred to as a Gene Locus (this is the ‘address’ of the gene, and the plural is ‘loci’). At least 14 different coat colour genes have been discovered in mammals (with another 6 or so possible colour genes), and all of them can occur in a number of different versions which have been caused by small changes (mutations) in the genetic code over the many thousands of years that domestic horses have existed. These different versions of the same gene are known as alleles of that gene, and it is possible for two identical alleles to be paired up (the alleles are homozygous) or two different alleles to be paired up (the alleles are heterozygous) on the chromosome pairs. When a pair of alleles is heterozygous, one of the alleles is normally found to completely over-ride the genetic information provided by its partner, and they are referred to as ‘dominant’ and ‘recessive’ respectively. This allows us to make a list of the different alleles of any particular gene in the order of their increasing dominance so that one knows at a glance which allele of a pair will be the one that decides the coat colour. Mostly it is the original ‘wild type’ allele that will be the most dominant of the group of alleles which may occur at that gene locus, but just occasionally it is a mutation that is the highest ranking allele. Genetecists symbolize genes with letters or abbreviations for the name of the Gene Locus written in italics; dominant alleles are labelled with a Capital letter eg. E, and recessive alleles with a small letter, eg.  e.

How Coat Colour is Produced in Horses
Colour in hair, skin, and eyes is caused by a pigment called melanin which is produced as little grain-like structures by cells called melanocytes that are spread thoughout the skin, and are found in the base of all normal hair follicles. In horses, melanin is found in two distinct forms, eumelanin, a black pigment, and phaeomelanin, a red or yellowish-red pigment. All the variations in colour that we see are due to one or more of the following:-

i) which of the two pigments, eumelanin and phaeomelanin, are present in the skin and hair and their location and distribution in the hair. A melanocyte cannot make both pigments at the same time, but certain genes can make melanocytes alternate between the pigments to produce bands of colour in individual hairs. Other genes can prevent any production of eumelanin in the hair thus giving a red coat colour, or restrict it to splotches and stripes as found in very rare brindle horses . These effects are controlled by two different genes, named the ‘A’ or Agouti locus and the ‘E’ or Extension locus. They work closely together even though they are located on different chromosome pairs.

ii) the number, size and shape of the pigment granules in the skin and hair. For example, if you reduce the number of yellow/red pigment granules in red hair you will get gold hair, or with even less pigment the hair looks cream.
ii-a) The number of granules present is controlled by the dilution genes at the ‘C’ or Cream locus and the newly discovered ‘Prl’ or Pearl locus.

ii-b) Alternatively if you change the shape of the eumelanin pigment granules from elongated to round, the colour changes from black to chocolate/liver. This is the function of the ‘B’ locus which is well known in Dogs and Cats, but has not yet been found in horses

iii) the way that the pigment granules are distributed within each individual hair. The ‘normal’ distribution is a regular one, but some gene mutations cause pigment to be laid down only in the tips of the hairs, others cause pigment to be laid down only along one side of the hair. Several genes in horses are thought to work in these ways, and the recent discoveries concerning Dun dilution have proven one of these ideas. (see DUN page)

iv) increasing the amount of pigment pushed into each hair which has the effect of darkening the colour visually. This is due to minor genes as yet unidentified.

v) the distribution of pigmented hairs across the horse’s body, ie. all over the body or interspersed with areas of white hair. It is important to remember that White is caused by the complete absence of melanocytes, and therefore pigment, in that area of skin and hair.
v-a) White areas in horses are determined by at least six gene loci, known as ‘To’ or Tobiano, ‘O’ or Overo, ‘the ‘Sb’ or Sabino, ‘Spl’ or Splashed White, ‘W’ or White, and ‘Lp’ or Leopard Spotting.
v-b) Patterns of individual white hairs sprinkled through the normal pigmented hairs are caused by the several genes, the best known is ‘Rn’ or Roan, another one which is rarer is ‘Rab’ or Rabicano which is also known by the less attractive name of ‘Skunk Tail !

vi) the progressive loss of pigmentation in the hair over time, usually many years, which can affect any of the base coats or their variations. This is caused by the dominant gene ‘G’ or Grey, perhaps better known as Progressive Greying because it is NOT a colour in its own right but rather causes the loss of colour in any horse that has this gene.

Ancestral Horse Colour and Modern Horse Colours

Wild ancestral horses in ancient cave paintings had a coat colour designed for camouflage against their predators. It was composed of red body hairs, darker red on the head, neck and along the back and lighter creamy red-gold along the underparts, with a black mane and tail, black dorsal stripe, and black hairs on the lower-legs, especially over the joints. This was usually accompanied by a pattern of zebra-like stripes down the legs and in other areas which helped to break up their outline.

In 2015 there was a research breakthrough by an international collaboration led by groups at Uppsala University, Uppsala, Sweden, and the Huntsville Institute of Biotechnology, Huntsville, Alabama, USA, which proved the exact location and nature of the Dun gene in modern Dun patterned horses. The research team also detected this exact same Dun gene in Przewalski Horses, and in 43,000 year old preserved horse remains (long before domestication). So now we know that the Dun dilution pattern combined with dark stripy primitive markings on a Bay basecoat is indeed the original ancestral colour of the equine species and the  modern horse.

Modern horses have evolved a wide range of beautiful coat colours through the many small mutations  in the structure of  the gene loci  involved in the creation of hair and pigments.  In the wild these colours would have caused the horse to standout  like a ‘sore thumb’ and be eaten rather quickly, but  people have kept and treasured new colours for their beauty and rarity.

Although the coat colour of modern horses varies a lot, it can be simplified into three modern equine base coat colours, BAY (nearest to ancestral wild type with a RED body and BLACK points), BLACK (Black body and black points), and Chestnut (RED body and red points).

All the other colourful alternative coat colours result from the processes described above in ‘How Coat Colour is Produced’ which,

1).DILUTE these three base coats in lots of different ways eg dun, grullo, buckskin, cremello,etc

2).DARKEN them by adding extra pigment, eg. liver chestnut, or add a black overmantle eg. sooty/shaded  bay

3).MIX the base colours with different patterns and amounts of white (unpigmented) hair, eg. tobiano, sabino, roan, rabicano, appaloosa