How they work

Highland Pony Colour Genetics

Base Coat Colour – All ponies start with one of the three base coat colours: Black, Bay or Chestnut. They can then inherit other colour genes that effect the base coat in different ways. Read below for a more in-depth explanation.

The Extension Gene – Black Factor.
This is called the Red/Black factor. All Highland Ponies coat colours begin with either red or black based pigmentation. Ponies can carry a number of dilution patterns and/or modifiers that can affect the overall look of a pony’s coat colour, but they all have genetics for red or black.

The Red/Black factor is tested through the extension gene.
EE = Homozygous for black pigmentation. This means this pony is unable to produce red based offspring no matter what colour the other parent is. EE ponies can be black, bay, brown, mouse dun, yellow dun and any pony carrying the silver dilution.
Ee = Heterozygous for black and red pigmentation. This means this pony has a 50% chance of either passing on the black or the red pigmentation gene to its offspring. Ee ponies can be black, bay, brown, mouse dun, yellow dun and any pony carrying the silver dilution.
ee = Homozygous for red pigmentation. This means this pony will pass on the red pigmentation gene no matter what as it has no black pigmentation gene. ee ponies can be chestnut and red/fox dun.

The Agouti Gene – Bay Factor.
The agouti gene controls the distribution of black pigmentation. On black based ponies (EE & Ee) the dominate agouti gene causes the distribution of black to the points of a pony (lower legs, manes and tails) On homozygous red based ponies (ee) agouti has no effect so fair for is hidden.

The Agouti gene
AA = Homozygous for dominate agouti. This means this pony will pass on a dominate agouti gene to its offspring. AA ponies can be bay, chestnut, yellow dun, red/fox dun and any of those colours carrying the silver dilution gene.
Aa = Heterozygous for dominate and recessive agouti. This means this pony has a 50% chance of passing on either agouti gene to its offspring. Aa ponies can be bay, chestnut, yellow dun, red/fox dun and any of those colours carrying the silver dilution gene.
aa = Homozygous for recessive agouti. This means this pony will pass on recessive agouti to its offspring. aa ponies can be black, chestnut, mouse dun, red/fox dun and any of those colours carrying the silver dilution gene.

A newer allele was suspected “the At” and sequenced as of 2009 with a genetic test developed, but the At test has been debunked due to its infrequent results.
It is still widely acknowledge that there is a genetic reason behind the seal brown colouring but it is now regarded as unknown. The At allele causes the Seal brown coat colour, these ponies are brown. Their muzzles, eyebrows, flanks, quarters and girth are lighten to a reddish or yellow (giving the pony a mealy appearance) while the black pigmentation is not restricted to only the points and will also be on the ponies body.

The Dun Dilution.
The dun dilution gene is a dominate gene and cannot be hidden on any coat colour, by lightening base body coat while leaving the legs, mane and tail darker. The gene is also associated with primitive markings and the dorsal strip down the middle of a ponies back is the most recognisable marking associated with being a dun. A pony can also show ear tipping, zebra striping to the legs, shoulder striping, guard hairs in the mane, tail and legs (guard hairs are a layer of pale outer hairs that sometimes can be very noticeable on certain dun ponies) and face masks.

The Dun gene
DD = Homozygous. This means this pony will pass on the dun gene to its offspring. DD ponies can be mouse dun, yellow dun, red/fox dun and any of those colours carrying the silver dilution gene.
Dd = Heterozygous. This means this pony has a 50% chance of passing on the dun gene to its offspring. Dd ponies can be mouse dun, yellow dun, red/fox dun and any of those colours carrying the silver dilution gene.
dd = Negative. This means this pony has no dun gene and cannot pass it on to its offspring. dd ponies can be black, bay, brown (seal brown) chestnut, and any of these colours also carrying the silver dilution gene.

It is important to note that some horses and ponies can show counter shading and primitive markings that give them the appearance of having the dun gene. This is known as the Nd1 gene (non-dun). You can tell a Nd1 equine from a true dun mainly by taking note of their dorsal strip. A true dun’s dorsal strip will continue through their tail, where as an Nd1 equine’s will not. As the dun gene is well known throughout the Highland Pony breed and the Nd1 gene is not known to be in the breed thus far, it is safe to assume if your pony looks like a dun, it is a dun.

The Silver Dilution.
The silver dilution gene is a dominate gene over black based ponies (EE & Ee), it does not show on red based ponies (ee) and therefore can be hidden. The silver gene varies greatly through the different coat colours but typically it will cause lightening of the mane and tails to give a silver/flaxen appearance and on a uniformly black pony it will typically cause the dilution of the ponies body to a chocolate colour (often with dapples), whereas on a bay pony you will get the lightening of the mane, tail and body, the same as a black, but also lightening of the legs, causing the pony to easily be mistaken for a liver chestnut. A yellow dun carrying the silver dilution gene can also easily be mistaken for a flaxen chestnut.

The Silver gene
ZZ = Homozygous. This means this pony will pass on the silver dilution gene to its offspring. This pony will show the silver dilution traits, mentioned above, unless they are a red based pony.
n/Z = Heterozygous. This means this pony has a 50% chance of passing on the silver dilution gene to its offspring. This pony will show the silver dilution traits, mentioned above, unless they are a red based pony.
nn = Negative. This means this pony carries no silver dilution gene and cannot pass it on to its offspring.

It is important to note that the silver dapple gene is also associated with an inherited ocular syndrome known as Multiple Congenital Anomalies (MCOA) A homozygous pony will have a high risk of more serve MCOA, so it is advised to avoid breeding two silver dapple ponies together.

The Grey Gene.
The grey gene is a dominate gene and is responsible for the progressive depigmentation of a pony’s coat colour resulting in the complete greying of any pony carry the gene.
The grey gene is considered to be the strongest of all the genes and will dominate over all coat colours and dilution genes. The process varies per pony some may take only a couple of years before turning completely grey and others may take ten years or more. You will hear terms such a cream dun, grey dun, steel grey, rose grey and dapple grey to name a few but in the end all of these ponies will eventually be completely grey.

The Grey gene
GG = Homozygous for grey. This means this pony will turn grey and will pass on the grey gene, meaning all its offspring will also turn grey.
Gg = Heterozygous for grey. This means this pony will turn grey and has a 50% chance of passing on the grey gene to its offspring.
gg = Negative for grey. This means this pony will not turn grey and cannot pass the grey gene on to its offspring.

It is important to note that ponies with that have the grey gene have a high risk of melanoma. 70% of pones over 15 will develop melanomas and ponies that are Homozygous for grey having an even high risk than those that are heterozygous. 

The Pangare Gene.
The pangare gene causes the mealy effect. It causes pale hairs around the eyes, muzzle and underbelly. These pale hairs can extend into the girth area, flanks, chest, throats and up the hind quarters. On red based ponies it can also lighten off the mane and tails giving a flaxen like appearance.