Thunder Hill Equine Drum Horses

Horse Base Colours: Bay, Black, and Red

Under Construction

This page is under construction. It will contain extensive information on the horse colours Bay, Black, and Red. We are looking for pictures of solid coloured horses that are representative of the various shades in each colour. For a photo to be chosen the horse must be clean, unclipped, and standing in a conformation type stance that best shows off the colour. We have provided information on these colours in an unfinished format for your initial learning enjoyment, with more to follow as the page evolves.

Base colour:

It has been determined that ancestrally all horses were Bay Dun (EE AA DD). All horse colour starts from this point of origin. Base colour is first determined by whether or not a horse can produce the two types of colour pigment: eumelanin (black/brown) and phaeomelanin (red/yellow). The type of colour pigment produced is controlled by the Extension (E) locus. Second, the base colour is determined by where the colour pigments can be expressed on the body of the horse. The location of the colour pigment is controlled by the Agouti (A) locus. The base colours are referred to as Bay, Black and Red, and sometimes Seal Brown. The base colour can then be changed by dilution genes, modifier genes and genes controlling hair structure anomalies.

Extension (E):The Extension (E) gene/allele controls the production of a horse’s base pigment. A horse with a dominant Extension (E) allele is capable of producing both black and red pigment. A horse will have a black base in both homozygous (EE) and heterozygous (Ee) forms as the amount of eumelanin (black) is extended in the hair coat, and will have a red base when the recessive is homozygous (ee) as it only produce phaeomelanin (red) in the coat, causing a diminishing of the amount of eumelanin (black) and restricting eumelanin (black) to the skin. Extension (E) is also referred to as black factor or red factor, referencing whether or not a horse produces black colours or only red. Red horses are often called chestnut or sorrel. Pigment intensity, also known as shade, varies in both Black and Red horses but the cause has not been determined as of yet. Black horse shades range from jet black to a light colour that appears brown. Red horse shades range from a very dark red that appears almost black known as liver chestnut, to a very pale shade that can appear similar to a blond diluted colour. Red horses can also have manes and tails that are body coloured, darker than the body or lighter than the body. Brown or Seal Brown is a colour typified by a dark horse that has red or tan colouring on the muzzle and in the stifle/flank area as opposed to black in these areas. There has been no genetic basis found to treat Brown horses as a separate colour to date. Most people consider Seal Brown as a very dark shade of Bay. Seal Brown could also be explained as Bay with Sooty or a form of Pangare/Mealy.

Genetics: A Black horse will have the genetic shortcut code of EE aa or Ee aa, the Agouti status is often not provided as it is known to always be (aa). A Bay horse can have the genetic shortcut codes of EE AA, EE Aa, Ee AA, or Ee Aa. In situations where the recessive status does not matter the shortcut code can be written as E- A-, because we know that all Bay horses will have at least 1 dominant (E) and (A). A Red horse has the genetic shortcut codes ee AA, ee Aa, ee aa, ee A-, or ee A?. The question mark is used in situations where an allele is hidden and the status will not be known unless genetic testing is done.

Extension (E) is dominant, and historical research has determined that the red coloured horse arose from a mutation to the Extension gene, MC1R, causing a recessive version to appear. A SNP missense mutation causing a serine amino acid to be substituted by a phenylalanine amino acid (p.Ser83Phe) (S83F) results in a horse that is unable to produce eumelanin (black). This mutation is located on gene MC1R at position C901T. A second mutation substituting an aspartic amino acid with an asparagine amino acid (p.Asp84Asn) (D84N) found mainly in Black Forest Horses (ea), creates a red horse with the standard (e) and a second mutation (a) that masks the (e) on some tests causing a false (E), or a Red horse that is reported as Black. This additional mutation is located on MC1R at position G903A.

The Extension gene, MC1R (Melanocyte-stimulating hormone receptor) is located on chromosome 3 and is quite small with only 1 exon. MC1R is also known as: MSH-R, MC1-R, Melanocortin 1 Receptor and Alpha Melanocyte Stimulating Hormone Receptor.

Cytogenetic Map Location: ECAp>3p12.
Molecular Location:
NCBI: Gene ID: 100136907; Location: Chr 3 NC_009146.2 (36259305…36260258); Length: 954 bp
Ensembl: Gene ID: ENSECAG 00000000900; Location: 36259276…36260354; Length: 1,078 bp

Agouti (A): The dominant Agouti (A) gene/allele controls the distribution of black pigment on a horse’s body. In its homozygous (AA) or heterozygous (Aa) forms it causes black pigment to be restricted to a horses points: ear rims, lower legs, mane and tail, creating what is referred to as a Bay. The recessive (a) mutation form of the gene can only be expressed in its homozygous (aa) state. The recessive (aa) has no ability to restrict black pigment, therefore the horse remains a solid black colour over its entire body. Since the Agouti gene only affects black pigment, a Red horse may have either form of the allele and pass it on to its offspring without showing any sign that it carries the allele itself. There are currently people who believe that there may be two other forms of Agouti: Wild Bay (A+) and Seal Brown (At).
Wild Bay (A+) is thought to be dominant to common Bay (AA, Aa) and may be found in Arabians and Thoroughbreds. It is theorized to be part of Agouti (A) or may be part of Extension (E). Wild Bay looks like a Bay with limited black on the legs (reaching to fetlock only), if black is farther up the leg it will be incomplete and not cover the leg fully on the front or back. Wild Bay has not been genetically located yet.
Seal Brown (At) seems to be a minimally expressed Bay, and is thought to be recessive to regular Bay. There are red hairs on the underbelly, stifle fold, and on the face around eyes and muzzle. It is proposed that Homozygous Seal Brown (AtAt) looks dark Bay, while Heterozygous (Atat) forms look almost black. There was a test on the market for Seal Brown but it has been discontinued due to inconclusive and controversial results.

Genetics: A Black horse will have the genetic shortcut code of EE aa or Ee aa, This means that both black and red pigment will be produced but black pigment is not restricted to only the horses points so any red pigment produced is hidden. A Bay horse has the shortcut codes of EE Aa, EE AA, Ee Aa, Ee AA and E- A-, which means that both black and red pigment will be produced and the black pigment will be restricted to the horses points. A Red horse will have the genetic shortcut code of ee aa, ee Aa or ee AA. Since Red horses have no black pigment that Agouti can act upon the actual Agouti status of a red horse may not be known. This causes the sometimes surprising appearance of a Bay foal from one Black parent and one Red parent.

It has been found that the deletion of 11 nucleotides (ADEx2) in exon 2 of the ASIP gene is the causative mutation for Black horses. This frameshift mutation creates a loss of function to the ASIP gene by changing the normal coding sequence through alteration of the regular amino acid sequence. The 11 bp deletion is located at position 191-201 of the exon count based on the start codon, or position 2174-2184 on the genomic DNA level.

The Agouti gene, ASIP (Agouti Signaling Protein) is located on chromosome 22 and has 3 exons. ASIP is commonly referred to as Agouti but is also known as ASP, non-agouti homolog and agouti switch protein.

Cytogenetic Map Location: ECA22q15
Molecular Location:
NCBI: Gene ID: 100054335; Location: Chr 22 NC_009165.2 (25167080…25171074); Length: 3,995 bp
Ensemble: Gene ID: ENSECAG 00000004241; Location: 25167080…25171074; Length: 3,995 bp

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