Homozygous black


Khartoon was tested and found to have a Red Factor Type of 'E'.   This means he is homozygous black, he will always throw the black gene and he cannot sire a chestnut foal regardless of the color of the mare.  Khartoon also tested 'A' for the Agouti gene which means he will always throw the agouti gene which will restrict the black to the points of the horse making a black horse, bay.   

Pikhasso++/ was tested and found to have a Red Factor Type of 'E',  also homozygous black.  He tested Aa for Agouti which means he may or may not throw the agouti gene allowing for the possibility of both bay and black foals.

The basic coat colors of chestnut, bay, brown and black horses are controlled by the interaction between two genes: Extension (gene symbol E) and Agouti (gene symbol A). The Extension gene (red factor) controls the production of red and black pigment. Agouti controls the distribution of black pigment either to a points pattern (mane, tail, lower legs, ear rims) or uniformly over the body. The effects of approximately 10 other genes may modify these pigments to provide an array of colors in the domestic horse ranging from white to black.

The basic colors can be diluted by at least four genes: Cream, Champagne, Dun and Silver. The Cream gene has a dosage effect in that a single copy of Cream produces palominos, buckskins and smoky blacks. Two doses of Cream produce cremellos, perlinos and smoky creams. Champagne, Dun and Silver do not show a dosage effect.

Most color assignments can be correctly made based on physical appearance or phenotype alone. However, genetic testing may be necessary to define phenotypes that are visually ambiguous, such as bays with flaxen manes and tails or chestnuts with dark manes and tails. The same holds true when it is desirable to know which coat colors can be produced by breeding stock. Researchers at the Veterinary Genetics Laboratory and other institutions are working towards the identification of the specific genes and mutations responsible for coat color traits in the horse. In the future, diagnostic tests may be available for all the major coat color genes. Currently, genetic tests are available for: Extension (Red Factor), Agouti, Cream Dilution and Lethal White Overo.

Introduction to Coat Color Genetics

Red Factor - Extension

The Extension gene (red factor) has two alternative states (alleles). The dominant allele E produces black pigment in the coat. The recessive allele e produces red pigment. Red horses (chestnuts, sorrels, palominos and red duns, to name a few) are homozygous, that is they have two alleles, for the recessive red allele ee. Black pigmented horses (black, bay, brown, buckskin and grullo, to name a few) have at least one E allele. They can be homozygous EE or heterozygous Ee. A horse that is homozygous EE will not produce red offspring, regardless of the color of the mate.

The DNA diagnostic test for red factor can be used to identify those black horses for which neither pedigree nor breeding records is informative for identifying carriers of the recessive red factor. Since red is inherited as a recessive trait, it is relatively easy to start up a breeding program that will produce only red horses. It has been more difficult to initiate a black breeding program as black Ee horses can produce red foals. Prior to the development of this test, only pedigree or breeding records, not phenotype, could provide information about whether black horses are EE or Ee.

Red Factor results are reported as:

  • e: Only the red factor detected. The horse can be assumed to be homozygous for red (ee). The basic color is sorrel or chestnut, but depending on genes at other color loci, the horse could be palomino, red dun, gray, cremello, white or any of these colors with the white hair patterns tobiano, overo, roan or appaloosa. 

  • Ee: Both black and red factors detected. The horse can be assumed to be heterozygous for the red factor (Ee). It can transmit either E or e to its offspring. The basic color of the horse will be black, bay or brown, but depending on genes at other color loci, the horse may be buckskin, zebra dun, grullo, perlino, gray, white or any of these colors with the white hair patterns tobiano, overo, roan or appaloosa.

  • E: No red factor detected. The horse can be assumed to be homozygous for black pigment (EE). It cannot have red foals, regardless of the color of the mate. The basic color of the horse will be black, bay or brown, but depending on genes at other color loci, the horse may be buckskin, zebra dun, grullo, perlino, gray, white or any of these colors with the white hair patterns tobiano, overo, roan or appaloosa. 

Agouti (Bay/Black)

The Agouti gene controls the distribution of black pigment. The dominant allele A restricts black pigment to the points of the horse (mane, tail, lower legs and ear rims), as seen, for example, in bays and buckskins. The recessive allele a uniformly distributes black pigment over the entire body.

Breeders interested in producing black horses need to have breeding stock carrying the a allele, in addition to the E allele of the Extension gene. Using results from the red factor and agouti tests, click here for a table of breeding schemes to produce black animals.

Agouti results are reported as:

A or Aa: Black pigment distributed in point pattern. The basic color of the horse will be bay or brown in the absence of other modifying genes. A has no effect on red pigment (ee). 

a: Only recessive allele detected. Black pigment distributed uniformly. The basic color of the horse will be black in the absence of other modifying genes.