Understanding Equine DNA and Agouti

Due to advances in the DNA technology during the last two decades, and with the recent identification of some genes and mutations causing differences in hair color or underlying certain disorders in Equines, DNA testing has become the method of choice, providing invaluable information for the owners and breeders.

Because practically all cells in the body of the same individual contain identical DNA, and the laboratory tests are extremely sensitive, any easily obtainable “live” material is useful as a source for DNA testing. The material of choice in equine testing is pulled hair from the mane or tail, and must contain intact root bulbs (follicles), which are the source of DNA. (Please note: a young foal’s mane hair is typically too fine, so the coarser tail hair should be used).

Like most animals, the horse has two pigments: black (eumelanin), and red/yellow (pheomelanin). The difference between the production of red alone, and red plus black together is controlled by two alternative forms (alleles) of the Extension gene. The dominant “E” allele determines the production of the black pigment in addition to red, whereas the recessive “e” allele (also called the Red Factor) permits the expression of red only. Consequently, e/e horses have only red pigmented hair (chestnut, sorrel), while horses heterozygous or homozygous for the dominant allele E (E/e or E/E) can produce both red and black pigment.

In a horse carrying at least one E allele, the body distribution of black pigmented hair is further controlled by alleles of the Agouti gene. A horse carrying the dominant “A” allele (either A/a or A/A) will have the black hair restricted to the points (mane, tail, legs) and the base color will be bay. In contrast, the recessive allele “a” does not restrict the black hair, and a homozygote (a/a) will have the black pigmented hair distributed evenly over the entire body, and the resulting base will be black.

The seal brown coat color is characterized by a dark/black body color, with a black mane, tail and legs, and reddish (tan) highlights of varying extent around the muzzle, eyes, on the flanks, belly, and inner thighs. It has been long believed that seal brown is caused by a third allele (At) of Agouti, but this has been the subject of debates and some controversy, in part due to the lack of DNA-based evidence.

In our recent research study we discovered that a specific DNA change in the Agouti locus is indeed responsible for At (a scientific manuscript is currently being prepared for publication).

The following article featuring our At test was published in the April 2010 issue of the Paint Horse Journal (www.painthorsejournal.com).

This article is posted here with the kind permission of the Paint Horse Journal: Brown Paint Horse Journal 0410.pdf

Hierarchy of interactions between Agouti alleles:

bay A > At > a (bay A is dominant over At and ‘a’; At is dominant over ‘a’)

Expected base colors of an E/e or E/E horse:

A/A, A/At, A/a = bay

At/At, At/a = seal brown

a/a = black

The ‘a’ and At alleles are caused by separate changes in Agouti, which do not overlap.

Thus to obtain a comprehensive Agouti allelic status (when it cannot be deduced from the breeding records), one has to perform two DNA tests, both offered by PDSAz:

  1. The standard/conventional Agouti test, specific for the recessive ‘a’. Everything that is not ‘a’ is interpreted as ‘A’ (but can be either bay-A, or seal brown-At).
  2.  The At-specific test will differentiate between bay A and At (this test done alone cannot distinguish between bay ‘A’ and ‘a’).