Published in the Morgan Horse Association of New Zealand magazine in Autumn 2011

Dr Jenny Cahill


Equine Parentage and Animal Genetic Services Centre

Massey University


Coat colour was one of the first genetic traits of horses to be investigated in depth, the responsible gene “defects” isolated and diagnostic screening tests created. Knowledge of the genetic colour profile of an individual is extremely important if colour is one of the desirable/undesirable outcomes of your breeding programme. And in some instances, such as the overo lethal white mutation in frame overo horses, vital to be able to identify carriers of hidden lethal genes.


At the Centre we are pleased to now be able to offer some of these colour tests to New Zealand horse breeders. We are currently offering the following tests:

-Extension/red/chestnut test

-Agouti/black test

-Cream dilution

-Overo Lethal White


-Silver dilution

All tests are $35, and details on sample collection and submission are available on our weblink or by emailing me at This email address is being protected from spambots. You need JavaScript enabled to view it. Depending on the number of samples we receive the turnaround time for tests will be between 5 and 10 working days once the samples reach the lab. As well as issuing a certificate with the test results/colour profile for your horse I will also include an interpretation of the results and possible mating outcomes.


What do the test names mean, and how do you choose the test or tests that will give you maximum information for your breeding programme?


Firstly some basic information explaining the genetic terms used in discussing the results.

Each colour site (or locus) tested has a pair of alleles (or markers) that we measure.

One of each pair has come from the dam and one from the sire.

The alleles are given letters – the dominant allele is in upper case, and the recessive allele in lower case.

Dominant allele – only needs one of the pair to produce the effect (in this case a colour variant)

Recessive – needs 2 copies of the pair to produce it’s effect

If the 2 alleles at the site are the same the horse is homozygous for that site.

If the 2 alleles of the pair are different the horse is heterozygous for that colour site.


The two basic coat colour tests are the Extension/red locus with the two alleles E and e, and the Agouti/black locus with the two alleles, A and a. The combination of these two markers determines the base coat colour of all horses – chestnut, bay or black.


Chestnuts are all ee, and have no black pigment.

One or two copies of E (EE or Ee) means that there will be black pigment.

BUT whether the horse is bay or black depends on it’s status for the Agouti locus.

aa will be black.

One or two copies of A (AA or Aa) will be bay. Black pigment is distributed to the points- head, legs, mane and tail.


The test to choose is whichever of the two markers is hidden by the base coat colour.

When you consider that a bay horse could be AAEE or AAEe or AaEE or Aaee, it is easy to see how a knowledge of the exact profile will helping predicting possible colour outcomes for offspring.

  • Chestnut horses are all ee for the Extension locus.
  • Want to test for the Agouti locus to see if the profile is AA or Aa or aa, in order to predict whether bay or black offspring are a possibility.
  • Bay horses, could be EE or Ee and AA or Aa.


    Want to test for Extension to see if there is one copy of the e allele, and therefore could produce chestnut offspring.

    Also may want to test for Agouti to see if it is AA with no chance of black offspring, or Aa, which could produce black offspring.

    • Black horses are all aa for Agouti.

    Want to test for Extension to see if EE or Ee, as only the profile with a copy of e could produce chestnut offspring.


    All of the above holds true for the many diluted and patterned variations in colour.


    Cream dilution, alleles C and Ccr

    With some of the more unusual faded colours it can be difficult to determine visually if there is a dilution present, or what the base coat colour is. The test tells us whether there is none, one or two copies of the cream dilution gene present.

    Chestnut plus one copy of cream results in palamino.


    Bay plus one copy of cream results in buckskin.

    haymeron park dream jeani

    Black with one copy leads to smoky black.

    Two copies of the cream dilution result in the very diluted versions of cremello (from chestnut), perlino (from bay) and smokey cream (from black). These can look similar, and so testing for cream in combination with Extension and Agouti is very useful.


    Overo Lethal White

    A relatively high proportion of horses with frame overo patterning carry a hidden gene for Overo Lethal White syndrome.

    The alleles are N – normal and O – overo lethal white mutation.

    NN – normal and noncarrier, solid or frame

    NO – frame overo pattern, carrier, and if mated to another carrier will produce a proportion of white foals with overo lethal white syndrome. Hence the importance of identifying these carriers, to allow for suitable matings to be chosen to eliminate the risk of this syndrome in foals.






    This locus determines whether a horse has tobiano patterning, and has the two alleles TO and to. TO is dominant and so horses with one or two copies of TO (TOTO or TOto) will be tobiano in appearance.

    BUT only the horse with 2 copies, TOTO (homozygous for tobiano) will produce all tobiano offspring. The heterozygous horse, TOto, will produce a percentage of tobiano foals, depending on the status of their mate.


    Silver dilution, alleles Z and z

    The silver dilution gene is dominant and has a dilution effect on black pigment, but no effect on red pigment. Unlike cream dilution there is no visible difference in coat colour between horses with 1 copy of the dominant silver dilution (Zz) and those with 2 copies (ZZ). There is however a difference in the frequency with which they will pass the dilution on to their offspring.

    A solid black horse will be chocolate coloured with lightened mane and tail. A bay horse will have the black pigment on lower legs, mane and tail lightened, and in some cases can be mistaken for chestnuts with flaxen mane and tail. A chestnut horse has no black pigment and so can carry the silver dilution with no apparent effect on coat colour. The silver dilution is known to occur in a range of breeds including Icelandic horses, Morgan horses, Miniature horses, Shetland ponies and Rocky Mountain horses


    Grey, alleles G and g

    The colour grey, or more accurately greying with age, has long been known to dominant, and epistatic over the 3 base coat colours. So regardless of whether a horse has chestnut, bay or black as its base coat colour, if it has 1 or 2 copies of the dominant grey gene it will be a grey horse. A diagnostic test is available to determine if grey horses have 1 or 2 copies of the grey gene, but it is not offered at this laboratory.

    • All grey horses must have at least 1 grey parent
    • Mating 2 non grey horses can never result in grey offspring



    If you have the full colour genetic profiles of both dam and sire you can then make very informed predictions of the outcomes of a mating with respect to colour of offspring

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