Case study: testing for agouti
We frequently test chestnut mares for agouti when their owners want to know if they
could potentially produce black foals.
Put simply, black horses have black pigment in their hair
and they aren't bay or brown.
This case study looks at the two genes that control the basic coat
colours (chestnut, bay or brown, and black) and how you can use information from a horse's
appearance combined with the results of the agouti test to make predictions about foal colour
from a chestnut mare.
Examples with other coat colours will be covered in future case studies.
Hair pigment in horses comes in two versions, red (the chestnut colour) and black.
Each horse has two copies of the gene that controls this hair pigment. Once copy is
inherited from the horse's dam and one from its sire. If either one copy or both copies
specify the black version of this gene, the horse will produce black pigment in its hair.
The mare in our illustration has two copies of the version of this gene that specify red
pigment instead, so she is chestnut.
For historical reasons the gene that specifies hair pigment colour is called extension.
The written short form of the two extension genotypes are big 'E' for black pigment and
little 'e' for red pigment.
The second requirement for a black horse is that they aren't bay or browm. At the moment there
are three testable versions of the gene that controls bay colouring, specifying bay, brown or black.
As was the case for extension, every horse has two copies
of this gene, with one being inherited from the dam and one from the sire. Black horses must inherit
two copies of the black version of this gene. This means they need to inherit the black version from both
The gene that controls bay colouring is called agouti. The written short form of
the three agouti genotypes are big 'A' for bay, 'At' for brown and little 'a' for black. (Note
that most testing labs including Practical Horse Genetics group 'A' and 'At' together as 'A'.
This isn't a problem if you primarily interested in black because your focus will be on whether
two copies of the 'a' form of agouti are present).
Each version of agouti requires black pigment to be present for its effect to be seen.
This means that for chestnut horses - which have no black pigment - there is no visual indication
of what versions of the agouti gene they carry. Genetic testing for agouti is usually the quickest
and cheapest way to find out.
Have a look at our chestnut mare in the illustration. She will pass on the version of the
extension gene that specifies
red pigment (an 'e' genotype) to her foal - but that's OK, because her foal could still be black if
it inherits the version for black pigment (an 'E' genotype) from its sire. It's easy to pick whether
a potential sire has an 'E' genotype to pass on just by looking at him: if he is black, brown or bay,
then he has at least one copy of 'E'.
But will she pass on the black version of agouti to her foal? This mare tested as having an
'A/a' genotype, meaning that she has one copy of agouti that specifies black colouring and one that
specifies bay or brown colouring. This means that yes, she could pass on an 'a' genotype. However
she is just as likely to pass on her 'A' genotype instead, which would mean a bay or brown foal instead
If her owner wants to maximise their chance of a black foal, they should use a black stallion.
Since he is black, we can tell without genetic testing that he carries two copies of the 'a' version
of agouti. This guarantees that he will pass on the 'a' version of agouti required for a black foal.
Ideally he would also have an 'E/E' extension genotype, guaranteeing that he passes an 'E' genotype
too. Genetic testing of his extension genotype is one way to find out if he is 'E/E', but he's also
very likely to be 'E/E' if he has had lots of foals and none are chestnut.
From a black 'E/E, a/a' stallion, this mare has a 50:50 chance of producing a black foal or
a bay foal. From a black 'E/e, a/a' stallion, this mare has a 50% chance of producing a chestnut
foal, a 25% chance of producing a black foal, and a 25% chance of a bay foal. From a bay stallion
with an 'E/E, A/a' genotype, she has a
25% chance of producing a black foal, and a 75% chance of a bay foal. All other options have even
less chance of producing a black foal!
Congratulations on making it all the way to the end! Do you need agouti testing for your
chestnut mare (or stallion)? Order it here.