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Basic Horse Genetics
ANR-1420
u
nderstanding the basic principles of genetics and
gene-selection methods is essential for people in
the horse-breeding business and is also beneficial to
any horse owner when it comes to making decisions
about a horse purchase, suitability, and utilization.
before getting into the basics of horse-breeding deci-
sions, however, it is important that breeders under-
stand the following terms.
Chromosome - a rod-like body found in the cell
nucleus that contains the genes. Chromosomes occur
in pairs in all cells, with the exception of the sex cells
(sperm and egg). Horses have 32 pairs of chromo-
somes, and donkeys have 31 pairs.
Gene - a small segment of chromosome (dnA) that
contains the genetic code. Genes occur in pairs, one
on each chromosome of a pair.
Alleles - the alternative states of a particular gene. the
gene located at a fixed position on a chromosome will
contain a particular gene or one of its alleles. multiple
alleles are possible.
Genotype - the genetic makeup of an individual. With
alleles A and a, three possible genotypes are AA, Aa,
and aa. not all of these pairs of alleles will result in
the same phenotype because pairs may have different
modes of action.
Phenotype - characteristics of an animal that can
be seen or measured—for example, color, birth
weight, speed.
Qualitative traits - traits that are controlled by a
single pair or a few pairs of genes. Qualitative traits are
easily sorted into distinct categories and are not highly
affected by environmental influences; therefore, it is
usually simple to determine an animal’s genotype for a
particular qualitative trait. An example of a qualitative
trait in horses is chestnut versus black coat color.
Quantitative traits - traits that show a continuous
range of phenotypic variation. Quantitative traits
usually are controlled by more than one gene pair
and are heavily influenced by environmental factors,
such as track condition, trainer expertise, and nutrition.
because of these conditions, quantitative traits cannot
be classified into distinct categories. Often, the impor-
tant economic traits of livestock are quantitative—for
example, cannon circumference and racing speed.
Heritability - the portion of the total phenotypic
difference (variation) among animals that is caused by
the part of its genetic makeup that can be passed from
generation to generation.
Homozygous - an individual whose genes for a
particular trait are the same. For example, a black horse
may be homozygous dominant for the black gene (ee),
while a chestnut horse is homozygous recessive for
that gene (ee).
Heterozygous - an individual whose genes for a
particular trait are different. For example, a phenotypi-
cally black horse may be heterozygous (ee) for the
black gene.
www.aces.edu
Selecting Qualitative Traits:
Basic Color Genetics
selecting qualitative traits is a good place to review
some basic genetic principles because most horse
colors are controlled by relatively few genes and
are easily identified phenotypically. the key to basic
genetics is to remember that the horse contributes
only one gene for any allele that he or she has to the
offspring. For example, the base coat color of any
horse may be either black with a genotype of ee or
ee or chestnut (sorrel) with a genotype of ee. the
homozygous black horse (ee) can contribute only an e
gene to the offspring. the homozygous chestnut horse
(ee) can contribute only the e gene to the offspring.
However, the heterozygous black horse (ee) can
contribute either an e or e to the offspring. this is an
example of simple dominant gene action. An easy way
to determine the chances of getting a black or chestnut
horse is to simply write down the possible genes
contributed from both parents (in bold letters below)
in a Punnett square as shown:
Dominant gene - an allele that is expressed when
carried by only one of a pair of chromosomes. For
example, the e allele for the black versus chestnut coat
color is dominant, while e is recessive. Horses that
have one copy of the dominant e allele (ee or ee) will
be black unless that color is modified by other genes.
Recessive gene - an allele that is expressed only
when the dominant allele is absent—for example, the
e allele for the black versus chestnut coat color. Horses
that have the e allele on both chromosomes of a pair
(ee) will be chestnut unless that color is modified by
other genes.
Additive – a gene effect that occurs when the
heterozygous phenotype is intermediate between the
two homozygous phenotypes—for example, aa = no
product; Aa = product; AA= two times the product.
many economically important traits in livestock are
influenced by many pairs of additive genes.
Locus – the place on a chromosome where a gene is
located. the plural of locus is loci.
Epistasis – one locus masks, or controls, the expres-
sion of another locus. A locus, or loci, controlling the
early steps in a pathway can be epistatic to genes
occurring later in the pathway. For example, in horses,
if an early step in a pathway that produces pigment
(color) precursors is masked by the dominant white
gene, it does not matter what base color the animal
was supposed to be—it will have a white coat.
black (EE) × black (EE) =
all offspring homozygous
black (EE)
black (Ee) × chestnut (ee) = ½
heterozygous black (Ee) and ½
chestnut (ee)
E
E
e
e
E
EE
EE
E
Ee
Ee
E
EE
EE
e
ee
ee
black (Ee) × black (Ee) =
¼ homozygous black (EE),
½ heterozygous black (Ee)
¼ chestnut (ee)
black (EE) × black (Ee) = all
offspring black; ½ homozy-
gous (EE), ½ heterzygous (Ee)
E
e
E
e
E
E
EE
Ee
EE
Ee
e
Ee
ee
E
EE
Ee
black (EE) × chestnut (ee) = all
offspring heterzygous black
(Ee)
chestnut (ee) × chestnut (ee) =
all offspring chestnut (ee)
e
e
e
e
E
Ee
Ee
e
ee
ee
E
Ee
Ee
e
ee
ee
2
Alabama Cooperative extension system
zations. A c
cr
contributed from each parent (a double
dose, c
cr
c
cr
) dilutes the chestnut color to cremello
(ivory coat, pink skin, blue eyes) and the bay color to
perlino (ivory coat, pink skin, blue eyes, and a darker
mane and tail). the silver dapple gene (Z) is also a
diluting gene that results in a dark chocolate color with
a black coat, a silver-maned bay on a bay coat, and no
effect on a chestnut coat. Horses with the silver dapple
gene do not have to be dappled, and the gene is most
commonly found in rocky mountain horses and shet-
land and icelandic ponies and is rarely seen in Quarter
Horses, morgans, and Peruvian Pasos.
Other genes that dilute the base coat color are the
Champagne (Ch) gene and the Pearl (Prl) gene.
Champagne is a dominant gene that can dilute any coat
color or modification of the base colors. Champagne
dilutes a black base coat to brown and a chestnut
coat to gold. Champagne horses have amber eyes
and lavender-colored skin that becomes speckled
with darker pigmented spots as the horse ages. the
Champagne dilution is common in tennessee Walking
Horses, missouri Fox trotters, miniatures, and spanish
mustangs. the Pearl gene is a rare dilution that is reces-
sive. that is, it takes two doses of the gene to change
a base chestnut coat to a light apricot color. A single
dose of the gene does not affect the horse’s base coat
color unless it is combined with the cream gene; then,
the resulting coat color is phenotypically similar to the
double cream dilution (perlino, cremello), but in effect,
the horse is a pseudo-cremello or pseudo-perlino. that
is, the color looks like cremello or perlino, but it is
caused by a different genetic action. the Pearl gene is
found in Andalusians, lusitanos, Quarter Horses, and
Paints. in Quarter Horses and Paints, it historically has
been referred to as the “barlink Factor.”
Another form of coat color modification is the grey
gene (G). the homozygous dominant (GG) and
heterozygous dominant (Gg) both result in a horse
that progressively develops more white hairs in its
coat with age. Grey horses are born with a normal, or
almost normal, coat color and eventually turn white
with advancing age. the skin and eyes of grey horses
remain dark. because the grey gene has a dominant
gene action, at least one parent of a grey horse must
be grey. Grey occurs in many breeds of horses, and
it is the predominant color in several breeds such as
lippizans and Andalusians. melanomas (skin tumors)
are more common in gray horses. While the condition
may be disfiguring, most of the tumors are benign.
the problem lies with identifying whether the parent
with the black base coat is homozygous or heterozy-
gous for that trait. since we know that chestnut horses
can only be homozygous recessive (ee), performing
test matings of a black horse to chestnut horses will
give the breeder a clue to the black horse’s genotype.
the more matings that are performed in which no
chestnut offspring are produced, the more assurance
there is that the black horse is homozygous (ee).
if even one chestnut horse is produced, we know
that the black horse has to be heterozygous (ee).
recent mapping of the horse’s genome has reduced
this tedious process to a simple dnA diagnostic
test performed on samples of the horse’s hair roots.
most breeds include both black and chestnut horses;
however, some breeds have been selected for only the
dominant allele, such as Friesians and Cleveland bays,
and others have been selected for only the recessive,
such as suffolks and Haflingers.
the next obvious question is, if the base coat color of
a horse is either black or chestnut, why are there so
few true black horses? it is because there are other
diluting genes that restrict or dilute the base coat color.
For example, the bay (agouti) gene (A), which has
several alleles (A, a+ and a), restricts the black color
to the “points” (the legs, ear rims, mane, and tail).
depending on the “dose” of the bay gene received by
the horse from its parents, a black horse can remain a
true black (eeaa or eeaa) or may become bay (strong
dilution with at least one parent contributing an A) or
seal brown (less dilution than bay with at least one
parent contributing an a+). it is not clear how, or even
if, this bay dilution gene interacts with the chestnut
base coat.
Another example of a diluting gene is the dun (d)
gene, which commonly is found in stock-type horses,
ponies, and the norwegian Fjord. the homozygous
dominant (dd) or heterozygous (dd) combination of
this gene dilutes the base coat to grullo if the horse is
black, to dun if the horse is bay, and to red dun if the
horse is chestnut. the d gene also contributes a darker
dorsal stripe and often darker shoulder and leg bars.
the cream gene (c
cr
) also dilutes the coat color and
has an additive, or dosage, effect. A single dose (Cc
cr
)
with a chestnut coat color results in a palomino and
with a bay color results in a buckskin. A single dose of
the cream gene on a black or seal brown coat results
in a horse that is phenotypically similar to black or seal
brown but is termed a smokey black by some organi-
Basic Horse Genetics
3
Basic colors and results from common modifications or dilutions
Base Color
Modified/diluted
with
Result
Further modified/
diluted with
Result
black
aa
black
dd
black
black
AA, Aa
+
, Aa
bay
dd
bay
black
a
+
a
+
, a
+
a
seal brown
dd
seal brown
black
AA, Aa
+
, Aa
bay
dd or dd
dun
black
a
+
a
+
, a
+
a
seal brown
dd or dd
dun or brown
grullo
black
aa
black
dd or dd
grullo
chestnut
dd
chestnut
chestnut
dd or dd
red dun
black
aa
black
CC
black
black
aa
black
Cc
cr
smokey black
black
AA, Aa
+
, Aa
bay
Cc
cr
buckskin
black
AA, Aa
+
, Aa
bay
c
cr
c
cr
perlino
black
a
+
a
+
, a
+
a
seal brown
Cc
cr
diluted seal brown
smokey black
chestnut
CC
chestnut
chestnut
Cc
cr
palomino
chestnut
c
cr
c
cr
cremello
black
aa
black
zz
black
black
aa
black
ZZ or Zz
chocolate with sil-
ver mane and tail
black
AA, Aa
+
, Aa
bay
ZZ or Zz
bay with lightened
points and silver
mane and tail
chestnut
zz
chestnut
chestnut
ZZ or Zz
chestnut
Champagne (Ch) dilution possibilities with basic colors. In this scheme, the recessive Ch gene is identified by N.
All offspring of homozygous dominant horses (ChCh) should show the Champagne dilution phenotypically.
(from Cook et al., 2008)
Base color
Modified with
Result
Further modified
with
Result
any
nn
homozygous
recessive for Ch.
no change in the
horse’s coat color
from Ch gene.
black
aa
nCh or ChCh
dark tan with
brown points
black
AA, Aa
+
, Aa
bay
nCh or ChCh
tan with brown
points
chestnut
nCh or ChCh
gold
4
Alabama Cooperative extension system
Pearl (Prl) dilution possibilities with basic coat colors. In this scheme, the dominant Prl gene is identified by N, and the reces-
sive is identified by Prl. (from Veterinary Genetics Laboratory, 2011)
Base color
Modified with
Result
Further modified
with
Result
any
nn or nPrl
no change
black
AA, Aa
+
, Aa
bay
nPrl and c
cr
pseudo-perlino
chestnut
nPrl and c
cr
pseudo-cremello
chestnut
PrlPrl
apricot body,
mane, and tail
Grey(G), Roan (RN) and White (W)
coat color modifications
Base color
Tobiano (TO) and Overo (O) spotting patterns
Base color
Modified
with
Result
Modified
with
Result
any
GG, Gg
grey
any
tOtO, tOto
tobiano
any
gg
no change
any
toto
no change
any
rnrn (prob-
ably lethal),
rnrn
roan
any
Oo
overo
any
oo
no change
any
rn
no change
any
Ww
white
the tobiano spotting color pattern (tO) in which white
crosses the horse’s back between the withers and tail
is found in horse breeds throughout the world. it is a
dominant trait that can occur on any coat color. the
overo spotting color pattern (Oo) in which white origi-
nates from the horse’s belly and usually does not cross
the back between its withers and tail also is found in
horse breeds throughout the world. because an overo
offspring can result infrequently from the mating of
two solid-colored horses, it had been assumed that
the overo color pattern is caused by the homozygous
recessive (oo). However, transmission of the overo
spotting pattern does not follow a recessive pattern and
is now known to be inherited as a dominant trait in
which the homozygous dominant is a lethal condition
in the early embryonic stage. this is not to be confused
with the lethal white foal syndrome, which also is
associated with the overo color pattern. Foals with the
lethal white foal syndrome are almost always the result
of two overo parents and are typically either blue-eyed
white foals or may have only a few colored spots
around the muzzle, ears, or tail. the lethal white foal
syndrome causes intestinal blockage due to missing
portions of the digestive tract or lack of nerve cells that
control movement of the intestinal tract. the sabino
color pattern is another spotting pattern in which the
horse has irregular spotting on the legs, belly, and
face and often has roaning in the colored portions of
its coat. sabino patterns in different breeds may be
controlled by different genes.
any
ww
no change
roan (rn) is another gene that lightens the base coat
color in horses by mixing white hairs and colored
hairs on the body. the amount of white hairs may vary
between the summer and winter coats, but overall,
the horse remains the same color throughout its life.
the head and leg colors of roan horses are darker
than the body. the roan color is a dominant trait, but
there is some controversy as to the possibility that the
homozygous dominant condition is lethal in the early
embryonic state. there are other genes that contribute
to an uneven roaning pattern, typically around the
flank, barrel, and top of the tail in horses.
the white gene (W) modifies the normal coat so
that the horse is white from birth. typically, this
gene results in pink skin and dark eyes. this is also
a dominant trait, but research indicates that the
homozygous dominant (WW) is a lethal condition in
early embryonic development. there is evidence that
two normal parents can produce a white foal, which
indicates that some white foals are produced from a
gene mutation. the W gene is rare in all breeds but
can be found in the tennessee Walking Horse, minia-
tures, and American Albino breeds and has occurred in
thoroughbreds, Arabians, and standardbreds.
Basic Horse Genetics
5
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