Equine Color Genetics for the Breeder

Written by:
Dr. Frederick Harper, Extension Horse Specialist
and Dr. Benny Bell, Associate Professor
Department of Animal Science
University of Tennessee.

A new born foal is an exciting and economically important event. The entire future of the horse industry hinges on this occurrence. The creation of prospective world grand champion Tennessee Walking Horses, Kentucky Derby winners, Olympic champions as well as pleasure and 4-H horses depends on the transmission of genes from one generation to the next.

These genetic circumstances are among the least understood of all aspects of horse production due to limited genetic research in horses. The lack of research is due to the high cost of maintaining breeding herds large enough to generate sufficient data for genetic studies and the lack of organized performance testing programs.

The generation interval is the time required to produce a generation and for them to reproduce. It can be expressed as the average time between birth of horses and the birth of their replacements. Low reproductive efficiency, reported to be 50 to 80 percent, results in a long generation interval in horses. Generation interval is nine to 12 years in horses. There are about nine generations per 100 years. The long generation interval results in slower genetic progress, which is also a cost factor as well as a genetic factor. However, these negative factors do not, and should not, prevent conscientious horse breeders from applying good genetic principles in their efforts to breed better horses and “champions.”

It is amazing that a number of breeders have been successful in continually breeding “champion” quality horses in each breed with little technical training in genetics and without the benefit of information from research.

Demand for high quality horses makes it imperative that each breeder judiciously establish specific breeding goals, apply genetic principles in making decisions and utilize the best available and affordable breeding stallions and mares.

This article outlines the basics of genetics and its application to horses. This information should allow horse breeders to understand genetic principles and apply these concepts in their efforts to breed better horses. Intelligent application of genetics combined with good management practices gives the horse breeder a better chance of success.

Basic Genetics

            Genes are the basic units of inheritance. They are located on chromosomes which are threadlike structures that exist in pairs. Each gene is located at a fixed position, called a locus, on a specific chromosome. A chromosome can be considered a linear arrangement of genes containing hundreds or probably even thousands of genes. Chromosomes are found in the nucleus of each body cell. The horse has 32 chromosome pairs or 64 chromosomes, compared to a human who has 23 pairs. One chromosome in each pair is inherited from the sire and the horse from the dam.

Like chromosomes, genes occur in pairs also. Each parent (sire and dam) contributes one gene of each pair. Sperm produced by the stallion and ovum (eggs) from the mare are sex cells. As sperm and eggs are formed, chromosome pairs separate so each sex cell contains only one member of each pair. Each sex cell contains a random sample of the animal’s genes. When the sperm unites with the ovum, at fertilization, the original chromosome number of 32 pairs is restored. Through this process the individual receives a random of half of each parent’s genes.

One pair of chromosomes determines the sex of the foal. The sex chromosomes are designated as X and Y. The mare possesses two X chromosomes, and the stallion has and X and a Y chromosome. The mare can contribute only an X chromosome to each of her foals. The stallion, by random chance, may contribute an X chromosome or a Y chromosome to each of his get. Therefore, the stallion determines the sex of the foal. Genes on the X chromosome are called sex-linked and consequently have different patterns of inheritance. Very few loci have been identified on the Y chromosome.

Genes carried on the same chromosome are physically linked together; however, this physical relationship does not mean that genes on he same chromosome always will be inherited together. During the formation of sex cells when chromosome pairs line-up and separate, chromosomes may break and rejoin. Therefore, when chromosomes separate, they may carry new combinations of genes. This process is called “crossing-over.”

Members of a gene pair at a given locus may take different forms. These forms are called alleles. Individuals with two different alleles at a particular locus are called heterozygous at the locus. If the two genes of a pair at the locus are the same, the animal is homozygous. Even though any one individual can only have two different alleles at a locus, the number of different alleles in a population for a given locus can be much greater than two.

Gene Expression

            Genes express themselves in different ways and to different degrees. An understanding of the expression or action of genes is fundamental in the development of a genetic improvement program. In order to discuss different types of gene action, it is necessary to understand two new terms. Genotype is the genetic make-up of an individual. Phenotype is the observable characteristics of an individual. The physical appearance, such as color or conformation, and performance traits are phenotypes. At times, the genotype for a trait can be determined by looking at the animal. But most of the time, it is impossible to know an individual’s genotype from its physical appearance. For some traits, the phenotype is influenced by environment as well as the animal’s genetic make-up.

How genes express themselves may be divided into two general categories: additive and non-additive. Additive gene expression occurs when the effect of one gene adds to the effect of its own allele or to other genes that affect a trait. Traits such as conformation, speed, and performance are largely affected by additive gene action. Typically such traits are controlled by large numbers of genes, and each gene contributes a certain amount to the animal’s genetic ability.

Each different gene adds to others to produce a more extreme phenotype with additive gene action. Speed in race horses appears to be affected by additive gene action. A large number of genes are involved in the inheritance of speed. However, only three gene pairs will be used to illustrate the effect of additive gene action.

ccddee = poor racing ability

Ccddee = below average racing ability

Ccddee = slightly below average racing ability

CCDdee = average racing ability

CCDDee = slightly above average racing ability

CCDDEe = above average racing ability

CCDDEE = superior racing ability


With each addition of a positive gene, there is improvement in racing ability. Most performance traits are due to this type of inheritance.

Non-additive gene action occurs when the phenotypic expression of one gene does not necessarily add to the expression of other genes. The gene may not be expressed at all. It may interact with its partner to give a certain unique phenotypic effect, or two entirely different gene pairs may interact with each other to produce a particular phenotype. Coat color is an example of how a trait is influenced by non-additive gene action. In non-additive gene expression, the effect of a gene is dependent on the specific combination of genes present. Phenotypes of traits affected by non-additive gene expression generally fall into rather specific classes such as body coat color. Phenotype of traits controlled by additive gene action are distributed over a continuous range such as show ring performance or jumping ability. These traits are called quantitative.

Some genes are dominant, which is an example of non-additive gene action. A dominant gene can hide or mask the expression of the other gene paired with it. The effect of the recessive gene is not observed if it is paired with a dominant gene. However, the recessive gene is present and can be transmitted by an individual to some of its foals. The only time a recessive gene is expressed is when both genes are recessive.

Black coat color is due to a dominant black gene (B). Dominant genes are noted by capital letters, while recessive genes are depicted by lower case letters (b). All black horses have at least one dominant (B) gene. A black horse may be homozygous dominant (BB) or heterozygous (Bb). If a horse is homozygous recessive (bb), it will be a chestnut. Every foal from a BB sire (or dame) will receive a B gene and be black. Half the foals from a Bb (black sire (or dame) will receive a B gene and the other half a b gene. If a black stallion of unknown genotype (B_) is mated to a chestnut (bb) mare, the foal is chestnut (bb), the stallion has to be heterozygous (Bb). Since the foal can only get a b gene from its dam, it also has to receive a b gene from its sire.

Certain genes or gene combinations may be lethal. A true lethal results in death prior to or shortly after birth. Most lethal genes are recessive and therefore are only expressed in homozygous recessive individuals. If dominant, the fetus would die and the gene be removed from the population.

Combined Immunodeficiency (CID) is a lethal which occurs in Arabians. Affected foals die four to five months after birth. There is a complete deficiency of both B- and T- lymphocytes, which have a key role in the defense reactions of immunology.

CID is caused by a single recessive gene resulting in the death of about 2.5 percent of all Arabian foals. However, about 25 percent of Arabians are carriers of the CID gene.

When a carrier is mated to another carrier, one foal in four is expected to have CID, two of four will be carriers and only one will not posses the gene. To determine the presence of this recessive lethal, progeny testing is needed. If a stallion sires or a mare produces one CID foal, they are carriers – and should not be used as breeding animals.

Another type of non-additive gene action is called co-dominance or partial dominance. In this case, the phenotype of the heterozygte (Oo) can be distinguished from the heterozygous dominant. Palomino coat color caused by the effects of a dilution gene (D) is an example of partial dominance. If a horse has the genetic makeup of chestnut (bb), and has one copy of dilution gene (Dd) then the horse will be palomino. If two copies (DD) are present, the horse will be nearly a white cremello color. The recessive dd has no effect on color, so the bbdd individual is chestnut.

Over-dominance occurs when the heterozygous individual (Qq) is superior to either the homozygous dominant (QQ) or the homozygous recessive (qq) individual.

Epistasis is the interaction of more than one gene pair to produce a unique phenotype. The genes at one locus may influence genetic expression of another gene pair. The palomino coat color is an example of such an interaction between genes at two loci. Another example is the bay color in horses. A bay horse has black points: mane, tail, and lower legs with a bay body color. If a horse is (A-) at the bay locus and is also (B-), the horse will be bay. If the horse is homozygous recessive (aa) at the bay locus and B- , it will be black.


Genotype                    Color (phenotype)

aaBB                            black

aaBb                            black

AaBB                           bay

AaBb                           bay

AABB                          bay

AABb                          bay


Quantitive Traits

For some traits, an animal’s phenotype is affected by the environment as well as its genotype. For example, a horse’s performance in three-day events is due to both it genetic make-up and its environment. An animal’s genotype can be thought of as its potential or ability for a specific trait. The environment represents the opportunity given the individual to express its genetic potential. Environmental factors include nutrition, health care, conditioning, and training. A draft horse no matter how well fed, conditioned, and trained will not win the Kentucky Derby. The best-bred Tennessee Walking Horse yearling, if not properly fed, conditioned and trained, can never reach its genetic potential of being a world champion.

Good environment is essential for a horse’s genetic potential to be expressed. However, the effects of environment are not genetically transmitted to foals. Progress made through genetics is permanent improvement and transmitted from generation to generation. However, improvement due to environment is temporary and cannot be transmitted to the offspring.

Environment can complicate one’s ability to measure a horse’s true breeding value (genotype). For example, a horse of average genetic merit that receives exceptional training may out perform another that is genetically superior but was managed by a less-skilled trainer. It is critical that breeders base selection decisions on estimates of a horse’s genetic merit and attempt to remove as many of the environmental influences as possible.

This effect can be minimized by comparing individuals which are in the same environment. This is very difficult, or nearly impossible, in the horse industry. A horse raised and trained on one farm has a different environment than one from another farm. The situation is very complex with management of horses today: a broodmare is shipped to a stud farm for foaling and re-breeding; returns home when the foal is 60+/- old; sold as a yearling, the horse is often kept at a training farm (stable); then goes to numerous race track or shows for two or more years; then is placed at stud or in the broodmare band.

An important parameter of a trait is called heritability. Heritability is the proportion or percentage of the difference in a trait which is due to additive genetic difference in horses. Some useful heritability estimates are listed in Table I.

The heritability of speed is 40 percent. This means that 40 percent of the variation in speed is due to genetic differences in the horses’ breeding values. Most of the remaining variation is due to environmental differences. Heritability estimates 40 percent or greater are relatively high. Those less than 10 percent are considered low. Traits that are more easily measured and defined typically have high heritability. When the criteria is subjective, such as show ring winnings, etc., it is difficult to make genetic progress due to low heritable traits. Traits such as reproductive performance and longevity fall into this low category. If a trait has a low heritability, the trait is influenced more by the environment.

Variation (differences) is the raw material with which the breeder works. If none of the variation is due to genetic differences, genetic improvement is not possible.

Heritability can be used to predict genetic improvement. Racing speed is highly heritable, about 40 percent. With racing Quarter Horses, a speed index (SI) measures a horses relative speed under certain conditions. The higher the SI, the faster the horse. The selection differential is the difference between the average merit of the stallions and mares selected as parents and the average of population from which they were chosen. If the average SI for all racing Quarter Horses is 75 and the sire’s SI is 99 and the dam’s SI is 90, the genetic change expected is as follows:

Genetic Change = Heritability X Sire’s Superiority + Dam’s superiority

Sire’s Superiority = Sire’s SI – Breed average SI

= 99-75 = 24

Dam’s Superiority – Dam’s SI – Breed average SI

= 90 – 75 = 15

=0.40   X   24 + 15 / 2

  =0.40 x  39 / 2 = 0.40 X 19.5 = 7.8

The foal should have an anticipated speed index of 83 (75 + 7.8).

Heritability estimates give the horse breeder several pieces of useful information: 1) it indicates how much additive gene action affects a specific trait;  2) the effect due to the environment;  3) it indicates the amount of progress that can be expected for a trait; and 4) it indicates the type of mating system to use.


TABLE I: Heritability Estimates for Horse

Trait         Degree of Heritability

Speed (racing)                      High

Cow Sense                            Medium to high

Intelligence                           Medium to high

Growth Rate                          Medium to high

Mature Size                           Medium to high

Type or conformation         Medium

Efficiency of growth            Medium

Fertility and vigor                Low


References and additional reading: Jones, W.E. 1982.

Genetics and Horse Breeding. Lea & Febiger, Philadelphia.

Equine Genetics and Selection Procedures. 1978

Equine Research, Inc., Carrollton, Texas.

2 comments on “Equine Color Genetics for the Breeder

  1. Cecile

    I’ve been trained as a steincist, of course I also believe that believing science is much much better than nonesense crap. What I tried to say was that if steincists often consider them to be eslites and everyone should just believe in science, it doesn’t help the development of science education actually. I think the society actually needs more rational discussions on most issues. In many cases, steincists should also learn the sources of lay people getting incorrect information in order to understand the real problems are and then have a better way to deliver correct information to the publics.

  2. PhoebeOQ

    Hi Haven’t we met before? My contact information on my profile



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