Equine Coat Color Genetics

Lesson One

Introduction to Horse Color Genetics

While the old saying is true that "a good horse is never a bad color", the colors of horses have been important to human beings as far back as when prehistoric people painted "polka-dotted" horses on their cave walls. Certainly today, when horses are valued for aesthetic as much as utilitarian purposes, there is a great deal of interest in identifying, and breeding for, colors.

Horse color genetics is a manifestation of the principles of genetics that is relatively easy to observe. To the "lay person", genetics can be a mysterious, confusing branch of science. It's true that it is incredibly complicated. And unless we work in an advanced genetics laboratory, we can't watch as the parts of chromosomes separate from pairs to single strands in the reproductive cells, then combine back into pairs again when a new life is created.

But a horse's color, in most cases, is easily observable, and is caused by relatively few genes, most of which are now well understood. The horse's color is a visible trait by which we can see genetics at work, and thus, more easily understand its principles.

Equine Genome Mapping Project

The Horse Genome Project is a collaborative effort by many research partners in North America, Europe, Asia, and Australia.

Scientists in recent years have been able to map the entire equine genome. More information on the Equine Genome Mapping project may be found at the University of Kentucky. Take a moment to review the site located here http://www.uky.edu/Ag/Horsemap/welcome.html and begin to get familiar with the project.

The Glossary associated with the Genome Mapping Project defines many of the terms used in this class. It is reproduced, with a few updates, below, for your convenience. It may also be found at the above link to the Equine Genome Project, on the web site of the University of Kentucky.

GENOMICS 101 - TERMS AND DEFINITIONS

Gene: a) hereditary determinant for a trait. b) piece of DNA with code for a protein. For example, genes are responsible for hair and skin color by directing the production of varying amounts and types of the pigment melanin.

Genome: The complete set of genes and associated regulatory DNA. The study of the genome is called genomics.

Chromosome: Large molecule that contains DNA (complexed with proteins) in a cell. Each horse cell has 32 pairs. Human cells have 23 pairs.

Allele: Form of a gene. For example, alternate forms of the gene called MC1R produce red or black pigment in hair. (Sometimes alleles are referred to, colloquially, as genes, as in "the gene for red hair" versus "the gene for black hair". Technically, allele is the correct term.)

Homozygous: All animals have two gene copies, one from the mother and one from the father. If both copies of the gene are the same, then the individual is said to be homozygous for that gene.

Heterozygous: All animals have two gene copies, one from the mother and one from the father. If both copies are different, then the individual is said to be heterozygous for that gene.

Dominant gene: An allele which is expressed whenever it is present.

Recessive gene: An allele which is expressed only in the absence of a dominant gene. Horses with one copy of a dominant allele and one copy of a recessive allele are said to be carriers of the recessive allele (gene).

Carriers: Individuals which do not possess a trait but can pass it to their offspring are said to be carriers for that genetic trait. This is characteristic of recessive genes.

Gene locus: The DNA site for a gene. For example, there is a locus for the gray gene and its two alleles are "the presence of graying" and "the absence of graying".

DNA: The molecule that contains hereditary material and the major constituent of chromosomes. DNA is composed of only 4 molecular units (bases) but the organization of the units is unique among genes and species. A gene may have 1000 to 2000 bases long. The whole genome of any mammal is composed of approximately 3 billion units of these 4 bases.

Mutation: A genetic variation in the gene that causes an alternative form of a trait within a species. This can also be called a genetic variant. Mutations can be identified as changes in the composition of the DNA at a unique site.

Proteins: Product of genes. Genes usually act by creating proteins which act as enzymes or which can be structural parts of cells.

Gene Map or Genome Map: The known order for a set of genes or DNA markers at intervals along a chromosome. A minimum density map will have 300 markers while a high density gene map will have 10,000 markers. Denser maps are more effective research tools.

Genome Sequence: The complete DNA sequence determined for all chromosomes in a cell for an individual, including all 20,000 genes and approximately 3 billion DNA bases.

* This class will not focus on the mapping project; however, references to findings will be noted.

Equine Coat Color Genetics and DNA Testing

Before we start discussing specific coat colors, a common understanding of how their genetics work in the Equine Species is valuable.

Genes are the basic units of inheritance. They are composed of DNA. Genes, linked together, form a chromosome -- similar to the way pearls are threaded together to make a strand.

Horses carry 32 pairs of chromosomes, for a total of 64 chromosomes. Each horse has inherited 32 chromosomes from each parent; it is these 64 chromosomes which carry the genetic makeup of each horse. Each gene on the chromosome has a mate, or allele, in exactly the same place or “locus” on the chromosome’s matched pair. It is these alleles which carry the genetic traits for the characteristics evidenced in a horse.

Each pair of genes codes the DNA for a specific job. A pair of genes can control something as obvious as whether or not a cow will have horns, or be as subtle as coding for a specific portion of a biological molecule.

During the cell division, when one cell divides into either two eggs or two sperm cells, only one member of each chromosome pair goes into each new cell. This provides every sperm and egg with only one copy of each gene. For example, suppose a stallion has at one gene location, along the chromosomes, a pair of genes (alleles) designated as “E” and “e”. When that chromosome pair divides into two sperm cells, one resulting sperm cell will get the chromosome with the “e”, and the other resulting sperm cell will get the other chromosome with the “E”. This same process takes place in the mare as she produces eggs.

Upon fertilization, the single chromosomes find their corresponding mate and pair back up. The resulting individual again has two genes at each location – one from its dam and one from its sire.

In this course, we will use the most widely accepted, scientifically sensible notation for the various genes/alleles. Do not get tunnel vision about genetic abbreviations. Different laboratories and registries abbreviate color genes differently; but with a little effort, you can learn to interpret each source's method.

Just what do we know about equine colors?

Equine coat colors have often been a great cause of confusion. There are tremendous ranges of shades within a color, and various colors without recognized names, and all of their methods of inheritance (especially of "shade") are not understood. Then there are colors which appear to the eye to be identical, but are caused by completely different genes/alleles. However, many of the genes causing various colors have been isolated and are well understood, even outside of the laboratory. The various genetic testing laboratories usually depend upon the experiences of "lay" horse breeders, "in the field", so to speak, to tell them what to look for in the laboratory. Then the lab is able to isolate the gene responsible for the observed color based on how it is inherited, and develop a test for it.

Breed associations have contributed to the confusion. The Jockey Club (Thoroughbred registry for racing), American Quarter Horse Association, American Paint Horse Association, and The Friesian Registry, for example, all recognize only a limited number of colors each, which vary from registry to registry, and sometimes change from year to year.

Equine Color Testing Resources

UC Davis : http://www.vgl.ucdavis.edu/services/horse.php
red, black, agouti (A / a only), cream, dun, pearl, silver, LWO, Sabino-1, Tobiano, gray, roan, & champagne

Pet DNA Services of Arizona : http://www.petdnaservicesaz.com/Equine.html
AGOUTI : (seal) brown (At) vs. bay (A)

Animal Genetics (in Florida) : http://www.animalgenetics.us/Equine.htm
Tobiano, E Locus (red gene), Agouti, Cream gene, Sabino, Overo, Lethal White Syndrome (OLWS), Silver Dapple (Z), Gray, Champagne

VetGen : http://www.vetgen.com/documents/order-form-equine.pdf
black, red, agouti, cream, silver

University of Kentucky : http://www.ca.uky.edu/gluck/AGTRL.asp#color
Champagne, Tobiano, E Locus (red gene), Agouti, Cream gene, Sabino, Overo Lethal White Syndrome (OLWS), Silver Dapple (Z)

Texas A & M : http://www.cvm.tamu.edu/vibs/
They offer tests for black/red, agouti, tobiano, cream, sabino, and silver.

More info from the University of California, Davis branch

Shown below is a partial listing of horse color genes and their alleles and descriptions originally taken from the University of California, Davis, web site http://www.vgl.ucdavis.edu/services/coatcolor.php in November 2013, edited for conformity and clarity.

The reference to the highly-controversial "dominant white" has been removed for now, pending an in-depth discussion of its true nature in later lessons.

* THIS IS BY NO MEANS AN EXHAUSTIVE LIST OF ALL KNOWN HORSE COLOR GENES.

Dominant forms of each gene begin with a capital (upper-case) letter (A, At, Cr)
and its recessive forms are represented by all-lower-case letters (a, cr).

Gene Relationships

Gene interactions can be complex, confusing and elusive. Fortunately, many horse color genes adhere to a relationship based on simple dominance.

Genes that interact under the terms of simple dominance exist in only two forms.

• One form of the gene is dominant. This means that its form will be expressed. Upper-case (capital) letters usually are used to indicate a dominant gene.

• The other form is recessive. Recessive genes are "submissive to" the dominant and are expressed in lower case letters.

When there are just two possible expressions for a specific gene, dominant or recessive, there are only three possible ways this matched pair can exist.

1. Both genes are in the dominant form (XX)

2. Both genes are in the recessive form (xx)

3. One member of the pair is in the dominant form and the other is in the recessive form (Xx) (the notation xX is not used)

Homozygous and heterozygous are words used to identify which gene combination is present. These words sound difficult, but the prefixes of the words are common in our language. The prefix “hetero-” means "different", and “homo-” means "the same".

Putting together the concepts of dominant vs. recessive and homozygous vs. heterozygous provides us with the language used by geneticists to describe gene relationships.

When both copies of the genes are in the dominant form the terminology used is "homozygous dominant". Foals that are homozygous for a particular dominant gene must have received one copy of that gene from each parent (sire and dam).

When both copies of the genes are in the recessive form the terminology used is "homozygous recessive". Foals that are homozygous recessive for a particular gene must have received one copy of that recessive gene from each parent (sire and dam).

Example: all red horses, commonly called sorrel or chestnut, are homozygous recessive for the red gene – “ee”.

When the pair exists in the dominant/recessive relationship the relationship is referred to as heterozygous. The dominant form is in control of the expression. Each offspring has a 50/50 chance of inheriting either the dominant or the recessive gene from a heterozygous parent.

Example: a black horse may be either homozygous dominant (EE) or heterozygous (Ee). Either way the dominant gene will be expressed.

Predicting Gene Combinations - The Punnett Square

The last concept to be mastered before we begin our discussion of the genetics of specific coat colors is how to predict the possible gene combinations that could occur from the mating of two horses. The Punnett Square is a tool that simplifies the process.

To use the Punnett Square, one draws a table with two (2) columns – one for each of the gene pairs contributed by the stallion – and two (2) rows, one for each of the gene pairs contributed by the mare. Each quadrant of the Punnett Square equals a 25% chance of that combination of the genes occurring.

(See following graphic.)

STEP 2

Across the top, place each one of the genes contributed by the stallion into a separate column.

For this example, let’s assume the stallion is homozygous recessive for pigment, or “ee”

STEP 3

Down the left side, place each one of the possible genes contributed by the mare into a separate row.

Let’s assume this mare is Heterozygous for pigment, or “Ee”

STEP 4

To create a mating, enter the gene notation from the top of the column into the blank boxes in the table.

STEP 5

Now add the gene notation at the left side of each row into each mating box.

The resulting table, above, indicates the E/e gene combinations possible from the mating of this stallion to this mare. In this example, foals from this cross have a 50% chance of getting the “Ee” combination (2 x 25%) and a 50% chance of getting the “ee” combination.

The concept of a "cross", as in a particular stallion crossed with a particular mare, is abbreviated "x". Thus, the mating above would be abbreviated ee x Ee = 50% Ee, 50% ee

A foal is considered to be by a stallion, and out of a mare. Thus, the foal resulting from the mating above is by an ee stallion, and out of an Ee mare. One easy way to remember how these terms are used is to keep in mind that the foal literally comes out of the mare when it is born.

ADDITIONAL READING:

http://www.horsecolors.us/genetics/genetics.htm

Click Here To Take Quiz

The next lesson will cover:

· the two basic coat pigment colors of all horses – Black (E) and Red (e), and

· the most basic modifiers of black pigment: bay and brown agouti (A) and (At)