Coat Color Genetics: Part I

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Coat Color Genetics: Part I

what color is your horse?
coat color genetics: part I

by anita enander from (ARABIAN HORSE WORLD – July 12)

This is the first in a series of articles on coat color. First up, the basics for purebred Arabians. Next month we’ll look at how breeders can apply this information to increase their chances of getting a particular coat color in a foal. Then we’ll tackle the complexities found in Half-Arabians, where genes for colors that are found in other breeds come into play.

Breeding Basics — Coat Color

Coat color in Arabian horses is a great topic for helping breeders to learn about genetics. Although many genes influence coat color in equines, there are only three genes that create the commonly observed colors of purebred Arabian horses. Understanding how these three genes work has benefits far beyond trying to predict foal color. Ultimately, it helps us understand heritability of genetic disorders, susceptibility to certain diseases, variable response to treatment, and much more. As scientists continue to study coat color, they are learning more about what turns genes on and off, how multiple genes interact, and how modifier genes and mutations affect other genes. By learning the basics of coat color heritability, breeders will be able to build more knowledge of genetics and apply it to breeding decisions and to horse care and management.

The three different genes we’ll consider are all “autosomal,” which means they occur on chromosomes other than the gender-determining chromosomes X and Y, and they operate independent of the gender of the horse; they are not sex-linked. Each of the three genes has at least two forms (alleles), which may be dominant or recessive. Every horse inherits one copy of a gene from the dam and one from the sire. A horse is “homozygous” for a gene if both copies are the same, or “heterozygous” if the two copies are different. (See sidebar on Genomic Terms for more.)

The genes that determine coat color are denoted by alphabetical letters. In Arabian horses these are A, E, and G (for the dominant version) and a, e, and g (for the recessive version). For those who remember the high school biology explanation of brown and blue eyes, brown is the dominant color and blue is the recessive. A blue-eyed person has two copies of the recessive form (allele) of the gene. A brown-eyed person may have two copies of the dominant form, or one copy of the dominant (brown) and one copy of the recessive (blue) allele, but the result will be the same — brown eyes.

Over the years, I’ve found it easiest for people who are trying to understand coat color if we consider the three genes in a specific order. Remember, a horse has two copies of each gene — one inherited from the sire and one from the dam.

Base coat color: black or chestnut (E or e)

Base coat color is created by melanin. Melanin in horses has two forms: eumelanin (black), and phaeomelanin (orange/red). The gene that determines whether a horse can make eumelanin is called “Extension” because the dominant version (allele), E, extends the black pigment (eumelanin) across the entire body, including mane and tail. The recessive allele, e, blocks the production of eumelanin, which means only the phaeomalenin shows — giving a chestnut base color. Even if a horse has just one E version (the dominant allele) of the gene, the base color will be black. The second may be E also (in which case the horse is “homozygous” for black); if the second allele is the e version, the horse will still have black coat color (because the other E is dominant), but the horse will be “heterozygous” for black. If the horse has two e copies, it is homozygous for the recessive form of the gene and will be chestnut. EE or Ee is black; ee is chestnut.

Agouti modifier: getting to bay (A or a)

A gene that affects the distribution of eumelanin was first identified in a rodent called an agouti. That association with the gene has stuck, even though the gene in horses is not the same as that in the agouti. For horses it is designated as A (dominant) or a (recessive). The dominant form of the gene causes the black hairs to be limited to the “points” (mane, tail, and lower legs) and causes a mix of red and brown/black hairs that gives the appearance of various brown shades in the body. Of course, this only affects horses with a basic coat color that is black (Ee or EE). So a bay horse will be either AA or Aa.

Because a chestnut horse has no black hairs to be influenced by the agouti gene, it can have any combination of the agouti alleles: AA, Aa, or aa. Therefore, a chestnut horse might “carry” the dominant form of agouti gene, but it is not visible in the color of the horse.

Going grey? (G or g)

Horses that gradually go grey carry a mutated form of a gene that causes a loss of hair color. This is true for Arabians and other breeds. This is not a “white” gene, but a gene that gradually causes loss of the pigment in the hair. This gene is labeled G in the mutated, dominant form or g for the normal form (no pigment loss). Like the agouti gene, it operates as a simple dominant — if the horse has one copy of the mutation, it will go grey. There is some research that supports the idea that a horse having two copies of the dominant form (GG) becomes grey more quickly than horses that are heterozygous (Gg). A horse can only become grey if it inherited at least one dominant G from one parent (and that parent would therefore be grey). Therefore, a horse that is grey MUST have had at least one parent that is grey.

This is an example of a mutation that has been selected for by breeders — think of all the mythology involving the desirable “white” horses.

What is the underlying genotype?

Breeders who may want to make breeding decisions that include consideration of color will want to know the genotype of their breeding stock. By knowing the genotype of both parents, breeders can improve the odds of getting the color they want. Fortunately, all three of these genes can be tested for. Of course, if you have a black, chestnut, or bay horse, you don’t need to test for grey, because you know the horse is gg.

On this page are all the possible combinations and the phenotypes you’ll see. Hold on to your hat, because there are 27 possibilities: 9 that are colored and 18 that are grey.

GENOMIC TERMS: Reproduced with permission from the Horse Genome Project website at the University of Kentucky,

GENE: 1) hereditary determinant for a trait. 2) 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 protein melatonin.

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 that is expressed whenever it is present.

RECESSIVE GENE: An allele that 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 that 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 grey gene, and its two alleles are the presence of grey and the absence of grey.

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 1,000 to 2,000 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 appearance 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.

Commonly asked questions:

Q: Why do some black horses fade in the sun more than others? Is it because the “faders” are heterozygous, or is there another gene involved?

A: Attempts to find a third form of the allele (or another gene) that would account for sun fading in black horses have failed; also, there are plenty of homozygous black horses that fade badly. Mineral intake may play a role, but researchers don’t have definitive answers.

Q: What accounts for the range in chestnut colors and the flaxen mane/tail?

A:. There is research under way to try to understand what causes the variation in chestnut colors, but there are no definitive answers for that either. Stay tuned.

Q: What causes seal brown or dark black/bay?

A: Researchers in France are studying the agouti gene in equines and have identified a third form (allele) of the agouti gene At that apparently causes the seal brown. By their research, a horse that either has two copies of this allele — or one At and one a — will be seal brown. If the horse has even one copy of the A it will be bay because the A form remains dominant over the At form. The same researchers have identified another form that accounts for the “wild bay” pattern.

Q: Why do some horses that go grey retain “fleabites” or have blotches of color like the “bloody shoulder”?

A: The complete influence of the mutation is still being studied. There may be other genes that affect the extent of color loss.

Q: Does the grey mutation have anything to do with the common occurrence of melanomas in grey horses?

A: Research suggests that horses that are homozygous (GG) are more prone to develop melanomas.

These are the 9 combinations that, with gg, will not result in a grey horse:

EEaagg — Black: Homozygous for black and homozygous for the recessive (no effect) agouti, so remains black.

Eeaagg — Black: Heterozygous for black and homozygous for the recessive (no effect) agouti, so remains black.

eeAAgg — Chestnut: Homozygous for the recessive chestnut and homozygous for agouti (which has no visible effect).

eeAagg — Chestnut: Homozygous for the recessive chestnut and heterozygous for agouti (which has no visible effect).

eeaagg — Chestnut: Homozygous for the recessive chestnut and homozygous for no agouti influence.

EEAAgg — Bay: Homozygous for black, but also homozygous for the dominant agouti gene that causes the bay.

EEAagg — Bay: Homozygous for black, but has one dominant agouti gene that causes the bay.

EeAAgg — Bay: Heterozygous for black, but also homozygous for the dominant agouti gene that causes the bay.

EeAagg — Bay: Heterozygous for black, but has one dominant agouti gene that causes the bay.


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