Horse Genetics. Ernest Bailey
noted in the previous chapter, each parent transmits one of its two chromosomes to its offspring. Every horse has two copies of every autosomal gene, one from its sire and one from its dam. If the two copies are identical, then the horse is said to be homozygous. If the two alleles are different, then the horse is said to be heterozygous for that trait. Homozygous and heterozygous are terms that refer to the genotype of the horse. Genotype describes the specific alleles present in the horse and is useful to predict what the parent will pass to offspring. Genotype could be called “the genetic recipe” of the individual for the locus. For Extension, the genotypes E/E and e/e would be homozygous genotypes because both alleles are the same. Horses that possess two different alleles at a locus, for example E and e, (genotype E/e) are heterozygotes. The symbols for each of the two alleles, one from the sire and one from the dam, are separated by a slash (/) by convention.
Dominant and recessive; phenotype and genotype
The phenotype of a horse is its measurable appearance. The Extension locus has three genotypes but only two phenotypes (Table 5.1). Why are there three genotypes and two phenotypes? Because the variant for black pigment is dominant over the variant for red pigment. It only takes a single allele for black to allow the horse to make black pigment. There is no difference in appearance between a horse homozygous for E or one that is heterozygous E/e; both will be equally able to make black pigment. In the absence of the gene for black pigment the horse will have the recessive phenotype, chestnut (genotype e/e). If you mate two chestnut horses, the offspring will always be chestnut because there is no way for their offspring to inherit the E allele. However, if you mate two black horses, you might produce a chestnut offspring. This will only happen if both parents are heterozygous (E/e) and can transmit the variant for e to the offspring resulting in a horse homozygous for the chestnut allele (e/e). The relationship of alleles, homozygous, heterozygous, phenotype, and genotype are summarized in Table 5.1 using Extension as an example.
Table 5.1. Chart showing the relationship of genotype to phenotype for the different combinations of the alleles E and e of the Extension gene for coat color.
| Genotype | Phenotype |
| E/E (homozygous for E) | Black and red pigment |
| E/e (heterozygous, both E and e) | Black and red pigment |
| e/e (homozygous for e) | Red pigment only |
A dominant allele is always expressed when present. A recessive allele is only expressed in the absence of a dominant allele. A characteristic that is often useful to know about a recessive trait is that it will always breed true—matings of chestnut horses will always produce chestnut offspring. However, horses with black can produce chestnuts if they are heterozygous. Heterozygous horses possessing recessive alleles hidden by the dominant alleles are called “carriers” for the recessive allele. Carrier means the allele is present but not seen in the phenotype.
It is important to realize that the terms have no meaning beyond the interaction of the two alleles at the same locus. Just as the term “allele” only refers to the relationship of variants at a single locus, dominant and recessive are terms that only apply to alleles at the same locus. Furthermore, dominant alleles and recessive alleles are equally likely to be inherited. Heterozygous transmit the dominant alleles to 50% of their offspring and the recessive allele to the other 50% of their offspring.
Breeding heterozygous and homozygous horses
One common question is: What are the chances of producing a particular phenotype when mating two horses? If you know the genotypes of the parents you can figure that out using a Punnett square. Reginald Punnett was a scientist in the early 1900s who popularized this form of analysis and has given his name to this approach. To begin with, the genotype tells us precisely what type of gametes a sire and dam will produce. Horses homozygous for E (E/E) will always produce eggs or sperm with the allele for E. Horses homozygous for e (e/e) will always produce eggs or sperm with the e allele. Horses that are heterozygous (E/e) will produce 50% eggs or sperm with E and 50% with e.
A more interesting situation occurs when mating two heterozygotes and this is when the Punnett square becomes useful to visualize the result. Table 5.2 shows a Punnett square for the mating of a heterozygous mare and stallion for the Extension locus. Each of them can produce gametes with ether e or E. Either possibility is equally likely. The sire’s contribution is listed on the left side of the table and his gamete contributions shaded. The squares below and across from the parental contributions are filled in with the result seen in the lower half. The upper left square shows that each parent can contribute the E allele and in this case the offspring will be homozygous E. The lower right square shows that the offspring will inherit the e allele from both parents and be homozygous e. The two other squares (lower left and upper right) show that the offspring could inherit alternate alleles from the parents and be heterozygous (E/e).
Table 5.2. Set-up for a Punnett square to predict genotypes of offspring.
In summary, when mating of two heterozygous parents, there is a 50% chance of producing heterozygous offspring (E/e) that would be phenotypically black since E is dominant, 25% chance of producing homozygous E/E (phenotypically black), and a 25% chance of producing offspring that are homozygous for the recessive allele (ee) and phenotypically chestnut.
You can also use a Punnett square to show the results from mating homozygotes for one allele to a heterozygote. (Hint: chestnut crossed with a heterozygote has a 50% chance of producing chestnut offspring.)
Of course, matings of homozygotes for the same alleles will always produce offspring homozygous for the allele. The parents only have the one allele to transmit to their offspring. Specifically, matings of E/E x E/E will always produce E/E offspring and e/e x e/e always produces e/e offspring. Matings of homozygotes for the opposite alleles will always produce heterozygous offspring because each parent only has the one type of allele to pass to their offspring: E/E x e/e produces all E/e offspring (heterozygotes).
Schematic representation of pedigrees
When we want to know if a trait is recessive or dominant, we can use family data in pedigrees. When using a pedigree to determine mode of inheritance we look for the following clues:
1. Dominant traits: affected offspring always have an affected parent.
2. Recessive traits: a) unaffected parents can have affected offspring (in this case we know the parents are heterozygous carriers of the gene for that trait); b) matings of affected parents always produce affected offspring.
These principles are illustrated in Figs 5.1 and 5.2.
Fig. 5.1. Pedigree representation illustrating the inheritance of a dominant trait. Squares represent males and circles represent females. The black shapes represent those individuals exhibiting the dominant trait. The open or clear shapes represent those without the trait.