A Very Basic Introduction to Genetics
You can’t learn about horse color without learning at least a little bit about equine genetics.
HOW IT ALL BEGINS
Genetic information that determines the traits of a living organism is stored in the nucleus of a cell. Using a microscope, it is possible to observe oblong structures in the nucleus during certain time periods in the life cycle of a cell. These structures, called chromosomes, contain deoxyribonucleic acid (DNA), which is the direct carrier of hereditary information. The molecular building blocks of DNA are the four nucleotides known as adenine, thymine, cytosine, and guanine. A DNA molecule has two strands aligned with each other (like the tracks of a train), forming the familiar double helix. Segments of DNA are called genes. They are essentially the ingredients for the recipe to make a living thing and determine the kind of “products” the cell will manufacture and the characteristics they determine—for example, eye or hair color.
SO…WHAT’S SO IMPORTANT ABOUT GENES?
The DNA sequence of an organism and the presence or absence of proteins that code for certain traits is called genotype; their external manifestation (the organism’s observable traits and characteristics) is phenotype. Most multicellular organisms obtain half of their chromosomes and genes from each parent. Horses have 32 pairs of chromosomes for 64 in total, and each gene normally exists in the same place on the same chromosome—this location is called the locus. The locus is the physical site on the chromosome where one form of a gene can be found. The different forms of genes that determine possible phenotypes are known as alleles. The alleles for a gene normally will be found in the same place on a chromosome from one parent as on the same chromosome from the other parent. As one locus is paired with another locus, the horse has two allelic genes matched from the series of alleles possible for a specific characteristic.
Alleles may be represented by a pair of letters: one letter denoting the allele donated by one parent and a second letter indicating the allele contributed by the other parent. If both alleles from both parents are identical, the animal has a homozygous genotype with two identical alleles at this locus (for example, AA or aa), but if they are different, then the individual is heterozygous (Aa or aA). When one of the alleles in a heterozygote completely determines the phenotype even when the second allele is present, the suppressing allele is said to be dominant and the suppressed allele is recessive. This phenomenon is called complete dominance. The completely dominant allele is designated by a capital letter (A), and the corresponding recessive allele is designated by a lowercase letter (a). In this scenario, the individual with the genotype “AA” has the same phenotype as individual with the genotype “Aa”—the recessive gene is hidden. But, while it doesn’t “show” in the individual, it could emerge as observable in offspring. This plays an important role in the probabilities of the inheritance of any trait.
When individuals with the genotype “AA” and “Aa” are phenotypically different, and the trait encoded by allele “A” is more weakly expressed in the heterozygous “Aa” individual than in the homozygous “AA” individual, then the allele “A” is designated as incompletely dominant. In this case the heterozygous individual has a phenotype that can be an intermediate phenotype (that is, an “average”) between individuals with the genotype “AA” and “aa.”
A LITTLE ABOUT TRAITS
Now let us discuss genes that can amplify, weaken, or otherwise modify the action of other genes. Such genes are called genetic modifiers. An organism’s phenotype can be formed by the action of two or more of these non-allelic or complementary genes, which in combination create an effect other than what the genes would on their own. Examples in horses are the genes Extension and Agouti, the first of which codes for the production of black pigment, and the second of which distributes the black pigment throughout the horse’s body. Another genetic modifier is a gene that masks the expression of non-allelic genes, called epistatic.
Traits in living organisms are divided into quantitative and qualitative. Quantitative traits can be measured—that is, they are the kind of trait where how much you have can vary: body weight, height, and the thickness of bones, for example. Quantitative traits are usually not the product of one gene, but instead are coded by several pairs of genes and have a so-called polygenetic inheritance.
Qualitative traits, on the other hand, are usually monogenetic or influenced by a single gene. The phenotype is either/or—that is, you have one variant of the gene or another that dictates how it manifests. Pigments and blood type are examples.
When it comes to genes working nicely together (or not), there are other terms to become familiar with and to aim to understand:
Penetrance is the ability of a gene to show itself phenotypically. It can be either complete (manifested in each individual that carries the gene) or incomplete (not phenotypically expressed by all carriers).
Pleiotropic action is when one gene is responsible for two or more phenotypic traits.
Some genes can lead to serious deviations from the norm, such as decreasing its viability (sub-lethal effect) or even leading to death (lethal effect). The loss of an animal due to an unfavorable genotype can occur either at the early stage of embryogenesis or sometime after its birth.
Some genes located on the same chromosome can be linked and transferred together to offspring. Their pattern of inheritance differs from that of unlinked genes.
A mutation is a change in the DNA sequence of a cell or its locus. The extent of mutations can range from a single or few nucleotides to entire chromosomes. Mutations lead to variation and ultimately the formation of alleles. The allele that exists in its original “normal” form in the species is called wild. Other alleles of the same gene are the product of mutations involving the wild allele.
With a basic grasp of the vocabulary I’ve introduced in this first chapter, you’ll be able to now appreciate the genetics of horse color as much as you appreciate the myriad colors themselves. In the next chapter we’ll examine over a hundred colors, how they manifest, and the genetic influences at play. Throughout you will find references to the color photographs you can view in the Color Photo Reference sections.
CHAPTER 2:
Horse Colors
Base Colors
As I mentioned in Chapter One: Introduction to Horse Color, in this book I am working with four base colors in horses: bay, black, seal brown, and chestnut. They are called “base colors” because any individual horse must have one of them; they are the basis for color effects of additional genes.
BLACK
Black color (Photo 1) is evident in the hair on the horse’s torso, head, legs, and also the mane and tail. The skin is dark gray, the eyes dark or hazelnut, the horn on hooves is pigmented, and the eyelashes are black. Faded black color usually develops