Color Genetics: Vol. I

Understanding the Basics

Introduction

It is easy to get overwhelmed when you first start taking a look at color genetics. Not only are there different genes that behave differently depending on what other elements are at play, but in some rare cases, the horse may not look at all like what their genes say they should. On top of all of this, some genes are not well understood or have little research to back up long-held beliefs about inheritance and expression.

In my experience, once you have a basic understanding of what each gene does and why, it becomes much easier to understand, predict, and seek out the outcomes you are looking for.

This guide will have 4 sections, with different subsections for each gene. We will start out talking about the Basics of horse color and review terms that will help your understanding of later sections. Next, we will talk about Dilutions that modify a horses base color. Then we will discuss White Patterns. Finally, we will talk about coat modifiers & other miscellaneous genes that are not yet fully understood. At the very end, I will include links to various resources as well as the references that I used.

Each post will have a section teaching you about the genes in question with various examples. A short, 5-question quiz will be included at the bottom for you to test yourself on what you've learned. You will be able to access the answer key by clicking on the show answer button. Each section will build on the previous section.

Looks vs Genes

Some basic terms to understand before we start going in depth. A horses phenotype is the way that they look, and is the way we often refer to a horse. For example, you wouldn't generally start listing off genes for a horse when you're describing them to someone else, you would call them bay or chestnut. Those are phenotypes. A horses genotype is the genes that control their color. Sometimes it is easy to tell what phenotype (looks) a horse is going to have based on their genotype, but not always. Things like the horses age, current season, health, and many other factors can all play a part in the way that a horse looks.

Inheritance

Each gene is controlled by two different alleles. A foal will inherit one allele from their sire and one from their dam. The easiest way to picture the way that inheritance works is with the use of a punnet square.

A gene might have multiple different alleles that are possible. Most genes follow a simple dominance pattern. Most simple dominant genes have only two possible alleles. You can think of them kind of like an on/off switch. For example, black is a simple dominant gene. A horse either does or does not have black. If they do not have black, they would be chestnut. In cases of simple dominance, we capitalize the dominant allele, E, and write it first. We use lowercase to indicate the less dominant allele, e, and write it to the right of the dominant allele. We may also refer to the least dominant allele as being recessive.

Other genes, such as Agouti, follow a more complex system of dominance. An incomplete dominant gene will have multiple different alleles that have their own system of dominance and are generally unique when compared to other genes. We will go over them when we speak about those specific genes.

When a horse has two copies of a dominant allele, we often call them homozygous. This means that they will only ever be able to pass on a copy of the dominant allele. In Example 1, you can see that the Dam is homozygous black with EE. The sire, even though he has two copies of the same allele (ee), would not be considered homozygous because E is more dominant than e. All of their foals will appear black, but because they have two different alleles, would be considered heterozygous.

In Example 2, we have two heterozygous parents who each have one copy of the dominant allele for black, E. If these two horses had foals, about 25% of them would be homozgyous black (EE), about 50% would be heterozygous black (Ee), and about 25% would be chestnut having not inherited black at all (ee).

It is worth noting that allele and gene are often used interchangeably in casual conversation, but for the sake of this guide, I will stick to referring to them separately to try and help reduce confusion.