Appaloosa Genetics: Part I


By Rebecca Bellone and Sheila Archer

Photos and illustrations provided by Cheryl Woods, Lisa Estridge, Petra Davidson, Kim Utke and Sheila Archer

In the spring of 2001, The Appaloosa Project was begun with a two-part goal. The first was to discover the genetic mechanisms underlying appaloosa spotting (also referred to as leopard complex spotting) and associated traits. The second goal was to share this information in a manner that would help those folks that could apply the science we discovered—the breeders. To this aim we have developed an electronic classroom where subscribers can ask questions. These questions often guide us to create additional educational material. Recently we prepared a three part video series answering the questions we are most frequently asked. These videos were broadcast at Equitana in New Zealand and later shared with breeders on the Web. The Appaloosa Horse Club has asked us to translate these videos into written material for their subscribers. This article is the first in a series of three short articles we have written to explore these questions. Each gives detailed but easily understood answers.

Here are the questions the three articles will address:

1. “How can two loudly patterned Appaloosas produce a solid, non-characteristic horse?”

2. “How can two loudly patterned Appaloosas end up producing a foal with very little coat pattern such as just a few white flecks on its rump?”

3. “How is night blindness related to Appaloosa coat patterns?”

Before we begin to discuss the first question, we need to explain the way that we use the terms “Appaloosa” vs. “appaloosa.” When this word is capitalized, we are referring to the breed of horse known as the Appaloosa. When we use the same word without capitalizing (appaloosa) we are referring to leopard complex spotting. Since “leopard complex spotting” isn’t a familiar term to most breeders, we find that using “appaloosa” works better, even though this type of spotting occurs in other breeds besides the Appaloosa.

In this article we plan to address the first question represented in Figure 1—how can this mating produce a solid non-characteristic horse? The answer is in the genes. But we’re not talking about jeans you wear. Instead, we’re talking about genes—those that are inherited. A gene is best defined as a discrete unit of heredity. It is a piece of DNA that codes for a trait and is passed on from both the mother and the father to their offspring. This is represented in Figure 2.

A gene. DNA is the cell’s genetic material which folds tightly to form structures called chromosomes. Shown here is a single chromosome with one section that is unfolded and has been zoomed in on and highlighted in green to represent a gene.

The gene that most Appaloosa breeders are interested in is the LP gene. Also referred to as “the appaloosa gene,” LP stands for “leopard complex spotting.” Gene names are often presented as symbols and italicized. The LP gene is the one that determines if a horse will inherit one of the appaloosa coat patterns, and it controls whether or not any appaloosa characteristics are visible. Breeders and enthusiasts know that Appaloosas can have a wide variety of coat patterns, from horses with just a few white flecks on the rump, all the way up to an animal that is almost completely white. Sometimes these animals will have pigmented spots in the white areas, and sometimes not.

Figure 3: Appaloosa coat patterns. These patterns can range from horses that have white covering most of the body to horses with just a few white flecks on the rump, as illustrated in all three panels below. The bottom panel represents those horses displaying minimal white patterning known as “white flecks on rump.” Additionally, white patterned areas can have pigmented spots (middle panel) while others do not (top panel). All of these patterns are inherited by the LP gene.

In addition to the coat pattern the LP gene is also responsible for other pigmentation traits that breeders refer to as “characteristics.” Also known as “LP-associated traits,” these include striped hooves, white sclera, mottled skin, and varnish roan patterning, as seen in Figure 4. Sometimes horses are born with striped hooves, mottling, and white sclera but no obvious coat pattern. These horses will develop varnish roaning with age, though the amount varies from one horse to the next.

Figure 4: LP characteristics. (From top to bottom) Striped hooves appear as bands of unpigmented material on a pigmented hoof. Readily visible white sclera. Mottling is pink skin with spots of pigment occurring around the anus, genitalia, eyes and muzzle. Varnish roan patterning occurs when horses progressively lose pigment in the hair throughout the coat but retain pigment in the bony surfaces of the body. Areas of retained pigment on the hips, face, etc. are known as varnish marks.

As mentioned, it is the LP gene that is responsible for both the coat patterns and characteristics. Whether or not a horse has these traits depends on which version of LP the horse inherits. Thus the LP gene comes in two forms, or as called by geneticists “alleles.” One form is said to be dominant and we symbolize this allele with capital letters—LP. The other form is the recessive, which we symbolize with lower case letters—lp (See Figure 5a and 5b).

Figure 5: The LP gene comes in two forms. As in Figure 2 we see our gene being represented on a chromosome, additionally here we see the two forms of the LP gene. Alternative forms of a gene are called alleles and here are represented by different colors. The dominant form (LP) is represented in green DNA whereas the recessive form (lp) is represented in purple DNA.

Alleles, or alternative forms of genes, have different functions. In the case of LP, the dominant version (shown in green in Figure 5) allows for the presence of appaloosa spotting and associated characteristics, while the recessive allele (shown in purple in Figure 5) does not. Horses have two alleles for every gene—one that they inherit from their sire and one they inherit from their dam. Thus, there are three possible genotypes (or genetic makeup) with regard to the LP gene. A horse can inherit two dominant forms of LP (one from its sire and one from its dam) resulting in the genotype LP/LP, also known as homozygous dominant as each allele is the same (homo meaning same, so two of the same form of the gene). A horse can inherit two recessive versions of the gene, resulting in the genotype lp/lp, and be homozygous recessive. Finally, a horse can inherit one version of each form, giving the genotype LP/lp, which is termed heterozygous (hetero meaning different). The LP form is said to be dominant over the lp form because if both are present, the instruction to be appaloosa spotted and have characteristics is dominant over the instructions to be solid without characteristics.

Figure 6: The LP gene is an incompletely dominant gene. The left horse is homozygous for the LP mutation (“fully on”) and has few to no pigment spots in the white area. The horse in the middle is heterozygous (“partially on”) for the LP mutation and has pigmented spots in the white patterned area. The horse on the right (“fully off”) is homozygous for the recessive form.

To complicate things a bit further, LP is actually incompletely dominant, which means that the three possible genotypes each have a different appearance. Homozygotes (two of the same allele) can look different than heterozygotes (two different alleles). To think about it a bit differently, when a horse is homozygous for the LP mutation (genotype LP/LP) they only have the instructions to be appaloosa spotted—consider this to be the “fully on” state. Horses with this genotype have few to no spots of pigment in their white areas, Horses that are heterozygous for the LP mutation have one allele giving instructions to allow for appaloosa spotting and another allele giving instructions for being solid—think about this being the state in which the combined instructions are “partially on.” This results in a horse with pigmented spots in their white patterned areas. Horses with the genotype lp/lp are homozygous recessive, so they only have the instructions to be fully pigmented and thus will be solid and non-characteristic—their instructions are “fully off” for appaloosa spotting. Now that we understand the basics of LP as a gene, we can return to our original question—how can two loudly patterned Appaloosas produce a foal that is what we call a “true solid?” This is a horse with no Appaloosa traits and no coat pattern that remains normally pigmented for its entire life. Since both parents described have pigmented spots in their white patterned areas we know that each parent is heterozygous for LP, meaning they each have one copy of the form of the gene that has the directions to be appaloosa spotted (LP) and one copy of the directions to be solid non-characteristic (lp). So in this case the sire can produce sperm with the recessive version (represented as a solid black sperm in figure 7) and sperm that carry the dominant allele (represented as the leopard spotted sperm in Figure 7). The same is true for the dam—she can produce eggs with lp or eggs with LP.

Figure 7: Mating between two heterozygous Appaloosas (LP/lp). The sire and the dam of this cross are both heterozygous for LP, thus the sire can produce two types of sperm, one carrying the LP allele (leopard spotted sperm) and the other one having the lp allele (solid black sperm). Likewise, the dam can produce two types of eggs, either with LP, or with lp.

When this type of cross results in offspring that are solid and non-characteristic, as shown in Figure 8, it is because both the sire and the dam have contributed the recessive allele. At the moment of conception, a “true solid” foal will be formed, when a sperm with the recessive form of the LP gene fertilizes the egg that happens to also contain the recessive form of LP. The resulting foal will have two recessive copies of the LP gene, one from each parent, and be normally pigmented with no appaloosa traits or coat patterning. Our hope is that this example has helped you to understand a little more about the genetics of LP. Next month we will tackle trying to explain a little bit more of what we know about the genetics of the variation in the patterns when we answer the question, “How can two loudly patterned Appaloosas produce an offspring with only a few white flecks on his rump?”

Figure 8: A true solid offspring resulting from crossing two horses heterozygous for LP. In this example cross the horse inherited the recessive form of LP from both its sire and its dam. This type of cross has a 1:4 chance of producing a solid non-characteristic offspring every time the cross is made.