Appaloosa coat patterns, coat colour genetics and practical information for breeders of spotted horses - The Appaloosa Project Appaloosa coat patterns, coat colour genetics and practical information for breeders of spotted horses - The Appaloosa Project
Appaloosa coat patterns, coat colour genetics and practical information for breeders of spotted horses - The Appaloosa Project
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The Appaloosa Project: Studies Currently Underway

What is the Appaloosa Project?

The Appaloosa Project is a research initiative being conducted by a team of researchers from Canada and the US. It is a long-term effort designed to investigate the nature of Appaloosa genetics. The goal of the project is to identify and isolate the main genes responsible for Appaloosa patterning, and to investigate key physical traits associated with these genes.

The Project is an example of new genetics in action. The old research paradigm was phenotype-based, that is, we had only the physical appearance of Appaloosas to make our judgments from. But, with recent developments in molecular biology, particularly with respect to gene mapping technology, scientists are now able to find genes in a way that was not previously possible. Now we can take phenotype evidence forward and verify it in the lab, finding the actual genetic mechanisms involved in the physical traits we observe. By doing so, the Appaloosa Project contributes to the worldwide effort to map the genome of the horse.

Sheila Archer - Researcher and Coordinator for "The Appaloosa Project"

1. Search for the LP Gene

To understand the importance of the search for this gene, you must first know what LP is and its significance for breeders. LP stands for “leopard complex”, and is the name assigned to the gene that a horse must have in order to look like an Appaloosa. "Leopard complex" refers to a large group of patterns, any of which may occur when LP is present, and “leopard” simply refers to the unique form of spotting common to them. LP acts as an "on-off" switch that when present in dominant form, activates Appaloosa characteristics (striped hooves, mottled skin, white sclera) and Appaloosa roaning (Sponenberg, Carr, Simak, Schwink. 1990. Journal of Heredity, 81: 323-331). It is hypothesized that LP acts together with modifying genes to produce variability in patterning.

In June of 2003, Dr. Rebecca Bellone (was Terry) and associates conducted a genome scan for LP. A genome scan is a method that molecular biologists use to map the location of a gene by comparing animals that have inherited a copy of that special form of the gene with animals from the same family that have not. The scan was successful, and LP was bracketed to a region of equine chromosome 1 (Terry, Archer, Brooks, Bernoco & Bailey. 2004. Animal Genetics: 35, 134-137).

Following the discovery of LP's location, candidate genes within the bracketed region were selected and investigated. In August of 2008, Dr. Bellone and associates published the findings of a gene expressional analysis which indicated that TRPM1 (Transient Receptor Potential Cation Channel, Subfamily M, Member 1) is the probable location of the causative mutation for both Appaloosa spotting and CSNB (congenital stationary night blindness).

Recent research using SNP fine mapping technology has allowed us to refine the location of the mutation to a small region of TRPM1 (Bellone et al, 2010).

In the November 2010 issue of "Animal Genetics", Dr. Bellone and associates published their discovery of three SNPs that are closely associated with the LP mutation. The full article can be found at this link:
Association analysis of candidate SNPs in TRPM1 with leopard complex spotting (LP ) and congenital stationary night blindness (CSNB) in horses (page 207)

Current Status: The recently discoverd SNPs in TRPM1 can be used as a DNA test for the LP mutation. However, work continues to sequence the specific region of TRPM1 indicated by these SNPs as the most likely location for the LP mutation. Identification of the causative mutation is an important step in understanding LP and its modifiers, as well as the physical traits associated with these genes.

Implications: Breeders will now be able to confirm if LP is present or not in young horses that do not immediately show the classic Appaloosa characteristics required for regular registration. The new DNA test will also allow for the accurate identification of horses that are homozygous for LP. Ultimately, with the causative mutation identified, we will be able to answer key questions about Appaloosa genetics.

2. E & A: Coat Colour Modifiers of White Patterning

The study of the effects of extension of black (E) and agouti (A, otherwise known as bay) on Appaloosa white patterning began in 1999 as a phenotype study. This work mirrored the findings of Woolf (1990-96) who observed that white face and leg markings in Arabians were expressed lowest in black, somewhat more in bay, and highest in chestnut horses.

Analysis of photographic data gathered from several Appaloosa families revealed the presence of some important effects on Appaloosa coat patterning. When inherited in dominant form, E seems to cause significant suppression of white patterning, which was lessened when agouti (A) was present in dominant form. The results paralleled those of Woolf (unpublished, Archer 2000).

What also became apparent during analysis were some strong family effects. In certain families, other factors obscured, and even reversed, the above-mentioned E-effect.

In order to get a more precise picture of the effects of both E and A on white patterning in Appaloosas, a new study is underway. It looks at a large sample of unrelated horses, selected randomly. Through this approach “family effects” should be avoided. 300 horses are included in this study, of which a subset of 50 will be DNA tested for E and A.

Current status: The data-gathering portion of this study is complete, and we are now involved in the analysis stage, with publication to follow.

Implications: The information obtained through this new research will allow a quantitative estimate of the impact on white patterning in Appaloosas. This will be of value to breeders when predicting breeding outcomes.

3. PATN-1: The “Leopard Family” Gene Study

White patterning in Appaloosas appears to be a polygenic (many gene) trait. If this is indeed the case, an Appaloosa will display some amount of white Appaloosa-type patterning at birth if it has inherited both LP and one or more of the genes that help to produce Appaloosa-type patterning. We have given the generic name “PATN” (for “pattern”) to these genes. Phenotype-based evidence suggests there are a variety of these, with varying amounts of effect. Some seem to produce large amounts of patterning, while others produce minor amounts.

The Appaloosa Project is working to identify the gene responsible for very high levels of expression found in “leopard lines”. These are families of horses that have very high white pattern levels, and include leopard and near-leopard as well as fewspot and near-fewspot horses. This gene’s proposed name is PATN-1 (see above image for proposed continuum of expression). The study involves analysis of DNA collected from large half-sibling families produced by fewspot stallions, bred to non-Appaloosa mares.

Current Status: Work in 2006 produced evidence in support of a location for a gene for leopard-specific patterning. We are now working to confirm and refine the location further so that we may select candidate genes for further analysis. To help narrow down the location of this modifiers, a new study has been designed and horses are now being selected, with molecular work to begin in 2011.

Implications: Isolation of the “leopard family” white pattern gene will allow for the development of a DNA test. A DNA test for PATN-1 will allow breeders to learn whether a horse is heterozygous or homozygous for this significant pattern causing gene. Also of value to breeders will be the ability to test true solid horses from programs that concentrate on producing this pattern, but that have not inherited LP (and thus are non-characteristic). Some of these solids will have inherited PATN-1, but until a test is available the only way to prove their colour production capability has been by test breeding.

4. Night Blindness Study

Congenital stationary night blindness (CSNB) affects various breeds of horses, but there appears to be a form that is specific to the Appaloosa. Since Witzel’s 1977 study of night blindness in Appaloosas, it has been known that some horses of this breed were affected. Since no other breed-specific research has been done, the mode of inheritance and the factors affecting the severity of the condition have remained unknown.

In 2005, veterinary ophthalmology researchers Dr. Lynne Sandmeyer, Dr. Bruce Grahn and Dr. Carrie Breaux of the Western College of Veterinary Medicine, University of Saskatchewan joined forces with Sheila Archer of the Appaloosa Project research team, and together conducted a study of CSNB in the Appaloosa.

Current Status:
This study is now complete and has been published by the Journal of the American College of Veterinary Ophthalmologists. Read about the findings here.

A second study of CSNB, this time in the miniature horse, is now underway. Examination of horses for this study will continue through the fall of 2010, with the goal of publishing the results in 2011.

Genetic testing to identify which horses are affected will allow owners and breeders to take measures to ensure the safety of night blind animals. In addition, we hope to pursue the possibility of gene therapy to treat this condition.

5. Genetic Origins of the Appaloosa

One of the goals of the Appaloosa Project is to discover the source(s) from which the present day Appaloosa was developed and its relationship to other breeds that have "leopard complex" patterning. We will attempt to determine the genetic connections between Appaloosas and the other apparent LP-carrying breeds of the world when LP and its major modifiers have been identified.

Current Status: This study began in 2004 with a phenotype-based survey involving a sample of 200 Appaloosas taken from the first horses registered with the ApHC. The conformation of these horses was analyzed using a physical trait analysis system developed from the work of Willoughby (1974). Distinct physical sub-types were identified, and compared to potential source breeds, in order to develop a list of breeds with which to eventually perform genotype comparisons.

At this time, horses descended from and displaying the three designated “founding” sub-types are being sampled. DNA is also being gathered from apparent LP-carrying breeds, including the Spanish Mustang, Knabstrupper, British Spotted Pony, Miniature Horse and others. Molecular work is currently on hold, as we wait for SNP technology to advance further, allowing us to obtain more information with less cost than is now possible.

Implications: Knowing more about the genetic origins of the North American Appaloosa will answer some long-standing questions regarding the “source of the spots”. It will also provide breeders interested in selecting for certain physical types and associated disciplines to make informed decisions regarding selection of breeding stock, both within and outside the breed.

Created on 02/04/2003 10:24 AM by admin
Updated on 11/13/2010 01:54 PM by SheilaArcher
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