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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What Does the LP SNP Discovery Mean?

Whether you are an Appaloosa breeder or an enthusiast, you have probably just heard about a possible DNA test becoming available for Appaloosa spotting. We would like to share with you some more information about this discovery, including how accurate a test this would be, and whether we are going to continue searching for the LP mutation.

Just What Has Been Found?

First, it is important to understand just what we have discovered. The newly published results of our LP research reveal that we have identified three SNPs (single nucleotide polymorphisms) which, in a test group of over 500 unrelated horses, are perfectly associated with the LP mutation.

That’s a big pile of technical language to process, so let us break this down by starting with defining what a “SNP” is: A Single Nucleotide Polymorphism, or SNP (pronounced "snip"), is a single genetic change, or variation, that can occur within a the DNA sequence of a gene. The genetic code is specified by the four nucleotides "letters" - A (adenine), C (cytosine), T (thymine), and G (guanine).

SNP variation occurs when one nucleotide replaces the other, changing the sequence. For example, consider what happens if the letter G replaces the letter C in the phrase, “TAG A CAT”. Now “TAG A CAT “becomes “TAG A GAT”, which no longer makes sense.

Sometimes, a SNP changes the sequence of a gene so that it can no longer function properly. However, it is also the case that sometimes a SNP doesn’t have a known biological consequence. For example, think in terms of “TACA” becoming “TAGA” - though neither has a function in the English language, they are still different from one another. These types of changes can be helpful “markers” that geneticists use to locate causative mutations.

At this time, we are not sure which is the case with respect to the three SNP’s we have identified. In other words, we don’t yet know if these are simply changes in the DNA that can be used as markers or changes that disrupt gene function. All three SNPs are located in and near the proposed gene for LP, known as TRPM1. Because all three of these SNPs are in perfect association for LP genotype in over 500 horses tested, any or all of the SNPs could be used as a DNA test until the causative mutation is identified and/or confirmed.

How Does This Kind of DNA Test Work - and is it Accurate?

What we mean by perfect association is that in the samples we tested, horses that were homozygous for LP (LP/LP, or carry two copies of the version of the gene that causes appaloosa spotting) were also homozygous for the changed version of all three SNPs. Heterozygotes for LP (LP/lp) were heterozygous for these three SNPs, meaning they had one copy of the original “letter” and one copy of the changed “letter”. Finally, horses that are not appaloosa spotted (lp/lp) have two copies of the original version of the SNPs.

You may be wondering how accurate a DNA test for LP would be using these three SNPs. In the 500 + horses we tested, from several breeds, we did not identify any exceptions to this association. Thus, the answer is that it is very accurate, based on the experiments we did, but we can’t say these markers are 100% accurate, unless it turns out that one of the SNPs is actually the causative LP mutation.

What Comes Next?

This is one of the reasons why determining the causative mutation is so important. We cannot stop and congratulate ourselves just yet! The champagne corks will not pop until we have confirmed the causative mutation. Therefore, we continue to work to investigate these mutations and TRPM1 itself, the gene in which they occur.

Aside from having a test that we can be sure is 100% accurate, there are other reasons why determining the causative mutation is important. Our previous work on TRPM1 and gene expression in Appaloosas affected with CSNB recently lead human researchers to investigate TRPM1 in night vision and CSNB in humans. We want to continue to enhance our understanding of this. As well, the role of TRPM1 in pigmentation has not been fully determined, thus identifying the causative mutation will help us and others to understand what role TRPM1 plays in pigmentation. It will also help us to understand what other genes might be involved in appaloosa spotting.

It is our hope that breeders and horses will continue to benefit from the results of our research findings. We are determined and anxious to take this all the way to the finish line!

Sheila Archer and Rebecca Bellone, Ph.D
November 13, 2010

Created on 08/11/2006 07:44 PM by adm1n
Updated on 02/06/2012 08:45 PM by PetraDavidson
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