Pandora's Box: Equine Genomics

Pandora's Box: Equine Genomics

Individuals have differences in DNA's nucleotide sequences. This is pretty obvious—we have chestnuts and greys, but they are all still horses.

Photo: iStock

The genetics of horses has been of great interest to humans for millennia. While we might not have used that term specifically, the recording of equine parentage, births, and deaths was a practice that pre-dated the compulsory recording of human births and deaths in Great Britain by over a century. The term “genomics” covers all aspects of genes, including their structure and function, not just the science of heredity.

The genome is all of the DNA, divided up and packaged as chromosomes, in each cell. The DNA molecule, the unit of heredity, is made up of four nucleotide bases—guanine (G), cytosine (C), adenine (A), and thymine (T)—in a sequence. The equine genome consists of about 2,700 million base pairs, which is similar in size to the human genome.

Less than 3% of the genome actually codes for proteins. The remaining 97% was formerly termed “junk DNA” but we now know it orchestrates the use of the entire genome, as regulatory elements. Individuals have differences in the sequences of the nucleotides. This is pretty obvious—we have greys and bays but they are still horses. However, not all of the sequence differences are that obvious, and sequence differences can be whole sections of sequence or just single nucleotides. A single nucleotide polymorphism (SNP, usually pronounced “snip”) is a single nucleotide in a sequence that differs between individuals at a low-population frequency.

Approximately 10 million SNPs have been found in the collective equine genome. It is important to remember that SNPs are not necessarily mutations that have any effect on the organism. Indeed, SNPs are less likely to be found in the protein coding genes of the genome as these areas have been heavily selected for functionality by evolution. Any change in DNA sequence that did not benefit the animal would reduce its chances of survival in the gene pool.

Science uses selected SNPs as a crude road map of the genome. By way of analogy, a set of directions are like a SNP map. If I gave you some directions, they might be: “Turn right at the pub, then take the second left after the church.” The pub and the church have no actual bearing on the destination, they are just guiding landmarks, and so it is with SNPs. SNPs that sit close together on a chromosome are likely to be inherited together. Using commercial SNP arrays (called “SNP chips”), molecular biology techniques can rapidly hone in on a region of the genome that is different between horses in terms of its SNP frequency.

SNP analysis is an immensely useful tool to narrow down the search for areas of the genome harboring genetic traits of interest, whether they be a trait relating to disease or a desired trait. Studies using this approach are called genome-wide association studies, or GWAS (pronounced “gee-waahs”).

The SNP-GWAS approach has helped identify regions of interest in the genome in diseases such as lavender foal syndrome, polysaccharide storage myopathy, recurrent laryngeal neuropathy, foal immunodeficiency syndrome in Fell and Dales ponies, osteochondrosis dissecans, guttural pouch tympany in Arabians and German warmbloods, recurrent uveitis in German warmbloods, insect bite hypersensitivity, and hydrocephalus in Friesians.

We have only just started to uncover the wealth of information the equine genome holds. Continued efforts for funding and research will yield more mind-blowing results than our imagination can fathom. Watch this space!

CONTACT: Emma N. Adam, BVetMed, MRCVS, DACVIM-LA, DACVS-LA, PhD—emma.adam@uky.edu—859/218-1175— University of Kentucky Maxwell H. Gluck Equine Research Center, Lexington


This is an excerpt from Equine Disease Quarterly, funded by underwriters at Lloyd’s, London.

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Equine Disease Quarterly

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