The State of the Equine Genome Sequence

The field of equine genetics got a huge boost back in 2007 when the first horse genome was successfully sequenced. Now, four years later, what is the state of that novel sequence? Nena Winand, DVM, PhD, a geneticist and assistant professor in the Department of Molecular Medicine at Cornell University in Ithaca, N.Y., and Ernie Bailey, PhD, geneticist and professor of veterinary science at the University of Kentucky's Gluck Equine Research Center, shed some light on where the genetic sequence is and where it could be going.

Currently, researchers only have the sequence from one horse, Twilight, a Thoroughbred mare produced by a special inbreeding program to try to make this horse homozygous for most traits. "People need to realize that the genome sequence is continuously being edited and improved," said Winand. "It's a work in progress. As a starting point in studying specific genes, for example, we first compare everything to Twilight's sequence."

She explained, "If I have a horse in which I want to look at a defect in a certain gene, I clone that gene, sequence that gene (in the horse I'm looking at), and then compare it to Twilight's sequence."

The genome sequence is a very useful tool to start with, but eventually, researchers would benefit from additional genetic information from different horses, she relayed.

"We can use Twilight's sequence as 'normal' for some things," Winand said. "However, if you were looking for something specific in a Thoroughbred, you'd start with Twilight as a comparison, but would ultimately use non-breed controls and then within-breed controls to answer some of these questions."

"We have the whole genome sequence, but the organization of the sequence can vary a lot between individuals," added Bailey. "Thus it will be useful to have additional horses sequenced. Our workshop is in the process of trying to sequence more horses." Then we'll know more about whether something in the sequence is typical of all horses or aberrant with that individual.

"It would be nice to know how Twilight's sequence compares to an Andalusian or a draft horse. We already know that all horses with the Tobiano color pattern have a major inversion in chromosome 3 of 50 million bases. It's minor in the whole scheme of things, but significant in how chromosome 3 compares with solid colored horses," says Bailey.

Researchers could find other variations in other breeds and types of horses as more horses are sequenced.

"The next few years will be exciting, because all these things are happening so quickly," Bailey concluded. "I think in the next two years we'll have five to 10 horses with their whole genome sequenced. Within the next four years I would assume we'll have 100."

About the Author

Heather Smith Thomas

Heather Smith Thomas ranches with her husband near Salmon, Idaho, raising cattle and a few horses. She has a B.A. in English and history from University of Puget Sound (1966). She has raised and trained horses for 50 years, and has been writing freelance articles and books nearly that long, publishing 20 books and more than 9,000 articles for horse and livestock publications. Some of her books include Understanding Equine Hoof Care, The Horse Conformation Handbook, Care and Management of Horses, Storey's Guide to Raising Horses and Storey's Guide to Training Horses. Besides having her own blog,, she writes a biweekly blog at that comes out on Tuesdays.

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