mare with foal


Horse Genome Project


International Equine Genome Mapping Workshop
The 8th Dorothy Russell Havemeyer Foundation International Equine Genome Mapping Workshop took place near Newmarket, UK from July 22 to 25, 2009...[more]

Writers at the Louisville Courier Journal recently won the 2008 Media Eclipse Award for journalism based on an article about Thoroughbred racing and break-downs. They published a 3 part story, including genetics, track surfaces and medications. In connection with the genetics section they interviewed several members of the Horse Genome Project. See the accompanying links for the full stories on the 2008 Media Eclipse Award and the article itself.

Courier-Journal Web site wins award for horse project
Genetics may hold key to Injury-prone horses
[December 2008]

The first draft of the horse genome sequence was recently completed and deposited...
[JAVMA News, April 2007]

Data on Equine Genome Freely Available to Researchers Worldwide
[NIH News, February 2007]

The first genome map of a horse is complete, providing scientists with new tools for investigating equine disease. [ April 2006]



The human genome project changed biology forever.  A plan was made to sequence the entire human genome in the late 1980s.   The plan was controversial. Some people thought it better to fund lots of individual research projects rather than a single large one.    But big ideas capture our imaginations and the project was approved for $3 billion and underway in 1990.

It was a bold project because, in 1990, the technical ability did not exist to sequence and assemble large sets of DNA.   Indeed, much of the $3 billion was devoted to developing computer programs, laboratory methods and research equipment to rapidly and inexpensively sequence and assemble DNA.

Nothing like this had been contemplated for animals.  Although horse breeders have successfully used genetic selection for centuries, many problems have been resistant to breeder’s methods or inventions of veterinary medicine and animal science.  Horse owners need better vaccines for infectious diseases, therapies for respiratory diseases and allergic diseases and more information about the occurrence, diagnosis and prognosis of developmental diseases of the horse.   Obviously, all these problems do not have simple hereditary causes. But many scientists believe tha genome information will help them find solutions.

The horse genome project was a result of the human genome project.  We already knew that the size and organization of the genome was very similar among all mammals. The programs, methods and tools developed for the human genome project could be used to study the genetics of any biological organism.  We could use the information from the human genome to predict the organization and sequence of horse genes. 
In October 1995, 70 scientists from 20 countries met in Lexington, Kentucky to make a plan for mapping the horse genome.  By the end of the meeting the Horse Genome Project was born.  We agreed to work together to make a genetic map (since none of us had the resources to do it alone), to share our research information before publication, and to encourage other scientists to develop and apply the gene map.  Friendly, and unfortunately sometimes not-so-friendly, competition is the norm in the scientific world, so agreement for these broad collaborations was truly remarkable and illustrated the importance we placed on this work.  Basically, we scientists agreed that while we might compete on other aspects of equine health research, we would enter into a strong collaboration to make a genetic map for the horse.

Meeting over a few beers


Between 1995 and 2007, seven workshop meetings were conducted under the auspices of the Dorothy Russell Havemeyer Foundation (an organization devoted to promoting equine health research)

1995 in Lexington/Kentucky
1997 in San Diego/ California
1999 in Uppsala/Sweden
2001 in Brisbane/Australia
2003 in Kruger Park/South Africa
2005 in Newbridge/Ireland
2007 at Lake Tahoe/California. 

These were international workshops and participating scientists came from the United States, United Kingdom, France, The Netherlands, Poland, Spain, Germany, Switzerland, Sweden, Denmark, Norway, Czech Republic, Italy, Portugal, Japan, Australia, New Zealand, China, Korea, South Africa, Brazil, Canada.

In 1996, the United States Department of Agriculture (USDA) invited the Horse Genome Project participants to join their program for studying genomics of agriculturally important species.   The horse genome community has met as a part of a USDA National Sponsored Research Project in San Diego, CA every January since 1997.  

The initial goal of the Horse Genome Project was limited to making a genetic map for the horse.  All 32 pairs of chromosomes would be identified and genetic landmarks identified on each chromosome so that points of reference could be established to the human genome sequence.  In this way, information from the human genome could be used without the great expense of sequencing the horse genome. 

A side benefit of the project was discovery of the genetic basis for many simple genetic traits in horses including coat color and several hereditary diseases.  Molecular tests were developed and are now commercially available to horse breeders.  (link to applications).

But the goals changed dramatically in 2005.   Research showed animal genomes were, at once, more simple and more complex than we thought.  First, there were only around 20,000 genes, not the 300,000 or 100,000 originally projected.  These genes only represented a 2% of the DNA on chromosomes.  This was astounding because we thought that once we knew the sequence of genes, we would be able to understand the secrets of heredity.  Instead, the key to understanding genes resides in the 98% of the genome that does not encode genes and which we had called “junk DNA”.  While genes are similar between species, the junk DNA is unique to each species.  So, to understand how genes work in horses, we needed horse “junk DNA” sequences.

In July 2005, the workshop participants submitted a white paper to the National Human Genome Research Institute (NHGRI) describing the benefits of sequencing the horse genome for medical and veterinary research.    Although the specific goal of NHGRI was to study the human genome, they were also sequencing genomes of 24 mammals to identify similarities and differences with the human genome. This information would identify the human DNA elements important for further study.  Mammals were selected to represent the diverse branches of the phylogenetic tree.  Horses belong to a family called perissodactyla, including equids, rhinoceros and tapirs.  No animal from that family had been sequenced and the white paper convinced them to choose the horse.

The project moved very rapidly from that point. The Broad Institute of MIT and Harvard, one of the sequencing centers for NHGRI, was especially intrigued with sequencing the horse.  In February, 2006, sequencing began and by that July the entire genome had been chopped into 30,000,000 pieces and the DNA sequence of every piece determined.  The next step was to assemble the sequences into the correct order.  This was completed in January 2007 and is now available online at

The next and most exciting phase of the project is just beginning.  The black box of genetics has been cracked open.  We hope the information will provide new approaches to old problems.


running horses

©2011 Horse Genome Project. All Rights Reserved
website last modified: 10/02/2014
Content Manager: E. Bailey | Webmaster: P. Dillon | Web pages by Cat's Cradle Design