The genetic puzzle

Costing some $15 million, researchers put the final piece of a scientific puzzle on the horse genome sequence that totalled 2.7 billion DNA base pairs.

The early February announcement from the Massachusetts Institute of Technology's (MIT) Broad Institute that Equus caballus was added to the growing list of species genetically sequenced followed last year's unveiling of the dog. The map went global and made available to genetics researchers to spur new studies.

The advancement for veterinary medicine ends more than a decade of research and opens possibilities as vast as the molecule of life itself. In other words, the map has been built, and it paves the way for faster, cheaper exploration.

Twilight's contribution: A blood sample was enough to give geneticists at MIT's Broad Institute the tools to sequence the equine genome. Twilight is a research Thoroughbred at Cornell University's College of Veterinary Medicine.

It's about recognizing changes at the genetic level that influences health and disease, says Doug Antczak, VMD, PhD, the Dorothy Havemeyer McConville Professor of Equine Medicine at Cornell's Baker Institute. Antczak's team participated in collaborative research and owned the DNA-donor Thoroughbred Twilight.

"I never expected to have this completed in my working lifetime. All the things that can be done at the genome level, you can do in horses. That was not true a year ago," Antczak tells DVM Newsmagazine.

There are 80 known conditions in horses that are genetically similar to disorders seen in humans. The list starts with musculoskeletal problems and ends with cardiovascular and respiratory diseases. The next leg of this trip will be aimed at diagnostic testing methods or continuing research into new treatments.

Likely outcomes:

• A DNA sequence from any gene in the library will be available to researchers so they can focus on that gene within the context of the horse. A process that used to take three months to identify will now only take technicians about 30 minutes.

• The development of an SNP chip, a collection of DNA spots on a slide for genome-wide molecular experiments, could lead to research investigating polymorphisms and variation in the genome or be directed toward gene expression. For example, researchers could be comparing lymphocytes from horses infected with herpes virus or free of herpes virus, or identify which genes are expressed when making an immune response to herpes (also called a gene expression array).

The findings are big, but the potential this work holds on improving the health of the horse is even bigger.

The sequencing is a culmination of work conducted by 20 institutions internationally and coordinated through Dr. Ernie Bailey of the University of Kentucky's Gluck Equine Research Center. Funded by the National Human Genome Research Institute, one of the National Institutes of Health, the genetics team at Broad carried out the sequencing and assembly of the horse genome.

"Just imagine yourself flying. We started this project at 30,000 feet. You can imagine that you don't see a great level of detail. Now with the sequence, we will be working at the ground level. That's a major accomplishment," Antczak says.

The landing took Broad's Kerstin Lindblad-Toh's team one year, a far faster and cheaper ride compared to the eye-watering 13-year, $2.7-billion price tag for the human genome still lauded as one of the greatest feats in science exploration. The process improved, Antczak reports, and the velocity of mapping work accelerated exponentially.

"The horse community really hit the jackpot last year when NIH added the species to the list they are sequencing," Antczak explains. "The horse became an attractive species to NIH both for its value to human medicine and its application to human medicine. But they did so on the basis of work that has gone on by horse geneticists in an organized fashion."

"I'm a senior scientist now, but I will be able to see applications of this work in my lifetime, Antczak says. "That is a fabulous feeling."

The genetic map was based around research of Thoroughbred Twilight, chosen from a small herd of horses selected and bred for more than 25 years to study mechanisms that prevent maternal immunological recognition and destruction of the developing fetus during mammalian pregnancy. The work, Antczak explains, has implications in reproduction, clinical organ transplantation and immune regulation.

The coverage of 6.8-fold is considered quite good, reports Claire M. Wade, PhD, a senior research scientist with the Broad Institute and Massachusetts General Hospital.

"The way I describe it, imagine you have a floor with nothing on it. And someone gives you sufficient decks of cards. When you throw them on the floor, that is the amount of coverage you get from 1x coverage. It is very discontiguous. You have islands with a little bit of coverage and other places that have no coverage at all. As you continue to throw more cards, you get better coverage and better linking of those cards. That is what we are aiming for."

In addition to sequencing the horse genome, Broad Institute officials report, a map was created of horse genetic variation using DNA samples from a variety of modern and ancestral breeds, including the Akel Teke, Andalusian, Arabian, Icelandic, Quarter, Standardbred and Thoroughbred. With 1 million signposts of variation called single nucleotide polymorphisms (SNPs), the map will offer scientists a genome-wide view of genetic variability in horses and help them identify the genetic contributions to physical and behavioral differences as well as disease susceptibility.

"The horse brings a lot from evolutionary and biomedical perspectives," Wade says. "It is the only sequenced representative of its mammalian order. From the biomedical standpoint, we can learn a lot about exercise physiology, allergies and arthritis, which are commonly suffered by horses, as well as infectious diseases."

During the next several months, researchers plan to improve the accuracy of the horse genome sequence and deposit an even higher resolution assembly in public databases. The result will be a tool to help veterinary researchers understand diseases that affect equines as well as implications for population genetics.

Dr. Doug Antczak

"The horse has had a fantastic set of pedigrees going over 300 years now that makes them attractive to the study of genetic traits and how they relate to performance," Antczak says. "There are lots of good pedigrees that are much better than any other domestic species."