The Harry M. Zweig Memorial Fund for Equine Research

Horse Genome Project: Functional Genomics of the Equine Immune System

Dr. Douglas F. Antczak

Objective: The overall objective of this project is to advance knowledge of the equine genome. Specifically, in the coming year we propose to concentrate our efforts on genes of the immune system of the horse. This focus will support the equine research of several established and new investigators at Cornell, and thus begin to fulfill the promise of practical application that justified the previous awards for the Horse Genome Project from the Zweig Fund.

Background and Significance: The Genome is the collection of all the genes of an organism. The comprehensive study of the Genome, that is, of all of the genetic material of a human, plant, or animal, is called Genomics. The term was coined to distinguish this type of investigation from the more familiar word Genetics, which refers to the study of the inheritance and function of individual genes. The Genome contains biological information – a blueprint or code that the cells of our bodies use to produce proteins and other molecules necessary for life. The information in the Genome is contained in the sequences of the chemical molecule DNA, which itself is packaged in long strands called chromosomes. For mammals, whose DNA contains over 3 billion bits of information and over 30,000 individual genes, studies of the Genome can be a daunting prospect. However, the development of new technologies for gene identification and sequencing has made possible rapid progress in the field of Genomics in a number of species, including the horse.

During the past seven years (1996-2002) Cornell has participated in and become a leading member of the International Horse Genome Project Workshop. This consortium of over 20 laboratories from more than a dozen countries has collaborated to produce the first genetic map of the horse. This map is already being used by equine scientists and there is potential for many more important applications in the future.

Specific Aims for 2003:

This application seeks continued support for Phase II of Cornell's participation in the international collaboration of the Horse Genome Project. Specifically, during 2003 we propose to work in the following areas:

1) Gene Discovery: Collaborating with other members of the Horse Genome Project, we would continue to increase the density of the horse gene map through high throughput sequencing and characterization of expressed horse genes contained in two gene libraries produced for us in 2001. It should be possible for the Horse Genome Project scientists to determine sequences from most of the predicted 30,000 equine genes within the next two years, adding to the 2000+ equine gene sequences already determined. These genes will be used to create so-called gene chip "microarrays" that can be used to assess the activity of thousands of genes in a single experiment. This technology should find wide application in many areas of equine medicine and surgery in the near future.

2) Focus on Genes of the Immune System. We would intensify our molecular studies of selected genes of the equine immune system by 'data mining' a new Bacterial Artificial Chromosome library (see progress report below). DNA clones containing the most important genes regulating immunity would be isolated from the library and assigned to horse chromosomes. With further characterization these genes would be used for the production of new antibody reagents that are required for clinical investigations of the immune system by our own laboratory group, and by other investigators at Cornell and elsewhere.

In partnership with the Havemeyer Foundation we have begun planning a small scientific workshop on genomic applications to equine immunity to be held at Cornell in the summer of 2003. The workshop will bring to Cornell the key scientists and clinicians from around the world with expertise and interest in the genes of the equine immune system. It is expected that this meeting will foster new collaborations that will speed progress in understanding and application of equine immune system genes to problems in clinical medicine.

Progress in 2002:

Horse Genome Project Workshop efforts: The Workshop group has completed a second generation linkage map and submitted it for publication. This map is now powerful enough to identify relatively short chromosome regions containing genes controlling physiological and pathological traits. In verification of this, the map has been used to pinpoint the regions containing the coat color genes for gray and palomino, and microsatellites developed at Cornell have proved to be the closest known markers to the controlling genes.

Cornell Laboratory research: Progress in our laboratory in the past year has been remarkable for two reasons:

1) The long-awaited Bacterial Artificial Chromosome (BAC) horse genomic library was completed by our colleague, Dr. Pieter de Jong of Children's Hospital of Oakland, California. This new resource contains all of the genetic material of one of Cornell's Thoroughbred stallions that has been selectively bred for its Major Histocompatibility Complex (MHC) genes. The MHC genes have been demonstrated to be associated with susceptibility to skin tumors in horses, and with other diseases involving the immune system. The genes in this library are in very accessible form, and we have begun to 'mine' this library for genes of the immune system of the horse.

2) Dr. Bettina Wagner of the Hannover Veterinary School in Germany joined our group in March of this year for an extended visit. Dr. Wagner has brought tremendous expertise in molecular aspects of antibody formation in the horse to Cornell, and we have taken full advantage of her stay to push forward with new studies of the genes controlling immune function.

In addition to these two new developments, our laboratory continued our very successful studies of equine MHC genes, and in particular, their mode of expression in the horse placenta. Two important papers on this topic were published, and another has just been submitted.

Other relevant information:

Staffing of our laboratory has been very good, with one postdoctoral fellow, one graduate student, and one full-time technician all working on equine genomics. In addition, the Project is supported by Dr. Wagner's efforts, and two Cornell Presidential Undergraduate Scholars are conducting honors projects in horse genomics.

The past year brought excellent publicity for and recognition of the efforts of the Horse Genome Project. In particular, the May 2001 New York Times Science Section article was followed by a 20 minute New York Times television program on the Horse Genome Project that aired on the National Geographic Channel in November 2001. This program featured the Cornell component of the project. In August of 2002 Dr. Antczak will be a featured speaker on equine genomics at the prestigious Jockey Club Round Table conference held each year in Saratoga.

Finally, funding sources for the Horse Genome Project continue to expand. The Havemeyer Foundation has pledged continuing support for the Horse Genome Project, with the understanding that overall success for this effort is dependent upon multiple sources of support. At present these include our participation in the USDA's National Animal Genome Project and a consortium grant from the Morris Animal Foundation that has just been renewed for an additional three years.


During the past 7 years the Horse Genome Project has achieved far more than was anticipated when it began in 1995. Cornell’s participation in this project has made equine genetics a flagship program of the College of Veterinary Medicine. This project has been funded longer than most Zweig Fund projects. However, consideration for its renewal is merited because of the special promise that studies of horse genomics hold for the equine industry. The growing group of investigators at Cornell who can take advantage of genomic information makes this project highly leveraged for future equine research projects. Finally, partnership with the other agencies supporting the Horse Genome Project extends the value of the Zweig Fund grant.