The Harry M. Zweig Memorial Fund for Equine Research

Horse Genome Project

Dr. Douglas F. Antczak

The goals of this project are to continue to develop a genetic map of the horse, and to apply information from the gene map in studies of the effects of imprinted genes on performance traits, and on selected inherited diseases of the horse. The first generation equine gene map developed during the past five years is already being used by equine scientists, clinicians, and horse breeders in the study of normal growth and development, in the diagnosis and management of genetically determined diseases, and in developing new breeding strategies, and there is potential for many more important applications of genetic knowledge of the horse in the future.

Background and Significance: During the past five years (1996-2000) Cornell has participated in and become a leading member of the international Horse Genome Project Workshop. This consortium of 22 laboratories from 12 countries has collaborated to produce the first genetic map of the horse. Advances in technology have greatly improved the efficiency of gene mapping and sequencing, thereby reducing costs and facilitating progress in this area. Moreover, information on the genome structure of other species, notably humans, cattle, and pigs, has been used to speed progress in defining the horse genome.

Benefits have already begun to accrue to the equine industry from genetic studies of the horse. During the 1990s genes causing three of the most important genetic diseases of the horse were identified: Severe Combined Immunodeficiency Disease (SCID) in Arabians, hyperkalemic periodic paralysis (HYPP) of Quarter Horses, and the Lethal White Syndrome of Paint horses. Genetic tests for these diseases are available commercially, and thus breeders and prospective buyers can choose to have their animals tested, so that they can make informed decisions concerning matings or purchases. The identification of mutant genes causing other autosomal recessive diseases can now be attempted using the markers currently available in the horse gene map.

A gene map can also help clinicians to diagnose and possibly to treat a variety of conditions caused not by a single gene defect, but by a number of genes acting together. Many important equine diseases, such as chronic respiratory disease (heaves), laminitis (founder), 'bleeders,' a number of immune deficiency conditions other than SCID, and a variety of musculo-skeletal disorders are thought to have a strong genetic component. A genetic map of the horse is necessary to identify the individual genes which contribute to multigenic traits.

Specific Aims: This proposal seeks continued support for Phase 2 of Cornell's participation in the international collaboration of the Horse Genome Project. Specifically, during the three year period 1999-2001 we are undertaking the following investigations:

1) We continue to contribute to the cooperative gene mapping effort of the Horse Genome Project Workshop through identification, characterization, and testing of equine microsatellite markers that form the backbone of the horse gene map.

2)We are also investigating polymorphism in imprinted genes that are known to affect growth and development. In these studies we are testing the hypothesis that polymorphic imprinted genes are responsible for the "Maternal Grandsire Effect" long recognized by Thoroughbred breeders.

3) We are following opportunities to study inherited diseases of the horse as those opportunities arise.

Plans for 2001: During the coming year we would continue to map the 200+ new microsatellite markers that we have identified during the past four years. The immediate goal for the Horse Genome Project Workshop is to complete a 500 marker linkage map by the end of 2001. In our new studies we are also investigating horse genes which show parent-of-origin effects in mice and humans. These imprinted genes behave differently from all other genes described during the past 100 years - their activity varies depending upon whether they are inherited from the paternal or maternal parent. Such genes could explain the pattern of performance inheritance shown in certain Thoroughbred lines. Secretariat, for example, although an outstanding performer himself, enjoyed much less success as a sire of performers. However, Secretariat is considered a leading sire of broodmares - that is, inheritance of his positive performance traits is manifest primarily in his daughters' offspring. Our hypothesis is that the activity of certain performance-enhancing genes is determined by the parent of origin. Imprinted genes behave in this way, and many of them control processes of growth and development, which could explain their effects on performance. In the coming year we would complete the development of gene probes for four major imprinted genes which have been shown to control growth and development in other species. These probes would be tested for imprinting of the target genes using equine tissues. If the genes prove to be imprinted, they would subsequently be tested for variation within Thoroughbreds as candidates for genes controlling the Maternal Grandsire Effect. Finally, we have begun a new investigation of a recently recognized genetic disease of Arabian horses, the so-called Lavender Foal Syndrome. Lavender Foals have neurologic and coat color abnormalities, and all die within 48 hours of birth. The genetic cause of this disease is unknown, and there is no genetic marker to test for carriers of this undesirable trait.

Progress in 2000: The past year has been an outstanding one for the Horse Genome Project, both here at Cornell, and at the level of the international Workshop. At the Baker Institute we have continued to produce and characterize microsatellite markers for their use in developing the gene map of the horse. As of this writing we have published 100 new equine microsatellite markers. This total makes us the leading laboratory world-wide for the identification of this important type of genetic marker. These markers have been mapped to individual horse chromosomes through collaboration with the Veterinary Genetics Laboratory at the University of California at Davis. They have also been linked to other genes on the Horse Genome Project's half sibling reference families and on the unique full sibling horse family developed by my long-standing colleague, Prof. W. R. Allen of Cambridge University in England. This has lead to two major publications, one of which was selected as the feature (cover) article in the June 2000 issue of the journal Genomics. That work was also featured in a recent article in the weekly Science Section of the London Times newspaper.

On the Maternal Grandsire Effect project we have begun to characterize four horse genes known to be imprinted in humans and mice. Related work by a Swedish laboratory has shown recently that the imprinted Insulin-like Growth Factor-2 (Igf2) gene we are studying can affect the size of heart and muscle mass in pigs. This is clearly a trait of interest to horsemen.

The Horse Genome Project has continued to attract outstanding students. Dr. Helen Bird, who completed a PhD in human genetics, has recently joined our laboratory as a postdoctoral fellow. She joins one PhD student, Ms. Becky Tallmadge, and three Cornell undergraduates who are currently working on equine genomics projects in our laboratory.

The Dorothy Russell Havemeyer Foundation, Inc. continues to support core activities of the Workshop at the level of $50,000 per year. This commitment began in 1995 and will continue through 2001, and possibly beyond that date. In 1997 the horse was accepted as a member species of NRSP-8, the National Animal Genome Research Project, along with cattle, sheep, pigs, and chickens. This US Department of Agriculture funded Regional Project was renewed in 1998 for a second five year term. It provides $45,000 per year in new funds for centralized facilities and special resources for the horse gene mappers. In July of 2000 a major two year grant to the US Horse Genome Project laboratories from the Morris Animal Foundation was announced. This will bring $20,000 per year to the Cornell Laboratory. Thus, the support from the Zweig Fund has had a multiplier effect in attracting much needed new resources to the international research effort in equine genomics.

Conclusions: Momentum for horse genome research continues to build, and the success of the
international collaboration among participating laboratories continues to attract new resources to this project. During the past five years the College of Veterinary Medicine at Cornell emerged as a leading participant in the Horse Genome Project, and progress in Cornell's laboratory continues to accelerate. Support from the Zweig Memorial Fund has been critical to this success.