Significance of the Equine Genome for the Horse Industry

Chapter 27 SIGNIFICANCE OF THE EQUINE GENOME FOR THE HORSE INDUSTRY



Doug F. Antczak


Over the past dozen years a consortium of veterinary geneticists and clinicians have worked together to advance knowledge of the genome of the horse. Participants in the Horse Genome Project from 22 laboratories in 12 countries collaborated to produce the initial linkage, physical, and comparative equine gene maps. This international cooperation has been essential to the success of the project. In early 2006 these efforts were given an enormous boost when the U.S. National Human Genome Research Institute of the National Institutes of Health added the horse to the list of mammalian species to be sequenced. Now, just 2 years later, a whole genome sequence of the horse has been produced and is available to researchers and clinicians worldwide in public DNA databases. The explosion in information about the equine genome has already produced important new diagnostic tests for inherited diseases that can be used clinically to eliminate genetically determined conditions through selective breeding. The future will no doubt bring even more rapid advances in genetic-based technologies that will have the power to transform traditional horse-breeding practices. This will lead to more interactions between geneticists and horse breeders who have the shared goal of “improving the breed.”



STATUS OF THE EQUINE GENOME AND GENOMIC RESOURCES


Characterization of the genome of the horse has progressed rapidly from a state <20 years ago, when only a handful of equine genes had been sequenced and mapped, to the situation today, where virtually the entire genome sequence is available online. The speed at which the equine genome has been characterized has produced some technologies and research tools that have become obsolete as quickly as they have been developed and defined. This makes it challenging to create a summary of the state-of-the-art technology that will have a long duration.


Like the various types of maps that are available for geographic information, different experimental approaches have yielded information that provides complementary views of the genomic landscape of the horse. Furthermore, increasing levels of resolution provide ever more detailed information. The linkage maps of the horse based on polymorphic microsatellites1,2 remain useful tools for mapping traits to chromosomes or to sub-chromosomal levels. Fine mapping and gene identification requires additional or alternative methods. Physical maps of many horse chromosomes have been produced, most from the research group at Texas A&M University (reviewed in Chowdhary and Raudsepp3). These include highly detailed maps of the equine X and Y chromosomes.4,5 Comparative maps made across genomes provide reference points and identify conserved chromosomal regions. So-called chromosome painting has been very informative in these studies. This technique uses fluorescently labeled gene probes from individual chromosomes or chromosome arms in hybridization experiments using chromosome smears from the same species used to generate the probes, or from different species. In the case of the horse, a high degree of conservation of gene content has been demonstrated between human and horse chromosomes.6,7 This has been very useful in predicting gene content and even gene order on individual horse chromosomes.


The U.S. Government–sponsored whole genome sequencing of the horse can be justified on the basis of the comparative genomic information obtained that will help decipher the secrets of the human genome. However, the benefits to the horse may be even more important. The whole genome sequencing effort undertaken at MIT’s Broad Institute produced a 6.8× coverage of the equine genome. On average, every section of DNA from the donor horse was sequenced 6.8 times. Some parts of the genome are more difficult to sequence than others, such as the genes of the immune system that are highly polymorphic, contain duplicated genes, and have many DNA repeat sequences. Overall, a 6.8× coverage of the equine genome means that about 85%–90% of the donor horse’s DNA has been determined. This is still a very high level of coverage compared with most mammals that have been sequenced, with the exception of humans and mice. The raw sequence data must be assembled into the order found on the chromosomes, and annotated, so that the 20,000+ genes of the horse can be named using a nomenclature system that is consistent with that used in other mammals. The assembly and annotation processes are very large and complex tasks, and refinements will continue for several years to come. We do know that the horse genome contains about 2.68 billion base pairs that are spread across 31 autosomes and the sex chromosomes. The overall polymorphism rate of 1/1500 base pairs in the equine genome has been estimated. Several relevant websites that contain information about the Horse Genome Project and the equine genome are listed in Box 27-1.



Box 27-1 Websites Relevant to Horse Genetics

























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Jun 8, 2016 | Posted by in EQUINE MEDICINE | Comments Off on Significance of the Equine Genome for the Horse Industry

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Horse Genome Project (HGP)

University of Kentucky
 http://www.uky.edu/Ag/Horsemap/
Horse Genome Resources (NIH) http://www.ncbi.nlm.nih.gov/genome/guide/horse/
Horse Genome Project (NIH) http://www.ncbi.nlm.nih.gov/sites/entrez?db=genomeprj&cmd=Retrieve&dopt=Overview&list_uids=11760
Horse Genome Browser Gateway(University of California Santa Cruz) http://genome.ucsc.edu/cgi-bin/hgGateway
Ensembl Horse Database http://www.ensembl.org/Equus_caballus/index.html
Horse Genome Project(MIT Broad Institute) http://www.broad.mit.edu/mammals/horse/
Horsemap Database(France)