The Equine Genetic Diversity Consortium

The Equine Genetic Diversity Consortium: an international collaboration to describe genetic variation in modern horse breeds

The Equine Genetic Diversity Consortium (EGDC) led by the University of Minnesota represents a collaborative international community of equine researchers who are working to build a comprehensive understanding of genetic diversity among equine populations across the world. The result of this project will positively impact our ability to define population-based issues, identify and preserve characteristics that define particular breeds, decipher the history of the modern horse, and uncover the genetic basis of numerous complex traits.

Diversity in the Modern Horse.

While several prior studies have focused upon maternal lineage diversity in horses (mitochondrial DNA, mtDNA), and small set of nuclear DNA markers, this project is the first to utilize whole-genome nuclear single nucleotide polymorphis (SNP) data to understand evolutionary relationships among equine populations. Each horse in the study (> 20 horses per breed) will be genotyped at over 54,000 SNP loci to determine diversity within and among breeds, quantify the relationships of breeds to one another, and evaluate admixture. We will also identify a set of ancestry informative markers (AIMs) that will be useful for future questions of population assignment and to correct for population structure in association studies. Once complete, this data set will stimulate new studies into the origins of breeds and breed-defining traits, and guide efforts to preserve genetic diversity.

Signatures of Selection in the Modern Horse.

Domestic animal populations provide the opportunity to study genomes that have undergone recent intense selection. Human husbandry in livestock and companion animal species has resulted in breeds that have been developed to uniformly exhibit particular traits through selective breeding practices and intensive inbreeding. Bred for athletic ability, particular performance traits, and metabolic efficiency, horses are an ideal for the identification of genes and genetic pathways underlying those phenotypes. The goal of this project is to identify genomic regions under selection in the domestic horse genome.

We are using two methods of identifying regions under selection. Mapping signatures of selection in the modern horse is the first step in the identification of genes important in the domestication and specialization of modern horse breeds. Specifically, we believe that this method will allow for the identification of genomic regions underlying important metabolic and performance traits in the horse that may also be important to understanding human disease.

Equine Genetic Diversity Consortium Members:

University of Minnesota, St Paul, MN
Jessica L. Petersen, Molly E. McCue, James R. Mickelson

Animal Health Trust, Suffolk, UK
Mark Vaudin, June E. Swinburne, Laura Fox-Clipsham

Equine Analysis Systems, Inc., Midway, KY
Matthew M. Binns

French National Institute for Agricultural Research, Jouy-en-Josas, France
Gérard Guérin

Japan Racing Association, Japan
Telhisa Hasegawa

Norwegian School of Veterinary Science, Oslo, Norway
Knut H. Røed

Royal Veterinary College, London, UK
Richard Piercy

San Diego Zoo’s Institute for Conservation Research, Escondido, CA
Oliver A. Ryder

Swedish University of Agricultural Sciences, Sweden
Lisa S. Andersson, Jeanette Axelsson, Gabriella Lindgren

Texas A&M University, College Station, TX
E. Gus Cothran

University College Dublin, Ireland
Emmeline W. Hill, Nick Orr, Pieter Brama, Beatrice McGivney

Universidade Estadual Paulista–Botucatu, São Paulo, Brazil
Alexandre Secorun Borges

University of Azores, Portugal
Artur da Câmara Machado, Maria Susana Lopes

University of Berne, Switzerland
Bianca Haase, Tosso Leeb

University of California, Davis, CA
Danika L. Bannasch, M. Cecilia T. Penedo

University of Helsinki, Helsinki, Finland
Karin Hemmann, Hannes Lohi

University of Kentucky, Lexington, KY
Ernest F. Bailey, Kathryn T. Graves

University of Perugia, Italy
Michela Felicetti, Maurizio Silvestrelli

University of Veterinary Medicine, Hannover, Germany
Ottmar Distl

Laboratory of Racing Chemistry, Japan
Teruaki Tozaki

University of Sydney, New South Wales, Australia
Claire M. Wade