James W. Kijas, CSIRO Livestock Industries
David Townley, CSIRO Livestock Industries
Brian P. Dalrymple, CSIRO Livestock Industries
Michael P. Heaton, USDA ARS Roman L. Hruska U.S. Meat Animal Research Center
Jillian F. Maddox, University of Melbourne
Annette McGrath, Australian Genome Research Facility Ltd
Peter Wilson, Australian Genome Research Facility Ltd
Roxann G. Ingersoll, Johns Hopkins University
Russell McCulloch, CSIRO Livestock Industries
Sean McWilliam, CSIRO Livestock Industries
Dave Tang, CSIRO Livestock Industries
John McEwan, AgResearch Invermay Agricultural Centre
Noelle Cockett, Utah State University
V. Hutton Oddy, University of New England Australia
Frank W. Nicholas, The University of Sydney
Herman Raadsma, The University of Sydney
Wes Barris, CSIRO Livestock Industries
Steve C. Bishop, University of Edinburgh, Roslin Institute
David Coltman, University of Alberta
Allan Crawford, AgResearch Invermay Agricultural Centre
André Eggen, Centre de Recherche INRAE Île-de-France - Jouy-en-Josas - Antony
Georg Erhardt, Justus Liebig University Giessen
Robert Forage, SheepGenomics
Olivier Hanotte, International Livestock Research Institute Nairobi
Peter Hunt, CSIRO Livestock Industries
Han Jianlin, Chinese Academy of Agricultural Sciences
Kui Li, Chinese Academy of Agricultural Sciences
Paolo Ajmone Marsan, Catholic University of the Sacred Heart, Piacenza
James E. Miller, School of Veterinary Medicine
Josephine Pemberton, The University of Edinburgh
Laurent Schibler, Centre de Recherche INRAE Île-de-France - Jouy-en-Josas - Antony

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The genetic structure of sheep reflects their domestication and subsequent formation into discrete breeds. Understanding genetic structure is essential for achieving genetic improvement through genome-wide association studies, genomic selection and the dissection of quantitative traits. After identifying the first genome-wide set of SNP for sheep, we report on levels of genetic variability both within and between a diverse sample of ovine populations. Then, using cluster analysis and the partitioning of genetic variation, we demonstrate sheep are characterised by weak phylogeographic structure, overlapping genetic similarity and generally low differentiation which is consistent with their short evolutionary history. The degree of population substructure was, however, sufficient to cluster individuals based on geographic origin and known breed history. Specifically, African and Asian populations clustered separately from breeds of European origin sampled from Australia, New Zealand, Europe and North America. Furthermore, we demonstrate the presence of stratification within some, but not all, ovine breeds. The results emphasize that careful documentation of genetic structure will be an essential prerequisite when mapping the genetic basis of complex traits. Furthermore, the identification of a subset of SNP able to assign individuals into broad groupings demonstrates even a small panel of markers may be suitable for applications such as traceability.

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