Developing a 670k genotyping array to tag ~2M SNPs across 24 horse breeds
Identifieur interne : 000A66 ( Pmc/Curation ); précédent : 000A65; suivant : 000A67Developing a 670k genotyping array to tag ~2M SNPs across 24 horse breeds
Auteurs : Robert J. Schaefer [États-Unis] ; Mikkel Schubert [Danemark] ; Ernest Bailey [États-Unis] ; Danika L. Bannasch [États-Unis] ; Eric Barrey [France] ; Gila Kahila Bar-Gal [Israël] ; Gottfried Brem [Autriche] ; Samantha A. Brooks [États-Unis] ; Ottmar Distl [Allemagne] ; Ruedi Fries [Allemagne] ; Carrie J. Finno [États-Unis] ; Vinzenz Gerber [Suisse] ; Bianca Haase ; Vidhya Jagannathan [Suisse] ; Ted Kalbfleisch [États-Unis] ; Tosso Leeb [Suisse] ; Gabriella Lindgren [Suède] ; Maria Susana Lopes [Portugal] ; Núria Mach [France] ; Artur Da Câmara Machado [Portugal] ; James N. Macleod [États-Unis] ; Annette Mccoy [États-Unis] ; Julia Metzger [Allemagne] ; Cecilia Penedo [États-Unis] ; Sagi Polani [Israël] ; Stefan Rieder [Suisse] ; Imke Tammen ; Jens Tetens [Allemagne] ; Georg Thaller [Allemagne] ; Andrea Verini-Supplizi [Italie] ; Claire M. Wade ; Barbara Wallner [Autriche] ; Ludovic Orlando [Danemark, France] ; James R. Mickelson [États-Unis] ; Molly E. Mccue [États-Unis]Source :
- BMC Genomics [ 1471-2164 ] ; 2017.
Abstract
To date, genome-scale analyses in the domestic horse have been limited by suboptimal single nucleotide polymorphism (SNP) density and uneven genomic coverage of the current SNP genotyping arrays. The recent availability of whole genome sequences has created the opportunity to develop a next generation, high-density equine SNP array.
Using whole genome sequence from 153 individuals representing 24 distinct breeds collated by the equine genomics community, we cataloged over 23 million de novo discovered genetic variants. Leveraging genotype data from individuals with both whole genome sequence, and genotypes from lower-density, legacy SNP arrays, a subset of ~5 million high-quality, high-density array candidate SNPs were selected based on breed representation and uniform spacing across the genome. Considering probe design recommendations from a commercial vendor (Affymetrix, now Thermo Fisher Scientific) a set of ~2 million SNPs were selected for a next-generation high-density SNP chip (MNEc2M). Genotype data were generated using the MNEc2M array from a cohort of 332 horses from 20 breeds and a lower-density array, consisting of ~670 thousand SNPs (MNEc670k), was designed for genotype imputation.
Here, we document the steps taken to design both the MNEc2M and MNEc670k arrays, report genomic and technical properties of these genotyping platforms, and demonstrate the imputation capabilities of these tools for the domestic horse.
The online version of this article (doi:10.1186/s12864-017-3943-8) contains supplementary material, which is available to authorized users.
Url:
DOI: 10.1186/s12864-017-3943-8
PubMed: 28750625
PubMed Central: 5530493
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</author>
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</institution-wrap>
Hermann-Rodewald-Strasse 6, 24098 Kiel, Germany</nlm:aff>
<country xml:lang="fr">Allemagne</country>
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<institution>Department of Animal Sciences, Functional Breeding Group,</institution>
<institution>Georg-August University Göttingen,</institution>
</institution-wrap>
Burckhardtweg 2, 37077 Göttingen, Germany</nlm:aff>
<country xml:lang="fr">Allemagne</country>
<wicri:regionArea>Burckhardtweg 2, 37077 Göttingen</wicri:regionArea>
</affiliation>
</author>
<author><name sortKey="Thaller, Georg" sort="Thaller, Georg" uniqKey="Thaller G" first="Georg" last="Thaller">Georg Thaller</name>
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<institution-id institution-id-type="GRID">grid.9764.c</institution-id>
<institution>Institute of Animal Breeding and Husbandry,</institution>
<institution>Christian-Albrechts-University Kiel,</institution>
</institution-wrap>
Hermann-Rodewald-Strasse 6, 24098 Kiel, Germany</nlm:aff>
<country xml:lang="fr">Allemagne</country>
<wicri:regionArea>Hermann-Rodewald-Strasse 6, 24098 Kiel</wicri:regionArea>
</affiliation>
</author>
<author><name sortKey="Verini Supplizi, Andrea" sort="Verini Supplizi, Andrea" uniqKey="Verini Supplizi A" first="Andrea" last="Verini-Supplizi">Andrea Verini-Supplizi</name>
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<institution>Department of Veterinary Medicine - Sport Horse Research Centre,</institution>
<institution>University of Perugia,</institution>
</institution-wrap>
Perugia, Italy</nlm:aff>
<country xml:lang="fr">Italie</country>
<wicri:regionArea>Perugia</wicri:regionArea>
</affiliation>
</author>
<author><name sortKey="Wade, Claire M" sort="Wade, Claire M" uniqKey="Wade C" first="Claire M." last="Wade">Claire M. Wade</name>
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<institution-id institution-id-type="GRID">grid.1013.3</institution-id>
<institution>School of Life and Environmental Sciences, Faculty of Veterinary Science,</institution>
<institution>University of Sydney,</institution>
</institution-wrap>
Regimental Drive, B19-301 RMC Gunn, Sydney, NSW 2006 Australia</nlm:aff>
<wicri:noCountry code="subfield">NSW 2006 Australia</wicri:noCountry>
</affiliation>
</author>
<author><name sortKey="Wallner, Barbara" sort="Wallner, Barbara" uniqKey="Wallner B" first="Barbara" last="Wallner">Barbara Wallner</name>
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<institution-id institution-id-type="GRID">grid.6583.8</institution-id>
<institution>Institute of Animal Breeding and Genetics, Department of Biomedical Sciences,</institution>
<institution>University of Veterinary Medicine Vienna,</institution>
</institution-wrap>
Vienna, Austria</nlm:aff>
<country xml:lang="fr">Autriche</country>
<wicri:regionArea>Vienna</wicri:regionArea>
</affiliation>
</author>
<author><name sortKey="Orlando, Ludovic" sort="Orlando, Ludovic" uniqKey="Orlando L" first="Ludovic" last="Orlando">Ludovic Orlando</name>
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<institution-id institution-id-type="GRID">grid.5254.6</institution-id>
<institution>Centre for GeoGenetics, Natural History Museum of Denmark,</institution>
<institution>University of Copenhagen,</institution>
</institution-wrap>
Copenhagen, Denmark</nlm:aff>
<country xml:lang="fr">Danemark</country>
<wicri:regionArea>Copenhagen</wicri:regionArea>
</affiliation>
<affiliation wicri:level="1"><nlm:aff id="Aff23">Laboratoire d’Anthropobiologie Moléculaire et d’Imagerie de Synthèse, CNRS UMR 5288, Université de Toulouse, Université Paul Sabatier, 31000 Toulouse, France</nlm:aff>
<country xml:lang="fr">France</country>
<wicri:regionArea>Laboratoire d’Anthropobiologie Moléculaire et d’Imagerie de Synthèse, CNRS UMR 5288, Université de Toulouse, Université Paul Sabatier, 31000 Toulouse</wicri:regionArea>
</affiliation>
</author>
<author><name sortKey="Mickelson, James R" sort="Mickelson, James R" uniqKey="Mickelson J" first="James R." last="Mickelson">James R. Mickelson</name>
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<institution>Department of Veterinary and Biomedical Sciences,</institution>
<institution>College of Veterinary Medicine, University of Minnesota,</institution>
</institution-wrap>
St. Paul, MN USA</nlm:aff>
<country>États-Unis</country>
<placeName><region type="state">Minnesota</region>
</placeName>
<wicri:cityArea>St. Paul</wicri:cityArea>
</affiliation>
</author>
<author><name sortKey="Mccue, Molly E" sort="Mccue, Molly E" uniqKey="Mccue M" first="Molly E." last="Mccue">Molly E. Mccue</name>
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<institution-id institution-id-type="GRID">grid.17635.36</institution-id>
<institution>Department of Veterinary Population Medicine,</institution>
<institution>College of Veterinary Medicine, University of Minnesota,</institution>
</institution-wrap>
St. Paul, MN USA</nlm:aff>
<country>États-Unis</country>
<placeName><region type="state">Minnesota</region>
</placeName>
<wicri:cityArea>St. Paul</wicri:cityArea>
</affiliation>
</author>
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<idno type="doi">10.1186/s12864-017-3943-8</idno>
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<sourceDesc><biblStruct><analytic><title xml:lang="en" level="a" type="main">Developing a 670k genotyping array to tag ~2M SNPs across 24 horse breeds</title>
<author><name sortKey="Schaefer, Robert J" sort="Schaefer, Robert J" uniqKey="Schaefer R" first="Robert J." last="Schaefer">Robert J. Schaefer</name>
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<institution-id institution-id-type="GRID">grid.17635.36</institution-id>
<institution>Department of Veterinary Population Medicine,</institution>
<institution>College of Veterinary Medicine, University of Minnesota,</institution>
</institution-wrap>
St. Paul, MN USA</nlm:aff>
<country>États-Unis</country>
<placeName><region type="state">Minnesota</region>
</placeName>
<wicri:cityArea>St. Paul</wicri:cityArea>
</affiliation>
</author>
<author><name sortKey="Schubert, Mikkel" sort="Schubert, Mikkel" uniqKey="Schubert M" first="Mikkel" last="Schubert">Mikkel Schubert</name>
<affiliation wicri:level="1"><nlm:aff id="Aff2"><institution-wrap><institution-id institution-id-type="ISNI">0000 0001 0674 042X</institution-id>
<institution-id institution-id-type="GRID">grid.5254.6</institution-id>
<institution>Centre for GeoGenetics, Natural History Museum of Denmark,</institution>
<institution>University of Copenhagen,</institution>
</institution-wrap>
Copenhagen, Denmark</nlm:aff>
<country xml:lang="fr">Danemark</country>
<wicri:regionArea>Copenhagen</wicri:regionArea>
</affiliation>
</author>
<author><name sortKey="Bailey, Ernest" sort="Bailey, Ernest" uniqKey="Bailey E" first="Ernest" last="Bailey">Ernest Bailey</name>
<affiliation wicri:level="2"><nlm:aff id="Aff3"><institution-wrap><institution-id institution-id-type="ISNI">0000 0004 1936 8438</institution-id>
<institution-id institution-id-type="GRID">grid.266539.d</institution-id>
<institution>Maxwell H. Gluck Equine Research Center,</institution>
<institution>Department of Veterinary Science, University of Kentucky,</institution>
</institution-wrap>
Lexington, KY USA</nlm:aff>
<country>États-Unis</country>
<placeName><region type="state">Kentucky</region>
</placeName>
<wicri:cityArea>Lexington</wicri:cityArea>
</affiliation>
</author>
<author><name sortKey="Bannasch, Danika L" sort="Bannasch, Danika L" uniqKey="Bannasch D" first="Danika L." last="Bannasch">Danika L. Bannasch</name>
<affiliation wicri:level="2"><nlm:aff id="Aff4"><institution-wrap><institution-id institution-id-type="ISNI">0000 0004 1936 9684</institution-id>
<institution-id institution-id-type="GRID">grid.27860.3b</institution-id>
<institution>School of Veterinary Medicine,</institution>
<institution>University of California-Davis,</institution>
</institution-wrap>
Davis, CA 95616 USA</nlm:aff>
<country xml:lang="fr">États-Unis</country>
<placeName><region type="state">Californie</region>
</placeName>
<wicri:cityArea>Davis</wicri:cityArea>
</affiliation>
</author>
<author><name sortKey="Barrey, Eric" sort="Barrey, Eric" uniqKey="Barrey E" first="Eric" last="Barrey">Eric Barrey</name>
<affiliation wicri:level="1"><nlm:aff id="Aff5"><institution-wrap><institution-id institution-id-type="ISNI">0000 0004 4910 6535</institution-id>
<institution-id institution-id-type="GRID">grid.460789.4</institution-id>
<institution>Unité de Génétique Animale et Biologie Intégrative- UMR1313, INRA,</institution>
<institution>Université Paris-Saclay,</institution>
</institution-wrap>
AgroParisTech, 78350 Jouy-en-Josas, France</nlm:aff>
<country xml:lang="fr">France</country>
<wicri:regionArea>AgroParisTech, 78350 Jouy-en-Josas</wicri:regionArea>
</affiliation>
</author>
<author><name sortKey="Bar Gal, Gila Kahila" sort="Bar Gal, Gila Kahila" uniqKey="Bar Gal G" first="Gila Kahila" last="Bar-Gal">Gila Kahila Bar-Gal</name>
<affiliation wicri:level="1"><nlm:aff id="Aff6"><institution-wrap><institution-id institution-id-type="ISNI">0000 0004 1937 0538</institution-id>
<institution-id institution-id-type="GRID">grid.9619.7</institution-id>
<institution>The Robert H. Smith Faculty of Agriculture, Food and Environment,</institution>
<institution>The Koret School of Veterinary Medicine, The Hebrew University,</institution>
</institution-wrap>
76100 Rehovot, Israel</nlm:aff>
<country xml:lang="fr">Israël</country>
<wicri:regionArea>76100 Rehovot</wicri:regionArea>
</affiliation>
</author>
<author><name sortKey="Brem, Gottfried" sort="Brem, Gottfried" uniqKey="Brem G" first="Gottfried" last="Brem">Gottfried Brem</name>
<affiliation wicri:level="1"><nlm:aff id="Aff7"><institution-wrap><institution-id institution-id-type="ISNI">0000 0000 9686 6466</institution-id>
<institution-id institution-id-type="GRID">grid.6583.8</institution-id>
<institution>Institute of Animal Breeding and Genetics, Department of Biomedical Sciences,</institution>
<institution>University of Veterinary Medicine Vienna,</institution>
</institution-wrap>
Vienna, Austria</nlm:aff>
<country xml:lang="fr">Autriche</country>
<wicri:regionArea>Vienna</wicri:regionArea>
</affiliation>
</author>
<author><name sortKey="Brooks, Samantha A" sort="Brooks, Samantha A" uniqKey="Brooks S" first="Samantha A." last="Brooks">Samantha A. Brooks</name>
<affiliation wicri:level="2"><nlm:aff id="Aff8"><institution-wrap><institution-id institution-id-type="ISNI">0000 0004 1936 8091</institution-id>
<institution-id institution-id-type="GRID">grid.15276.37</institution-id>
<institution>Department of Animal Science,</institution>
<institution>University of Florida,</institution>
</institution-wrap>
Gainesville, FL USA</nlm:aff>
<country>États-Unis</country>
<placeName><region type="state">Floride</region>
</placeName>
<wicri:cityArea>Gainesville</wicri:cityArea>
</affiliation>
</author>
<author><name sortKey="Distl, Ottmar" sort="Distl, Ottmar" uniqKey="Distl O" first="Ottmar" last="Distl">Ottmar Distl</name>
<affiliation wicri:level="1"><nlm:aff id="Aff9"><institution-wrap><institution-id institution-id-type="ISNI">0000 0001 0126 6191</institution-id>
<institution-id institution-id-type="GRID">grid.412970.9</institution-id>
<institution>Institute for Animal Breeding and Genetics,</institution>
<institution>University of Veterinary Medicine,</institution>
</institution-wrap>
Hannover, Germany</nlm:aff>
<country xml:lang="fr">Allemagne</country>
<wicri:regionArea>Hannover</wicri:regionArea>
</affiliation>
</author>
<author><name sortKey="Fries, Ruedi" sort="Fries, Ruedi" uniqKey="Fries R" first="Ruedi" last="Fries">Ruedi Fries</name>
<affiliation wicri:level="1"><nlm:aff id="Aff10">Lehrstuhl für Tierzucht der Technischen Universität München, Liesel-Beckmann-Strasse 1, 85354 Freising, Germany</nlm:aff>
<country xml:lang="fr">Allemagne</country>
<wicri:regionArea>Lehrstuhl für Tierzucht der Technischen Universität München, Liesel-Beckmann-Strasse 1, 85354 Freising</wicri:regionArea>
</affiliation>
</author>
<author><name sortKey="Finno, Carrie J" sort="Finno, Carrie J" uniqKey="Finno C" first="Carrie J." last="Finno">Carrie J. Finno</name>
<affiliation wicri:level="2"><nlm:aff id="Aff4"><institution-wrap><institution-id institution-id-type="ISNI">0000 0004 1936 9684</institution-id>
<institution-id institution-id-type="GRID">grid.27860.3b</institution-id>
<institution>School of Veterinary Medicine,</institution>
<institution>University of California-Davis,</institution>
</institution-wrap>
Davis, CA 95616 USA</nlm:aff>
<country xml:lang="fr">États-Unis</country>
<placeName><region type="state">Californie</region>
</placeName>
<wicri:cityArea>Davis</wicri:cityArea>
</affiliation>
</author>
<author><name sortKey="Gerber, Vinzenz" sort="Gerber, Vinzenz" uniqKey="Gerber V" first="Vinzenz" last="Gerber">Vinzenz Gerber</name>
<affiliation wicri:level="1"><nlm:aff id="Aff11">Swiss Institute of Equine Medicine, Department of Clinical Veterinary Medicine, Vetsuisse Faculty, University of Bern, and Agroscope, Länggassstrasse 124, 3001 Bern, Switzerland</nlm:aff>
<country xml:lang="fr">Suisse</country>
<wicri:regionArea>Swiss Institute of Equine Medicine, Department of Clinical Veterinary Medicine, Vetsuisse Faculty, University of Bern, and Agroscope, Länggassstrasse 124, 3001 Bern</wicri:regionArea>
</affiliation>
</author>
<author><name sortKey="Haase, Bianca" sort="Haase, Bianca" uniqKey="Haase B" first="Bianca" last="Haase">Bianca Haase</name>
<affiliation><nlm:aff id="Aff12"><institution-wrap><institution-id institution-id-type="ISNI">0000 0004 1936 834X</institution-id>
<institution-id institution-id-type="GRID">grid.1013.3</institution-id>
<institution>School of Life and Environmental Sciences, Faculty of Veterinary Science,</institution>
<institution>University of Sydney,</institution>
</institution-wrap>
Regimental Drive, B19-301 RMC Gunn, Sydney, NSW 2006 Australia</nlm:aff>
<wicri:noCountry code="subfield">NSW 2006 Australia</wicri:noCountry>
</affiliation>
</author>
<author><name sortKey="Jagannathan, Vidhya" sort="Jagannathan, Vidhya" uniqKey="Jagannathan V" first="Vidhya" last="Jagannathan">Vidhya Jagannathan</name>
<affiliation wicri:level="1"><nlm:aff id="Aff13"><institution-wrap><institution-id institution-id-type="ISNI">0000 0001 0726 5157</institution-id>
<institution-id institution-id-type="GRID">grid.5734.5</institution-id>
<institution>Institute of Genetics,</institution>
<institution>University of Bern,</institution>
</institution-wrap>
3001 Bern, Switzerland</nlm:aff>
<country xml:lang="fr">Suisse</country>
<wicri:regionArea>3001 Bern</wicri:regionArea>
</affiliation>
</author>
<author><name sortKey="Kalbfleisch, Ted" sort="Kalbfleisch, Ted" uniqKey="Kalbfleisch T" first="Ted" last="Kalbfleisch">Ted Kalbfleisch</name>
<affiliation wicri:level="2"><nlm:aff id="Aff14"><institution-wrap><institution-id institution-id-type="ISNI">0000 0001 2113 1622</institution-id>
<institution-id institution-id-type="GRID">grid.266623.5</institution-id>
<institution>Department of Biochemistry and Molecular Biology, School of Medicine,</institution>
<institution>University of Louisville,</institution>
</institution-wrap>
Louisville, KY 40202 USA</nlm:aff>
<country xml:lang="fr">États-Unis</country>
<placeName><region type="state">Kentucky</region>
</placeName>
<wicri:cityArea>Louisville</wicri:cityArea>
</affiliation>
</author>
<author><name sortKey="Leeb, Tosso" sort="Leeb, Tosso" uniqKey="Leeb T" first="Tosso" last="Leeb">Tosso Leeb</name>
<affiliation wicri:level="1"><nlm:aff id="Aff13"><institution-wrap><institution-id institution-id-type="ISNI">0000 0001 0726 5157</institution-id>
<institution-id institution-id-type="GRID">grid.5734.5</institution-id>
<institution>Institute of Genetics,</institution>
<institution>University of Bern,</institution>
</institution-wrap>
3001 Bern, Switzerland</nlm:aff>
<country xml:lang="fr">Suisse</country>
<wicri:regionArea>3001 Bern</wicri:regionArea>
</affiliation>
</author>
<author><name sortKey="Lindgren, Gabriella" sort="Lindgren, Gabriella" uniqKey="Lindgren G" first="Gabriella" last="Lindgren">Gabriella Lindgren</name>
<affiliation wicri:level="1"><nlm:aff id="Aff15"><institution-wrap><institution-id institution-id-type="ISNI">0000 0000 8578 2742</institution-id>
<institution-id institution-id-type="GRID">grid.6341.0</institution-id>
<institution>Department of Animal Breeding and Genetics,</institution>
<institution>Swedish University of Agricultural Sciences,</institution>
</institution-wrap>
Uppsala, Sweden</nlm:aff>
<country xml:lang="fr">Suède</country>
<wicri:regionArea>Uppsala</wicri:regionArea>
</affiliation>
</author>
<author><name sortKey="Lopes, Maria Susana" sort="Lopes, Maria Susana" uniqKey="Lopes M" first="Maria Susana" last="Lopes">Maria Susana Lopes</name>
<affiliation wicri:level="1"><nlm:aff id="Aff16"><institution-wrap><institution-id institution-id-type="ISNI">0000 0001 2096 9474</institution-id>
<institution-id institution-id-type="GRID">grid.7338.f</institution-id>
<institution>Biotechnology Centre of Azores,</institution>
<institution>University of Azores,</institution>
</institution-wrap>
Angra do heroísmo, Portugal</nlm:aff>
<country xml:lang="fr">Portugal</country>
<wicri:regionArea>Angra do heroísmo</wicri:regionArea>
</affiliation>
</author>
<author><name sortKey="Mach, Nuria" sort="Mach, Nuria" uniqKey="Mach N" first="Núria" last="Mach">Núria Mach</name>
<affiliation wicri:level="1"><nlm:aff id="Aff5"><institution-wrap><institution-id institution-id-type="ISNI">0000 0004 4910 6535</institution-id>
<institution-id institution-id-type="GRID">grid.460789.4</institution-id>
<institution>Unité de Génétique Animale et Biologie Intégrative- UMR1313, INRA,</institution>
<institution>Université Paris-Saclay,</institution>
</institution-wrap>
AgroParisTech, 78350 Jouy-en-Josas, France</nlm:aff>
<country xml:lang="fr">France</country>
<wicri:regionArea>AgroParisTech, 78350 Jouy-en-Josas</wicri:regionArea>
</affiliation>
</author>
<author><name sortKey="Da Camara Machado, Artur" sort="Da Camara Machado, Artur" uniqKey="Da Camara Machado A" first="Artur" last="Da Câmara Machado">Artur Da Câmara Machado</name>
<affiliation wicri:level="1"><nlm:aff id="Aff16"><institution-wrap><institution-id institution-id-type="ISNI">0000 0001 2096 9474</institution-id>
<institution-id institution-id-type="GRID">grid.7338.f</institution-id>
<institution>Biotechnology Centre of Azores,</institution>
<institution>University of Azores,</institution>
</institution-wrap>
Angra do heroísmo, Portugal</nlm:aff>
<country xml:lang="fr">Portugal</country>
<wicri:regionArea>Angra do heroísmo</wicri:regionArea>
</affiliation>
</author>
<author><name sortKey="Macleod, James N" sort="Macleod, James N" uniqKey="Macleod J" first="James N." last="Macleod">James N. Macleod</name>
<affiliation wicri:level="2"><nlm:aff id="Aff3"><institution-wrap><institution-id institution-id-type="ISNI">0000 0004 1936 8438</institution-id>
<institution-id institution-id-type="GRID">grid.266539.d</institution-id>
<institution>Maxwell H. Gluck Equine Research Center,</institution>
<institution>Department of Veterinary Science, University of Kentucky,</institution>
</institution-wrap>
Lexington, KY USA</nlm:aff>
<country>États-Unis</country>
<placeName><region type="state">Kentucky</region>
</placeName>
<wicri:cityArea>Lexington</wicri:cityArea>
</affiliation>
</author>
<author><name sortKey="Mccoy, Annette" sort="Mccoy, Annette" uniqKey="Mccoy A" first="Annette" last="Mccoy">Annette Mccoy</name>
<affiliation wicri:level="2"><nlm:aff id="Aff17"><institution-wrap><institution-id institution-id-type="ISNI">0000 0004 1936 9991</institution-id>
<institution-id institution-id-type="GRID">grid.35403.31</institution-id>
<institution>Department of Veterinary Clinical Medicine,</institution>
<institution>College of Veterinary Medicine, University of Illinois at Urbana-Champaign,</institution>
</institution-wrap>
Champaign, IL 61802 USA</nlm:aff>
<country xml:lang="fr">États-Unis</country>
<placeName><region type="state">Illinois</region>
</placeName>
<wicri:cityArea>Champaign</wicri:cityArea>
</affiliation>
</author>
<author><name sortKey="Metzger, Julia" sort="Metzger, Julia" uniqKey="Metzger J" first="Julia" last="Metzger">Julia Metzger</name>
<affiliation wicri:level="1"><nlm:aff id="Aff9"><institution-wrap><institution-id institution-id-type="ISNI">0000 0001 0126 6191</institution-id>
<institution-id institution-id-type="GRID">grid.412970.9</institution-id>
<institution>Institute for Animal Breeding and Genetics,</institution>
<institution>University of Veterinary Medicine,</institution>
</institution-wrap>
Hannover, Germany</nlm:aff>
<country xml:lang="fr">Allemagne</country>
<wicri:regionArea>Hannover</wicri:regionArea>
</affiliation>
</author>
<author><name sortKey="Penedo, Cecilia" sort="Penedo, Cecilia" uniqKey="Penedo C" first="Cecilia" last="Penedo">Cecilia Penedo</name>
<affiliation wicri:level="2"><nlm:aff id="Aff18"><institution-wrap><institution-id institution-id-type="ISNI">0000 0004 1936 9684</institution-id>
<institution-id institution-id-type="GRID">grid.27860.3b</institution-id>
<institution>Veterinary Genetics Laboratory,</institution>
<institution>University of California Davis,</institution>
</institution-wrap>
Davis, CA USA</nlm:aff>
<country>États-Unis</country>
<placeName><region type="state">Californie</region>
</placeName>
<wicri:cityArea>Davis</wicri:cityArea>
</affiliation>
</author>
<author><name sortKey="Polani, Sagi" sort="Polani, Sagi" uniqKey="Polani S" first="Sagi" last="Polani">Sagi Polani</name>
<affiliation wicri:level="1"><nlm:aff id="Aff6"><institution-wrap><institution-id institution-id-type="ISNI">0000 0004 1937 0538</institution-id>
<institution-id institution-id-type="GRID">grid.9619.7</institution-id>
<institution>The Robert H. Smith Faculty of Agriculture, Food and Environment,</institution>
<institution>The Koret School of Veterinary Medicine, The Hebrew University,</institution>
</institution-wrap>
76100 Rehovot, Israel</nlm:aff>
<country xml:lang="fr">Israël</country>
<wicri:regionArea>76100 Rehovot</wicri:regionArea>
</affiliation>
</author>
<author><name sortKey="Rieder, Stefan" sort="Rieder, Stefan" uniqKey="Rieder S" first="Stefan" last="Rieder">Stefan Rieder</name>
<affiliation wicri:level="1"><nlm:aff id="Aff19"><institution-wrap><institution-id institution-id-type="ISNI">0000 0004 4681 910X</institution-id>
<institution-id institution-id-type="GRID">grid.417771.3</institution-id>
<institution></institution>
<institution>Agroscope, Swiss National Stud Farm,</institution>
</institution-wrap>
1580 Avenches, Switzerland</nlm:aff>
<country xml:lang="fr">Suisse</country>
<wicri:regionArea>1580 Avenches</wicri:regionArea>
</affiliation>
</author>
<author><name sortKey="Tammen, Imke" sort="Tammen, Imke" uniqKey="Tammen I" first="Imke" last="Tammen">Imke Tammen</name>
<affiliation><nlm:aff id="Aff12"><institution-wrap><institution-id institution-id-type="ISNI">0000 0004 1936 834X</institution-id>
<institution-id institution-id-type="GRID">grid.1013.3</institution-id>
<institution>School of Life and Environmental Sciences, Faculty of Veterinary Science,</institution>
<institution>University of Sydney,</institution>
</institution-wrap>
Regimental Drive, B19-301 RMC Gunn, Sydney, NSW 2006 Australia</nlm:aff>
<wicri:noCountry code="subfield">NSW 2006 Australia</wicri:noCountry>
</affiliation>
</author>
<author><name sortKey="Tetens, Jens" sort="Tetens, Jens" uniqKey="Tetens J" first="Jens" last="Tetens">Jens Tetens</name>
<affiliation wicri:level="1"><nlm:aff id="Aff20"><institution-wrap><institution-id institution-id-type="ISNI">0000 0001 2153 9986</institution-id>
<institution-id institution-id-type="GRID">grid.9764.c</institution-id>
<institution>Institute of Animal Breeding and Husbandry,</institution>
<institution>Christian-Albrechts-University Kiel,</institution>
</institution-wrap>
Hermann-Rodewald-Strasse 6, 24098 Kiel, Germany</nlm:aff>
<country xml:lang="fr">Allemagne</country>
<wicri:regionArea>Hermann-Rodewald-Strasse 6, 24098 Kiel</wicri:regionArea>
</affiliation>
<affiliation wicri:level="1"><nlm:aff id="Aff21"><institution-wrap><institution-id institution-id-type="ISNI">0000 0001 2364 4210</institution-id>
<institution-id institution-id-type="GRID">grid.7450.6</institution-id>
<institution>Department of Animal Sciences, Functional Breeding Group,</institution>
<institution>Georg-August University Göttingen,</institution>
</institution-wrap>
Burckhardtweg 2, 37077 Göttingen, Germany</nlm:aff>
<country xml:lang="fr">Allemagne</country>
<wicri:regionArea>Burckhardtweg 2, 37077 Göttingen</wicri:regionArea>
</affiliation>
</author>
<author><name sortKey="Thaller, Georg" sort="Thaller, Georg" uniqKey="Thaller G" first="Georg" last="Thaller">Georg Thaller</name>
<affiliation wicri:level="1"><nlm:aff id="Aff20"><institution-wrap><institution-id institution-id-type="ISNI">0000 0001 2153 9986</institution-id>
<institution-id institution-id-type="GRID">grid.9764.c</institution-id>
<institution>Institute of Animal Breeding and Husbandry,</institution>
<institution>Christian-Albrechts-University Kiel,</institution>
</institution-wrap>
Hermann-Rodewald-Strasse 6, 24098 Kiel, Germany</nlm:aff>
<country xml:lang="fr">Allemagne</country>
<wicri:regionArea>Hermann-Rodewald-Strasse 6, 24098 Kiel</wicri:regionArea>
</affiliation>
</author>
<author><name sortKey="Verini Supplizi, Andrea" sort="Verini Supplizi, Andrea" uniqKey="Verini Supplizi A" first="Andrea" last="Verini-Supplizi">Andrea Verini-Supplizi</name>
<affiliation wicri:level="1"><nlm:aff id="Aff22"><institution-wrap><institution-id institution-id-type="ISNI">0000 0004 1757 3630</institution-id>
<institution-id institution-id-type="GRID">grid.9027.c</institution-id>
<institution>Department of Veterinary Medicine - Sport Horse Research Centre,</institution>
<institution>University of Perugia,</institution>
</institution-wrap>
Perugia, Italy</nlm:aff>
<country xml:lang="fr">Italie</country>
<wicri:regionArea>Perugia</wicri:regionArea>
</affiliation>
</author>
<author><name sortKey="Wade, Claire M" sort="Wade, Claire M" uniqKey="Wade C" first="Claire M." last="Wade">Claire M. Wade</name>
<affiliation><nlm:aff id="Aff12"><institution-wrap><institution-id institution-id-type="ISNI">0000 0004 1936 834X</institution-id>
<institution-id institution-id-type="GRID">grid.1013.3</institution-id>
<institution>School of Life and Environmental Sciences, Faculty of Veterinary Science,</institution>
<institution>University of Sydney,</institution>
</institution-wrap>
Regimental Drive, B19-301 RMC Gunn, Sydney, NSW 2006 Australia</nlm:aff>
<wicri:noCountry code="subfield">NSW 2006 Australia</wicri:noCountry>
</affiliation>
</author>
<author><name sortKey="Wallner, Barbara" sort="Wallner, Barbara" uniqKey="Wallner B" first="Barbara" last="Wallner">Barbara Wallner</name>
<affiliation wicri:level="1"><nlm:aff id="Aff7"><institution-wrap><institution-id institution-id-type="ISNI">0000 0000 9686 6466</institution-id>
<institution-id institution-id-type="GRID">grid.6583.8</institution-id>
<institution>Institute of Animal Breeding and Genetics, Department of Biomedical Sciences,</institution>
<institution>University of Veterinary Medicine Vienna,</institution>
</institution-wrap>
Vienna, Austria</nlm:aff>
<country xml:lang="fr">Autriche</country>
<wicri:regionArea>Vienna</wicri:regionArea>
</affiliation>
</author>
<author><name sortKey="Orlando, Ludovic" sort="Orlando, Ludovic" uniqKey="Orlando L" first="Ludovic" last="Orlando">Ludovic Orlando</name>
<affiliation wicri:level="1"><nlm:aff id="Aff2"><institution-wrap><institution-id institution-id-type="ISNI">0000 0001 0674 042X</institution-id>
<institution-id institution-id-type="GRID">grid.5254.6</institution-id>
<institution>Centre for GeoGenetics, Natural History Museum of Denmark,</institution>
<institution>University of Copenhagen,</institution>
</institution-wrap>
Copenhagen, Denmark</nlm:aff>
<country xml:lang="fr">Danemark</country>
<wicri:regionArea>Copenhagen</wicri:regionArea>
</affiliation>
<affiliation wicri:level="1"><nlm:aff id="Aff23">Laboratoire d’Anthropobiologie Moléculaire et d’Imagerie de Synthèse, CNRS UMR 5288, Université de Toulouse, Université Paul Sabatier, 31000 Toulouse, France</nlm:aff>
<country xml:lang="fr">France</country>
<wicri:regionArea>Laboratoire d’Anthropobiologie Moléculaire et d’Imagerie de Synthèse, CNRS UMR 5288, Université de Toulouse, Université Paul Sabatier, 31000 Toulouse</wicri:regionArea>
</affiliation>
</author>
<author><name sortKey="Mickelson, James R" sort="Mickelson, James R" uniqKey="Mickelson J" first="James R." last="Mickelson">James R. Mickelson</name>
<affiliation wicri:level="2"><nlm:aff id="Aff24"><institution-wrap><institution-id institution-id-type="ISNI">0000000419368657</institution-id>
<institution-id institution-id-type="GRID">grid.17635.36</institution-id>
<institution>Department of Veterinary and Biomedical Sciences,</institution>
<institution>College of Veterinary Medicine, University of Minnesota,</institution>
</institution-wrap>
St. Paul, MN USA</nlm:aff>
<country>États-Unis</country>
<placeName><region type="state">Minnesota</region>
</placeName>
<wicri:cityArea>St. Paul</wicri:cityArea>
</affiliation>
</author>
<author><name sortKey="Mccue, Molly E" sort="Mccue, Molly E" uniqKey="Mccue M" first="Molly E." last="Mccue">Molly E. Mccue</name>
<affiliation wicri:level="2"><nlm:aff id="Aff1"><institution-wrap><institution-id institution-id-type="ISNI">0000000419368657</institution-id>
<institution-id institution-id-type="GRID">grid.17635.36</institution-id>
<institution>Department of Veterinary Population Medicine,</institution>
<institution>College of Veterinary Medicine, University of Minnesota,</institution>
</institution-wrap>
St. Paul, MN USA</nlm:aff>
<country>États-Unis</country>
<placeName><region type="state">Minnesota</region>
</placeName>
<wicri:cityArea>St. Paul</wicri:cityArea>
</affiliation>
</author>
</analytic>
<series><title level="j">BMC Genomics</title>
<idno type="eISSN">1471-2164</idno>
<imprint><date when="2017">2017</date>
</imprint>
</series>
</biblStruct>
</sourceDesc>
</fileDesc>
<profileDesc><textClass></textClass>
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</teiHeader>
<front><div type="abstract" xml:lang="en"><sec><title>Background</title>
<p id="Par1">To date, genome-scale analyses in the domestic horse have been limited by suboptimal single nucleotide polymorphism (SNP) density and uneven genomic coverage of the current SNP genotyping arrays. The recent availability of whole genome sequences has created the opportunity to develop a next generation, high-density equine SNP array.</p>
</sec>
<sec><title>Results</title>
<p id="Par2">Using whole genome sequence from 153 individuals representing 24 distinct breeds collated by the equine genomics community, we cataloged over 23 million de novo discovered genetic variants. Leveraging genotype data from individuals with both whole genome sequence, and genotypes from lower-density, legacy SNP arrays, a subset of ~5 million high-quality, high-density array candidate SNPs were selected based on breed representation and uniform spacing across the genome. Considering probe design recommendations from a commercial vendor (Affymetrix, now Thermo Fisher Scientific) a set of ~2 million SNPs were selected for a next-generation high-density SNP chip (MNEc2M). Genotype data were generated using the MNEc2M array from a cohort of 332 horses from 20 breeds and a lower-density array, consisting of ~670 thousand SNPs (MNEc670k), was designed for genotype imputation.</p>
</sec>
<sec><title>Conclusions</title>
<p id="Par3">Here, we document the steps taken to design both the MNEc2M and MNEc670k arrays, report genomic and technical properties of these genotyping platforms, and demonstrate the imputation capabilities of these tools for the domestic horse.</p>
</sec>
<sec><title>Electronic supplementary material</title>
<p>The online version of this article (doi:10.1186/s12864-017-3943-8) contains supplementary material, which is available to authorized users.</p>
</sec>
</div>
</front>
<back><div1 type="bibliography"><listBibl><biblStruct></biblStruct>
<biblStruct></biblStruct>
<biblStruct><analytic><author><name sortKey="Mccoy, Am" uniqKey="Mccoy A">AM McCoy</name>
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<author><name sortKey="Mccue, Me" uniqKey="Mccue M">ME McCue</name>
</author>
</analytic>
</biblStruct>
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<biblStruct><analytic><author><name sortKey="Howie, Bn" uniqKey="Howie B">BN Howie</name>
</author>
<author><name sortKey="Carlson, Cs" uniqKey="Carlson C">CS Carlson</name>
</author>
<author><name sortKey="Rieder, Mj" uniqKey="Rieder M">MJ Rieder</name>
</author>
<author><name sortKey="Nickerson, Da" uniqKey="Nickerson D">DA Nickerson</name>
</author>
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<biblStruct><analytic><author><name sortKey="Lu, D" uniqKey="Lu D">D Lu</name>
</author>
<author><name sortKey="Akanno, Ec" uniqKey="Akanno E">EC Akanno</name>
</author>
<author><name sortKey="Crowley, Jj" uniqKey="Crowley J">JJ Crowley</name>
</author>
<author><name sortKey="Schenkel, F" uniqKey="Schenkel F">F Schenkel</name>
</author>
<author><name sortKey="Li, H" uniqKey="Li H">H Li</name>
</author>
<author><name sortKey="De Pauw, M" uniqKey="De Pauw M">M De Pauw</name>
</author>
</analytic>
</biblStruct>
<biblStruct></biblStruct>
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<biblStruct></biblStruct>
<biblStruct><analytic><author><name sortKey="Browning, Sr" uniqKey="Browning S">SR Browning</name>
</author>
<author><name sortKey="Browning, Bl" uniqKey="Browning B">BL Browning</name>
</author>
</analytic>
</biblStruct>
<biblStruct><analytic><author><name sortKey="Danecek, P" uniqKey="Danecek P">P Danecek</name>
</author>
<author><name sortKey="Auton, A" uniqKey="Auton A">A Auton</name>
</author>
<author><name sortKey="Abecasis, G" uniqKey="Abecasis G">G Abecasis</name>
</author>
<author><name sortKey="Albers, Ca" uniqKey="Albers C">CA Albers</name>
</author>
<author><name sortKey="Banks, E" uniqKey="Banks E">E Banks</name>
</author>
<author><name sortKey="Depristo, Ma" uniqKey="Depristo M">MA DePristo</name>
</author>
</analytic>
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<pmc article-type="research-article"><pmc-dir>properties open_access</pmc-dir>
<front><journal-meta><journal-id journal-id-type="nlm-ta">BMC Genomics</journal-id>
<journal-id journal-id-type="iso-abbrev">BMC Genomics</journal-id>
<journal-title-group><journal-title>BMC Genomics</journal-title>
</journal-title-group>
<issn pub-type="epub">1471-2164</issn>
<publisher><publisher-name>BioMed Central</publisher-name>
<publisher-loc>London</publisher-loc>
</publisher>
</journal-meta>
<article-meta><article-id pub-id-type="pmid">28750625</article-id>
<article-id pub-id-type="pmc">5530493</article-id>
<article-id pub-id-type="publisher-id">3943</article-id>
<article-id pub-id-type="doi">10.1186/s12864-017-3943-8</article-id>
<article-categories><subj-group subj-group-type="heading"><subject>Research Article</subject>
</subj-group>
</article-categories>
<title-group><article-title>Developing a 670k genotyping array to tag ~2M SNPs across 24 horse breeds</article-title>
</title-group>
<contrib-group><contrib contrib-type="author"><name><surname>Schaefer</surname>
<given-names>Robert J.</given-names>
</name>
<address><email>schae234@umn.edu</email>
</address>
<xref ref-type="aff" rid="Aff1">1</xref>
</contrib>
<contrib contrib-type="author"><name><surname>Schubert</surname>
<given-names>Mikkel</given-names>
</name>
<xref ref-type="aff" rid="Aff2">2</xref>
</contrib>
<contrib contrib-type="author"><name><surname>Bailey</surname>
<given-names>Ernest</given-names>
</name>
<xref ref-type="aff" rid="Aff3">3</xref>
</contrib>
<contrib contrib-type="author"><name><surname>Bannasch</surname>
<given-names>Danika L.</given-names>
</name>
<xref ref-type="aff" rid="Aff4">4</xref>
</contrib>
<contrib contrib-type="author"><name><surname>Barrey</surname>
<given-names>Eric</given-names>
</name>
<xref ref-type="aff" rid="Aff5">5</xref>
</contrib>
<contrib contrib-type="author"><name><surname>Bar-Gal</surname>
<given-names>Gila Kahila</given-names>
</name>
<xref ref-type="aff" rid="Aff6">6</xref>
</contrib>
<contrib contrib-type="author"><name><surname>Brem</surname>
<given-names>Gottfried</given-names>
</name>
<xref ref-type="aff" rid="Aff7">7</xref>
</contrib>
<contrib contrib-type="author"><name><surname>Brooks</surname>
<given-names>Samantha A.</given-names>
</name>
<xref ref-type="aff" rid="Aff8">8</xref>
</contrib>
<contrib contrib-type="author"><name><surname>Distl</surname>
<given-names>Ottmar</given-names>
</name>
<xref ref-type="aff" rid="Aff9">9</xref>
</contrib>
<contrib contrib-type="author"><name><surname>Fries</surname>
<given-names>Ruedi</given-names>
</name>
<xref ref-type="aff" rid="Aff10">10</xref>
</contrib>
<contrib contrib-type="author"><name><surname>Finno</surname>
<given-names>Carrie J.</given-names>
</name>
<xref ref-type="aff" rid="Aff4">4</xref>
</contrib>
<contrib contrib-type="author"><name><surname>Gerber</surname>
<given-names>Vinzenz</given-names>
</name>
<xref ref-type="aff" rid="Aff11">11</xref>
</contrib>
<contrib contrib-type="author"><name><surname>Haase</surname>
<given-names>Bianca</given-names>
</name>
<xref ref-type="aff" rid="Aff12">12</xref>
</contrib>
<contrib contrib-type="author"><name><surname>Jagannathan</surname>
<given-names>Vidhya</given-names>
</name>
<xref ref-type="aff" rid="Aff13">13</xref>
</contrib>
<contrib contrib-type="author"><name><surname>Kalbfleisch</surname>
<given-names>Ted</given-names>
</name>
<xref ref-type="aff" rid="Aff14">14</xref>
</contrib>
<contrib contrib-type="author"><name><surname>Leeb</surname>
<given-names>Tosso</given-names>
</name>
<xref ref-type="aff" rid="Aff13">13</xref>
</contrib>
<contrib contrib-type="author"><name><surname>Lindgren</surname>
<given-names>Gabriella</given-names>
</name>
<xref ref-type="aff" rid="Aff15">15</xref>
</contrib>
<contrib contrib-type="author"><name><surname>Lopes</surname>
<given-names>Maria Susana</given-names>
</name>
<xref ref-type="aff" rid="Aff16">16</xref>
</contrib>
<contrib contrib-type="author"><name><surname>Mach</surname>
<given-names>Núria</given-names>
</name>
<xref ref-type="aff" rid="Aff5">5</xref>
</contrib>
<contrib contrib-type="author"><name><surname>da Câmara Machado</surname>
<given-names>Artur</given-names>
</name>
<xref ref-type="aff" rid="Aff16">16</xref>
</contrib>
<contrib contrib-type="author"><name><surname>MacLeod</surname>
<given-names>James N.</given-names>
</name>
<xref ref-type="aff" rid="Aff3">3</xref>
</contrib>
<contrib contrib-type="author"><name><surname>McCoy</surname>
<given-names>Annette</given-names>
</name>
<xref ref-type="aff" rid="Aff17">17</xref>
</contrib>
<contrib contrib-type="author"><name><surname>Metzger</surname>
<given-names>Julia</given-names>
</name>
<xref ref-type="aff" rid="Aff9">9</xref>
</contrib>
<contrib contrib-type="author"><name><surname>Penedo</surname>
<given-names>Cecilia</given-names>
</name>
<xref ref-type="aff" rid="Aff18">18</xref>
</contrib>
<contrib contrib-type="author"><name><surname>Polani</surname>
<given-names>Sagi</given-names>
</name>
<xref ref-type="aff" rid="Aff6">6</xref>
</contrib>
<contrib contrib-type="author"><name><surname>Rieder</surname>
<given-names>Stefan</given-names>
</name>
<xref ref-type="aff" rid="Aff19">19</xref>
</contrib>
<contrib contrib-type="author"><name><surname>Tammen</surname>
<given-names>Imke</given-names>
</name>
<xref ref-type="aff" rid="Aff12">12</xref>
</contrib>
<contrib contrib-type="author"><name><surname>Tetens</surname>
<given-names>Jens</given-names>
</name>
<xref ref-type="aff" rid="Aff20">20</xref>
<xref ref-type="aff" rid="Aff21">21</xref>
</contrib>
<contrib contrib-type="author"><name><surname>Thaller</surname>
<given-names>Georg</given-names>
</name>
<xref ref-type="aff" rid="Aff20">20</xref>
</contrib>
<contrib contrib-type="author"><name><surname>Verini-Supplizi</surname>
<given-names>Andrea</given-names>
</name>
<xref ref-type="aff" rid="Aff22">22</xref>
</contrib>
<contrib contrib-type="author"><name><surname>Wade</surname>
<given-names>Claire M.</given-names>
</name>
<xref ref-type="aff" rid="Aff12">12</xref>
</contrib>
<contrib contrib-type="author"><name><surname>Wallner</surname>
<given-names>Barbara</given-names>
</name>
<xref ref-type="aff" rid="Aff7">7</xref>
</contrib>
<contrib contrib-type="author"><name><surname>Orlando</surname>
<given-names>Ludovic</given-names>
</name>
<xref ref-type="aff" rid="Aff2">2</xref>
<xref ref-type="aff" rid="Aff23">23</xref>
</contrib>
<contrib contrib-type="author"><name><surname>Mickelson</surname>
<given-names>James R.</given-names>
</name>
<xref ref-type="aff" rid="Aff24">24</xref>
</contrib>
<contrib contrib-type="author" corresp="yes"><name><surname>McCue</surname>
<given-names>Molly E.</given-names>
</name>
<address><email>mccu0173@umn.edu</email>
</address>
<xref ref-type="aff" rid="Aff1">1</xref>
</contrib>
<aff id="Aff1"><label>1</label>
<institution-wrap><institution-id institution-id-type="ISNI">0000000419368657</institution-id>
<institution-id institution-id-type="GRID">grid.17635.36</institution-id>
<institution>Department of Veterinary Population Medicine,</institution>
<institution>College of Veterinary Medicine, University of Minnesota,</institution>
</institution-wrap>
St. Paul, MN USA</aff>
<aff id="Aff2"><label>2</label>
<institution-wrap><institution-id institution-id-type="ISNI">0000 0001 0674 042X</institution-id>
<institution-id institution-id-type="GRID">grid.5254.6</institution-id>
<institution>Centre for GeoGenetics, Natural History Museum of Denmark,</institution>
<institution>University of Copenhagen,</institution>
</institution-wrap>
Copenhagen, Denmark</aff>
<aff id="Aff3"><label>3</label>
<institution-wrap><institution-id institution-id-type="ISNI">0000 0004 1936 8438</institution-id>
<institution-id institution-id-type="GRID">grid.266539.d</institution-id>
<institution>Maxwell H. Gluck Equine Research Center,</institution>
<institution>Department of Veterinary Science, University of Kentucky,</institution>
</institution-wrap>
Lexington, KY USA</aff>
<aff id="Aff4"><label>4</label>
<institution-wrap><institution-id institution-id-type="ISNI">0000 0004 1936 9684</institution-id>
<institution-id institution-id-type="GRID">grid.27860.3b</institution-id>
<institution>School of Veterinary Medicine,</institution>
<institution>University of California-Davis,</institution>
</institution-wrap>
Davis, CA 95616 USA</aff>
<aff id="Aff5"><label>5</label>
<institution-wrap><institution-id institution-id-type="ISNI">0000 0004 4910 6535</institution-id>
<institution-id institution-id-type="GRID">grid.460789.4</institution-id>
<institution>Unité de Génétique Animale et Biologie Intégrative- UMR1313, INRA,</institution>
<institution>Université Paris-Saclay,</institution>
</institution-wrap>
AgroParisTech, 78350 Jouy-en-Josas, France</aff>
<aff id="Aff6"><label>6</label>
<institution-wrap><institution-id institution-id-type="ISNI">0000 0004 1937 0538</institution-id>
<institution-id institution-id-type="GRID">grid.9619.7</institution-id>
<institution>The Robert H. Smith Faculty of Agriculture, Food and Environment,</institution>
<institution>The Koret School of Veterinary Medicine, The Hebrew University,</institution>
</institution-wrap>
76100 Rehovot, Israel</aff>
<aff id="Aff7"><label>7</label>
<institution-wrap><institution-id institution-id-type="ISNI">0000 0000 9686 6466</institution-id>
<institution-id institution-id-type="GRID">grid.6583.8</institution-id>
<institution>Institute of Animal Breeding and Genetics, Department of Biomedical Sciences,</institution>
<institution>University of Veterinary Medicine Vienna,</institution>
</institution-wrap>
Vienna, Austria</aff>
<aff id="Aff8"><label>8</label>
<institution-wrap><institution-id institution-id-type="ISNI">0000 0004 1936 8091</institution-id>
<institution-id institution-id-type="GRID">grid.15276.37</institution-id>
<institution>Department of Animal Science,</institution>
<institution>University of Florida,</institution>
</institution-wrap>
Gainesville, FL USA</aff>
<aff id="Aff9"><label>9</label>
<institution-wrap><institution-id institution-id-type="ISNI">0000 0001 0126 6191</institution-id>
<institution-id institution-id-type="GRID">grid.412970.9</institution-id>
<institution>Institute for Animal Breeding and Genetics,</institution>
<institution>University of Veterinary Medicine,</institution>
</institution-wrap>
Hannover, Germany</aff>
<aff id="Aff10"><label>10</label>
Lehrstuhl für Tierzucht der Technischen Universität München, Liesel-Beckmann-Strasse 1, 85354 Freising, Germany</aff>
<aff id="Aff11"><label>11</label>
Swiss Institute of Equine Medicine, Department of Clinical Veterinary Medicine, Vetsuisse Faculty, University of Bern, and Agroscope, Länggassstrasse 124, 3001 Bern, Switzerland</aff>
<aff id="Aff12"><label>12</label>
<institution-wrap><institution-id institution-id-type="ISNI">0000 0004 1936 834X</institution-id>
<institution-id institution-id-type="GRID">grid.1013.3</institution-id>
<institution>School of Life and Environmental Sciences, Faculty of Veterinary Science,</institution>
<institution>University of Sydney,</institution>
</institution-wrap>
Regimental Drive, B19-301 RMC Gunn, Sydney, NSW 2006 Australia</aff>
<aff id="Aff13"><label>13</label>
<institution-wrap><institution-id institution-id-type="ISNI">0000 0001 0726 5157</institution-id>
<institution-id institution-id-type="GRID">grid.5734.5</institution-id>
<institution>Institute of Genetics,</institution>
<institution>University of Bern,</institution>
</institution-wrap>
3001 Bern, Switzerland</aff>
<aff id="Aff14"><label>14</label>
<institution-wrap><institution-id institution-id-type="ISNI">0000 0001 2113 1622</institution-id>
<institution-id institution-id-type="GRID">grid.266623.5</institution-id>
<institution>Department of Biochemistry and Molecular Biology, School of Medicine,</institution>
<institution>University of Louisville,</institution>
</institution-wrap>
Louisville, KY 40202 USA</aff>
<aff id="Aff15"><label>15</label>
<institution-wrap><institution-id institution-id-type="ISNI">0000 0000 8578 2742</institution-id>
<institution-id institution-id-type="GRID">grid.6341.0</institution-id>
<institution>Department of Animal Breeding and Genetics,</institution>
<institution>Swedish University of Agricultural Sciences,</institution>
</institution-wrap>
Uppsala, Sweden</aff>
<aff id="Aff16"><label>16</label>
<institution-wrap><institution-id institution-id-type="ISNI">0000 0001 2096 9474</institution-id>
<institution-id institution-id-type="GRID">grid.7338.f</institution-id>
<institution>Biotechnology Centre of Azores,</institution>
<institution>University of Azores,</institution>
</institution-wrap>
Angra do heroísmo, Portugal</aff>
<aff id="Aff17"><label>17</label>
<institution-wrap><institution-id institution-id-type="ISNI">0000 0004 1936 9991</institution-id>
<institution-id institution-id-type="GRID">grid.35403.31</institution-id>
<institution>Department of Veterinary Clinical Medicine,</institution>
<institution>College of Veterinary Medicine, University of Illinois at Urbana-Champaign,</institution>
</institution-wrap>
Champaign, IL 61802 USA</aff>
<aff id="Aff18"><label>18</label>
<institution-wrap><institution-id institution-id-type="ISNI">0000 0004 1936 9684</institution-id>
<institution-id institution-id-type="GRID">grid.27860.3b</institution-id>
<institution>Veterinary Genetics Laboratory,</institution>
<institution>University of California Davis,</institution>
</institution-wrap>
Davis, CA USA</aff>
<aff id="Aff19"><label>19</label>
<institution-wrap><institution-id institution-id-type="ISNI">0000 0004 4681 910X</institution-id>
<institution-id institution-id-type="GRID">grid.417771.3</institution-id>
<institution></institution>
<institution>Agroscope, Swiss National Stud Farm,</institution>
</institution-wrap>
1580 Avenches, Switzerland</aff>
<aff id="Aff20"><label>20</label>
<institution-wrap><institution-id institution-id-type="ISNI">0000 0001 2153 9986</institution-id>
<institution-id institution-id-type="GRID">grid.9764.c</institution-id>
<institution>Institute of Animal Breeding and Husbandry,</institution>
<institution>Christian-Albrechts-University Kiel,</institution>
</institution-wrap>
Hermann-Rodewald-Strasse 6, 24098 Kiel, Germany</aff>
<aff id="Aff21"><label>21</label>
<institution-wrap><institution-id institution-id-type="ISNI">0000 0001 2364 4210</institution-id>
<institution-id institution-id-type="GRID">grid.7450.6</institution-id>
<institution>Department of Animal Sciences, Functional Breeding Group,</institution>
<institution>Georg-August University Göttingen,</institution>
</institution-wrap>
Burckhardtweg 2, 37077 Göttingen, Germany</aff>
<aff id="Aff22"><label>22</label>
<institution-wrap><institution-id institution-id-type="ISNI">0000 0004 1757 3630</institution-id>
<institution-id institution-id-type="GRID">grid.9027.c</institution-id>
<institution>Department of Veterinary Medicine - Sport Horse Research Centre,</institution>
<institution>University of Perugia,</institution>
</institution-wrap>
Perugia, Italy</aff>
<aff id="Aff23"><label>23</label>
Laboratoire d’Anthropobiologie Moléculaire et d’Imagerie de Synthèse, CNRS UMR 5288, Université de Toulouse, Université Paul Sabatier, 31000 Toulouse, France</aff>
<aff id="Aff24"><label>24</label>
<institution-wrap><institution-id institution-id-type="ISNI">0000000419368657</institution-id>
<institution-id institution-id-type="GRID">grid.17635.36</institution-id>
<institution>Department of Veterinary and Biomedical Sciences,</institution>
<institution>College of Veterinary Medicine, University of Minnesota,</institution>
</institution-wrap>
St. Paul, MN USA</aff>
</contrib-group>
<pub-date pub-type="epub"><day>27</day>
<month>7</month>
<year>2017</year>
</pub-date>
<pub-date pub-type="pmc-release"><day>27</day>
<month>7</month>
<year>2017</year>
</pub-date>
<pub-date pub-type="collection"><year>2017</year>
</pub-date>
<volume>18</volume>
<elocation-id>565</elocation-id>
<history><date date-type="received"><day>20</day>
<month>2</month>
<year>2017</year>
</date>
<date date-type="accepted"><day>13</day>
<month>7</month>
<year>2017</year>
</date>
</history>
<permissions><copyright-statement>© The Author(s). 2017</copyright-statement>
<license license-type="OpenAccess"><license-p><bold>Open Access</bold>
This article is distributed under the terms of the Creative Commons Attribution 4.0 International License (<ext-link ext-link-type="uri" xlink:href="http://creativecommons.org/licenses/by/4.0/">http://creativecommons.org/licenses/by/4.0/</ext-link>
), which permits unrestricted use, distribution, and reproduction in any medium, provided you give appropriate credit to the original author(s) and the source, provide a link to the Creative Commons license, and indicate if changes were made. The Creative Commons Public Domain Dedication waiver (<ext-link ext-link-type="uri" xlink:href="http://creativecommons.org/publicdomain/zero/1.0/">http://creativecommons.org/publicdomain/zero/1.0/</ext-link>
) applies to the data made available in this article, unless otherwise stated.</license-p>
</license>
</permissions>
<abstract id="Abs1"><sec><title>Background</title>
<p id="Par1">To date, genome-scale analyses in the domestic horse have been limited by suboptimal single nucleotide polymorphism (SNP) density and uneven genomic coverage of the current SNP genotyping arrays. The recent availability of whole genome sequences has created the opportunity to develop a next generation, high-density equine SNP array.</p>
</sec>
<sec><title>Results</title>
<p id="Par2">Using whole genome sequence from 153 individuals representing 24 distinct breeds collated by the equine genomics community, we cataloged over 23 million de novo discovered genetic variants. Leveraging genotype data from individuals with both whole genome sequence, and genotypes from lower-density, legacy SNP arrays, a subset of ~5 million high-quality, high-density array candidate SNPs were selected based on breed representation and uniform spacing across the genome. Considering probe design recommendations from a commercial vendor (Affymetrix, now Thermo Fisher Scientific) a set of ~2 million SNPs were selected for a next-generation high-density SNP chip (MNEc2M). Genotype data were generated using the MNEc2M array from a cohort of 332 horses from 20 breeds and a lower-density array, consisting of ~670 thousand SNPs (MNEc670k), was designed for genotype imputation.</p>
</sec>
<sec><title>Conclusions</title>
<p id="Par3">Here, we document the steps taken to design both the MNEc2M and MNEc670k arrays, report genomic and technical properties of these genotyping platforms, and demonstrate the imputation capabilities of these tools for the domestic horse.</p>
</sec>
<sec><title>Electronic supplementary material</title>
<p>The online version of this article (doi:10.1186/s12864-017-3943-8) contains supplementary material, which is available to authorized users.</p>
</sec>
</abstract>
<kwd-group xml:lang="en"><title>Keywords</title>
<kwd>Equine genomics</kwd>
<kwd>Whole genome sequence</kwd>
<kwd>SNP-tagging</kwd>
<kwd>SNP chip</kwd>
<kwd>Variant recalibration</kwd>
<kwd>SNP discovery</kwd>
<kwd>SNP informativeness</kwd>
<kwd>SNP validation</kwd>
<kwd>Linkage disequilibrium</kwd>
</kwd-group>
<funding-group><award-group><funding-source><institution>USDA NIFA</institution>
</funding-source>
<award-id>2012-67015-19432</award-id>
</award-group>
<award-group><funding-source><institution>Minnesota Agricultural Experiment Station Multistate Project</institution>
</funding-source>
<award-id>MIN-62-090</award-id>
</award-group>
<award-group><funding-source><institution>The National Animal Genome Project (NRSP8)</institution>
</funding-source>
<award-id>USDA-NSRP8</award-id>
</award-group>
<award-group><funding-source><institution>Danish Council of Independent Research, Natural Sciences</institution>
</funding-source>
<award-id>Grant 4002-00152B</award-id>
</award-group>
<award-group><funding-source><institution>Danish Research Foundation</institution>
</funding-source>
<award-id>DNRF94</award-id>
</award-group>
<award-group><funding-source><institution>Initiative d'Excellence Chaires d'attractivité</institution>
</funding-source>
</award-group>
<award-group><funding-source><institution>Université de Toulouse (OURASI)</institution>
</funding-source>
</award-group>
<award-group><funding-source><institution>European Research Council</institution>
</funding-source>
<award-id>(ERC-CoG-2015-681605)</award-id>
</award-group>
<award-group><funding-source><institution>Bavarian Ministry State Ministry for Food and Agriculture, and Forestry</institution>
</funding-source>
<award-id>A/13/39</award-id>
</award-group>
<award-group><funding-source><institution>The Swedish Research Council Formas</institution>
</funding-source>
<award-id>221-2013-1661</award-id>
</award-group>
<award-group><funding-source><institution>The Swedish Research Council VR</institution>
</funding-source>
<award-id>621-2012-4666</award-id>
</award-group>
</funding-group>
<custom-meta-group><custom-meta><meta-name>issue-copyright-statement</meta-name>
<meta-value>© The Author(s) 2017</meta-value>
</custom-meta>
</custom-meta-group>
</article-meta>
</front>
</pmc>
</record>
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