A High Density SNP Array for the Domestic Horse and Extant Perissodactyla: Utility for Association Mapping, Genetic Diversity, and Phylogeny Studies
Identifieur interne : 002730 ( Pmc/Curation ); précédent : 002729; suivant : 002731A High Density SNP Array for the Domestic Horse and Extant Perissodactyla: Utility for Association Mapping, Genetic Diversity, and Phylogeny Studies
Auteurs : Molly E. Mccue [États-Unis] ; Danika L. Bannasch [États-Unis] ; Jessica L. Petersen [États-Unis] ; Jessica Gurr [Australie] ; Ernie Bailey [États-Unis] ; Matthew M. Binns [États-Unis] ; Ottmar Distl [Allemagne] ; Gérard Guérin [France] ; Telhisa Hasegawa [Japon] ; Emmeline W. Hill [Irlande (pays)] ; Tosso Leeb [Suisse] ; Gabriella Lindgren [Suède] ; M. Cecilia T. Penedo [États-Unis] ; Knut H. R Ed [Norvège] ; Oliver A. Ryder [États-Unis] ; June E. Swinburne [Royaume-Uni] ; Teruaki Tozaki [Japon] ; Stephanie J. Valberg [États-Unis] ; Mark Vaudin [Royaume-Uni] ; Kerstin Lindblad-Toh [Suède, États-Unis] ; Claire M. Wade [Australie] ; James R. Mickelson [États-Unis]Source :
- PLoS Genetics [ 1553-7390 ] ; 2012.
Abstract
An equine SNP genotyping array was developed and evaluated on a panel of samples representing 14 domestic horse breeds and 18 evolutionarily related species. More than 54,000 polymorphic SNPs provided an average inter-SNP spacing of ∼43 kb. The mean minor allele frequency across domestic horse breeds was 0.23, and the number of polymorphic SNPs within breeds ranged from 43,287 to 52,085. Genome-wide linkage disequilibrium (LD) in most breeds declined rapidly over the first 50–100 kb and reached background levels within 1–2 Mb. The extent of LD and the level of inbreeding were highest in the Thoroughbred and lowest in the Mongolian and Quarter Horse. Multidimensional scaling (MDS) analyses demonstrated the tight grouping of individuals within most breeds, close proximity of related breeds, and less tight grouping in admixed breeds. The close relationship between the Przewalski's Horse and the domestic horse was demonstrated by pair-wise genetic distance and MDS. Genotyping of other Perissodactyla (zebras, asses, tapirs, and rhinoceros) was variably successful, with call rates and the number of polymorphic loci varying across taxa. Parsimony analysis placed the modern horse as sister taxa to
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DOI: 10.1371/journal.pgen.1002451
PubMed: 22253606
PubMed Central: 3257288
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Hill</name><affiliation wicri:level="1"><nlm:aff id="aff9"><addr-line>Animal Genomics Laboratory, School of Agriculture and Food Science, University College Dublin, Dublin, Ireland</addr-line></nlm:aff><country xml:lang="fr">Irlande (pays)</country><wicri:regionArea>Animal Genomics Laboratory, School of Agriculture and Food Science, University College Dublin, Dublin</wicri:regionArea></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="aff10"><addr-line>Institute of Genetics, Vetsuisse Faculty, University of Bern, Berne, Switzerland</addr-line></nlm:aff><country xml:lang="fr">Suisse</country><wicri:regionArea>Institute of Genetics, Vetsuisse Faculty, University of Bern, Berne</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="aff11"><addr-line>Department of Animal Breeding and Genetics, Swedish University of Agricultural Sciences, Uppsala, Sweden</addr-line></nlm:aff><country xml:lang="fr">Suède</country><wicri:regionArea>Department of Animal Breeding and Genetics, Swedish University of Agricultural Sciences, Uppsala</wicri:regionArea></affiliation></author><author><name sortKey="Penedo, M Cecilia T" sort="Penedo, M Cecilia T" uniqKey="Penedo M" first="M. 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Ryder</name><affiliation wicri:level="1"><nlm:aff id="aff14"><addr-line>San Diego Zoo's Institute for Conservation Research, Escondido, California, United States of America</addr-line></nlm:aff><country xml:lang="fr">États-Unis</country><wicri:regionArea>San Diego Zoo's Institute for Conservation Research, Escondido, California</wicri:regionArea></affiliation></author><author><name sortKey="Swinburne, June E" sort="Swinburne, June E" uniqKey="Swinburne J" first="June E." last="Swinburne">June E. 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Mccue</name><affiliation wicri:level="1"><nlm:aff id="aff1"><addr-line>College of Veterinary Medicine, University of Minnesota, St. Paul, Minnesota, United States of America</addr-line></nlm:aff><country xml:lang="fr">États-Unis</country><wicri:regionArea>College of Veterinary Medicine, University of Minnesota, St. Paul, Minnesota</wicri:regionArea></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="1"><nlm:aff id="aff2"><addr-line>Department of Population Health and Reproduction, School of Veterinary Medicine, University of California Davis, Davis, California, United States of America</addr-line></nlm:aff><country xml:lang="fr">États-Unis</country><wicri:regionArea>Department of Population Health and Reproduction, School of Veterinary Medicine, University of California Davis, Davis, California</wicri:regionArea></affiliation></author><author><name sortKey="Petersen, Jessica L" sort="Petersen, Jessica L" uniqKey="Petersen J" first="Jessica L." last="Petersen">Jessica L. Petersen</name><affiliation wicri:level="1"><nlm:aff id="aff1"><addr-line>College of Veterinary Medicine, University of Minnesota, St. Paul, Minnesota, United States of America</addr-line></nlm:aff><country xml:lang="fr">États-Unis</country><wicri:regionArea>College of Veterinary Medicine, University of Minnesota, St. Paul, Minnesota</wicri:regionArea></affiliation></author><author><name sortKey="Gurr, Jessica" sort="Gurr, Jessica" uniqKey="Gurr J" first="Jessica" last="Gurr">Jessica Gurr</name><affiliation wicri:level="1"><nlm:aff id="aff3"><addr-line>Faculty of Veterinary Science, University of Sydney, Sydney, Australia</addr-line></nlm:aff><country xml:lang="fr">Australie</country><wicri:regionArea>Faculty of Veterinary Science, University of Sydney, Sydney</wicri:regionArea></affiliation></author><author><name sortKey="Bailey, Ernie" sort="Bailey, Ernie" uniqKey="Bailey E" first="Ernie" last="Bailey">Ernie Bailey</name><affiliation wicri:level="1"><nlm:aff id="aff4"><addr-line>Maxwell H. Gluck Equine Research Center, Department of Veterinary Science, University of Kentucky, Lexington, Kentucky, United States of America</addr-line></nlm:aff><country xml:lang="fr">États-Unis</country><wicri:regionArea>Maxwell H. Gluck Equine Research Center, Department of Veterinary Science, University of Kentucky, Lexington, Kentucky</wicri:regionArea></affiliation></author><author><name sortKey="Binns, Matthew M" sort="Binns, Matthew M" uniqKey="Binns M" first="Matthew M." last="Binns">Matthew M. Binns</name><affiliation wicri:level="1"><nlm:aff id="aff5"><addr-line>Equine Analysis Systems, Midway, Kentucky, United States of America</addr-line></nlm:aff><country xml:lang="fr">États-Unis</country><wicri:regionArea>Equine Analysis Systems, Midway, Kentucky</wicri:regionArea></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="aff6"><addr-line>Institute of Animal Breeding and Genetics, University of Veterinary Medicine Hannover, Hannover, Germany</addr-line></nlm:aff><country xml:lang="fr">Allemagne</country><wicri:regionArea>Institute of Animal Breeding and Genetics, University of Veterinary Medicine Hannover, Hannover</wicri:regionArea></affiliation></author><author><name sortKey="Guerin, Gerard" sort="Guerin, Gerard" uniqKey="Guerin G" first="Gérard" last="Guérin">Gérard Guérin</name><affiliation wicri:level="1"><nlm:aff id="aff7"><addr-line>INRA, UMR 1313, Génétique Animale et Biologie Intégrative, Biologie Intégrative et Génétique Equine, Jouy-en-Josas, France</addr-line></nlm:aff><country xml:lang="fr">France</country><wicri:regionArea>INRA, UMR 1313, Génétique Animale et Biologie Intégrative, Biologie Intégrative et Génétique Equine, Jouy-en-Josas</wicri:regionArea></affiliation></author><author><name sortKey="Hasegawa, Telhisa" sort="Hasegawa, Telhisa" uniqKey="Hasegawa T" first="Telhisa" last="Hasegawa">Telhisa Hasegawa</name><affiliation wicri:level="1"><nlm:aff id="aff8"><addr-line>Equine Research Institute, Japan Racing Association, Utsunomiya, Japan</addr-line></nlm:aff><country xml:lang="fr">Japon</country><wicri:regionArea>Equine Research Institute, Japan Racing Association, Utsunomiya</wicri:regionArea></affiliation></author><author><name sortKey="Hill, Emmeline W" sort="Hill, Emmeline W" uniqKey="Hill E" first="Emmeline W." last="Hill">Emmeline W. Hill</name><affiliation wicri:level="1"><nlm:aff id="aff9"><addr-line>Animal Genomics Laboratory, School of Agriculture and Food Science, University College Dublin, Dublin, Ireland</addr-line></nlm:aff><country xml:lang="fr">Irlande (pays)</country><wicri:regionArea>Animal Genomics Laboratory, School of Agriculture and Food Science, University College Dublin, Dublin</wicri:regionArea></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="aff10"><addr-line>Institute of Genetics, Vetsuisse Faculty, University of Bern, Berne, Switzerland</addr-line></nlm:aff><country xml:lang="fr">Suisse</country><wicri:regionArea>Institute of Genetics, Vetsuisse Faculty, University of Bern, Berne</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="aff11"><addr-line>Department of Animal Breeding and Genetics, Swedish University of Agricultural Sciences, Uppsala, Sweden</addr-line></nlm:aff><country xml:lang="fr">Suède</country><wicri:regionArea>Department of Animal Breeding and Genetics, Swedish University of Agricultural Sciences, Uppsala</wicri:regionArea></affiliation></author><author><name sortKey="Penedo, M Cecilia T" sort="Penedo, M Cecilia T" uniqKey="Penedo M" first="M. Cecilia T." last="Penedo">M. Cecilia T. Penedo</name><affiliation wicri:level="1"><nlm:aff id="aff12"><addr-line>Veterinary Genetics Laboratory, University of California Davis, Davis, California, United States of America</addr-line></nlm:aff><country xml:lang="fr">États-Unis</country><wicri:regionArea>Veterinary Genetics Laboratory, University of California Davis, Davis, California</wicri:regionArea></affiliation></author><author><name sortKey="R Ed, Knut H" sort="R Ed, Knut H" uniqKey="R Ed K" first="Knut H." last="R Ed">Knut H. R Ed</name><affiliation wicri:level="1"><nlm:aff id="aff13"><addr-line>Department of Basic Sciences and Aquatic Medicine, Norwegian School of Veterinary Science, Oslo, Norway</addr-line></nlm:aff><country xml:lang="fr">Norvège</country><wicri:regionArea>Department of Basic Sciences and Aquatic Medicine, Norwegian School of Veterinary Science, Oslo</wicri:regionArea></affiliation></author><author><name sortKey="Ryder, Oliver A" sort="Ryder, Oliver A" uniqKey="Ryder O" first="Oliver A." last="Ryder">Oliver A. Ryder</name><affiliation wicri:level="1"><nlm:aff id="aff14"><addr-line>San Diego Zoo's Institute for Conservation Research, Escondido, California, United States of America</addr-line></nlm:aff><country xml:lang="fr">États-Unis</country><wicri:regionArea>San Diego Zoo's Institute for Conservation Research, Escondido, California</wicri:regionArea></affiliation></author><author><name sortKey="Swinburne, June E" sort="Swinburne, June E" uniqKey="Swinburne J" first="June E." last="Swinburne">June E. Swinburne</name><affiliation wicri:level="1"><nlm:aff id="aff15"><addr-line>Animal Health Trust, Suffolk, United Kingdom</addr-line></nlm:aff><country xml:lang="fr">Royaume-Uni</country><wicri:regionArea>Animal Health Trust, Suffolk</wicri:regionArea></affiliation></author><author><name sortKey="Tozaki, Teruaki" sort="Tozaki, Teruaki" uniqKey="Tozaki T" first="Teruaki" last="Tozaki">Teruaki Tozaki</name><affiliation wicri:level="1"><nlm:aff id="aff16"><addr-line>Department of Molecular Genetics, Laboratory of Racing Chemistry, Utsunomiya, Japan</addr-line></nlm:aff><country xml:lang="fr">Japon</country><wicri:regionArea>Department of Molecular Genetics, Laboratory of Racing Chemistry, Utsunomiya</wicri:regionArea></affiliation></author><author><name sortKey="Valberg, Stephanie J" sort="Valberg, Stephanie J" uniqKey="Valberg S" first="Stephanie J." last="Valberg">Stephanie J. Valberg</name><affiliation wicri:level="1"><nlm:aff id="aff1"><addr-line>College of Veterinary Medicine, University of Minnesota, St. Paul, Minnesota, United States of America</addr-line></nlm:aff><country xml:lang="fr">États-Unis</country><wicri:regionArea>College of Veterinary Medicine, University of Minnesota, St. Paul, Minnesota</wicri:regionArea></affiliation></author><author><name sortKey="Vaudin, Mark" sort="Vaudin, Mark" uniqKey="Vaudin M" first="Mark" last="Vaudin">Mark Vaudin</name><affiliation wicri:level="1"><nlm:aff id="aff15"><addr-line>Animal Health Trust, Suffolk, United Kingdom</addr-line></nlm:aff><country xml:lang="fr">Royaume-Uni</country><wicri:regionArea>Animal Health Trust, Suffolk</wicri:regionArea></affiliation></author><author><name sortKey="Lindblad Toh, Kerstin" sort="Lindblad Toh, Kerstin" uniqKey="Lindblad Toh K" first="Kerstin" last="Lindblad-Toh">Kerstin Lindblad-Toh</name><affiliation wicri:level="1"><nlm:aff id="aff17"><addr-line>Science for Life Laboratory, Department of Medical Biochemistry and Microbiology, Uppsala University, Uppsala, Sweden</addr-line></nlm:aff><country xml:lang="fr">Suède</country><wicri:regionArea>Science for Life Laboratory, Department of Medical Biochemistry and Microbiology, Uppsala University, Uppsala</wicri:regionArea></affiliation><affiliation wicri:level="1"><nlm:aff id="aff18"><addr-line>Broad Institute, Cambridge, Massachusetts, United States of America</addr-line></nlm:aff><country xml:lang="fr">États-Unis</country><wicri:regionArea>Broad Institute, Cambridge, Massachusetts</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 wicri:level="1"><nlm:aff id="aff3"><addr-line>Faculty of Veterinary Science, University of Sydney, Sydney, Australia</addr-line></nlm:aff><country xml:lang="fr">Australie</country><wicri:regionArea>Faculty of Veterinary Science, University of Sydney, Sydney</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="1"><nlm:aff id="aff1"><addr-line>College of Veterinary Medicine, University of Minnesota, St. Paul, Minnesota, United States of America</addr-line></nlm:aff><country xml:lang="fr">États-Unis</country><wicri:regionArea>College of Veterinary Medicine, University of Minnesota, St. Paul, Minnesota</wicri:regionArea></affiliation></author></analytic><series><title level="j">PLoS Genetics</title><idno type="ISSN">1553-7390</idno><idno type="eISSN">1553-7404</idno><imprint><date when="2012">2012</date></imprint></series></biblStruct></sourceDesc></fileDesc><profileDesc><textClass></textClass></profileDesc></teiHeader><front><div type="abstract" xml:lang="en"><p>An equine SNP genotyping array was developed and evaluated on a panel of samples representing 14 domestic horse breeds and 18 evolutionarily related species. More than 54,000 polymorphic SNPs provided an average inter-SNP spacing of ∼43 kb. The mean minor allele frequency across domestic horse breeds was 0.23, and the number of polymorphic SNPs within breeds ranged from 43,287 to 52,085. Genome-wide linkage disequilibrium (LD) in most breeds declined rapidly over the first 50–100 kb and reached background levels within 1–2 Mb. The extent of LD and the level of inbreeding were highest in the Thoroughbred and lowest in the Mongolian and Quarter Horse. Multidimensional scaling (MDS) analyses demonstrated the tight grouping of individuals within most breeds, close proximity of related breeds, and less tight grouping in admixed breeds. The close relationship between the Przewalski's Horse and the domestic horse was demonstrated by pair-wise genetic distance and MDS. Genotyping of other Perissodactyla (zebras, asses, tapirs, and rhinoceros) was variably successful, with call rates and the number of polymorphic loci varying across taxa. Parsimony analysis placed the modern horse as sister taxa to <italic>Equus przewalski</italic>. The utility of the SNP array in genome-wide association was confirmed by mapping the known recessive chestnut coat color locus (<italic>MC1R</italic>) and defining a conserved haplotype of ∼750 kb across all breeds. These results demonstrate the high quality of this SNP genotyping resource, its usefulness in diverse genome analyses of the horse, and potential use in related species.</p></div></front><back><div1 type="bibliography"><listBibl><biblStruct><analytic><author><name sortKey="Olsen, So" uniqKey="Olsen S">SO Olsen</name></author></analytic></biblStruct><biblStruct><analytic><author><name sortKey="Hendricks, B" uniqKey="Hendricks B">B Hendricks</name></author></analytic></biblStruct><biblStruct><analytic><author><name sortKey="Wade, Cm" uniqKey="Wade C">CM Wade</name></author><author><name sortKey="Giulotto, E" uniqKey="Giulotto E">E Giulotto</name></author><author><name sortKey="Sigurdsson, S" uniqKey="Sigurdsson S">S Sigurdsson</name></author><author><name sortKey="Zoli, M" uniqKey="Zoli M">M Zoli</name></author><author><name sortKey="Gnerre, S" uniqKey="Gnerre S">S Gnerre</name></author></analytic></biblStruct><biblStruct><analytic><author><name sortKey="Price, Sa" uniqKey="Price S">SA 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article-type="research-article"><pmc-dir>properties open_access</pmc-dir>
<front><journal-meta><journal-id journal-id-type="nlm-ta">PLoS Genet</journal-id><journal-id journal-id-type="iso-abbrev">PLoS Genet</journal-id><journal-id journal-id-type="publisher-id">plos</journal-id><journal-id journal-id-type="pmc">plosgen</journal-id><journal-title-group><journal-title>PLoS Genetics</journal-title></journal-title-group><issn pub-type="ppub">1553-7390</issn><issn pub-type="epub">1553-7404</issn><publisher><publisher-name>Public Library of Science</publisher-name><publisher-loc>San Francisco, USA</publisher-loc></publisher></journal-meta><article-meta><article-id pub-id-type="pmid">22253606</article-id><article-id pub-id-type="pmc">3257288</article-id><article-id pub-id-type="publisher-id">PGENETICS-D-10-00603</article-id><article-id pub-id-type="doi">10.1371/journal.pgen.1002451</article-id><article-categories><subj-group subj-group-type="heading"><subject>Research Article</subject></subj-group><subj-group subj-group-type="Discipline-v2"><subject>Agriculture</subject></subj-group><subj-group subj-group-type="Discipline-v2"><subject>Biology</subject><subj-group><subject>Genetics</subject></subj-group><subj-group><subject>Genomics</subject></subj-group><subj-group><subject>Population Biology</subject></subj-group></subj-group><subj-group subj-group-type="Discipline-v2"><subject>Veterinary Science</subject><subj-group><subject>Animal Types</subject></subj-group></subj-group></article-categories><title-group><article-title>A High Density SNP Array for the Domestic Horse and Extant Perissodactyla: Utility for Association Mapping, Genetic Diversity, and Phylogeny Studies</article-title><alt-title alt-title-type="running-head">Development and Use of an Equine SNP Array</alt-title></title-group><contrib-group><contrib contrib-type="author"><name><surname>McCue</surname><given-names>Molly E.</given-names></name><xref ref-type="aff" rid="aff1"><sup>1</sup></xref><xref ref-type="corresp" rid="cor1"><sup>*</sup></xref></contrib><contrib contrib-type="author"><name><surname>Bannasch</surname><given-names>Danika L.</given-names></name><xref ref-type="aff" rid="aff2"><sup>2</sup></xref></contrib><contrib contrib-type="author"><name><surname>Petersen</surname><given-names>Jessica L.</given-names></name><xref ref-type="aff" rid="aff1"><sup>1</sup></xref></contrib><contrib contrib-type="author"><name><surname>Gurr</surname><given-names>Jessica</given-names></name><xref ref-type="aff" rid="aff3"><sup>3</sup></xref></contrib><contrib contrib-type="author"><name><surname>Bailey</surname><given-names>Ernie</given-names></name><xref ref-type="aff" rid="aff4"><sup>4</sup></xref></contrib><contrib contrib-type="author"><name><surname>Binns</surname><given-names>Matthew M.</given-names></name><xref ref-type="aff" rid="aff5"><sup>5</sup></xref></contrib><contrib contrib-type="author"><name><surname>Distl</surname><given-names>Ottmar</given-names></name><xref ref-type="aff" rid="aff6"><sup>6</sup></xref></contrib><contrib contrib-type="author"><name><surname>Guérin</surname><given-names>Gérard</given-names></name><xref ref-type="aff" rid="aff7"><sup>7</sup></xref></contrib><contrib contrib-type="author"><name><surname>Hasegawa</surname><given-names>Telhisa</given-names></name><xref ref-type="aff" rid="aff8"><sup>8</sup></xref></contrib><contrib contrib-type="author"><name><surname>Hill</surname><given-names>Emmeline W.</given-names></name><xref ref-type="aff" rid="aff9"><sup>9</sup></xref></contrib><contrib contrib-type="author"><name><surname>Leeb</surname><given-names>Tosso</given-names></name><xref ref-type="aff" rid="aff10"><sup>10</sup></xref></contrib><contrib contrib-type="author"><name><surname>Lindgren</surname><given-names>Gabriella</given-names></name><xref ref-type="aff" rid="aff11"><sup>11</sup></xref></contrib><contrib contrib-type="author"><name><surname>Penedo</surname><given-names>M. Cecilia T.</given-names></name><xref ref-type="aff" rid="aff12"><sup>12</sup></xref></contrib><contrib contrib-type="author"><name><surname>Røed</surname><given-names>Knut H.</given-names></name><xref ref-type="aff" rid="aff13"><sup>13</sup></xref></contrib><contrib contrib-type="author"><name><surname>Ryder</surname><given-names>Oliver A.</given-names></name><xref ref-type="aff" rid="aff14"><sup>14</sup></xref></contrib><contrib contrib-type="author"><name><surname>Swinburne</surname><given-names>June E.</given-names></name><xref ref-type="aff" rid="aff15"><sup>15</sup></xref></contrib><contrib contrib-type="author"><name><surname>Tozaki</surname><given-names>Teruaki</given-names></name><xref ref-type="aff" rid="aff16"><sup>16</sup></xref></contrib><contrib contrib-type="author"><name><surname>Valberg</surname><given-names>Stephanie J.</given-names></name><xref ref-type="aff" rid="aff1"><sup>1</sup></xref></contrib><contrib contrib-type="author"><name><surname>Vaudin</surname><given-names>Mark</given-names></name><xref ref-type="aff" rid="aff15"><sup>15</sup></xref></contrib><contrib contrib-type="author"><name><surname>Lindblad-Toh</surname><given-names>Kerstin</given-names></name><xref ref-type="aff" rid="aff17"><sup>17</sup></xref><xref ref-type="aff" rid="aff18"><sup>18</sup></xref></contrib><contrib contrib-type="author" equal-contrib="yes"><name><surname>Wade</surname><given-names>Claire M.</given-names></name><xref ref-type="aff" rid="aff3"><sup>3</sup></xref></contrib><contrib contrib-type="author" equal-contrib="yes"><name><surname>Mickelson</surname><given-names>James R.</given-names></name><xref ref-type="aff" rid="aff1"><sup>1</sup></xref></contrib></contrib-group><aff id="aff1"><label>1</label><addr-line>College of Veterinary Medicine, University of Minnesota, St. Paul, Minnesota, United States of America</addr-line></aff><aff id="aff2"><label>2</label><addr-line>Department of Population Health and Reproduction, School of Veterinary Medicine, University of California Davis, Davis, California, United States of America</addr-line></aff><aff id="aff3"><label>3</label><addr-line>Faculty of Veterinary Science, University of Sydney, Sydney, Australia</addr-line></aff><aff id="aff4"><label>4</label><addr-line>Maxwell H. Gluck Equine Research Center, Department of Veterinary Science, University of Kentucky, Lexington, Kentucky, United States of America</addr-line></aff><aff id="aff5"><label>5</label><addr-line>Equine Analysis Systems, Midway, Kentucky, United States of America</addr-line></aff><aff id="aff6"><label>6</label><addr-line>Institute of Animal Breeding and Genetics, University of Veterinary Medicine Hannover, Hannover, Germany</addr-line></aff><aff id="aff7"><label>7</label><addr-line>INRA, UMR 1313, Génétique Animale et Biologie Intégrative, Biologie Intégrative et Génétique Equine, Jouy-en-Josas, France</addr-line></aff><aff id="aff8"><label>8</label><addr-line>Equine Research Institute, Japan Racing Association, Utsunomiya, Japan</addr-line></aff><aff id="aff9"><label>9</label><addr-line>Animal Genomics Laboratory, School of Agriculture and Food Science, University College Dublin, Dublin, Ireland</addr-line></aff><aff id="aff10"><label>10</label><addr-line>Institute of Genetics, Vetsuisse Faculty, University of Bern, Berne, Switzerland</addr-line></aff><aff id="aff11"><label>11</label><addr-line>Department of Animal Breeding and Genetics, Swedish University of Agricultural Sciences, Uppsala, Sweden</addr-line></aff><aff id="aff12"><label>12</label><addr-line>Veterinary Genetics Laboratory, University of California Davis, Davis, California, United States of America</addr-line></aff><aff id="aff13"><label>13</label><addr-line>Department of Basic Sciences and Aquatic Medicine, Norwegian School of Veterinary Science, Oslo, Norway</addr-line></aff><aff id="aff14"><label>14</label><addr-line>San Diego Zoo's Institute for Conservation Research, Escondido, California, United States of America</addr-line></aff><aff id="aff15"><label>15</label><addr-line>Animal Health Trust, Suffolk, United Kingdom</addr-line></aff><aff id="aff16"><label>16</label><addr-line>Department of Molecular Genetics, Laboratory of Racing Chemistry, Utsunomiya, Japan</addr-line></aff><aff id="aff17"><label>17</label><addr-line>Science for Life Laboratory, Department of Medical Biochemistry and Microbiology, Uppsala University, Uppsala, Sweden</addr-line></aff><aff id="aff18"><label>18</label><addr-line>Broad Institute, Cambridge, Massachusetts, United States of America</addr-line></aff><contrib-group><contrib contrib-type="editor"><name><surname>Georges</surname><given-names>Michel</given-names></name><role>Editor</role><xref ref-type="aff" rid="edit1"></xref></contrib></contrib-group><aff id="edit1">University of Liège, Belgium</aff><author-notes><corresp id="cor1">* E-mail: <email>mccu0173@umn.edu</email></corresp><fn fn-type="con"><p>Conceived and designed the experiments: MEM DLB MMB KL-T CMW JRM OAR. Analyzed the data: MEM JLP JG DLB CMW. Contributed reagents/materials/analysis tools: EB MMB OD GG TH EWH TL GL MCTP KHR OAR JES TT SJV MV. Wrote the paper: MEM JLP JRM.</p></fn></author-notes><pub-date pub-type="collection"><month>1</month><year>2012</year></pub-date><pub-date pub-type="epub"><day>12</day><month>1</month><year>2012</year></pub-date><volume>8</volume><issue>1</issue><elocation-id>e1002451</elocation-id><history><date date-type="received"><day>22</day><month>12</month><year>2010</year></date><date date-type="accepted"><day>21</day><month>11</month><year>2011</year></date></history><permissions><copyright-statement>McCue et al.</copyright-statement><copyright-year>2012</copyright-year><license xlink:href="http://creativecommons.org/licenses/by/4.0/"><license-p>This is an open-access article distributed under the terms of the Creative Commons Attribution License, which permits unrestricted use, distribution, and reproduction in any medium, provided the original author and source are properly credited.</license-p></license></permissions><abstract><p>An equine SNP genotyping array was developed and evaluated on a panel of samples representing 14 domestic horse breeds and 18 evolutionarily related species. More than 54,000 polymorphic SNPs provided an average inter-SNP spacing of ∼43 kb. The mean minor allele frequency across domestic horse breeds was 0.23, and the number of polymorphic SNPs within breeds ranged from 43,287 to 52,085. Genome-wide linkage disequilibrium (LD) in most breeds declined rapidly over the first 50–100 kb and reached background levels within 1–2 Mb. The extent of LD and the level of inbreeding were highest in the Thoroughbred and lowest in the Mongolian and Quarter Horse. Multidimensional scaling (MDS) analyses demonstrated the tight grouping of individuals within most breeds, close proximity of related breeds, and less tight grouping in admixed breeds. The close relationship between the Przewalski's Horse and the domestic horse was demonstrated by pair-wise genetic distance and MDS. Genotyping of other Perissodactyla (zebras, asses, tapirs, and rhinoceros) was variably successful, with call rates and the number of polymorphic loci varying across taxa. Parsimony analysis placed the modern horse as sister taxa to <italic>Equus przewalski</italic>. The utility of the SNP array in genome-wide association was confirmed by mapping the known recessive chestnut coat color locus (<italic>MC1R</italic>) and defining a conserved haplotype of ∼750 kb across all breeds. These results demonstrate the high quality of this SNP genotyping resource, its usefulness in diverse genome analyses of the horse, and potential use in related species.</p></abstract><abstract abstract-type="summary"><title>Author Summary</title><p>We utilized the previously generated horse genome sequence and a large SNP database to design an ∼54,000 SNP assay for use in the domestic horse and related species. The utility of this SNP array was demonstrated through genome-wide linkage disequilibrium, inbreeding and genetic distance measurements within breeds, as well as multidimensional scaling and parsimony analysis. Association mapping confirmed a large conserved segment containing the chestnut coat color locus in domestic horses. We also assess the utility of the SNP array in related species, including the Przewalski's Horse, zebras, asses, tapirs, and rhinoceros. This SNP genotyping tool will facilitate many genetics applications in equids, including identification of genes for health and performance traits, and compelling studies of the origins of the domestic horse, diversity within breeds, and evolutionary relationships among related species.</p></abstract><counts><page-count count="14"></page-count></counts></article-meta></front></pmc></record>Pour manipuler ce document sous Unix (Dilib)
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