Design of a Bovine Low-Density SNP Array Optimized for Imputation
Identifieur interne : 002856 ( Pmc/Curation ); précédent : 002855; suivant : 002857Design of a Bovine Low-Density SNP Array Optimized for Imputation
Auteurs : Didier Boichard [France] ; Hoyoung Chung [Corée du Sud, États-Unis] ; Romain Dassonneville [France] ; Xavier David [France] ; André Eggen [États-Unis] ; Sébastien Fritz [France] ; Kimberly J. Gietzen [États-Unis] ; Ben J. Hayes [Australie] ; Cynthia T. Lawley [États-Unis] ; Tad S. Sonstegard [États-Unis] ; Curtis P. Van Tassell [États-Unis] ; Paul M. Vanraden [États-Unis] ; Karine A. Viaud-Martinez [États-Unis] ; George R. Wiggans [États-Unis]Source :
- PLoS ONE [ 1932-6203 ] ; 2012.
Abstract
The Illumina BovineLD BeadChip was designed to support imputation to higher density genotypes in dairy and beef breeds by including single-nucleotide polymorphisms (SNPs) that had a high minor allele frequency as well as uniform spacing across the genome except at the ends of the chromosome where densities were increased. The chip also includes SNPs on the Y chromosome and mitochondrial DNA loci that are useful for determining subspecies classification and certain paternal and maternal breed lineages. The total number of SNPs was 6,909. Accuracy of imputation to Illumina BovineSNP50 genotypes using the BovineLD chip was over 97% for most dairy and beef populations. The BovineLD imputations were about 3 percentage points more accurate than those from the Illumina GoldenGate Bovine3K BeadChip across multiple populations. The improvement was greatest when neither parent was genotyped. The minor allele frequencies were similar across taurine beef and dairy breeds as was the proportion of SNPs that were polymorphic. The new BovineLD chip should facilitate low-cost genomic selection in taurine beef and dairy cattle.
Url:
DOI: 10.1371/journal.pone.0034130
PubMed: 22470530
PubMed Central: 3314603
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wicri:level="1"><nlm:aff id="aff2"><addr-line>Animal Genetic Improvement Division, National Institute of Animal Science, Seonghwan, Cheonan, Republic of Korea</addr-line></nlm:aff><country xml:lang="fr">Corée du Sud</country><wicri:regionArea>Animal Genetic Improvement Division, National Institute of Animal Science, Seonghwan, Cheonan</wicri:regionArea></affiliation><affiliation wicri:level="1"><nlm:aff id="aff3"><addr-line>Bovine Functional Genomics Laboratory, Agricultural Research Service, United States Department of Agriculture, Beltsville, Maryland, United States of America</addr-line></nlm:aff><country xml:lang="fr">États-Unis</country><wicri:regionArea>Bovine Functional Genomics Laboratory, Agricultural Research Service, United States Department of Agriculture, Beltsville, Maryland</wicri:regionArea></affiliation></author><author><name sortKey="Dassonneville, Romain" sort="Dassonneville, Romain" uniqKey="Dassonneville R" first="Romain" last="Dassonneville">Romain Dassonneville</name><affiliation wicri:level="1"><nlm:aff id="aff1"><addr-line>UMR1313 Animal Genetics and Integrative Biology, National Institute for Agricultural Research (INRA), Jouy-en-Josas, France</addr-line></nlm:aff><country xml:lang="fr">France</country><wicri:regionArea>UMR1313 Animal Genetics and Integrative Biology, National Institute for Agricultural Research (INRA), Jouy-en-Josas</wicri:regionArea></affiliation><affiliation wicri:level="1"><nlm:aff id="aff4"><addr-line>Institut de l'Elevage, Paris, France</addr-line></nlm:aff><country xml:lang="fr">France</country><wicri:regionArea>Institut de l'Elevage, Paris</wicri:regionArea></affiliation></author><author><name sortKey="David, Xavier" sort="David, Xavier" uniqKey="David X" first="Xavier" last="David">Xavier David</name><affiliation wicri:level="1"><nlm:aff id="aff5"><addr-line>National Association of Livestock and Artificial Insemination Cooperatives (UNCEIA), Paris, France</addr-line></nlm:aff><country 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Insemination Cooperatives (UNCEIA), Paris</wicri:regionArea></affiliation></author><author><name sortKey="Gietzen, Kimberly J" sort="Gietzen, Kimberly J" uniqKey="Gietzen K" first="Kimberly J." last="Gietzen">Kimberly J. 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Hayes</name><affiliation wicri:level="1"><nlm:aff id="aff7"><addr-line>Biosciences Research Division, Department of Primary Industries Victoria, Melbourne, Victoria, Australia</addr-line></nlm:aff><country xml:lang="fr">Australie</country><wicri:regionArea>Biosciences Research Division, Department of Primary Industries Victoria, Melbourne, Victoria</wicri:regionArea></affiliation><affiliation wicri:level="1"><nlm:aff id="aff8"><addr-line>Dairy Futures Cooperative Research Centre, Bundoora, Victoria, Australia</addr-line></nlm:aff><country xml:lang="fr">Australie</country><wicri:regionArea>Dairy Futures Cooperative Research Centre, Bundoora, Victoria</wicri:regionArea></affiliation><affiliation wicri:level="1"><nlm:aff id="aff9"><addr-line>La Trobe University, Bundoora, Victoria, Australia</addr-line></nlm:aff><country xml:lang="fr">Australie</country><wicri:regionArea>La Trobe University, Bundoora, Victoria</wicri:regionArea></affiliation></author><author><name sortKey="Lawley, Cynthia T" sort="Lawley, Cynthia T" uniqKey="Lawley C" first="Cynthia T." last="Lawley">Cynthia T. 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Sonstegard</name><affiliation wicri:level="1"><nlm:aff id="aff3"><addr-line>Bovine Functional Genomics Laboratory, Agricultural Research Service, United States Department of Agriculture, Beltsville, Maryland, United States of America</addr-line></nlm:aff><country xml:lang="fr">États-Unis</country><wicri:regionArea>Bovine Functional Genomics Laboratory, Agricultural Research Service, United States Department of Agriculture, Beltsville, Maryland</wicri:regionArea></affiliation></author><author><name sortKey="Van Tassell, Curtis P" sort="Van Tassell, Curtis P" uniqKey="Van Tassell C" first="Curtis P." last="Van Tassell">Curtis P. Van Tassell</name><affiliation wicri:level="1"><nlm:aff id="aff3"><addr-line>Bovine Functional Genomics Laboratory, Agricultural Research Service, United States Department of Agriculture, Beltsville, Maryland, United States of America</addr-line></nlm:aff><country xml:lang="fr">États-Unis</country><wicri:regionArea>Bovine Functional Genomics Laboratory, Agricultural Research Service, United States Department of Agriculture, Beltsville, Maryland</wicri:regionArea></affiliation></author><author><name sortKey="Vanraden, Paul M" sort="Vanraden, Paul M" uniqKey="Vanraden P" first="Paul M." last="Vanraden">Paul M. Vanraden</name><affiliation wicri:level="1"><nlm:aff id="aff10"><addr-line>Animal Improvement Programs Laboratory, Agricultural Research Service, United States Department of Agriculture, Beltsville, Maryland, United States of America</addr-line></nlm:aff><country xml:lang="fr">États-Unis</country><wicri:regionArea>Animal Improvement Programs Laboratory, Agricultural Research Service, United States Department of Agriculture, Beltsville, Maryland</wicri:regionArea></affiliation></author><author><name sortKey="Viaud Martinez, Karine A" sort="Viaud Martinez, Karine A" uniqKey="Viaud Martinez K" first="Karine A." last="Viaud-Martinez">Karine A. Viaud-Martinez</name><affiliation wicri:level="1"><nlm:aff id="aff6"><addr-line>Illumina, San Diego, California, United States of America</addr-line></nlm:aff><country xml:lang="fr">États-Unis</country><wicri:regionArea>Illumina, San Diego, California</wicri:regionArea></affiliation></author><author><name sortKey="Wiggans, George R" sort="Wiggans, George R" uniqKey="Wiggans G" first="George R." last="Wiggans">George R. Wiggans</name><affiliation wicri:level="1"><nlm:aff id="aff10"><addr-line>Animal Improvement Programs Laboratory, Agricultural Research Service, United States Department of Agriculture, Beltsville, Maryland, United States of America</addr-line></nlm:aff><country xml:lang="fr">États-Unis</country><wicri:regionArea>Animal Improvement Programs Laboratory, Agricultural Research Service, United States Department of Agriculture, Beltsville, Maryland</wicri:regionArea></affiliation></author></analytic><series><title level="j">PLoS ONE</title><idno type="eISSN">1932-6203</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>The Illumina BovineLD BeadChip was designed to support imputation to higher density genotypes in dairy and beef breeds by including single-nucleotide polymorphisms (SNPs) that had a high minor allele frequency as well as uniform spacing across the genome except at the ends of the chromosome where densities were increased. The chip also includes SNPs on the Y chromosome and mitochondrial DNA loci that are useful for determining subspecies classification and certain paternal and maternal breed lineages. The total number of SNPs was 6,909. Accuracy of imputation to Illumina BovineSNP50 genotypes using the BovineLD chip was over 97% for most dairy and beef populations. The BovineLD imputations were about 3 percentage points more accurate than those from the Illumina GoldenGate Bovine3K BeadChip across multiple populations. The improvement was greatest when neither parent was genotyped. The minor allele frequencies were similar across taurine beef and dairy breeds as was the proportion of SNPs that were polymorphic. The new BovineLD chip should facilitate low-cost genomic selection in taurine beef and dairy cattle.</p></div></front><back><div1 type="bibliography"><listBibl><biblStruct><analytic><author><name sortKey="Meuwissen, The" uniqKey="Meuwissen T">THE Meuwissen</name></author><author><name sortKey="Hayes, Bj" uniqKey="Hayes B">BJ Hayes</name></author><author><name sortKey="Goddard, Me" uniqKey="Goddard M">ME Goddard</name></author></analytic></biblStruct><biblStruct><analytic><author><name sortKey="Heffner, El" uniqKey="Heffner E">EL Heffner</name></author><author><name sortKey="Jannink, Jl" uniqKey="Jannink J">JL Jannink</name></author><author><name sortKey="Sorrells, Me" uniqKey="Sorrells M">ME Sorrells</name></author></analytic></biblStruct><biblStruct><analytic><author><name sortKey="Wiggans, Gr" uniqKey="Wiggans G">GR Wiggans</name></author><author><name sortKey="Vanraden, Pm" uniqKey="Vanraden P">PM VanRaden</name></author><author><name sortKey="Cooper, Ta" uniqKey="Cooper T">TA 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<front><journal-meta><journal-id journal-id-type="nlm-ta">PLoS One</journal-id><journal-id journal-id-type="iso-abbrev">PLoS ONE</journal-id><journal-id journal-id-type="publisher-id">plos</journal-id><journal-id journal-id-type="pmc">plosone</journal-id><journal-title-group><journal-title>PLoS ONE</journal-title></journal-title-group><issn pub-type="epub">1932-6203</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">22470530</article-id><article-id pub-id-type="pmc">3314603</article-id><article-id pub-id-type="publisher-id">PONE-D-11-24812</article-id><article-id pub-id-type="doi">10.1371/journal.pone.0034130</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><subject>Agricultural Biotechnology</subject></subj-group><subj-group><subject>Agricultural Production</subject></subj-group><subj-group><subject>Animal Management</subject></subj-group></subj-group><subj-group subj-group-type="Discipline-v2"><subject>Biology</subject><subj-group><subject>Computational Biology</subject><subj-group><subject>Genomics</subject></subj-group></subj-group><subj-group><subject>Genetics</subject><subj-group><subject>Population Genetics</subject></subj-group></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>Design of a Bovine Low-Density SNP Array Optimized for Imputation</article-title><alt-title alt-title-type="running-head">Bovine SNP Array for Accurate Imputation</alt-title></title-group><contrib-group><contrib contrib-type="author"><name><surname>Boichard</surname><given-names>Didier</given-names></name><xref ref-type="aff" rid="aff1"><sup>1</sup></xref></contrib><contrib contrib-type="author"><name><surname>Chung</surname><given-names>Hoyoung</given-names></name><xref ref-type="aff" rid="aff2"><sup>2</sup></xref><xref ref-type="aff" rid="aff3"><sup>3</sup></xref></contrib><contrib contrib-type="author"><name><surname>Dassonneville</surname><given-names>Romain</given-names></name><xref ref-type="aff" rid="aff1"><sup>1</sup></xref><xref ref-type="aff" rid="aff4"><sup>4</sup></xref></contrib><contrib contrib-type="author"><name><surname>David</surname><given-names>Xavier</given-names></name><xref ref-type="aff" rid="aff5"><sup>5</sup></xref></contrib><contrib contrib-type="author"><name><surname>Eggen</surname><given-names>André</given-names></name><xref ref-type="aff" rid="aff6"><sup>6</sup></xref></contrib><contrib contrib-type="author"><name><surname>Fritz</surname><given-names>Sébastien</given-names></name><xref ref-type="aff" rid="aff5"><sup>5</sup></xref></contrib><contrib contrib-type="author"><name><surname>Gietzen</surname><given-names>Kimberly J.</given-names></name><xref ref-type="aff" rid="aff6"><sup>6</sup></xref></contrib><contrib contrib-type="author"><name><surname>Hayes</surname><given-names>Ben J.</given-names></name><xref ref-type="aff" rid="aff7"><sup>7</sup></xref><xref ref-type="aff" rid="aff8"><sup>8</sup></xref><xref ref-type="aff" rid="aff9"><sup>9</sup></xref><xref ref-type="corresp" rid="cor1"><sup>*</sup></xref></contrib><contrib contrib-type="author"><name><surname>Lawley</surname><given-names>Cynthia T.</given-names></name><xref ref-type="aff" rid="aff6"><sup>6</sup></xref></contrib><contrib contrib-type="author"><name><surname>Sonstegard</surname><given-names>Tad S.</given-names></name><xref ref-type="aff" rid="aff3"><sup>3</sup></xref></contrib><contrib contrib-type="author"><name><surname>Van Tassell</surname><given-names>Curtis P.</given-names></name><xref ref-type="aff" rid="aff3"><sup>3</sup></xref></contrib><contrib contrib-type="author"><name><surname>VanRaden</surname><given-names>Paul M.</given-names></name><xref ref-type="aff" rid="aff10"><sup>10</sup></xref></contrib><contrib contrib-type="author"><name><surname>Viaud-Martinez</surname><given-names>Karine A.</given-names></name><xref ref-type="aff" rid="aff6"><sup>6</sup></xref></contrib><contrib contrib-type="author"><name><surname>Wiggans</surname><given-names>George R.</given-names></name><xref ref-type="aff" rid="aff10"><sup>10</sup></xref></contrib><contrib contrib-type="author"><collab>for the Bovine LD Consortium</collab></contrib></contrib-group><aff id="aff1"><label>1</label><addr-line>UMR1313 Animal Genetics and Integrative Biology, National Institute for Agricultural Research (INRA), Jouy-en-Josas, France</addr-line></aff><aff id="aff2"><label>2</label><addr-line>Animal Genetic Improvement Division, National Institute of Animal Science, Seonghwan, Cheonan, Republic of Korea</addr-line></aff><aff id="aff3"><label>3</label><addr-line>Bovine Functional Genomics Laboratory, Agricultural Research Service, United States Department of Agriculture, Beltsville, Maryland, United States of America</addr-line></aff><aff id="aff4"><label>4</label><addr-line>Institut de l'Elevage, Paris, France</addr-line></aff><aff id="aff5"><label>5</label><addr-line>National Association of Livestock and Artificial Insemination Cooperatives (UNCEIA), Paris, France</addr-line></aff><aff id="aff6"><label>6</label><addr-line>Illumina, San Diego, California, United States of America</addr-line></aff><aff id="aff7"><label>7</label><addr-line>Biosciences Research Division, Department of Primary Industries Victoria, Melbourne, Victoria, Australia</addr-line></aff><aff id="aff8"><label>8</label><addr-line>Dairy Futures Cooperative Research Centre, Bundoora, Victoria, Australia</addr-line></aff><aff id="aff9"><label>9</label><addr-line>La Trobe University, Bundoora, Victoria, Australia</addr-line></aff><aff id="aff10"><label>10</label><addr-line>Animal Improvement Programs Laboratory, Agricultural Research Service, United States Department of Agriculture, Beltsville, Maryland, United States of America</addr-line></aff><contrib-group><contrib contrib-type="editor"><name><surname>Liu</surname><given-names>Zhanjiang</given-names></name><role>Editor</role><xref ref-type="aff" rid="edit1"></xref></contrib></contrib-group><aff id="edit1">Auburn University, United States of America</aff><author-notes><corresp id="cor1">* E-mail: <email>ben.hayes@dpi.vic.gov.au</email></corresp><fn fn-type="con"><p>Conceived and designed the experiments: DB XD BJH TSS CPV. Performed the experiments: XD AE CTL TSS CPV HC SF GRW. Analyzed the data: RD BJH PMV GRW. Contributed reagents/materials/analysis tools: KJG KVM CTL. Wrote the paper: DB RD AE BJH CTL TSS CPV PMV GRW.</p></fn></author-notes><pub-date pub-type="collection"><year>2012</year></pub-date><pub-date pub-type="epub"><day>28</day><month>3</month><year>2012</year></pub-date><volume>7</volume><issue>3</issue><elocation-id>e34130</elocation-id><history><date date-type="received"><day>11</day><month>12</month><year>2011</year></date><date date-type="accepted"><day>22</day><month>2</month><year>2012</year></date></history><permissions><copyright-statement>This is an open-access article, free of all copyright, and may be freely reproduced, distributed, transmitted, modified, built upon, or otherwise used by anyone for any lawful purpose. The work is made available under the Creative Commons CC0 public domain dedication.</copyright-statement><copyright-year>2012</copyright-year></permissions><abstract><p>The Illumina BovineLD BeadChip was designed to support imputation to higher density genotypes in dairy and beef breeds by including single-nucleotide polymorphisms (SNPs) that had a high minor allele frequency as well as uniform spacing across the genome except at the ends of the chromosome where densities were increased. The chip also includes SNPs on the Y chromosome and mitochondrial DNA loci that are useful for determining subspecies classification and certain paternal and maternal breed lineages. The total number of SNPs was 6,909. Accuracy of imputation to Illumina BovineSNP50 genotypes using the BovineLD chip was over 97% for most dairy and beef populations. The BovineLD imputations were about 3 percentage points more accurate than those from the Illumina GoldenGate Bovine3K BeadChip across multiple populations. The improvement was greatest when neither parent was genotyped. The minor allele frequencies were similar across taurine beef and dairy breeds as was the proportion of SNPs that were polymorphic. The new BovineLD chip should facilitate low-cost genomic selection in taurine beef and dairy cattle.</p></abstract><counts><page-count count="10"></page-count></counts></article-meta></front></pmc></record>Pour manipuler ce document sous Unix (Dilib)
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