Design of a bovine low-density SNP array optimized for imputation
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 de...
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Published in | PloS one Vol. 7; no. 3; p. e34130 |
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Main Authors | , , , , , , , , , , , , , |
Format | Journal Article |
Language | English |
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Public Library of Science
28.03.2012
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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. |
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AbstractList | 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. |
Audience | Academic |
Author | Viaud-Martinez, Karine A Boichard, Didier Gietzen, Kimberly J Wiggans, George R David, Xavier Hayes, Ben J Sonstegard, Tad S Eggen, André Chung, Hoyoung Fritz, Sébastien Lawley, Cynthia T Van Tassell, Curtis P Dassonneville, Romain VanRaden, Paul M |
AuthorAffiliation | 5 National Association of Livestock and Artificial Insemination Cooperatives (UNCEIA), Paris, France 3 Bovine Functional Genomics Laboratory, Agricultural Research Service, United States Department of Agriculture, Beltsville, Maryland, United States of America 9 La Trobe University, Bundoora, Victoria, Australia 7 Biosciences Research Division, Department of Primary Industries Victoria, Melbourne, Victoria, Australia Auburn University, United States of America 10 Animal Improvement Programs Laboratory, Agricultural Research Service, United States Department of Agriculture, Beltsville, Maryland, United States of America 1 UMR1313 Animal Genetics and Integrative Biology, National Institute for Agricultural Research (INRA), Jouy-en-Josas, France 6 Illumina, San Diego, California, United States of America 4 Institut de l'Elevage, Paris, France 2 Animal Genetic Improvement Division, National Institute of Animal Science, Seonghwan, Cheonan, Republic of Korea 8 Dairy Futures Cooperative Research Centre |
AuthorAffiliation_xml | – name: 8 Dairy Futures Cooperative Research Centre, Bundoora, Victoria, Australia – name: 7 Biosciences Research Division, Department of Primary Industries Victoria, Melbourne, Victoria, Australia – name: 10 Animal Improvement Programs Laboratory, Agricultural Research Service, United States Department of Agriculture, Beltsville, Maryland, United States of America – name: 5 National Association of Livestock and Artificial Insemination Cooperatives (UNCEIA), Paris, France – name: 3 Bovine Functional Genomics Laboratory, Agricultural Research Service, United States Department of Agriculture, Beltsville, Maryland, United States of America – name: 1 UMR1313 Animal Genetics and Integrative Biology, National Institute for Agricultural Research (INRA), Jouy-en-Josas, France – name: Auburn University, United States of America – name: 2 Animal Genetic Improvement Division, National Institute of Animal Science, Seonghwan, Cheonan, Republic of Korea – name: 6 Illumina, San Diego, California, United States of America – name: 4 Institut de l'Elevage, Paris, France – name: 9 La Trobe University, Bundoora, Victoria, Australia |
Author_xml | – sequence: 1 givenname: Didier surname: Boichard fullname: Boichard, Didier organization: UMR1313 Animal Genetics and Integrative Biology, National Institute for Agricultural Research (INRA), Jouy-en-Josas, France – sequence: 2 givenname: Hoyoung surname: Chung fullname: Chung, Hoyoung – sequence: 3 givenname: Romain surname: Dassonneville fullname: Dassonneville, Romain – sequence: 4 givenname: Xavier surname: David fullname: David, Xavier – sequence: 5 givenname: André surname: Eggen fullname: Eggen, André – sequence: 6 givenname: Sébastien surname: Fritz fullname: Fritz, Sébastien – sequence: 7 givenname: Kimberly J surname: Gietzen fullname: Gietzen, Kimberly J – sequence: 8 givenname: Ben J surname: Hayes fullname: Hayes, Ben J – sequence: 9 givenname: Cynthia T surname: Lawley fullname: Lawley, Cynthia T – sequence: 10 givenname: Tad S surname: Sonstegard fullname: Sonstegard, Tad S – sequence: 11 givenname: Curtis P surname: Van Tassell fullname: Van Tassell, Curtis P – sequence: 12 givenname: Paul M surname: VanRaden fullname: VanRaden, Paul M – sequence: 13 givenname: Karine A surname: Viaud-Martinez fullname: Viaud-Martinez, Karine A – sequence: 14 givenname: George R surname: Wiggans fullname: Wiggans, George R |
BackLink | https://www.ncbi.nlm.nih.gov/pubmed/22470530$$D View this record in MEDLINE/PubMed https://hal.science/hal-01019774$$DView record in HAL |
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ContentType | Journal Article |
Copyright | COPYRIGHT 2012 Public Library of Science 2012. 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. Notwithstanding the ProQuest Terms and Conditions, you may use this content in accordance with the terms of the License. Distributed under a Creative Commons Attribution 4.0 International License 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. 2012 |
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CorporateAuthor | Bovine LD Consortium for the Bovine LD Consortium |
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DocumentTitleAlternate | Bovine SNP Array for Accurate Imputation |
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Keywords | snps illumina bovineld beadchip beef breed genotype dairy breed |
Language | English |
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Notes | ObjectType-Article-1 SourceType-Scholarly Journals-1 ObjectType-Feature-2 content type line 23 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. |
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SubjectTerms | Accuracy Agricultural sciences Agriculture Algorithms Alleles Animals Beef Biology Bovidae Breeding - methods Cattle Chromosomes Consortia Dairy cattle Dairy industry Deoxyribonucleic acid DNA DNA, Mitochondrial - genetics Expected values Gene Frequency Genetics Genome Genomes Genomics Genotype Genotypes Haplotypes Laboratories Life Sciences Livestock Methods Mitochondrial DNA Oligonucleotide Array Sequence Analysis - instrumentation Polymorphism, Single Nucleotide Population Populations Single nucleotide polymorphisms Single-nucleotide polymorphism Taurine Veterinary Science Y Chromosomes |
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Title | Design of a bovine low-density SNP array optimized for imputation |
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