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dc.contributor.authorMcclure, Matthew C-
dc.contributor.authorSonstegard, Tad S-
dc.contributor.authorWiggans, George R-
dc.contributor.authorVan Eenennaam, Alison L-
dc.contributor.authorWeber, Kristina L-
dc.contributor.authorPenedo, Cecilia T-
dc.contributor.authorBerry, Donagh P-
dc.contributor.authorFlynn, John-
dc.contributor.authorGarcia, José Fernando-
dc.contributor.authorCarmo, Adriana S-
dc.contributor.authorRegitano, Luciana C A-
dc.contributor.authorAlbuquerque, Milla-
dc.contributor.authorSilva, Marcos V G B-
dc.contributor.authorMachado, Marco A-
dc.contributor.authorCoffey, Mike-
dc.contributor.authorMoore, Kirsty-
dc.contributor.authorBoscher, Marie-yvonne-
dc.contributor.authorGenestout, Lucie-
dc.contributor.authorMazza, Raffaele-
dc.contributor.authorTaylor, Jeremy F-
dc.contributor.authorSchnabel, Robert D-
dc.contributor.authorSimpson, Barry-
dc.contributor.authorMarques, Elisa-
dc.contributor.authorMcewan, John C-
dc.contributor.authorCromie, Andrew-
dc.contributor.authorCoutinho, Luiz L-
dc.contributor.authorKuehn, Larry A-
dc.contributor.authorKeele, John W-
dc.contributor.authorPiper, Emily K-
dc.contributor.authorCook, Jim-
dc.contributor.authorWilliams, Robert-
dc.contributor.authorVan Tassell, Curtis P-
dc.identifier.citationFrontiers in Genetics, v. 4, p. 176-11, 2013.-
dc.description.abstractTo assist cattle producers transition from microsatellite (MS) to single nucleotide polymorphism (SNP) genotyping for parental verification we previously devised an effective and inexpensive method to impute MS alleles from SNP haplotypes. While the reported method was verified with only a limited data set (N = 479) from Brown Swiss, Guernsey, Holstein, and Jersey cattle, some of the MS-SNP haplotype associations were concordant across these phylogenetically diverse breeds. This implied that some haplotypes predate modern breed formation and remain in strong linkage disequilibrium. To expand the utility of MS allele imputation across breeds, MS and SNP data from more than 8000 animals representing 39 breeds (Bos taurus and B. indicus) were used to predict 9410 SNP haplotypes, incorporating an average of 73 SNPs per haplotype, for which alleles from 12 MS markers could be accurately be imputed. Approximately 25% of the MS-SNP haplotypes were present in multiple breeds (N = 2 to 36 breeds). These shared haplotypes allowed for MS imputation in breeds that were not represented in the reference population with only a small increase in Mendelian inheritance inconsistancies. Our reported reference haplotypes can be used for any cattle breed and the reported methods can be applied to any species to aid the transition from MS to SNP genetic markers. While ~91% of the animals with imputed alleles for 12 MS markers had ≤1 Mendelian inheritance conflicts with their parents' reported MS genotypes, this figure was 96% for our reference animals, indicating potential errors in the reported MS genotypes. The workflow we suggest autocorrects for genotyping errors and rare haplotypes, by MS genotyping animals whose imputed MS alleles fail parentage verification, and then incorporating those animals into the reference dataset.en
dc.description.sponsorshipUSDA National Research Initiative Competitive Integrated-
dc.sourceCurrículo Lattes-
dc.titleImputation of microsatellite alleles from dense SNP genotypes for parentage verification across multiple Bos taurus and Bos indicus breedsen
dc.contributor.institutionUnited States Department of Agriculture-
dc.contributor.institutionUniversity of California-Davis-
dc.contributor.institutionAnimal and Grassland Research and Innovation Centre-
dc.contributor.institutionWeatherbys DNA Laboratory-
dc.contributor.institutionUniversidade Estadual Paulista (UNESP)-
dc.contributor.institutionDeoxi Biotecnologia-
dc.contributor.institutionEmbrapa Pecuária Sudeste (Embrapa)-
dc.contributor.institutionUniversidade de São Paulo (USP)-
dc.contributor.institutionScotland's Rural College (SRUC)-
dc.contributor.institutionItalian Breeders Association-
dc.contributor.institutionUniversity of Missouri-Columbia-
dc.contributor.institutionNeogen Company-
dc.contributor.institutionInvermay Agricultural Centre-
dc.contributor.institutionIrish Cattle Breeding Federation-
dc.contributor.institutionUniversity of Queensland-
dc.contributor.institutionUniversity of New England-
dc.contributor.institutionAmerican-International Charolais Association-
dc.description.affiliationBovine Functional Genomics Laboratory, BARC, Agriculture Research Service, United States Department of Agriculture, Beltsville, MD, USA-
dc.description.affiliationAnimal Improvement Programs Laboratory, BARC, Agriculture Research Service, United States Department of Agriculture, Beltsville, MD, USA-
dc.description.affiliationDepartment of Animal Science, University of California-Davis, Davis, CA, USA-
dc.description.affiliationVeterinary Genetics Laboratory, School of Veterinary Medicine, University of California-Davis, Davis, CA, USA-
dc.description.affiliationAnimal and Bioscience Research Department, Animal and Grassland Research and Innovation Centre, Teagasc, Moorepark, Ireland-
dc.description.affiliationWeatherbys DNA Laboratory, Kildare, Ireland-
dc.description.affiliationUniversidade Estadual Paulista Júlio de Mesquita Filho, Departamento de Apoio a Produção e Saúde Animal, Faculdade de Medicina Veterinária, Araçatuba, Rua Clóvis Pestana, 793 - Laboratório de Bioquímica e Biologia Molecular Animal, Jardim Dona Amélia, CEP 16050680, SP, Brasil-
dc.description.affiliationDeoxi Biotecnologia, Araçatuba, Brazil-
dc.description.affiliationEmbrapa Pecuária Sudeste, São Carlos, Brazil-
dc.description.affiliationDepartment of Animal Science, College of Agriculture, University of Sao Paulo, Piracicaba, Brazil-
dc.description.affiliationEmbrapa Gado de Leite, Juiz de Fora, Brazil-
dc.description.affiliationAnimal and Veterinary Science, SRUC, Midlothian, Scotland-
dc.description.affiliationLABOGENA, Jouy-en-Josas, France-
dc.description.affiliationCoordinatore Laboratorio Genetica e Servizi, Associazione Italiana Allevatori - Italian Breeders Association, Roma, Italy-
dc.description.affiliationDivision of Animal Science, University of Missouri-Columbia, Columbia, MO, USA-
dc.description.affiliationGeneSeek, Neogen Company, Lincoln, NE, USA-
dc.description.affiliationAgResearch, Invermay Agricultural Centre, Mosgiel, New Zealand-
dc.description.affiliationIrish Cattle Breeding Federation, Bandon, Ireland-
dc.description.affiliationESALQ – USP, Piracicaba, SP, Brazil-
dc.description.affiliationGenetics, Breeding, and Animal Health Research Unit, U.S. Meat Animal Research Center, USDA-ARS, Clay Center, NE, USA-
dc.description.affiliationAnimal Genetics Laboratory, School of Veterinary Science, The University of Queensland, Gatton, QLD, Australia-
dc.description.affiliationAnimal Genetics and Breeding Unit, University of New England, Armidale, NSW, Australia-
dc.description.affiliationAmerican-International Charolais Association, Kansas City, MO, USA-
dc.description.affiliationUnespUniversidade Estadual Paulista Júlio de Mesquita Filho, Departamento de Apoio a Produção e Saúde Animal, Faculdade de Medicina Veterinária, Araçatuba, Rua Clóvis Pestana, 793 - Laboratório de Bioquímica e Biologia Molecular Animal, Jardim Dona Amélia, CEP 16050680, SP, Brasil-
dc.description.sponsorshipIdUSDA-ARS: 1265-31000-104-00D-
dc.description.sponsorshipIdUSDA National Research Initiative Competitive Integrated: 2009-55205-05057 and 2009-65205-05635-
dc.rights.accessRightsAcesso restrito-
dc.relation.ispartofFrontiers in Genetics-
Appears in Collections:Artigos, TCCs, Teses e Dissertações da Unesp

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