Imputation of microsatellite alleles from dense SNP genotypes for parentage verification across multiple Bos taurus and Bos indicus breeds

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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 [UNESP]
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.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.institutionJouy-en-Josas
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.date.accessioned2016-01-28T16:53:20Z
dc.date.available2016-01-28T16:53:20Z
dc.date.issued2013
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.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.sponsorshipUSDA-ARS
dc.description.sponsorshipUSDA National Research Initiative Competitive Integrated
dc.description.sponsorshipIdUSDA-ARS: 1265-31000-104-00D
dc.description.sponsorshipIdUSDA National Research Initiative Competitive Integrated: 2009-55205-05057 and 2009-65205-05635
dc.format.extent176-11
dc.identifierhttp://dx.doi.org/10.3389/fgene.2013.00176
dc.identifier.citationFrontiers in Genetics, v. 4, p. 176-11, 2013.
dc.identifier.doi10.3389/fgene.2013.00176
dc.identifier.issn1664-8021
dc.identifier.lattes9991374083045897
dc.identifier.urihttp://hdl.handle.net/11449/133041
dc.language.isoeng
dc.relation.ispartofFrontiers in Genetics
dc.relation.ispartofjcr4.151
dc.relation.ispartofsjr2,274
dc.rights.accessRightsAcesso restrito
dc.sourceCurrículo Lattes
dc.titleImputation of microsatellite alleles from dense SNP genotypes for parentage verification across multiple Bos taurus and Bos indicus breedsen
dc.typeArtigo
unesp.author.lattes9991374083045897
unesp.campusUniversidade Estadual Paulista (Unesp), Faculdade de Medicina Veterinária, Araçatubapt
unesp.departmentApoio a Produção e Saúde Animalpt

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