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

dc.contributorUnited States Department of Agriculture
dc.contributorUniversity of California-Davis
dc.contributorAnimal and Grassland Research and Innovation Centre
dc.contributorWeatherbys DNA Laboratory
dc.contributorUniversidade Estadual Paulista (Unesp)
dc.contributorDeoxi Biotecnologia
dc.contributorEmbrapa Pecuária Sudeste (Embrapa)
dc.contributorUniversidade de São Paulo (USP)
dc.contributorScotland's Rural College (SRUC)
dc.contributorJouy-en-Josas
dc.contributorItalian Breeders Association
dc.contributorUniversity of Missouri-Columbia
dc.contributorNeogen Company
dc.contributorInvermay Agricultural Centre
dc.contributorIrish Cattle Breeding Federation
dc.contributorUniversity of Queensland
dc.contributorUniversity of New England
dc.contributorAmerican-International Charolais Association
dc.creatorMcclure, Matthew C
dc.creatorSonstegard, Tad S
dc.creatorWiggans, George R
dc.creatorVan Eenennaam, Alison L
dc.creatorWeber, Kristina L
dc.creatorPenedo, Cecilia T
dc.creatorBerry, Donagh P
dc.creatorFlynn, John
dc.creatorGarcia, José Fernando [UNESP]
dc.creatorCarmo, Adriana S
dc.creatorRegitano, Luciana C A
dc.creatorAlbuquerque, Milla
dc.creatorSilva, Marcos V G B
dc.creatorMachado, Marco A
dc.creatorCoffey, Mike
dc.creatorMoore, Kirsty
dc.creatorBoscher, Marie-yvonne
dc.creatorGenestout, Lucie
dc.creatorMazza, Raffaele
dc.creatorTaylor, Jeremy F
dc.creatorSchnabel, Robert D
dc.creatorSimpson, Barry
dc.creatorMarques, Elisa
dc.creatorMcewan, John C
dc.creatorCromie, Andrew
dc.creatorCoutinho, Luiz L
dc.creatorKuehn, Larry A
dc.creatorKeele, John W
dc.creatorPiper, Emily K
dc.creatorCook, Jim
dc.creatorWilliams, Robert
dc.creatorVan Tassell, Curtis P
dc.date2016-01-28T16:53:20Z
dc.date2016-01-28T16:53:20Z
dc.date2013
dc.date.accessioned2023-09-12T08:02:30Z
dc.date.available2023-09-12T08:02:30Z
dc.identifierhttp://dx.doi.org/10.3389/fgene.2013.00176
dc.identifierFrontiers in Genetics, v. 4, p. 176-11, 2013.
dc.identifier1664-8021
dc.identifierhttp://hdl.handle.net/11449/133041
dc.identifier10.3389/fgene.2013.00176
dc.identifier9991374083045897
dc.identifier.urihttps://repositorioslatinoamericanos.uchile.cl/handle/2250/8782303
dc.descriptionTo 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.
dc.descriptionUSDA-ARS
dc.descriptionUSDA National Research Initiative Competitive Integrated
dc.descriptionBovine Functional Genomics Laboratory, BARC, Agriculture Research Service, United States Department of Agriculture, Beltsville, MD, USA
dc.descriptionAnimal Improvement Programs Laboratory, BARC, Agriculture Research Service, United States Department of Agriculture, Beltsville, MD, USA
dc.descriptionDepartment of Animal Science, University of California-Davis, Davis, CA, USA
dc.descriptionVeterinary Genetics Laboratory, School of Veterinary Medicine, University of California-Davis, Davis, CA, USA
dc.descriptionAnimal and Bioscience Research Department, Animal and Grassland Research and Innovation Centre, Teagasc, Moorepark, Ireland
dc.descriptionWeatherbys DNA Laboratory, Kildare, Ireland
dc.descriptionUniversidade 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.descriptionDeoxi Biotecnologia, Araçatuba, Brazil
dc.descriptionEmbrapa Pecuária Sudeste, São Carlos, Brazil
dc.descriptionDepartment of Animal Science, College of Agriculture, University of Sao Paulo, Piracicaba, Brazil
dc.descriptionEmbrapa Gado de Leite, Juiz de Fora, Brazil
dc.descriptionAnimal and Veterinary Science, SRUC, Midlothian, Scotland
dc.descriptionLABOGENA, Jouy-en-Josas, France
dc.descriptionCoordinatore Laboratorio Genetica e Servizi, Associazione Italiana Allevatori - Italian Breeders Association, Roma, Italy
dc.descriptionDivision of Animal Science, University of Missouri-Columbia, Columbia, MO, USA
dc.descriptionGeneSeek, Neogen Company, Lincoln, NE, USA
dc.descriptionAgResearch, Invermay Agricultural Centre, Mosgiel, New Zealand
dc.descriptionIrish Cattle Breeding Federation, Bandon, Ireland
dc.descriptionESALQ – USP, Piracicaba, SP, Brazil
dc.descriptionGenetics, Breeding, and Animal Health Research Unit, U.S. Meat Animal Research Center, USDA-ARS, Clay Center, NE, USA
dc.descriptionAnimal Genetics Laboratory, School of Veterinary Science, The University of Queensland, Gatton, QLD, Australia
dc.descriptionAnimal Genetics and Breeding Unit, University of New England, Armidale, NSW, Australia
dc.descriptionAmerican-International Charolais Association, Kansas City, MO, USA
dc.descriptionUniversidade 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.descriptionUSDA-ARS: 1265-31000-104-00D
dc.descriptionUSDA National Research Initiative Competitive Integrated: 2009-55205-05057 and 2009-65205-05635
dc.format176-11
dc.languageeng
dc.relationFrontiers in Genetics
dc.relation4.151
dc.relation2,274
dc.rightsAcesso restrito
dc.sourceCurrículo Lattes
dc.titleImputation of microsatellite alleles from dense SNP genotypes for parentage verification across multiple Bos taurus and Bos indicus breeds
dc.typeArtigo


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