Accuracy of genomic predictions in Bos indicus (Nellore) cattle

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dc.contributor.authorNeves, Haroldo H. R. [UNESP]
dc.contributor.authorCarvalheiro, Roberto [UNESP]
dc.contributor.authorPerez O'Brien, Ana M.
dc.contributor.authorUtsunomiya, Yuri T. [UNESP]
dc.contributor.authorCarmo, Adriana S. do [UNESP]
dc.contributor.authorSchenkel, Flavio S.
dc.contributor.authorSoelkner, Johann
dc.contributor.authorMcEwan, John C.
dc.contributor.authorVan Tassell, Curtis P.
dc.contributor.authorCole, John B.
dc.contributor.authorSilva, Marcos V. G. B. da
dc.contributor.authorQueiroz, Sandra A. [UNESP]
dc.contributor.authorSonstegard, Tad S.
dc.contributor.authorGarcia, José Fernando [UNESP]
dc.contributor.institutionUniversidade Estadual Paulista (Unesp)
dc.contributor.institutionGenSys Consultores Assoc SC Ltda
dc.contributor.institutionUniv Nat Resources & Life Sci
dc.contributor.institutionUniversity of Guelph
dc.contributor.institutionAgResearch
dc.contributor.institutionARS
dc.contributor.institutionEmpresa Brasileira de Pesquisa Agropecuária (EMBRAPA)
dc.date.accessioned2014-12-03T13:07:04Z
dc.date.available2014-12-03T13:07:04Z
dc.date.issued2014-02-27
dc.description.abstractBackground: Nellore cattle play an important role in beef production in tropical systems and there is great interest in determining if genomic selection can contribute to accelerate genetic improvement of production and fertility in this breed. We present the first results of the implementation of genomic prediction in a Bos indicus (Nellore) population.Methods: Influential bulls were genotyped with the Illumina Bovine HD chip in order to assess genomic predictive ability for weight and carcass traits, gestation length, scrotal circumference and two selection indices. 685 samples and 320 238 single nucleotide polymorphisms (SNPs) were used in the analyses. A forward-prediction scheme was adopted to predict the genomic breeding values (DGV). In the training step, the estimated breeding values (EBV) of bulls were deregressed (dEBV) and used as pseudo-phenotypes to estimate marker effects using four methods: genomic BLUP with or without a residual polygenic effect (GBLUP20 and GBLUP0, respectively), a mixture model (Bayes C) and Bayesian LASSO (BLASSO). Empirical accuracies of the resulting genomic predictions were assessed based on the correlation between DGV and dEBV for the testing group.Results: Accuracies of genomic predictions ranged from 0.17 (navel at weaning) to 0.74 (finishing precocity). Across traits, Bayesian regression models (Bayes C and BLASSO) were more accurate than GBLUP. The average empirical accuracies were 0.39 (GBLUP0), 0.40 (GBLUP20) and 0.44 (Bayes C and BLASSO). Bayes C and BLASSO tended to produce deflated predictions (i. e. slope of the regression of dEBV on DGV greater than 1). Further analyses suggested that higher-than-expected accuracies were observed for traits for which EBV means differed significantly between two breeding subgroups that were identified in a principal component analysis based on genomic relationships.Conclusions: Bayesian regression models are of interest for future applications of genomic selection in this population, but further improvements are needed to reduce deflation of their predictions. Recurrent updates of the training population would be required to enable accurate prediction of the genetic merit of young animals. The technical feasibility of applying genomic prediction in a Bos indicus (Nellore) population was demonstrated. Further research is needed to permit cost-effective selection decisions using genomic information.en
dc.description.affiliationUniv Estadual Paulista, UNESP, Fac Ciencias Agr & Vet, BR-14884900 Sao Paulo, Brazil
dc.description.affiliationGenSys Consultores Assoc SC Ltda, BR-90680000 Porto Alegre, RS, Brazil
dc.description.affiliationUniv Nat Resources & Life Sci, Div Livestock Sci, Dept Sustainable Agr Syst BOKU, A-1180 Vienna, Austria
dc.description.affiliationUniv Guelph, Ctr Genet Improvement Livestock, Guelph, ON N1G 2W1, Canada
dc.description.affiliationAgResearch, Ctr Reprod & Genom, Invermay, Mosgiel, New Zealand
dc.description.affiliationARS, USDA, Bovine Funct Genom Lab, Beltsville, MD 20705 USA
dc.description.affiliationARS, Anim Improvement Programs Lab, USDA, Beltsville, MD 20705 USA
dc.description.affiliationEmbrapa DairyCattle, Bioinformat & Anim Genom Lab, Juiz De Fora, MG, Brazil
dc.description.affiliationUniv Estadual Paulista, UNESP, Fac Med Vet Aracatuba, BR-16050680 Sao Paulo, Brazil
dc.description.affiliationUnespUniv Estadual Paulista, UNESP, Fac Ciencias Agr & Vet, BR-14884900 Sao Paulo, Brazil
dc.description.affiliationUnespUniv Estadual Paulista, UNESP, Fac Med Vet Aracatuba, BR-16050680 Sao Paulo, Brazil
dc.description.sponsorshipConselho Nacional de Desenvolvimento Científico e Tecnológico (CNPq)
dc.description.sponsorshipFundação de Amparo à Pesquisa do Estado de São Paulo (FAPESP)
dc.description.sponsorship(BFGL) from the USDA Agricultural Research Service
dc.description.sponsorshipIdCNPq: 560922/2010-8
dc.description.sponsorshipIdCNPq: 483590/2010-0
dc.description.sponsorshipIdFAPESP: 10/06185-4
dc.description.sponsorshipIdFAPESP: 11/16643-2
dc.description.sponsorshipIdFAPESP: 10/52030-2
dc.description.sponsorshipId(BFGL) from the USDA Agricultural Research Service1265-31000-104D
dc.format.extent13
dc.identifierhttp://dx.doi.org/10.1186/1297-9686-46-17
dc.identifier.citationGenetics Selection Evolution. London: Biomed Central Ltd, v. 46, 13 p., 2014.
dc.identifier.doi10.1186/1297-9686-46-17
dc.identifier.fileWOS000333517900001.pdf
dc.identifier.issn0999-193X
dc.identifier.lattes9991374083045897
dc.identifier.urihttp://hdl.handle.net/11449/111217
dc.identifier.wosWOS:000333517900001
dc.language.isoeng
dc.publisherBiomed Central Ltd.
dc.relation.ispartofGenetics Selection Evolution
dc.relation.ispartofjcr3.743
dc.rights.accessRightsAcesso aberto
dc.sourceWeb of Science
dc.titleAccuracy of genomic predictions in Bos indicus (Nellore) cattleen
dc.typeArtigo
dcterms.rightsHolderBiomed Central Ltd
unesp.author.lattes9991374083045897
unesp.campusUniversidade Estadual Paulista (Unesp), Faculdade de Medicina Veterinária, Araçatubapt

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