Accuracy of genomic predictions in Bos indicus (Nellore) cattle.
Autor(a) principal: | |
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Data de Publicação: | 2014 |
Outros Autores: | , , , , , , , , , , , , |
Tipo de documento: | Artigo |
Idioma: | eng |
Título da fonte: | Repositório Institucional da EMBRAPA (Repository Open Access to Scientific Information from EMBRAPA - Alice) |
Texto Completo: | http://www.alice.cnptia.embrapa.br/alice/handle/doc/987574 https://doi.org/10.1186/1297-9686-46-17 |
Resumo: | Background- 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. |
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Accuracy of genomic predictions in Bos indicus (Nellore) cattle.Nellore cattleGenomic selectionBackground- 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.Haroldo HR Neves; Roberto Carvalheiro; Ana M Pérez O'Brien; Yuri T Utsunomiya; Adriana S. do Carmo; Flávio S Schenkel; Johann Sölkner; John C McEwan; Curtis P Van Tassell; John B Cole; MARCOS VINICIUS GUALBERTO B SILVA, CNPGL; Sandra A Queiroz; Tad S Sonstegard; José Fernando Garcia.NEVES, H. H.CARVALHEIRO, R.O'BRIEN, A. M.UTSUNOMIYA, Y. T.CARMO, A. S. doSCHENKEL, F. S.SÖLKNER, J.MCEWAN, J. C.VAN TASSELL, C. P.COLE, J. B.SILVA, M. V. G. B.QUEIROZ, S. A.SONSTEGARD, T. S.GARCIA, J. F.2015-01-25T08:43:51Z2015-01-25T08:43:51Z2014-06-0420142015-01-25T08:43:51Zinfo:eu-repo/semantics/publishedVersioninfo:eu-repo/semantics/articleGenetics Selection Evolution, v. 46, article 17, 2014.http://www.alice.cnptia.embrapa.br/alice/handle/doc/987574https://doi.org/10.1186/1297-9686-46-17enginfo:eu-repo/semantics/openAccessreponame:Repositório Institucional da EMBRAPA (Repository Open Access to Scientific Information from EMBRAPA - Alice)instname:Empresa Brasileira de Pesquisa Agropecuária (Embrapa)instacron:EMBRAPA2017-08-16T02:03:03Zoai:www.alice.cnptia.embrapa.br:doc/987574Repositório InstitucionalPUBhttps://www.alice.cnptia.embrapa.br/oai/requestcg-riaa@embrapa.bropendoar:21542017-08-16T02:03:03Repositório Institucional da EMBRAPA (Repository Open Access to Scientific Information from EMBRAPA - Alice) - Empresa Brasileira de Pesquisa Agropecuária (Embrapa)false |
dc.title.none.fl_str_mv |
Accuracy of genomic predictions in Bos indicus (Nellore) cattle. |
title |
Accuracy of genomic predictions in Bos indicus (Nellore) cattle. |
spellingShingle |
Accuracy of genomic predictions in Bos indicus (Nellore) cattle. NEVES, H. H. Nellore cattle Genomic selection |
title_short |
Accuracy of genomic predictions in Bos indicus (Nellore) cattle. |
title_full |
Accuracy of genomic predictions in Bos indicus (Nellore) cattle. |
title_fullStr |
Accuracy of genomic predictions in Bos indicus (Nellore) cattle. |
title_full_unstemmed |
Accuracy of genomic predictions in Bos indicus (Nellore) cattle. |
title_sort |
Accuracy of genomic predictions in Bos indicus (Nellore) cattle. |
author |
NEVES, H. H. |
author_facet |
NEVES, H. H. CARVALHEIRO, R. O'BRIEN, A. M. UTSUNOMIYA, Y. T. CARMO, A. S. do SCHENKEL, F. S. SÖLKNER, J. MCEWAN, J. C. VAN TASSELL, C. P. COLE, J. B. SILVA, M. V. G. B. QUEIROZ, S. A. SONSTEGARD, T. S. GARCIA, J. F. |
author_role |
author |
author2 |
CARVALHEIRO, R. O'BRIEN, A. M. UTSUNOMIYA, Y. T. CARMO, A. S. do SCHENKEL, F. S. SÖLKNER, J. MCEWAN, J. C. VAN TASSELL, C. P. COLE, J. B. SILVA, M. V. G. B. QUEIROZ, S. A. SONSTEGARD, T. S. GARCIA, J. F. |
author2_role |
author author author author author author author author author author author author author |
dc.contributor.none.fl_str_mv |
Haroldo HR Neves; Roberto Carvalheiro; Ana M Pérez O'Brien; Yuri T Utsunomiya; Adriana S. do Carmo; Flávio S Schenkel; Johann Sölkner; John C McEwan; Curtis P Van Tassell; John B Cole; MARCOS VINICIUS GUALBERTO B SILVA, CNPGL; Sandra A Queiroz; Tad S Sonstegard; José Fernando Garcia. |
dc.contributor.author.fl_str_mv |
NEVES, H. H. CARVALHEIRO, R. O'BRIEN, A. M. UTSUNOMIYA, Y. T. CARMO, A. S. do SCHENKEL, F. S. SÖLKNER, J. MCEWAN, J. C. VAN TASSELL, C. P. COLE, J. B. SILVA, M. V. G. B. QUEIROZ, S. A. SONSTEGARD, T. S. GARCIA, J. F. |
dc.subject.por.fl_str_mv |
Nellore cattle Genomic selection |
topic |
Nellore cattle Genomic selection |
description |
Background- 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. |
publishDate |
2014 |
dc.date.none.fl_str_mv |
2014-06-04 2014 2015-01-25T08:43:51Z 2015-01-25T08:43:51Z 2015-01-25T08:43:51Z |
dc.type.status.fl_str_mv |
info:eu-repo/semantics/publishedVersion |
dc.type.driver.fl_str_mv |
info:eu-repo/semantics/article |
format |
article |
status_str |
publishedVersion |
dc.identifier.uri.fl_str_mv |
Genetics Selection Evolution, v. 46, article 17, 2014. http://www.alice.cnptia.embrapa.br/alice/handle/doc/987574 https://doi.org/10.1186/1297-9686-46-17 |
identifier_str_mv |
Genetics Selection Evolution, v. 46, article 17, 2014. |
url |
http://www.alice.cnptia.embrapa.br/alice/handle/doc/987574 https://doi.org/10.1186/1297-9686-46-17 |
dc.language.iso.fl_str_mv |
eng |
language |
eng |
dc.rights.driver.fl_str_mv |
info:eu-repo/semantics/openAccess |
eu_rights_str_mv |
openAccess |
dc.source.none.fl_str_mv |
reponame:Repositório Institucional da EMBRAPA (Repository Open Access to Scientific Information from EMBRAPA - Alice) instname:Empresa Brasileira de Pesquisa Agropecuária (Embrapa) instacron:EMBRAPA |
instname_str |
Empresa Brasileira de Pesquisa Agropecuária (Embrapa) |
instacron_str |
EMBRAPA |
institution |
EMBRAPA |
reponame_str |
Repositório Institucional da EMBRAPA (Repository Open Access to Scientific Information from EMBRAPA - Alice) |
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Repositório Institucional da EMBRAPA (Repository Open Access to Scientific Information from EMBRAPA - Alice) |
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Repositório Institucional da EMBRAPA (Repository Open Access to Scientific Information from EMBRAPA - Alice) - Empresa Brasileira de Pesquisa Agropecuária (Embrapa) |
repository.mail.fl_str_mv |
cg-riaa@embrapa.br |
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1817695364842520576 |