Prediction of genomic breeding values of milk traits in Brazilian Saanen goats
Autor(a) principal: | |
---|---|
Data de Publicação: | 2021 |
Outros Autores: | , |
Tipo de documento: | Artigo |
Idioma: | eng |
Título da fonte: | Repositório Institucional da UNESP |
Texto Completo: | http://dx.doi.org/10.1111/jbg.12550 http://hdl.handle.net/11449/209331 |
Resumo: | The study's objective was to compare the genomic prediction ability methods for the traits milk yield, milk composition and somatic cell count of Saanen Brazilian goats. Nine hundred forty goats, genotyped with an Axiom_OviCap (Caprine) panel, Affimetrix customized array with 62,557 single nucleotide polymorphisms (SNPs), were used for the genomic selection analyses. The genomic methods studied to estimate the effects of SNPs and direct genomic values (DGV) were as follows: (a) genomic BLUP (GBLUP), (b) Bayes C pi and (c) Bayesian Lasso (BLASSO). Estimated breeding values (EBV) and deregressed estimated breeding values (dEBV) were used as response variables for the genomic predictions. The prediction ability was assessed by Pearson's correlation between DGV and response variables (EBV and dEBV). Regression coefficients of the response variables on the DGV were obtained to verify if the genomic predictions were biased. In addition, the mean square error of prediction (MSE) was used as a measure of verification of model fit to the data. The means of prediction accuracy, when EBV was used as a response variable, were 0.68, 0.68 and 0.67 for GBLUP, Bayes C pi and BLASSO, respectively. With dEBV, the mean prediction accuracy was 0.50 for all models. The averages of the EBV regression coefficients on DGV were 1.08 for all models (GBLUP, Bayes C pi and BLASSO), higher than those obtained for the regression coefficient of dEBV on DGV, which presented values of 1.05, 1.05 and 1.08 for GBLUP, Bayes C pi and BLASSO, respectively. None of the methods stood out in terms of prediction ability; however, the GBLUP method was the most appropriate for estimating the DGV, in a slightly more reliable and less biased way, besides presenting the lowest computational cost. In the context of the present study, EBV was the preferred response variables considering the genomic prediction accuracy despite dEBV also presented lower bias. |
id |
UNSP_a23320cdb703d7df0c8065d6140efd07 |
---|---|
oai_identifier_str |
oai:repositorio.unesp.br:11449/209331 |
network_acronym_str |
UNSP |
network_name_str |
Repositório Institucional da UNESP |
repository_id_str |
2946 |
spelling |
Prediction of genomic breeding values of milk traits in Brazilian Saanen goatsBayesian methodsgenome‐wide selectionmulti‐stepprediction abilitysmall populationsThe study's objective was to compare the genomic prediction ability methods for the traits milk yield, milk composition and somatic cell count of Saanen Brazilian goats. Nine hundred forty goats, genotyped with an Axiom_OviCap (Caprine) panel, Affimetrix customized array with 62,557 single nucleotide polymorphisms (SNPs), were used for the genomic selection analyses. The genomic methods studied to estimate the effects of SNPs and direct genomic values (DGV) were as follows: (a) genomic BLUP (GBLUP), (b) Bayes C pi and (c) Bayesian Lasso (BLASSO). Estimated breeding values (EBV) and deregressed estimated breeding values (dEBV) were used as response variables for the genomic predictions. The prediction ability was assessed by Pearson's correlation between DGV and response variables (EBV and dEBV). Regression coefficients of the response variables on the DGV were obtained to verify if the genomic predictions were biased. In addition, the mean square error of prediction (MSE) was used as a measure of verification of model fit to the data. The means of prediction accuracy, when EBV was used as a response variable, were 0.68, 0.68 and 0.67 for GBLUP, Bayes C pi and BLASSO, respectively. With dEBV, the mean prediction accuracy was 0.50 for all models. The averages of the EBV regression coefficients on DGV were 1.08 for all models (GBLUP, Bayes C pi and BLASSO), higher than those obtained for the regression coefficient of dEBV on DGV, which presented values of 1.05, 1.05 and 1.08 for GBLUP, Bayes C pi and BLASSO, respectively. None of the methods stood out in terms of prediction ability; however, the GBLUP method was the most appropriate for estimating the DGV, in a slightly more reliable and less biased way, besides presenting the lowest computational cost. In the context of the present study, EBV was the preferred response variables considering the genomic prediction accuracy despite dEBV also presented lower bias.Conselho Nacional de Desenvolvimento Científico e Tecnológico (CNPq)Coordenação de Aperfeiçoamento de Pessoal de Nível Superior (CAPES)Univ Fed Ceara, Dept Anim Sci, Fortaleza, Ceara, BrazilSao Paulo State Univ Julio de Mesquita Filho, Fac Agr & Vet Sci Jaboticabal, Anim Sci Dept 1, Jaboticabal, BrazilBrazilian Agr Res Corp EMBRAPA, Embrapa Caprinos & Ovinos, Estr Sobral Groairas, Sobral, BrazilNatl Council Sci & Technol Dev CNPq, Lago Sul, BrazilSao Paulo State Univ Julio de Mesquita Filho, Fac Agr & Vet Sci Jaboticabal, Anim Sci Dept 1, Jaboticabal, BrazilWiley-BlackwellUniv Fed CearaUniversidade Estadual Paulista (Unesp)Empresa Brasileira de Pesquisa Agropecuária (EMBRAPA)Natl Council Sci & Technol Dev CNPqSousa, Diego Rodrigues deNascimento, Andre Vieira do [UNESP]Lobo, Raimundo Nonato Braga2021-06-25T11:56:34Z2021-06-25T11:56:34Z2021-04-16info:eu-repo/semantics/publishedVersioninfo:eu-repo/semantics/article11http://dx.doi.org/10.1111/jbg.12550Journal Of Animal Breeding And Genetics. Hoboken: Wiley, 11 p., 2021.0931-2668http://hdl.handle.net/11449/20933110.1111/jbg.12550WOS:000640685300001Web of Sciencereponame:Repositório Institucional da UNESPinstname:Universidade Estadual Paulista (UNESP)instacron:UNESPengJournal Of Animal Breeding And Geneticsinfo:eu-repo/semantics/openAccess2021-10-23T19:28:03Zoai:repositorio.unesp.br:11449/209331Repositório InstitucionalPUBhttp://repositorio.unesp.br/oai/requestopendoar:29462021-10-23T19:28:03Repositório Institucional da UNESP - Universidade Estadual Paulista (UNESP)false |
dc.title.none.fl_str_mv |
Prediction of genomic breeding values of milk traits in Brazilian Saanen goats |
title |
Prediction of genomic breeding values of milk traits in Brazilian Saanen goats |
spellingShingle |
Prediction of genomic breeding values of milk traits in Brazilian Saanen goats Sousa, Diego Rodrigues de Bayesian methods genome‐ wide selection multi‐ step prediction ability small populations |
title_short |
Prediction of genomic breeding values of milk traits in Brazilian Saanen goats |
title_full |
Prediction of genomic breeding values of milk traits in Brazilian Saanen goats |
title_fullStr |
Prediction of genomic breeding values of milk traits in Brazilian Saanen goats |
title_full_unstemmed |
Prediction of genomic breeding values of milk traits in Brazilian Saanen goats |
title_sort |
Prediction of genomic breeding values of milk traits in Brazilian Saanen goats |
author |
Sousa, Diego Rodrigues de |
author_facet |
Sousa, Diego Rodrigues de Nascimento, Andre Vieira do [UNESP] Lobo, Raimundo Nonato Braga |
author_role |
author |
author2 |
Nascimento, Andre Vieira do [UNESP] Lobo, Raimundo Nonato Braga |
author2_role |
author author |
dc.contributor.none.fl_str_mv |
Univ Fed Ceara Universidade Estadual Paulista (Unesp) Empresa Brasileira de Pesquisa Agropecuária (EMBRAPA) Natl Council Sci & Technol Dev CNPq |
dc.contributor.author.fl_str_mv |
Sousa, Diego Rodrigues de Nascimento, Andre Vieira do [UNESP] Lobo, Raimundo Nonato Braga |
dc.subject.por.fl_str_mv |
Bayesian methods genome‐ wide selection multi‐ step prediction ability small populations |
topic |
Bayesian methods genome‐ wide selection multi‐ step prediction ability small populations |
description |
The study's objective was to compare the genomic prediction ability methods for the traits milk yield, milk composition and somatic cell count of Saanen Brazilian goats. Nine hundred forty goats, genotyped with an Axiom_OviCap (Caprine) panel, Affimetrix customized array with 62,557 single nucleotide polymorphisms (SNPs), were used for the genomic selection analyses. The genomic methods studied to estimate the effects of SNPs and direct genomic values (DGV) were as follows: (a) genomic BLUP (GBLUP), (b) Bayes C pi and (c) Bayesian Lasso (BLASSO). Estimated breeding values (EBV) and deregressed estimated breeding values (dEBV) were used as response variables for the genomic predictions. The prediction ability was assessed by Pearson's correlation between DGV and response variables (EBV and dEBV). Regression coefficients of the response variables on the DGV were obtained to verify if the genomic predictions were biased. In addition, the mean square error of prediction (MSE) was used as a measure of verification of model fit to the data. The means of prediction accuracy, when EBV was used as a response variable, were 0.68, 0.68 and 0.67 for GBLUP, Bayes C pi and BLASSO, respectively. With dEBV, the mean prediction accuracy was 0.50 for all models. The averages of the EBV regression coefficients on DGV were 1.08 for all models (GBLUP, Bayes C pi and BLASSO), higher than those obtained for the regression coefficient of dEBV on DGV, which presented values of 1.05, 1.05 and 1.08 for GBLUP, Bayes C pi and BLASSO, respectively. None of the methods stood out in terms of prediction ability; however, the GBLUP method was the most appropriate for estimating the DGV, in a slightly more reliable and less biased way, besides presenting the lowest computational cost. In the context of the present study, EBV was the preferred response variables considering the genomic prediction accuracy despite dEBV also presented lower bias. |
publishDate |
2021 |
dc.date.none.fl_str_mv |
2021-06-25T11:56:34Z 2021-06-25T11:56:34Z 2021-04-16 |
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 |
http://dx.doi.org/10.1111/jbg.12550 Journal Of Animal Breeding And Genetics. Hoboken: Wiley, 11 p., 2021. 0931-2668 http://hdl.handle.net/11449/209331 10.1111/jbg.12550 WOS:000640685300001 |
url |
http://dx.doi.org/10.1111/jbg.12550 http://hdl.handle.net/11449/209331 |
identifier_str_mv |
Journal Of Animal Breeding And Genetics. Hoboken: Wiley, 11 p., 2021. 0931-2668 10.1111/jbg.12550 WOS:000640685300001 |
dc.language.iso.fl_str_mv |
eng |
language |
eng |
dc.relation.none.fl_str_mv |
Journal Of Animal Breeding And Genetics |
dc.rights.driver.fl_str_mv |
info:eu-repo/semantics/openAccess |
eu_rights_str_mv |
openAccess |
dc.format.none.fl_str_mv |
11 |
dc.publisher.none.fl_str_mv |
Wiley-Blackwell |
publisher.none.fl_str_mv |
Wiley-Blackwell |
dc.source.none.fl_str_mv |
Web of Science reponame:Repositório Institucional da UNESP instname:Universidade Estadual Paulista (UNESP) instacron:UNESP |
instname_str |
Universidade Estadual Paulista (UNESP) |
instacron_str |
UNESP |
institution |
UNESP |
reponame_str |
Repositório Institucional da UNESP |
collection |
Repositório Institucional da UNESP |
repository.name.fl_str_mv |
Repositório Institucional da UNESP - Universidade Estadual Paulista (UNESP) |
repository.mail.fl_str_mv |
|
_version_ |
1799965354578935808 |