Evaluation of imputation accuracy using the combination of two high-density panels in nelore beef cattle.

Detalhes bibliográficos
Autor(a) principal: BERNARDES
Data de Publicação: 2019
Outros Autores: NASCIMENTO, G. B. do, SAVEGNAGO, R. P., BUZANSKAS, M. E., WATANABE, R. N., REGITANO, L. C. de A., COUTINHO, L. L., GONDRO, C., MUNARI, D. P.
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/1115563
Resumo: this study compared imputation from lower-density commercial and customized panels to high-density panels and a combined panel (Illumina and Affymetrix) in Nelore beef cattle. Additionally, linkage disequilibrium and haplotype block conformation were estimated in individual high-density panels and compared with corresponding values in the combined panel after imputation. Overall, 814 animals were genotyped using BovineHD BeadChip (IllumHD), and 93 of these animals were also genotyped using the Axion Genome-Wide BOS 1 Array Plate (AffyHD). In general, customization considering linkage disequilibrium and minor allele frequency had the highest accuracies. The IllumHD panel had higher values of linkage disequilibrium for short distances between SNPs than AffyHD and the combined panel. The combined panel had an increased number of small haplotype blocks. The use of a combined panel is recommended due to its increased density and number of haplotype blocks, which in turn increase the probability of a marker being close to a quantitative trait locus of interest. Considering common SNPs between IllumHD and AffyHD for the customization of a low-density panel increases the imputation accuracy for IllumHD, AffyHD and the combined panel.
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spelling Evaluation of imputation accuracy using the combination of two high-density panels in nelore beef cattle.BovinoGado de CorteBeef cattleAnimal breedingthis study compared imputation from lower-density commercial and customized panels to high-density panels and a combined panel (Illumina and Affymetrix) in Nelore beef cattle. Additionally, linkage disequilibrium and haplotype block conformation were estimated in individual high-density panels and compared with corresponding values in the combined panel after imputation. Overall, 814 animals were genotyped using BovineHD BeadChip (IllumHD), and 93 of these animals were also genotyped using the Axion Genome-Wide BOS 1 Array Plate (AffyHD). In general, customization considering linkage disequilibrium and minor allele frequency had the highest accuracies. The IllumHD panel had higher values of linkage disequilibrium for short distances between SNPs than AffyHD and the combined panel. The combined panel had an increased number of small haplotype blocks. The use of a combined panel is recommended due to its increased density and number of haplotype blocks, which in turn increase the probability of a marker being close to a quantitative trait locus of interest. Considering common SNPs between IllumHD and AffyHD for the customization of a low-density panel increases the imputation accuracy for IllumHD, AffyHD and the combined panel.Priscila Arrigucci Bernardes, UNESP; Guilherme Batista do Nascimento, Centro Universitário de Adamantina; Rodrigo Pelicioni Savegnago, Instituto de Zootecnia; Marcos Eli Buzanskas, Universidade Federal da Paraiba; Rafael Nakamura Watanabe, UNESP; LUCIANA CORREIA DE ALMEIDA REGITANO, CPPSE; Luiz Lehmann Coutinho, USP; Cedric Gondro, Michigan State University; Danísio Prado Munari, UNESP.BERNARDESNASCIMENTO, G. B. doSAVEGNAGO, R. P.BUZANSKAS, M. E.WATANABE, R. N.REGITANO, L. C. de A.COUTINHO, L. L.GONDRO, C.MUNARI, D. P.2019-11-30T00:36:19Z2019-11-30T00:36:19Z2019-11-2920192020-01-10T11:11:11Zinfo:eu-repo/semantics/publishedVersioninfo:eu-repo/semantics/articleScientific Reports, v. 9, 17920, 2019.http://www.alice.cnptia.embrapa.br/alice/handle/doc/1115563doi.org/10.1038/s41598-019-54382-wenginfo: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:EMBRAPA2019-11-30T00:36:26Zoai:www.alice.cnptia.embrapa.br:doc/1115563Repositório InstitucionalPUBhttps://www.alice.cnptia.embrapa.br/oai/requestopendoar:21542019-11-30T00:36:26falseRepositório InstitucionalPUBhttps://www.alice.cnptia.embrapa.br/oai/requestcg-riaa@embrapa.bropendoar:21542019-11-30T00:36:26Repositório 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 Evaluation of imputation accuracy using the combination of two high-density panels in nelore beef cattle.
title Evaluation of imputation accuracy using the combination of two high-density panels in nelore beef cattle.
spellingShingle Evaluation of imputation accuracy using the combination of two high-density panels in nelore beef cattle.
BERNARDES
Bovino
Gado de Corte
Beef cattle
Animal breeding
title_short Evaluation of imputation accuracy using the combination of two high-density panels in nelore beef cattle.
title_full Evaluation of imputation accuracy using the combination of two high-density panels in nelore beef cattle.
title_fullStr Evaluation of imputation accuracy using the combination of two high-density panels in nelore beef cattle.
title_full_unstemmed Evaluation of imputation accuracy using the combination of two high-density panels in nelore beef cattle.
title_sort Evaluation of imputation accuracy using the combination of two high-density panels in nelore beef cattle.
author BERNARDES
author_facet BERNARDES
NASCIMENTO, G. B. do
SAVEGNAGO, R. P.
BUZANSKAS, M. E.
WATANABE, R. N.
REGITANO, L. C. de A.
COUTINHO, L. L.
GONDRO, C.
MUNARI, D. P.
author_role author
author2 NASCIMENTO, G. B. do
SAVEGNAGO, R. P.
BUZANSKAS, M. E.
WATANABE, R. N.
REGITANO, L. C. de A.
COUTINHO, L. L.
GONDRO, C.
MUNARI, D. P.
author2_role author
author
author
author
author
author
author
author
dc.contributor.none.fl_str_mv Priscila Arrigucci Bernardes, UNESP; Guilherme Batista do Nascimento, Centro Universitário de Adamantina; Rodrigo Pelicioni Savegnago, Instituto de Zootecnia; Marcos Eli Buzanskas, Universidade Federal da Paraiba; Rafael Nakamura Watanabe, UNESP; LUCIANA CORREIA DE ALMEIDA REGITANO, CPPSE; Luiz Lehmann Coutinho, USP; Cedric Gondro, Michigan State University; Danísio Prado Munari, UNESP.
dc.contributor.author.fl_str_mv BERNARDES
NASCIMENTO, G. B. do
SAVEGNAGO, R. P.
BUZANSKAS, M. E.
WATANABE, R. N.
REGITANO, L. C. de A.
COUTINHO, L. L.
GONDRO, C.
MUNARI, D. P.
dc.subject.por.fl_str_mv Bovino
Gado de Corte
Beef cattle
Animal breeding
topic Bovino
Gado de Corte
Beef cattle
Animal breeding
description this study compared imputation from lower-density commercial and customized panels to high-density panels and a combined panel (Illumina and Affymetrix) in Nelore beef cattle. Additionally, linkage disequilibrium and haplotype block conformation were estimated in individual high-density panels and compared with corresponding values in the combined panel after imputation. Overall, 814 animals were genotyped using BovineHD BeadChip (IllumHD), and 93 of these animals were also genotyped using the Axion Genome-Wide BOS 1 Array Plate (AffyHD). In general, customization considering linkage disequilibrium and minor allele frequency had the highest accuracies. The IllumHD panel had higher values of linkage disequilibrium for short distances between SNPs than AffyHD and the combined panel. The combined panel had an increased number of small haplotype blocks. The use of a combined panel is recommended due to its increased density and number of haplotype blocks, which in turn increase the probability of a marker being close to a quantitative trait locus of interest. Considering common SNPs between IllumHD and AffyHD for the customization of a low-density panel increases the imputation accuracy for IllumHD, AffyHD and the combined panel.
publishDate 2019
dc.date.none.fl_str_mv 2019-11-30T00:36:19Z
2019-11-30T00:36:19Z
2019-11-29
2019
2020-01-10T11:11:11Z
dc.type.driver.fl_str_mv info:eu-repo/semantics/publishedVersion
info:eu-repo/semantics/article
format article
status_str publishedVersion
dc.identifier.uri.fl_str_mv Scientific Reports, v. 9, 17920, 2019.
http://www.alice.cnptia.embrapa.br/alice/handle/doc/1115563
doi.org/10.1038/s41598-019-54382-w
identifier_str_mv Scientific Reports, v. 9, 17920, 2019.
doi.org/10.1038/s41598-019-54382-w
url http://www.alice.cnptia.embrapa.br/alice/handle/doc/1115563
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)
collection Repositório Institucional da EMBRAPA (Repository Open Access to Scientific Information from EMBRAPA - Alice)
repository.name.fl_str_mv 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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