Genomic selection for boar taint and carcass traits in a commercial pig line
Autor(a) principal: | |
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Data de Publicação: | 2012 |
Tipo de documento: | Dissertação |
Idioma: | por |
Título da fonte: | LOCUS Repositório Institucional da UFV |
Texto Completo: | http://locus.ufv.br/handle/123456789/5750 |
Resumo: | From the beginning of the century, advances in genotyping enabled the development of new classes of markers, among which stand out single nucleotide polymorphisms (SNPs). Due to the availability of these markers it has been proposed genomic selection, consisting of simultaneous analysis of large number of markers distributed throughout the genome; its success depends on the method used for prediction of genomic breeding values. The objective of this study was to compare the methods RR-BLUP and Bayesian LASSO to calculate estimated genomic breeding values (GEBVs) and also to determine which method provides more accurate results for genomic selection in pigs. A total of 622 boarswere genotyped for 2,500 SNPs, and phenotyped for the following traits: concentration of androstenone, concentration of skatole, backfat thickness and loin depth. The R software packages rrBLUP and BLR were used respectively for the implementation of the RR-BLUP method and Bayesian LASSO method. Genetic correlations between the traits were calculated by the correlation between the vectors of GEBVs. The Bayesian LASSO method reached higher accuracy values in three traits: concentration of androstenone (0.65), concentration of skatole (0.58) and loin depth (0.33), and RR-BLUP was more accurate (0.61) for backfat thickness. Genetic correlations calculated, show that exists a small genetic correlation (0.03) between backfat thickness and loin depth. Between the concentrations of androstenone and skatole also exists a genetic correlation (0.24)that is consistent with results from other studies. Thus, concerning to the estimates of effects of markers, for all traits the found peaks were in regions where are reported QTLs inPIGQTLdatabase and other studies. |
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Campos, Carolina Filardi dehttp://lattes.cnpq.br/4344854254887585Silva, Fabyano Fonseca ehttp://buscatextual.cnpq.br/buscatextual/visualizacv.do?id=K4766260Z2Lopes, Paulo Sáviohttp://buscatextual.cnpq.br/buscatextual/visualizacv.do?id=K4783377H1Guimarães, Simone Eliza Facionihttp://buscatextual.cnpq.br/buscatextual/visualizacv.do?id=K4782526Y2Gasparino, Elianehttp://lattes.cnpq.br/93590555815115572015-03-26T13:55:13Z2013-04-162015-03-26T13:55:13Z2012-07-23CAMPOS, Carolina Filardi de. Genomic selection for boar taint and carcass traits in a commercial pig line. 2012. 47 f. Dissertação (Mestrado em Genética e Melhoramento de Animais Domésticos; Nutrição e Alimentação Animal; Pastagens e Forragicul) - Universidade Federal de Viçosa, Viçosa, 2012.http://locus.ufv.br/handle/123456789/5750From the beginning of the century, advances in genotyping enabled the development of new classes of markers, among which stand out single nucleotide polymorphisms (SNPs). Due to the availability of these markers it has been proposed genomic selection, consisting of simultaneous analysis of large number of markers distributed throughout the genome; its success depends on the method used for prediction of genomic breeding values. The objective of this study was to compare the methods RR-BLUP and Bayesian LASSO to calculate estimated genomic breeding values (GEBVs) and also to determine which method provides more accurate results for genomic selection in pigs. A total of 622 boarswere genotyped for 2,500 SNPs, and phenotyped for the following traits: concentration of androstenone, concentration of skatole, backfat thickness and loin depth. The R software packages rrBLUP and BLR were used respectively for the implementation of the RR-BLUP method and Bayesian LASSO method. Genetic correlations between the traits were calculated by the correlation between the vectors of GEBVs. The Bayesian LASSO method reached higher accuracy values in three traits: concentration of androstenone (0.65), concentration of skatole (0.58) and loin depth (0.33), and RR-BLUP was more accurate (0.61) for backfat thickness. Genetic correlations calculated, show that exists a small genetic correlation (0.03) between backfat thickness and loin depth. Between the concentrations of androstenone and skatole also exists a genetic correlation (0.24)that is consistent with results from other studies. Thus, concerning to the estimates of effects of markers, for all traits the found peaks were in regions where are reported QTLs inPIGQTLdatabase and other studies.A partir do início do século XXI, avanços na genotipagem permitiram o desenvolvimento de novas classes de marcadores, entre os quais se destacam os polimorfismos de nucleotídeos simples (SNPs). Devido à disponibilidade desses marcadores, foi proposta a Seleção Genômica, que consiste em uma análise simultânea de um grande número de marcadores distribuídos ao longo do genoma, cujo sucesso depende do método utilizado de predição de valores genéticos genômicos. O objetivo deste estudo foi comparar os métodos RR-BLUP e LASSO Bayesiano para cálculo dos valores genéticos genômicos estimados (GEBVs) e determinar qual método apresenta resultados mais acurados para a seleção genômica em suínos. Foram genotipados 622 suínos machos não castrados para 2.500 SNPs, e fenotipados para as seguintes características: concentração de androstenona, concentração de skatol, espessura de gordura subcutânea e profundidade de lombo. Os pacotes rrBLUP e BLR do software R foram utilizados respectivamente para a implementação do método RR-BLUP e LASSO Bayesiano. As correlações genéticas entre as característicasforam calculadas por meio da correlação entre os vetores de GEBVs. O método LASSO Bayesiano apresentou valores mais elevados de acurácia em três características: concentração de androstenona (0,65), concentração deskatol (0,58), e profundidade de lombo (0,33), e o RR-BLUP foi mais acurado para espessura de gordura subcutânea (0,61). As correlações genéticas calculadas, mostram que existe uma pequena correlação genética entre espessura de gordura subcutânea e profundidade de lombo (0,03). Entre as concentrações de androstenona e skatol também existe correlação genética (0,24) que é consistente com os resultados de outros estudos. Assim, com relação às estimativas de efeitos de marcadores, para todas as características os picos encontrados estão em regiões onde se encontram QTLs relatados no PIGQTLdatabase e em outros estudos.Fundação de Amparo a Pesquisa do Estado de Minas Geraisapplication/pdfporUniversidade Federal de ViçosaMestrado em ZootecniaUFVBRGenética e Melhoramento de Animais Domésticos; Nutrição e Alimentação Animal; Pastagens e ForragiculSeleção genômica amplaProdução de suínosMarcadores molecularesSNPsSelection genomeProduction of pigsMolecular markers, SNPsCNPQ::CIENCIAS AGRARIAS::ZOOTECNIA::GENETICA E MELHORAMENTO DOS ANIMAIS DOMESTICOSGenomic selection for boar taint and carcass traits in a commercial pig lineSeleção genômica para características relacionadas ao odor da carne e características de carcaça em uma linhagem comercial de suínosinfo:eu-repo/semantics/publishedVersioninfo:eu-repo/semantics/masterThesisinfo:eu-repo/semantics/openAccessreponame:LOCUS Repositório Institucional da UFVinstname:Universidade Federal de Viçosa (UFV)instacron:UFVORIGINALtexto completo.pdfapplication/pdf833034https://locus.ufv.br//bitstream/123456789/5750/1/texto%20completo.pdfc1160b57dd7b16db04bc27109bc4f8f1MD51TEXTtexto completo.pdf.txttexto completo.pdf.txtExtracted texttext/plain67885https://locus.ufv.br//bitstream/123456789/5750/2/texto%20completo.pdf.txt4ee9503f2fc0eb6bc40480766a4d5a94MD52THUMBNAILtexto completo.pdf.jpgtexto completo.pdf.jpgIM Thumbnailimage/jpeg3588https://locus.ufv.br//bitstream/123456789/5750/3/texto%20completo.pdf.jpg1074b55e0eeeae5badf107b1b4e618f8MD53123456789/57502016-05-19 06:41:03.208oai:locus.ufv.br:123456789/5750Repositório InstitucionalPUBhttps://www.locus.ufv.br/oai/requestfabiojreis@ufv.bropendoar:21452016-05-19T09:41:03LOCUS Repositório Institucional da UFV - Universidade Federal de Viçosa (UFV)false |
dc.title.por.fl_str_mv |
Genomic selection for boar taint and carcass traits in a commercial pig line |
dc.title.alternative.eng.fl_str_mv |
Seleção genômica para características relacionadas ao odor da carne e características de carcaça em uma linhagem comercial de suínos |
title |
Genomic selection for boar taint and carcass traits in a commercial pig line |
spellingShingle |
Genomic selection for boar taint and carcass traits in a commercial pig line Campos, Carolina Filardi de Seleção genômica ampla Produção de suínos Marcadores moleculares SNPs Selection genome Production of pigs Molecular markers, SNPs CNPQ::CIENCIAS AGRARIAS::ZOOTECNIA::GENETICA E MELHORAMENTO DOS ANIMAIS DOMESTICOS |
title_short |
Genomic selection for boar taint and carcass traits in a commercial pig line |
title_full |
Genomic selection for boar taint and carcass traits in a commercial pig line |
title_fullStr |
Genomic selection for boar taint and carcass traits in a commercial pig line |
title_full_unstemmed |
Genomic selection for boar taint and carcass traits in a commercial pig line |
title_sort |
Genomic selection for boar taint and carcass traits in a commercial pig line |
author |
Campos, Carolina Filardi de |
author_facet |
Campos, Carolina Filardi de |
author_role |
author |
dc.contributor.authorLattes.por.fl_str_mv |
http://lattes.cnpq.br/4344854254887585 |
dc.contributor.author.fl_str_mv |
Campos, Carolina Filardi de |
dc.contributor.advisor-co1.fl_str_mv |
Silva, Fabyano Fonseca e |
dc.contributor.advisor-co1Lattes.fl_str_mv |
http://buscatextual.cnpq.br/buscatextual/visualizacv.do?id=K4766260Z2 |
dc.contributor.advisor-co2.fl_str_mv |
Lopes, Paulo Sávio |
dc.contributor.advisor-co2Lattes.fl_str_mv |
http://buscatextual.cnpq.br/buscatextual/visualizacv.do?id=K4783377H1 |
dc.contributor.advisor1.fl_str_mv |
Guimarães, Simone Eliza Facioni |
dc.contributor.advisor1Lattes.fl_str_mv |
http://buscatextual.cnpq.br/buscatextual/visualizacv.do?id=K4782526Y2 |
dc.contributor.referee1.fl_str_mv |
Gasparino, Eliane |
dc.contributor.referee1Lattes.fl_str_mv |
http://lattes.cnpq.br/9359055581511557 |
contributor_str_mv |
Silva, Fabyano Fonseca e Lopes, Paulo Sávio Guimarães, Simone Eliza Facioni Gasparino, Eliane |
dc.subject.por.fl_str_mv |
Seleção genômica ampla Produção de suínos Marcadores moleculares SNPs |
topic |
Seleção genômica ampla Produção de suínos Marcadores moleculares SNPs Selection genome Production of pigs Molecular markers, SNPs CNPQ::CIENCIAS AGRARIAS::ZOOTECNIA::GENETICA E MELHORAMENTO DOS ANIMAIS DOMESTICOS |
dc.subject.eng.fl_str_mv |
Selection genome Production of pigs Molecular markers, SNPs |
dc.subject.cnpq.fl_str_mv |
CNPQ::CIENCIAS AGRARIAS::ZOOTECNIA::GENETICA E MELHORAMENTO DOS ANIMAIS DOMESTICOS |
description |
From the beginning of the century, advances in genotyping enabled the development of new classes of markers, among which stand out single nucleotide polymorphisms (SNPs). Due to the availability of these markers it has been proposed genomic selection, consisting of simultaneous analysis of large number of markers distributed throughout the genome; its success depends on the method used for prediction of genomic breeding values. The objective of this study was to compare the methods RR-BLUP and Bayesian LASSO to calculate estimated genomic breeding values (GEBVs) and also to determine which method provides more accurate results for genomic selection in pigs. A total of 622 boarswere genotyped for 2,500 SNPs, and phenotyped for the following traits: concentration of androstenone, concentration of skatole, backfat thickness and loin depth. The R software packages rrBLUP and BLR were used respectively for the implementation of the RR-BLUP method and Bayesian LASSO method. Genetic correlations between the traits were calculated by the correlation between the vectors of GEBVs. The Bayesian LASSO method reached higher accuracy values in three traits: concentration of androstenone (0.65), concentration of skatole (0.58) and loin depth (0.33), and RR-BLUP was more accurate (0.61) for backfat thickness. Genetic correlations calculated, show that exists a small genetic correlation (0.03) between backfat thickness and loin depth. Between the concentrations of androstenone and skatole also exists a genetic correlation (0.24)that is consistent with results from other studies. Thus, concerning to the estimates of effects of markers, for all traits the found peaks were in regions where are reported QTLs inPIGQTLdatabase and other studies. |
publishDate |
2012 |
dc.date.issued.fl_str_mv |
2012-07-23 |
dc.date.available.fl_str_mv |
2013-04-16 2015-03-26T13:55:13Z |
dc.date.accessioned.fl_str_mv |
2015-03-26T13:55:13Z |
dc.type.status.fl_str_mv |
info:eu-repo/semantics/publishedVersion |
dc.type.driver.fl_str_mv |
info:eu-repo/semantics/masterThesis |
format |
masterThesis |
status_str |
publishedVersion |
dc.identifier.citation.fl_str_mv |
CAMPOS, Carolina Filardi de. Genomic selection for boar taint and carcass traits in a commercial pig line. 2012. 47 f. Dissertação (Mestrado em Genética e Melhoramento de Animais Domésticos; Nutrição e Alimentação Animal; Pastagens e Forragicul) - Universidade Federal de Viçosa, Viçosa, 2012. |
dc.identifier.uri.fl_str_mv |
http://locus.ufv.br/handle/123456789/5750 |
identifier_str_mv |
CAMPOS, Carolina Filardi de. Genomic selection for boar taint and carcass traits in a commercial pig line. 2012. 47 f. Dissertação (Mestrado em Genética e Melhoramento de Animais Domésticos; Nutrição e Alimentação Animal; Pastagens e Forragicul) - Universidade Federal de Viçosa, Viçosa, 2012. |
url |
http://locus.ufv.br/handle/123456789/5750 |
dc.language.iso.fl_str_mv |
por |
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por |
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info:eu-repo/semantics/openAccess |
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openAccess |
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application/pdf |
dc.publisher.none.fl_str_mv |
Universidade Federal de Viçosa |
dc.publisher.program.fl_str_mv |
Mestrado em Zootecnia |
dc.publisher.initials.fl_str_mv |
UFV |
dc.publisher.country.fl_str_mv |
BR |
dc.publisher.department.fl_str_mv |
Genética e Melhoramento de Animais Domésticos; Nutrição e Alimentação Animal; Pastagens e Forragicul |
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Universidade Federal de Viçosa |
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