Linkage disequilibrium patterns and persistence of phase in purebred and crossbred pig (Sus scrofa) populations

Detalhes bibliográficos
Autor(a) principal: Veroneze, Renata
Data de Publicação: 2014
Outros Autores: Bastiaansen, John WM, Knol, Egbert F, Guimarães, Simone EF, Silva, Fabyano F, Harlizius, Barbara, Lopes, Marcos S, Lopes, Paulo S
Tipo de documento: Artigo
Idioma: eng
Título da fonte: LOCUS Repositório Institucional da UFV
Texto Completo: https://doi.org/10.1186/s12863-014-0126-3
http://www.locus.ufv.br/handle/123456789/12715
Resumo: Genomic selection and genomic wide association studies are widely used methods that aim to exploit the linkage disequilibrium (LD) between markers and quantitative trait loci (QTL). Securing a sufficiently large set of genotypes and phenotypes can be a limiting factor that may be overcome by combining data from multiple breeds or using crossbred information. However, the estimated effect of a marker in one breed or a crossbred can only be useful for the selection of animals in another breed if there is a correspondence of the phase between the marker and the QTL across breeds. Using data of five pure pig (Sus scrofa) lines (SL1, SL2, SL3, DL1, DL2), one F1 cross (DLF1) and two commercial finishing crosses (TER1 and TER2), the objectives of this study were: (i) to compare the equality of LD decay curves of different pig populations; and (ii) to evaluate the persistence of the LD phase across lines or final crosses. Almost all of the lines presented different extents of LD, except for the SL2 and DL3, both of which exhibited the same extent of LD. Similar levels of LD over large distances were found in crossbred and pure lines. The crossbred animals (DLF1, TER1 and TER2) presented a high persistence of phase with their parental lines, suggesting that the available porcine single nucleotide polymorphism (SNP) chip should be dense enough to include markers that have the same LD phase with QTL across crossbred and parental pure lines. The persistence of phase across pure lines varied considerably between the different line comparisons; however, correlations were above 0.8 for all line comparisons when marker distances were smaller than 50 kb. This study showed that crossbred populations could be very useful as a reference for the selection of pure lines by means of the available SNP chip panel. Here, we also pinpoint pure lines that could be combined in a multiline training population. However, if multiline reference populations are used for genomic selection, the required density of SNP panels should be higher compared with a single breed reference population.
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spelling Linkage disequilibrium patterns and persistence of phase in purebred and crossbred pig (Sus scrofa) populationsNonlinear modelSingle nucleotide polymorphismSNPGenomic selectionGenomic selection and genomic wide association studies are widely used methods that aim to exploit the linkage disequilibrium (LD) between markers and quantitative trait loci (QTL). Securing a sufficiently large set of genotypes and phenotypes can be a limiting factor that may be overcome by combining data from multiple breeds or using crossbred information. However, the estimated effect of a marker in one breed or a crossbred can only be useful for the selection of animals in another breed if there is a correspondence of the phase between the marker and the QTL across breeds. Using data of five pure pig (Sus scrofa) lines (SL1, SL2, SL3, DL1, DL2), one F1 cross (DLF1) and two commercial finishing crosses (TER1 and TER2), the objectives of this study were: (i) to compare the equality of LD decay curves of different pig populations; and (ii) to evaluate the persistence of the LD phase across lines or final crosses. Almost all of the lines presented different extents of LD, except for the SL2 and DL3, both of which exhibited the same extent of LD. Similar levels of LD over large distances were found in crossbred and pure lines. The crossbred animals (DLF1, TER1 and TER2) presented a high persistence of phase with their parental lines, suggesting that the available porcine single nucleotide polymorphism (SNP) chip should be dense enough to include markers that have the same LD phase with QTL across crossbred and parental pure lines. The persistence of phase across pure lines varied considerably between the different line comparisons; however, correlations were above 0.8 for all line comparisons when marker distances were smaller than 50 kb. This study showed that crossbred populations could be very useful as a reference for the selection of pure lines by means of the available SNP chip panel. Here, we also pinpoint pure lines that could be combined in a multiline training population. However, if multiline reference populations are used for genomic selection, the required density of SNP panels should be higher compared with a single breed reference population.BioMed Central Genetics2017-11-01T16:18:46Z2017-11-01T16:18:46Z2014-11-25info:eu-repo/semantics/publishedVersioninfo:eu-repo/semantics/articlepdfapplication/pdf1471-2156https://doi.org/10.1186/s12863-014-0126-3http://www.locus.ufv.br/handle/123456789/12715engv. 15, n. 126, Nov. 2014Veroneze, RenataBastiaansen, John WMKnol, Egbert FGuimarães, Simone EFSilva, Fabyano FHarlizius, BarbaraLopes, Marcos SLopes, Paulo Sinfo:eu-repo/semantics/openAccessreponame:LOCUS Repositório Institucional da UFVinstname:Universidade Federal de Viçosa (UFV)instacron:UFV2024-07-12T08:45:53Zoai:locus.ufv.br:123456789/12715Repositório InstitucionalPUBhttps://www.locus.ufv.br/oai/requestfabiojreis@ufv.bropendoar:21452024-07-12T08:45:53LOCUS Repositório Institucional da UFV - Universidade Federal de Viçosa (UFV)false
dc.title.none.fl_str_mv Linkage disequilibrium patterns and persistence of phase in purebred and crossbred pig (Sus scrofa) populations
title Linkage disequilibrium patterns and persistence of phase in purebred and crossbred pig (Sus scrofa) populations
spellingShingle Linkage disequilibrium patterns and persistence of phase in purebred and crossbred pig (Sus scrofa) populations
Veroneze, Renata
Nonlinear model
Single nucleotide polymorphism
SNP
Genomic selection
title_short Linkage disequilibrium patterns and persistence of phase in purebred and crossbred pig (Sus scrofa) populations
title_full Linkage disequilibrium patterns and persistence of phase in purebred and crossbred pig (Sus scrofa) populations
title_fullStr Linkage disequilibrium patterns and persistence of phase in purebred and crossbred pig (Sus scrofa) populations
title_full_unstemmed Linkage disequilibrium patterns and persistence of phase in purebred and crossbred pig (Sus scrofa) populations
title_sort Linkage disequilibrium patterns and persistence of phase in purebred and crossbred pig (Sus scrofa) populations
author Veroneze, Renata
author_facet Veroneze, Renata
Bastiaansen, John WM
Knol, Egbert F
Guimarães, Simone EF
Silva, Fabyano F
Harlizius, Barbara
Lopes, Marcos S
Lopes, Paulo S
author_role author
author2 Bastiaansen, John WM
Knol, Egbert F
Guimarães, Simone EF
Silva, Fabyano F
Harlizius, Barbara
Lopes, Marcos S
Lopes, Paulo S
author2_role author
author
author
author
author
author
author
dc.contributor.author.fl_str_mv Veroneze, Renata
Bastiaansen, John WM
Knol, Egbert F
Guimarães, Simone EF
Silva, Fabyano F
Harlizius, Barbara
Lopes, Marcos S
Lopes, Paulo S
dc.subject.por.fl_str_mv Nonlinear model
Single nucleotide polymorphism
SNP
Genomic selection
topic Nonlinear model
Single nucleotide polymorphism
SNP
Genomic selection
description Genomic selection and genomic wide association studies are widely used methods that aim to exploit the linkage disequilibrium (LD) between markers and quantitative trait loci (QTL). Securing a sufficiently large set of genotypes and phenotypes can be a limiting factor that may be overcome by combining data from multiple breeds or using crossbred information. However, the estimated effect of a marker in one breed or a crossbred can only be useful for the selection of animals in another breed if there is a correspondence of the phase between the marker and the QTL across breeds. Using data of five pure pig (Sus scrofa) lines (SL1, SL2, SL3, DL1, DL2), one F1 cross (DLF1) and two commercial finishing crosses (TER1 and TER2), the objectives of this study were: (i) to compare the equality of LD decay curves of different pig populations; and (ii) to evaluate the persistence of the LD phase across lines or final crosses. Almost all of the lines presented different extents of LD, except for the SL2 and DL3, both of which exhibited the same extent of LD. Similar levels of LD over large distances were found in crossbred and pure lines. The crossbred animals (DLF1, TER1 and TER2) presented a high persistence of phase with their parental lines, suggesting that the available porcine single nucleotide polymorphism (SNP) chip should be dense enough to include markers that have the same LD phase with QTL across crossbred and parental pure lines. The persistence of phase across pure lines varied considerably between the different line comparisons; however, correlations were above 0.8 for all line comparisons when marker distances were smaller than 50 kb. This study showed that crossbred populations could be very useful as a reference for the selection of pure lines by means of the available SNP chip panel. Here, we also pinpoint pure lines that could be combined in a multiline training population. However, if multiline reference populations are used for genomic selection, the required density of SNP panels should be higher compared with a single breed reference population.
publishDate 2014
dc.date.none.fl_str_mv 2014-11-25
2017-11-01T16:18:46Z
2017-11-01T16:18:46Z
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 1471-2156
https://doi.org/10.1186/s12863-014-0126-3
http://www.locus.ufv.br/handle/123456789/12715
identifier_str_mv 1471-2156
url https://doi.org/10.1186/s12863-014-0126-3
http://www.locus.ufv.br/handle/123456789/12715
dc.language.iso.fl_str_mv eng
language eng
dc.relation.none.fl_str_mv v. 15, n. 126, Nov. 2014
dc.rights.driver.fl_str_mv info:eu-repo/semantics/openAccess
eu_rights_str_mv openAccess
dc.format.none.fl_str_mv pdf
application/pdf
dc.publisher.none.fl_str_mv BioMed Central Genetics
publisher.none.fl_str_mv BioMed Central Genetics
dc.source.none.fl_str_mv reponame:LOCUS Repositório Institucional da UFV
instname:Universidade Federal de Viçosa (UFV)
instacron:UFV
instname_str Universidade Federal de Viçosa (UFV)
instacron_str UFV
institution UFV
reponame_str LOCUS Repositório Institucional da UFV
collection LOCUS Repositório Institucional da UFV
repository.name.fl_str_mv LOCUS Repositório Institucional da UFV - Universidade Federal de Viçosa (UFV)
repository.mail.fl_str_mv fabiojreis@ufv.br
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