Study of whole genome linkage disequilibrium in Nellore cattle
Autor(a) principal: | |
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Data de Publicação: | 2013 |
Outros Autores: | , , , , , , , , , , , , |
Tipo de documento: | Artigo |
Idioma: | eng |
Título da fonte: | Repositório Institucional da UNESP |
Texto Completo: | http://dx.doi.org/10.1186/1471-2164-14-305 http://hdl.handle.net/11449/75351 |
Resumo: | Background: Knowledge of the linkage disequilibrium (LD) between markers is important to establish the number of markers necessary for association studies and genomic selection. The objective of this study was to evaluate the extent of LD in Nellore cattle using a high density SNP panel and 795 genotyped steers.Results: After data editing, 446,986 SNPs were used for the estimation of LD, comprising 2508.4 Mb of the genome. The mean distance between adjacent markers was 4.90 ± 2.89 kb. The minor allele frequency (MAF) was less than 0.20 in a considerable proportion of SNPs. The overall mean LD between marker pairs measured by r2 and |D'| was 0.17 and 0.52, respectively. The LD (r2) decreased with increasing physical distance between markers from 0.34 (1 kb) to 0.11 (100 kb). In contrast to this clear decrease of LD measured by r2, the changes in |D'| indicated a less pronounced decline of LD. Chromosomes BTA1, BTA27, BTA28 and BTA29 showed lower levels of LD at any distance between markers. Except for these four chromosomes, the level of LD (r2) was higher than 0.20 for markers separated by less than 20 kb. At distances < 3 kb, the level of LD was higher than 0.30. The LD (r2) between markers was higher when the MAF threshold was high (0.15), especially when the distance between markers was short.Conclusions: The level of LD estimated for markers separated by less than 30 kb indicates that the High Density Bovine SNP BeadChip will likely be a suitable tool for prediction of genomic breeding values in Nellore cattle. © 2013 Espigolan et al.; licensee BioMed Central Ltd. |
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Study of whole genome linkage disequilibrium in Nellore cattleBeef cattleGenomeLinkage disequilibriumMolecular markersanimal geneticscattlechromosomechromosome analysischromosome BTA1chromosome BTA27chromosome BTA28chromosome BTA29gene frequencygene linkage disequilibriumgenetic distancegenetic markergenotypenonhumansingle nucleotide polymorphismBosBovinaeBackground: Knowledge of the linkage disequilibrium (LD) between markers is important to establish the number of markers necessary for association studies and genomic selection. The objective of this study was to evaluate the extent of LD in Nellore cattle using a high density SNP panel and 795 genotyped steers.Results: After data editing, 446,986 SNPs were used for the estimation of LD, comprising 2508.4 Mb of the genome. The mean distance between adjacent markers was 4.90 ± 2.89 kb. The minor allele frequency (MAF) was less than 0.20 in a considerable proportion of SNPs. The overall mean LD between marker pairs measured by r2 and |D'| was 0.17 and 0.52, respectively. The LD (r2) decreased with increasing physical distance between markers from 0.34 (1 kb) to 0.11 (100 kb). In contrast to this clear decrease of LD measured by r2, the changes in |D'| indicated a less pronounced decline of LD. Chromosomes BTA1, BTA27, BTA28 and BTA29 showed lower levels of LD at any distance between markers. Except for these four chromosomes, the level of LD (r2) was higher than 0.20 for markers separated by less than 20 kb. At distances < 3 kb, the level of LD was higher than 0.30. The LD (r2) between markers was higher when the MAF threshold was high (0.15), especially when the distance between markers was short.Conclusions: The level of LD estimated for markers separated by less than 30 kb indicates that the High Density Bovine SNP BeadChip will likely be a suitable tool for prediction of genomic breeding values in Nellore cattle. © 2013 Espigolan et al.; licensee BioMed Central Ltd.Conselho Nacional de Desenvolvimento Científico e Tecnológico (CNPq)Faculdade de Ciências Agrárias e Veterinárias UNESP, Jaboticabal, SP 14884-000Instituto Nacional de Ciência e Tecnologia - Ciência Animal (INCT- CA), Viçosa, MG 36570 000Departamento de Nutrição e Produção Animal Faculdade de Medicina Veterinária e Zootecnia USP, Pirassununga, SPCentre for Genetic Improvement of Livestock Department of Animal and Poultry Science University of Guelph, Guelph, ONCNPq Fellowship National Council of Technological and Scientific Development SHIS QI 1, Conjunto B, 71605-001, Brasília, DFGenSys Consultores Associados, Porto AlegreFaculdade de Ciências Agrárias e Veterinárias UNESP, Jaboticabal, SP 14884-000Universidade Estadual Paulista (Unesp)Instituto Nacional de Ciência e Tecnologia - Ciência Animal (INCT- CA)Universidade de São Paulo (USP)University of GuelphSHIS QI 1GenSys Consultores AssociadosEspigolan, Rafael [UNESP]Baldi, Fernando [UNESP]Boligon, Arione A. [UNESP]Souza, Fabio R.P. [UNESP]Gordo, Daniel G.M. [UNESP]Tonussi, Rafael L. [UNESP]Cardoso, Diércles F. [UNESP]Oliveira, Henrique N. [UNESP]Tonhati, Humberto [UNESP]Sargolzaei, MehdiSchenkel, Flavio S.Carvalheiro, RobertoFerro, Jesus A. [UNESP]Albuquerque, Lucia G. [UNESP]2014-05-27T11:29:06Z2014-05-27T11:29:06Z2013-05-05info:eu-repo/semantics/publishedVersioninfo:eu-repo/semantics/articleapplication/pdfhttp://dx.doi.org/10.1186/1471-2164-14-305BMC Genomics, v. 14, n. 1, 2013.1471-2164http://hdl.handle.net/11449/7535110.1186/1471-2164-14-305WOS:0003194078000012-s2.0-848769753742-s2.0-84876975374.pdf7445254960858159Scopusreponame:Repositório Institucional da UNESPinstname:Universidade Estadual Paulista (UNESP)instacron:UNESPengBMC Genomics3.7302,110info:eu-repo/semantics/openAccess2023-10-30T06:12:53Zoai:repositorio.unesp.br:11449/75351Repositório InstitucionalPUBhttp://repositorio.unesp.br/oai/requestopendoar:29462023-10-30T06:12:53Repositório Institucional da UNESP - Universidade Estadual Paulista (UNESP)false |
dc.title.none.fl_str_mv |
Study of whole genome linkage disequilibrium in Nellore cattle |
title |
Study of whole genome linkage disequilibrium in Nellore cattle |
spellingShingle |
Study of whole genome linkage disequilibrium in Nellore cattle Espigolan, Rafael [UNESP] Beef cattle Genome Linkage disequilibrium Molecular markers animal genetics cattle chromosome chromosome analysis chromosome BTA1 chromosome BTA27 chromosome BTA28 chromosome BTA29 gene frequency gene linkage disequilibrium genetic distance genetic marker genotype nonhuman single nucleotide polymorphism Bos Bovinae |
title_short |
Study of whole genome linkage disequilibrium in Nellore cattle |
title_full |
Study of whole genome linkage disequilibrium in Nellore cattle |
title_fullStr |
Study of whole genome linkage disequilibrium in Nellore cattle |
title_full_unstemmed |
Study of whole genome linkage disequilibrium in Nellore cattle |
title_sort |
Study of whole genome linkage disequilibrium in Nellore cattle |
author |
Espigolan, Rafael [UNESP] |
author_facet |
Espigolan, Rafael [UNESP] Baldi, Fernando [UNESP] Boligon, Arione A. [UNESP] Souza, Fabio R.P. [UNESP] Gordo, Daniel G.M. [UNESP] Tonussi, Rafael L. [UNESP] Cardoso, Diércles F. [UNESP] Oliveira, Henrique N. [UNESP] Tonhati, Humberto [UNESP] Sargolzaei, Mehdi Schenkel, Flavio S. Carvalheiro, Roberto Ferro, Jesus A. [UNESP] Albuquerque, Lucia G. [UNESP] |
author_role |
author |
author2 |
Baldi, Fernando [UNESP] Boligon, Arione A. [UNESP] Souza, Fabio R.P. [UNESP] Gordo, Daniel G.M. [UNESP] Tonussi, Rafael L. [UNESP] Cardoso, Diércles F. [UNESP] Oliveira, Henrique N. [UNESP] Tonhati, Humberto [UNESP] Sargolzaei, Mehdi Schenkel, Flavio S. Carvalheiro, Roberto Ferro, Jesus A. [UNESP] Albuquerque, Lucia G. [UNESP] |
author2_role |
author author author author author author author author author author author author author |
dc.contributor.none.fl_str_mv |
Universidade Estadual Paulista (Unesp) Instituto Nacional de Ciência e Tecnologia - Ciência Animal (INCT- CA) Universidade de São Paulo (USP) University of Guelph SHIS QI 1 GenSys Consultores Associados |
dc.contributor.author.fl_str_mv |
Espigolan, Rafael [UNESP] Baldi, Fernando [UNESP] Boligon, Arione A. [UNESP] Souza, Fabio R.P. [UNESP] Gordo, Daniel G.M. [UNESP] Tonussi, Rafael L. [UNESP] Cardoso, Diércles F. [UNESP] Oliveira, Henrique N. [UNESP] Tonhati, Humberto [UNESP] Sargolzaei, Mehdi Schenkel, Flavio S. Carvalheiro, Roberto Ferro, Jesus A. [UNESP] Albuquerque, Lucia G. [UNESP] |
dc.subject.por.fl_str_mv |
Beef cattle Genome Linkage disequilibrium Molecular markers animal genetics cattle chromosome chromosome analysis chromosome BTA1 chromosome BTA27 chromosome BTA28 chromosome BTA29 gene frequency gene linkage disequilibrium genetic distance genetic marker genotype nonhuman single nucleotide polymorphism Bos Bovinae |
topic |
Beef cattle Genome Linkage disequilibrium Molecular markers animal genetics cattle chromosome chromosome analysis chromosome BTA1 chromosome BTA27 chromosome BTA28 chromosome BTA29 gene frequency gene linkage disequilibrium genetic distance genetic marker genotype nonhuman single nucleotide polymorphism Bos Bovinae |
description |
Background: Knowledge of the linkage disequilibrium (LD) between markers is important to establish the number of markers necessary for association studies and genomic selection. The objective of this study was to evaluate the extent of LD in Nellore cattle using a high density SNP panel and 795 genotyped steers.Results: After data editing, 446,986 SNPs were used for the estimation of LD, comprising 2508.4 Mb of the genome. The mean distance between adjacent markers was 4.90 ± 2.89 kb. The minor allele frequency (MAF) was less than 0.20 in a considerable proportion of SNPs. The overall mean LD between marker pairs measured by r2 and |D'| was 0.17 and 0.52, respectively. The LD (r2) decreased with increasing physical distance between markers from 0.34 (1 kb) to 0.11 (100 kb). In contrast to this clear decrease of LD measured by r2, the changes in |D'| indicated a less pronounced decline of LD. Chromosomes BTA1, BTA27, BTA28 and BTA29 showed lower levels of LD at any distance between markers. Except for these four chromosomes, the level of LD (r2) was higher than 0.20 for markers separated by less than 20 kb. At distances < 3 kb, the level of LD was higher than 0.30. The LD (r2) between markers was higher when the MAF threshold was high (0.15), especially when the distance between markers was short.Conclusions: The level of LD estimated for markers separated by less than 30 kb indicates that the High Density Bovine SNP BeadChip will likely be a suitable tool for prediction of genomic breeding values in Nellore cattle. © 2013 Espigolan et al.; licensee BioMed Central Ltd. |
publishDate |
2013 |
dc.date.none.fl_str_mv |
2013-05-05 2014-05-27T11:29:06Z 2014-05-27T11:29:06Z |
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/10.1186/1471-2164-14-305 BMC Genomics, v. 14, n. 1, 2013. 1471-2164 http://hdl.handle.net/11449/75351 10.1186/1471-2164-14-305 WOS:000319407800001 2-s2.0-84876975374 2-s2.0-84876975374.pdf 7445254960858159 |
url |
http://dx.doi.org/10.1186/1471-2164-14-305 http://hdl.handle.net/11449/75351 |
identifier_str_mv |
BMC Genomics, v. 14, n. 1, 2013. 1471-2164 10.1186/1471-2164-14-305 WOS:000319407800001 2-s2.0-84876975374 2-s2.0-84876975374.pdf 7445254960858159 |
dc.language.iso.fl_str_mv |
eng |
language |
eng |
dc.relation.none.fl_str_mv |
BMC Genomics 3.730 2,110 |
dc.rights.driver.fl_str_mv |
info:eu-repo/semantics/openAccess |
eu_rights_str_mv |
openAccess |
dc.format.none.fl_str_mv |
application/pdf |
dc.source.none.fl_str_mv |
Scopus 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 |
|
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1799964761773834240 |