Linkage disequilibrium and haplotype block structure in a composite beef cattle breed
Autor(a) principal: | |
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Data de Publicação: | 2014 |
Outros Autores: | , , , , , , , , , , , , , |
Tipo de documento: | Artigo |
Idioma: | eng |
Título da fonte: | Repositório Institucional da UNESP |
Texto Completo: | http://dx.doi.org/10.1186/1471-2164-15-S7-S6 http://hdl.handle.net/11449/117310 |
Resumo: | Background: The development of linkage disequilibrium (LD) maps and the characterization of haplotype block structure at the population level are useful parameters for guiding genome wide association (GWA) studies, and for understanding the nature of non-linear association between phenotypes and genes. The elucidation of haplotype block structure can reduce the information of several single nucleotide polymorphisms (SNP) into the information of a haplotype block, reducing the number of SNPs in a coherent way for consideration in GWA and genomic selection studies.Results: The maximum average LD, measured by r(2) varied between 0.33 to 0.40 at a distance of < 2.5 kb, and the minimum average values of r(2) varied between 0.05 to 0.07 at distances ranging from 400 to 500 kb, clearly showing that the average r(2) reduced with the increase in SNP pair distances. The persistence of LD phase showed higher values at shorter genomic distances, decreasing with the increase in physical distance, varying from 0.96 at a distance of < 2.5 kb to 0.66 at a distance from 400 to 500 kb. A total of 78% of all SNPs were clustered into haplotype blocks, covering 1,57 Mb of the total autosomal genome size.Conclusions: This study presented the first high density linkage disequilibrium map and haplotype block structure for a composite beef cattle population, and indicates that the high density SNP panel over 700 k can be used for genomic selection implementation and GWA studies for Canchim beef cattle. |
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Repositório Institucional da UNESP |
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2946 |
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Linkage disequilibrium and haplotype block structure in a composite beef cattle breedBackground: The development of linkage disequilibrium (LD) maps and the characterization of haplotype block structure at the population level are useful parameters for guiding genome wide association (GWA) studies, and for understanding the nature of non-linear association between phenotypes and genes. The elucidation of haplotype block structure can reduce the information of several single nucleotide polymorphisms (SNP) into the information of a haplotype block, reducing the number of SNPs in a coherent way for consideration in GWA and genomic selection studies.Results: The maximum average LD, measured by r(2) varied between 0.33 to 0.40 at a distance of < 2.5 kb, and the minimum average values of r(2) varied between 0.05 to 0.07 at distances ranging from 400 to 500 kb, clearly showing that the average r(2) reduced with the increase in SNP pair distances. The persistence of LD phase showed higher values at shorter genomic distances, decreasing with the increase in physical distance, varying from 0.96 at a distance of < 2.5 kb to 0.66 at a distance from 400 to 500 kb. A total of 78% of all SNPs were clustered into haplotype blocks, covering 1,57 Mb of the total autosomal genome size.Conclusions: This study presented the first high density linkage disequilibrium map and haplotype block structure for a composite beef cattle population, and indicates that the high density SNP panel over 700 k can be used for genomic selection implementation and GWA studies for Canchim beef cattle.Coordenação de Aperfeiçoamento de Pessoal de Nível Superior (CAPES)Embrapa (Brazilian Agricultural Research Corporation)Conselho Nacional de Desenvolvimento Científico e Tecnológico (CNPq)Univ Fed Sao Carlos, Dept Genet & Evolut, BR-13565905 Sao Carlos, SP, BrazilUniv Estadual Paulista, Fac Ciencias Agr & Vet, Dept Ciencias Exatas, BR-14884900 Jaboticabal, SP, BrazilEmbrapa Southeast Livestock, BR-13560970 Sao Carlos, SP, BrazilUniv Guelph, Ctr Genet Improvement Livestock, Guelph, ON N1G 2W1, CanadaEmbrapa Agr Informat, BR-13083886 Campinas, SP, BrazilUniv Fed Lavras, Dept Anim Sci, BR-3720000 Lavras, BrazilEmbrapa Dairy Cattle, BR-36038330 Juiz De Fora, BrazilUniv Estadual Paulista, Fac Ciencias Agr & Vet, Dept Ciencias Exatas, BR-14884900 Jaboticabal, SP, BrazilCAPES: 02663/09-0CNPq: 142053/2010-4CAPES: 5285-11-9Biomed Central LtdUniversidade Federal de São Carlos (UFSCar)Universidade Estadual Paulista (Unesp)Empresa Brasileira de Pesquisa Agropecuária (EMBRAPA)Univ GuelphUniversidade Federal de Lavras (UFLA)Mokry, Fabiana BarichelloBuzanskas, Marcos Eli [UNESP]Mudadu, Mauricio de AlvarengaGrossi, Daniela do AmaralHiga, Roberto HiroshiVentura, Ricardo VieiraLima, Andressa Oliveira deSargolzaei, MehdiConceicao Meirelles, Sarah LagunaSchenkel, Flavio SchrammGualberto Barbosa da Silva, Marcos ViniciusMeo Niciura, Simone CristinaAlencar, Mauricio Mello deMunari, Danisio Prado [UNESP]Almeida Regitano, Luciana Correia de2015-03-18T15:55:48Z2015-03-18T15:55:48Z2014-10-27info:eu-repo/semantics/publishedVersioninfo:eu-repo/semantics/article9application/pdfhttp://dx.doi.org/10.1186/1471-2164-15-S7-S6Bmc Genomics. London: Biomed Central Ltd, v. 15, 9 p., 2014.1471-2164http://hdl.handle.net/11449/11731010.1186/1471-2164-15-S7-S6WOS:000345683300006WOS000345683300006.pdf6064277731903249Web of Sciencereponame:Repositório Institucional da UNESPinstname:Universidade Estadual Paulista (UNESP)instacron:UNESPengBmc Genomics3.7302,110info:eu-repo/semantics/openAccess2024-06-06T13:42:01Zoai:repositorio.unesp.br:11449/117310Repositório InstitucionalPUBhttp://repositorio.unesp.br/oai/requestopendoar:29462024-08-05T14:14:44.959326Repositório Institucional da UNESP - Universidade Estadual Paulista (UNESP)false |
dc.title.none.fl_str_mv |
Linkage disequilibrium and haplotype block structure in a composite beef cattle breed |
title |
Linkage disequilibrium and haplotype block structure in a composite beef cattle breed |
spellingShingle |
Linkage disequilibrium and haplotype block structure in a composite beef cattle breed Mokry, Fabiana Barichello |
title_short |
Linkage disequilibrium and haplotype block structure in a composite beef cattle breed |
title_full |
Linkage disequilibrium and haplotype block structure in a composite beef cattle breed |
title_fullStr |
Linkage disequilibrium and haplotype block structure in a composite beef cattle breed |
title_full_unstemmed |
Linkage disequilibrium and haplotype block structure in a composite beef cattle breed |
title_sort |
Linkage disequilibrium and haplotype block structure in a composite beef cattle breed |
author |
Mokry, Fabiana Barichello |
author_facet |
Mokry, Fabiana Barichello Buzanskas, Marcos Eli [UNESP] Mudadu, Mauricio de Alvarenga Grossi, Daniela do Amaral Higa, Roberto Hiroshi Ventura, Ricardo Vieira Lima, Andressa Oliveira de Sargolzaei, Mehdi Conceicao Meirelles, Sarah Laguna Schenkel, Flavio Schramm Gualberto Barbosa da Silva, Marcos Vinicius Meo Niciura, Simone Cristina Alencar, Mauricio Mello de Munari, Danisio Prado [UNESP] Almeida Regitano, Luciana Correia de |
author_role |
author |
author2 |
Buzanskas, Marcos Eli [UNESP] Mudadu, Mauricio de Alvarenga Grossi, Daniela do Amaral Higa, Roberto Hiroshi Ventura, Ricardo Vieira Lima, Andressa Oliveira de Sargolzaei, Mehdi Conceicao Meirelles, Sarah Laguna Schenkel, Flavio Schramm Gualberto Barbosa da Silva, Marcos Vinicius Meo Niciura, Simone Cristina Alencar, Mauricio Mello de Munari, Danisio Prado [UNESP] Almeida Regitano, Luciana Correia de |
author2_role |
author author author author author author author author author author author author author author |
dc.contributor.none.fl_str_mv |
Universidade Federal de São Carlos (UFSCar) Universidade Estadual Paulista (Unesp) Empresa Brasileira de Pesquisa Agropecuária (EMBRAPA) Univ Guelph Universidade Federal de Lavras (UFLA) |
dc.contributor.author.fl_str_mv |
Mokry, Fabiana Barichello Buzanskas, Marcos Eli [UNESP] Mudadu, Mauricio de Alvarenga Grossi, Daniela do Amaral Higa, Roberto Hiroshi Ventura, Ricardo Vieira Lima, Andressa Oliveira de Sargolzaei, Mehdi Conceicao Meirelles, Sarah Laguna Schenkel, Flavio Schramm Gualberto Barbosa da Silva, Marcos Vinicius Meo Niciura, Simone Cristina Alencar, Mauricio Mello de Munari, Danisio Prado [UNESP] Almeida Regitano, Luciana Correia de |
description |
Background: The development of linkage disequilibrium (LD) maps and the characterization of haplotype block structure at the population level are useful parameters for guiding genome wide association (GWA) studies, and for understanding the nature of non-linear association between phenotypes and genes. The elucidation of haplotype block structure can reduce the information of several single nucleotide polymorphisms (SNP) into the information of a haplotype block, reducing the number of SNPs in a coherent way for consideration in GWA and genomic selection studies.Results: The maximum average LD, measured by r(2) varied between 0.33 to 0.40 at a distance of < 2.5 kb, and the minimum average values of r(2) varied between 0.05 to 0.07 at distances ranging from 400 to 500 kb, clearly showing that the average r(2) reduced with the increase in SNP pair distances. The persistence of LD phase showed higher values at shorter genomic distances, decreasing with the increase in physical distance, varying from 0.96 at a distance of < 2.5 kb to 0.66 at a distance from 400 to 500 kb. A total of 78% of all SNPs were clustered into haplotype blocks, covering 1,57 Mb of the total autosomal genome size.Conclusions: This study presented the first high density linkage disequilibrium map and haplotype block structure for a composite beef cattle population, and indicates that the high density SNP panel over 700 k can be used for genomic selection implementation and GWA studies for Canchim beef cattle. |
publishDate |
2014 |
dc.date.none.fl_str_mv |
2014-10-27 2015-03-18T15:55:48Z 2015-03-18T15:55:48Z |
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/10.1186/1471-2164-15-S7-S6 Bmc Genomics. London: Biomed Central Ltd, v. 15, 9 p., 2014. 1471-2164 http://hdl.handle.net/11449/117310 10.1186/1471-2164-15-S7-S6 WOS:000345683300006 WOS000345683300006.pdf 6064277731903249 |
url |
http://dx.doi.org/10.1186/1471-2164-15-S7-S6 http://hdl.handle.net/11449/117310 |
identifier_str_mv |
Bmc Genomics. London: Biomed Central Ltd, v. 15, 9 p., 2014. 1471-2164 10.1186/1471-2164-15-S7-S6 WOS:000345683300006 WOS000345683300006.pdf 6064277731903249 |
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 |
9 application/pdf |
dc.publisher.none.fl_str_mv |
Biomed Central Ltd |
publisher.none.fl_str_mv |
Biomed Central Ltd |
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_ |
1808128335179415552 |