Linkage disequilibrium and haplotype block structure in a composite beef cattle breed

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 gen...

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Detalles Bibliográficos
Autores: 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
Tipo de recurso: artículo
Estado:Versión publicada
Fecha de publicación:2014
País:Brasil
Institución:Universidade Estadual Paulista (UNESP)
Repositorio:Repositório Institucional da UNESP
Idioma:inglés
OAI Identifier:oai:repositorio.unesp.br:11449/117310
Acceso en línea:http://dx.doi.org/10.1186/1471-2164-15-S7-S6
http://hdl.handle.net/11449/117310
Access Level:acceso abierto
Descripción
Sumario: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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