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, Mudadu, Maurício de Alvarenga, Grossi, Daniela do Amaral, Higa, Roberto Hiroshi, Ventura, Ricardo Vieira, Lima, Andressa Oliveira de, Sargolzaei, Mehdi, Meirelles, Sarah Laguna Conceição, Schenkel, Flávio Schramm, Silva, Marcos Vinicius Gualberto Barbosa da, Niciura, Simone Cristina Méo, Alencar, Maurício Mello de, Munari, Danísio Prado, Regitano, Luciana Correia de Almeida
Tipo de recurso: artículo
Estado:Versión publicada
Fecha de publicación:2014
País:Brasil
Institución:Universidade Federal de Lavras (UFLA)
Repositorio:Repositório Institucional da UFLA
Idioma:inglés
OAI Identifier:oai:repositorio.ufla.br:1/41910
Acceso en línea:https://repositorio.ufla.br//handle/1/41910
Access Level:acceso abierto
Palabra clave:Animal breeding
Bovine
Canchim
Consistency of gametic phase
Single nucleotide polymorphism
Persistence of LD phase
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 r2 varied between 0.33 to 0.40 at a distance of < 2.5 kb, and the minimum average values of r2 varied between 0.05 to 0.07 at distances ranging from 400 to 500 kb, clearly showing that the average r2 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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