Abstract

Doc number: S6

Abstract

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.

Details

Title
Linkage disequilibrium and haplotype block structure in a composite beef cattle breed
Author
Mokry, Fabiana Barichello; Buzanskas, Marcos Eli; de Alvarenga Mudadu, Maurício; do Amaral Grossi, Daniela; Higa, Roberto Hiroshi; Ventura, Ricardo Vieira; de Lima, Andressa Oliveira; Sargolzaei, Mehdi; Conceição Meirelles, Sarah Laguna; Schenkel, Flávio Schramm; da Silva, Marcos Vinicius Gualberto Barbosa; Méo Niciura, Simone Cristina; de Alencar, Maurício Mello; Munari, Danísio Prado; de Almeida Regitano, Luciana Correia
Publication year
2014
Publication date
2014
Publisher
BioMed Central
e-ISSN
14712164
Source type
Scholarly Journal
Language of publication
English
ProQuest document ID
1617563459
Copyright
© 2014 Mokry et al.; licensee BioMed Central Ltd. This is an Open Access article distributed under the terms of the Creative Commons Attribution License (http://creativecommons.org/licenses/by/4.0), which permits unrestricted use, distribution, and reproduction in any medium, provided the original work is properly cited. The Creative Commons Public Domain Dedication waiver (http://creativecommons.org/publicdomain/zero/1.0/) applies to the data made available in this article, unless otherwise stated.