Genome-wide and local pattern of linkage disequilibrium and persistence of phase for 3 Danish pig breeds
Open Access
- 1 January 2013
- journal article
- research article
- Published by Springer Nature in BMC Genetics
- Vol. 14 (1) , 115
Abstract
The extent of linkage disequilibrium (LD) is of critical importance for genomic selection and marker assisted selection. The primary purpose of this study is to examine patterns of LD in three Danish pig breeds (Duroc, Landrace and Yorkshire); we also examine patterns of persistence of phase between the breeds. We quantify local LD by fitting a model relating LD to physical distance between markers in sliding windows, and use this to visualize how LD varies according to physical position. We use a similar method to examine local persistence of phase.Keywords
This publication has 21 references indexed in Scilit:
- A high density recombination map of the pig reveals a correlation between sex-specific recombination and GC contentBMC Genomics, 2012
- Analyses of pig genomes provide insight into porcine demography and evolutionNature, 2012
- Estimation of linkage disequilibrium in four US pig breedsBMC Genomics, 2012
- Optimizing illumina next-generation sequencing library preparation for extremely at-biased genomesBMC Genomics, 2012
- Recombination rates across porcine autosomes inferred from high‐density linkage mapsAnimal Genetics, 2011
- Extent of linkage disequilibrium and effective population size in Finnish Landrace and Finnish Yorkshire pig breeds1Journal of Animal Science, 2011
- Design of a High Density SNP Genotyping Assay in the Pig Using SNPs Identified and Characterized by Next Generation Sequencing TechnologyPLOS ONE, 2009
- A Unified Approach to Genotype Imputation and Haplotype-Phase Inference for Large Data Sets of Trios and Unrelated IndividualsThe American Journal of Human Genetics, 2009
- Linkage Disequilibrium and Persistence of Phase in Holstein–Friesian, Jersey and Angus CattleGenetics, 2008
- Haploview: analysis and visualization of LD and haplotype mapsBioinformatics, 2004