Characterizing Linkage Disequilibrium in Pig Populations

Knowledge of the extent and range of linkage disequilibrium (LD), defined as non-random association of alleles at two or more loci, in animal populations is extremely valuable in localizing genes affecting quantitative traits, identifying chromosomal regions under selection, studying population hist...

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Main Authors:	Du, Feng-Xing, Clutter, Archie C., Lohuis, Michael M.
Format:	Online
Language:	English
Published:	Ivyspring International Publisher 2007
Online Access:	https://www.ncbi.nlm.nih.gov/pmc/articles/PMC1802018/

id	pubmed-1802018
recordtype	oai_dc
spelling	pubmed-18020182007-03-23 Characterizing Linkage Disequilibrium in Pig Populations Du, Feng-Xing Clutter, Archie C. Lohuis, Michael M. Review Knowledge of the extent and range of linkage disequilibrium (LD), defined as non-random association of alleles at two or more loci, in animal populations is extremely valuable in localizing genes affecting quantitative traits, identifying chromosomal regions under selection, studying population history, and characterizing/managing genetic resources and diversity. Two commonly used LD measures, r2 and D', and their permutation based adjustments, were evaluated using genotypes of more than 6,000 pigs from six commercial lines (two terminal sire lines and four maternal lines) at ~4,500 autosomal SNPs (single nucleotide polymorphisms). The results indicated that permutation only partially removed the dependency of D' on allele frequency and that r2 is a considerably more robust LD measure. The maximum r2 was derived as a function of allele frequency. Using the same genotype dataset, the extent of LD in these pig populations was estimated for all possible syntenic SNP pairs using r2 and the ratio of r2 over its theoretical maximum. As expected, the extent of LD highest for SNP pairs was found in tightest linkage and decreased as their map distance increased. The level of LD found in these pig populations appears to be lower than previously implied in several other studies using microsatellite genotype data. For all pairs of SNPs approximately 3 centiMorgan (cM) apart, the average r2 was equal to 0.1. Based on the average population-wise LD found in these six commercial pig lines, we recommend a spacing of 0.1 to 1 cM for a whole genome association study in pig populations. Ivyspring International Publisher 2007-02-10 /pmc/articles/PMC1802018/ /pubmed/17384735 Text en © Ivyspring International Publisher. This is an open-access article distributed under the terms of the Creative Commons License (http://creativecommons.org/licenses/by-nc-nd/3.0/). Reproduction is permitted for personal, noncommercial use, provided that the article is in whole, unmodified, and properly cited.
repository_type	Open Access Journal
institution_category	Foreign Institution
institution	US National Center for Biotechnology Information
building	NCBI PubMed
collection	Online Access
language	English
format	Online
author	Du, Feng-Xing Clutter, Archie C. Lohuis, Michael M.
spellingShingle	Du, Feng-Xing Clutter, Archie C. Lohuis, Michael M. Characterizing Linkage Disequilibrium in Pig Populations
author_facet	Du, Feng-Xing Clutter, Archie C. Lohuis, Michael M.
author_sort	Du, Feng-Xing
title	Characterizing Linkage Disequilibrium in Pig Populations
title_short	Characterizing Linkage Disequilibrium in Pig Populations
title_full	Characterizing Linkage Disequilibrium in Pig Populations
title_fullStr	Characterizing Linkage Disequilibrium in Pig Populations
title_full_unstemmed	Characterizing Linkage Disequilibrium in Pig Populations
title_sort	characterizing linkage disequilibrium in pig populations
description	Knowledge of the extent and range of linkage disequilibrium (LD), defined as non-random association of alleles at two or more loci, in animal populations is extremely valuable in localizing genes affecting quantitative traits, identifying chromosomal regions under selection, studying population history, and characterizing/managing genetic resources and diversity. Two commonly used LD measures, r2 and D', and their permutation based adjustments, were evaluated using genotypes of more than 6,000 pigs from six commercial lines (two terminal sire lines and four maternal lines) at ~4,500 autosomal SNPs (single nucleotide polymorphisms). The results indicated that permutation only partially removed the dependency of D' on allele frequency and that r2 is a considerably more robust LD measure. The maximum r2 was derived as a function of allele frequency. Using the same genotype dataset, the extent of LD in these pig populations was estimated for all possible syntenic SNP pairs using r2 and the ratio of r2 over its theoretical maximum. As expected, the extent of LD highest for SNP pairs was found in tightest linkage and decreased as their map distance increased. The level of LD found in these pig populations appears to be lower than previously implied in several other studies using microsatellite genotype data. For all pairs of SNPs approximately 3 centiMorgan (cM) apart, the average r2 was equal to 0.1. Based on the average population-wise LD found in these six commercial pig lines, we recommend a spacing of 0.1 to 1 cM for a whole genome association study in pig populations.
publisher	Ivyspring International Publisher
publishDate	2007
url	https://www.ncbi.nlm.nih.gov/pmc/articles/PMC1802018/
_version_	1611394413214302208

Characterizing Linkage Disequilibrium in Pig Populations

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