Characterizing Linkage Disequilibrium in Pig Populations

Abstract

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, r 2 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 r 2 is a considerably more robust LD measure. The maximum r 2 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 r 2 and the ratio of r 2 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 r 2 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.

Linkage Disequilibrium Decay and Haplotype Block Structure in the Pig

“…The observed pattern of decay of LD is similar to what has been observed in previous studies in humans (Daly et al 2001), cattle (Farnir et al 2000), chickens (Aerts et al2007), and pigs (Du et al 2007).…”

“…Assessing the extent of useful LD: The threshold for useful LD that was chosen in this study was the same as previously used in LD studies of pig populations using r 2 as a measure of LD ( Jungerius et al 2005;Du et al 2007). With a threshold of 0.3, and considering that on average 1 cM is equivalent to 1 Mb, LD extended in the European breeds over 0.5-2 cM on SSC18 and 0.1-1 cM on SSC3.…”

“…In this study, r 2 was chosen because it is very useful in the case of biallelic markers such as SNPs and because it is independent from sample size (Devlin and Risch 1995). Further, Du et al (2007) evaluated recently how r 2 and D9 are affected by several levels of minor allele frequency (MAF). Their results suggest that D9 is highly dependent on levels of MAF, whereas r 2 is less.…”

“…With the commercial lines possibly containing the larger extent of LD in the species, we examined three genomic regions, each 1-3 cM, at a higher SNP density than previous studies (Nsengimana et al 2004;Du et al 2007). This study provides insight into the extent of useful LD across a wide range of breeds and the required sample sizes and number of markers for association studies.…”

Use of field data in pig genomic selection schemes: a simulation study

“…The total number of markers used for genomic evaluation was hence 9000 (500 markers × 18 chromosomes), which is considerably lower than what is usually used for genomic selection purposes. However, the linkage disequilibrium between adjacent markers was on average r 2 = 0.453, higher than expected from the low marker density (Lillehammer et al, 2011b) and similar to what would be expected if using a 50k SNP chip on a pig population (Du et al, 2007).…”