Linkage Disequilibrium in the Domesticated Pig

Abstract

This study investigated the extent of linkage disequilibrium (LD) in two genomic regions (on chromosomes 4 and 7) in five populations of domesticated pigs. LD was measured with DЈ and tested for significance with the Fisher exact test. Effects of genetic (linkage) distance, chromosome, population, and their interactions on DЈ were tested both through a linear model analysis of covariance and by a theoretical nonlinear model. The overall result was that (1) the distance explained most of the variability of DЈ, (2) the effect of chromosome was significant, and (3) the effect of population was significant. The significance of the chromosome effect may have resulted from selection and the significance of the population effect illustrates the effects of population structures and effective population sizes on LD. These results suggest that mapping methods based on LD may be valuable even with only moderately dense marker spacing in pigs.

Power of QTL mapping experiments in commercial Atlantic salmon populations, exploiting linkage and linkage disequilibrium and effect of limited recombination in males

“…In livestock populations, for example, recent effective population sizes are often quite small. As a result, the extent of LD can be considerable, with measurable LD (eg useable for detection of QTL) for up to tens of cM in cattle (Farnir et al, 2000), sheep (McRae et al, 2001), and pigs (Nsengimana et al, 2004). This is in sharp contrast to the situation in humans, where recent effective population sizes have been large, and consequently measurable LD often only extends a few 100 kb (eg Dunning et al, 2000;Reich et al, 2001).…”

Examination of a region showing linkage map discrepancies across sheep breeds

“…While single-locus methods such as regression of trait values on genotype do not directly require linkage information for their use, the following attempts to characterize the underlying genetic variants in the detected region may be hampered without this information. Also, given the large amount of variability in the amount of linkage disequilibrium between pairs of loci separated by a fixed distance in livestock populations (Farnir et al 2000;McRae et al 2002;Nsengimana et al 2004), multilocus methods that average out this variability are likely to be more powerful than single locus methods. All multilocus methods will require a genetic map to be known accurately so the appropriate weighting of information at each locus is achieved.…”

Linkage disequilibrium on chromosome 6 in Australian Holstein-Friesian cattle

“…This statistic has been used to measure the extent of LD in human [3] and livestock populations in a range of studies (e.g. [10,28,34,42]), thereby facilitating the comparison of the results in this study with other studies. D allows LD to be measured with highly polymorphic markers and is less sensitive to variation in marker allele frequencies than other measures of LD [14,46].…”

“…The extent of LD in livestock is expected to be higher than in humans, since the forces producing LD (admixture, selection and small effective population sizes) are more extreme in livestock populations [33]. The evidence supporting this expectation is accumulating: high levels of LD have been found to extend for many centimorgans in dairy cattle [10], sheep [28], pigs [34] and horses [43]. These studies used family information to infer the most likely phase of the dams' haplotypes.…”

“…Sutter et al [41] used several samples of unrelated animals to estimate LD in a range of dog breeds. Studies in humans, dogs and pigs indicate that the pattern and extent of the LD is often population-specific [19,34,37]. This emphasises that estimates of LD in specific populations are required before carrying out LD-based fine-mapping studies in those populations.…”