Quantitative Traint Loci and Single Nucleotide Polymorphism

An important piece of that information is the level of population-wide linkage disequilibrium (LD) in the region. Linkage disequilibrium refers to the non-random association of alleles at different loci and quantifies the level of informativeness between different markers. As such, it dictates marker density in marker-based studies (Goldstein and Weale, 2001; Weiss and Clark, 2002). A long extent of LD may be beneficiary for an initial survey on the genomic location of a quantitative trait locus (QTL) because only a limited number of markers has to be tested. On the other hand, a long extent of LD may be problematic for fine-mapping of a QTL, because association may be detected at a distance far from the causative locus. The average extent of LD (i.e. the dependence of LD on the separation distance between markers) has been investigated for several organisms, including human (Reich et al., 2001) and some domesticated animals (Farnir et al., 2000; Nsengimana et al., 2004; Sutter et al., 2004; Jungerius et al., Abstract. Many of the economically important traits in chicken are multifactorial and governed by multiple genes located at different quantitative trait loci (QTLs). The optimal marker density to identify these QTLs in linkage and association studies is largely determined by the extent of linkage disequilibrium (LD) around them. In this study, we investigated the extent of LD on two chromosomes in a white layer and two broiler chicken breeds. Pairwise levels of LD were calculated for 33 and 36 markers on chromosomes 10 and 28, respectively. We found that useful LD (i.e. an r 2 value higher than 0.3) in Nutreco chicken breed E5 (inbred) can extend to around 1 cM on chromosomes 10 and