Power of Linkage Disequilibrium Mapping to Detect a Quantitative Trait Locus (QTL) in Selected Samples of Unrelated Individuals

We considered a strategy to map quantitative trait loci (QTLs) using linkage disequilibrium (LD) when the QTL and marker locus were multiallelic. The strategy involved phenotyping a large number of unrelated individuals and genotyping only selected individuals from the two tails of the trait distribution. Power to detect trait-marker association was assessed as a function of the number of QTL and marker alleles. Two patterns of LD were used to study their influence on power. When the frequency of the QTL allele with the largest effect and that of the marker allele linked in coupling were equal, power was maximum. In this case, increasing the number of QTL alleles reduced the power. The maximum difference in power between the two LD patterns studied was ∼30%. For low QTL heritabilities (h2QTL < 0.1) and single trait studies we recommend selecting around 5 % of the upper and lower tails of the trait distribution