High-resolution gene mapping using admixture linkage disequilibrium

This note reports simulation study on the rate of decay in linkage disequilibrium (LD) in mixed populations over multiple discrete generations and explores the usefulness of the LD analysis in high-resolution gene mapping. The results indicate that the smaller the recombination fraction and the fewer generations since admixture event, the higher power of the approach in gene mapping. The expected estimate of recombination fraction would give an estimate that is slightly biased upwards, if relevant genes are in tight linkage. The estimated recombination fraction is usually larger than the true value within 2-5 generations. From generations 10-20, the mean estimates are in good agreement with the true value. The method presented here enables estimation of means and corresponding confidence intervals of the recombination fraction at any number of generations.