Prediction of the confidence interval of quantitative trait loci location

In 1997, Darvasi and Soller presented empirical predictions of the confidence interval of quantitative trait loci (QTL) location for dense marker maps in experimental crosses. They showed from simulation results for backcross and F-2 populations from inbred lines that the 95% confidence interval was a simple function of sample size and the effect of the QTL. In this study, we derive by theory simple equations that can be used to predict any confidence interval and show that for the 95% confidence interval, they are in good agreement with the empirical results given by Darvasi and Soller. A general form of the confidence interval is given that also applies to other population structures ( e. g., collections of sib pairs). Furthermore, the expected shape of the likelihood-ratio-test around the true QTL location is derived, which is shown to be extremely leptokurtic. It is shown that this shape explains why confidence intervals from the Log of Odds (LOD) drop-off method and bootstrap results frequently differ for real data sets.