Limitations of a two-step moment method for mapping linked multiple QTL

As an alternative to multiple-interval mapping a two-step moment method was recently proposed to map linked multiple quantitative trait loci (QTLs). The advantage of this moment method was supposed to be its simplicity and computational efficiency, especially in detecting closely linked QTLs within a marker bracket, but also in mapping QTLs in different marker intervals. Using simulations it is shown that the two-step moment method may give poor results compared with multiple-interval mapping, irrespective of whether the QTLs are in the same or in different marker intervals, especially if linked QTLs are in repulsion. The criteria of comparison are number of identified QTLs, likelihood ratio test statistics, means and empirical standard errors of the QTL position and QTL effects estimates, and the accuracy of the residual variance estimates. Further, the joint conditional probabilities of QTL genotypes for two putative QTLs within a marker interval were derived and compared with the unmodified approach ignoring the non-independence of the conditional probabilities.