PERMUTATION TESTS FOR MULTIPLE LOCI AFFECTING A QUANTITATIVE CHARACTER

The problem of detecting minor quantitative trait loci (QTL) responsib le for genetic variation not explained by major QTL is of importance i n the complete dissection of quantitative characters. Two extensions o f the permutation-based method for estimating empirical threshold valu es are presented. These methods, the conditional empirical threshold ( GET) and the residual empirical threshold (RET), yield critical values that can be used to construct tests for the presence of minor QTL eff ects while accounting for effects of known major QTL. The CET provides a completely nonparametric test through conditioning on markers linke d to major QTL. It allows for general nonadditive interactions among Q TL, but its practical application is restricted to regions of the geno me that are unlinked to the major QTL. The RET assumes a structural mo del for the effect of major QTL, and a threshold is constructed using residuals from this structural model. The search space for minor QTL i s unrestricted, and RET-based tests may be more powerful than the GET- based test when the structural model is approximately true.