Numerical comparison between powers of maximum likelihood and analysis of variance methods for QTL detection in progeny test designs: the case of monogenic inheritance.

Simulations are used to compare four statistics for the detection of a quantitative trait locus (QTL) in daughter and grand-daughter designs as defined by Soller and Genizi (1978) and Weller et al. (1990): (1) the Fisher test of a linear model including a marker effect within sire or grand-sire effect; (2) the likelihood ratio test of a segregation analysis without the information given by the marker; (3) the likelihood ratio test of a segregation analysis considering the information from the marker; and (4) the lod score which is the likelihood ratio test of absence of linkage between the marker and the QTL. In all cases the two segregation analyses are more powerful for QTL detection than are either the linear method or the lod score. The differences in power are generally limited but may be significant (in a ratio of 1 to 3 or 4) when the QTL has a small effect (0.2 standard deviations) and is not closely linked to the marker (recombination rate of 20% or more).