Use of sib-pair linkage methods for the estimation of the genetic variance at a quantitative trait locus

Until recently, the sib-pair linkage method of Haseman and Elston could only be used for the detection of linkage between a quantitative trait locus (QTL) and a marker locus. It was not possible to estimate the amount of genetic variance contributed by the QTL or its recombination fraction with the marker locus. With the advent of dense marker maps for nearly every domestic species, every QTL should be located between 2 flanking markers. In this situation, the Haseman-Elston test can be modified to estimate the variance of a putative QTL as well as its recombination fractions with the 2 flanking markers. In the present paper, we derive 2 different estimation methods for the QTL variance based on the squared performance of full sibs: in one only the QTL variance is estimated, while in the other both the QTL variance and the recombination fractions are estimated. The method that estimates only the QTL variance turns out to be more powerful than the other. With respect to the estimation of QTL variance both methods give results close to the true values. However, the estimation of recombination fractions resulted in an overall underestimation of the true parameters.