Estimation of the average effects of specific alleles detected by the pseudo-testcross QTL mapping strategy

Abstract

In a full-sib progeny of a mating between heterozygous parents, the analysis of marker-trait associations using dominant RAPD (random amplified polymorphic DNA) markers allows the detection of specific quantitative trait loci (QTL) for each parent of the cross. Here we develop a method aimed at estimating the breeding value of such QTL alleles in the population, for the incorporation of marker-assisted selection in operational forest tree-breeding programs. The proposed methodology expands on the pseudo-testcross QTL mapping strategy which is based on the selection of single dose markers present in one parent and absent in the other. It specifically exploits the fact that one of the parents of the full-sib family is double null for the RAPD markers bracketing the QTL so that, by looking at its half-sib family, 'band present' allele frequencies of the two markers can be obtained at the population level. The half-sib family of the other parent, which is doubly heterozygous, is then used to estimate the average effect (ie, the additive effect) of the two QTL alleles.