Effect of family relatedness on characteristics of estimated IBD probabilities in relation to precision of QTL estimates

The study based on nine multi-generational family structures, similar to a pedigree structure of a real dairy population, distinguished by an increased level of inbreeding from zero to 28% across the studied population. Highest inbreeding level in the pedigree, connected with highest relatedness, was accompanied by highest IBD probabilities of two alleles at the same locus, and by lower relative variation coefficients. Profiles of correlation coefficients of IBD probabilities along the marked chromosomal segment with those at the true QTL position were steepest when the inbreeding coefficient in the pedigree was highest. Precision of estimated QTL location increased with increasing inbreeding and pedigree relatedness. A method to assess the optimum level of inbreeding for QTL detection is proposed, depending on population parameters.An increased overall relationship in a QTL mapping design has positive effects on precision of QTL position estimates. But the relationship of inbreeding level and the capacity for QTL detection depending on the recombination rate of QTL and adjacent informative marker is not linear.Studies on quantitative trait loci (QTL) in dairy cattle are performed almost exclusively on data from commercial populations. Setting up experimental populations is highly expensive and time consuming. Therefore, the simplest and most popular design for QTL mapping in dairy cattle was the granddaughter design (GDD, [1]). Single grandsires establish their "own families" with a number of sons (sires) genotyped for a marker panel, involving phenotypic information on the quantitative trait, based on several hundreds of cows ((grand)daughters).The methodology to detect QTL in general pedigrees exploiting polymorphism of genetic markers was proposed by Fernando et al. (1989), based on a model where both the allelic QTL effects and the polygenic component are assumed to be random normal deviates [2]. The covariance between individuals for a putative QTL is modeled