Comparison of granddaughter design and general pedigree design analysis of QTL in dairy cattle: a simulation study

Traditional methods for detection and mapping of quantitative trait loci (QTL) in dairy cattle populations are usually based on daughter design (DD) or granddaughter design (GDD). Although these designs are well established and usually successful in detecting QTL, they consider sire families independently of each other, thereby ignoring relationships among other animals in the population and consequently, reducing the power of QTL detection. In this study we compared a traditional GDD with a general pedigree design (GPD) and assessed the precision and power of both methods for detecting and locating QTL in a simulated complex pedigree. QTL analyses were performed under the variance component model containing a random QTL and a random polygenic effect. The covariance matrix of the polygenic effect was a standard additive relationship matrix. The (co)variance matrix of the random QTL effect contained probabilities that QTL alleles shared by two individuals were identical by descent (IBD). In the GDD analysis, IBD probabilities were calculated using sires' and daughters' marker genotypes. In the GPD analysis, IBD probabilities were obtained using a deterministic approach. The estimation of QTL position and variance components was conducted using REML algorithm. Although both methods were able to locate the region of the QTL properly, the GPD method showed better precision of QTL position estimates in most cases and significantly higher power than the GDD method.