Mapping of multiple quantitative trait loci for growth and carcass traits in a complex commercial sheep pedigree

The confirmation of the segregation of experimentally discovered quantitative trait loci (QTL) in a variety of commercial populations is required before their commercial significance can be fully realized. The use of complex pedigrees in the design of such confirmation experiments has the potential to increase the probability of the QTL segregating within the pedigree while maintaining the power to detect this segregation. Here a QTL analysis is applied across candidate chromosomes of a complex pedigree of 570 Charollais sheep from commercial flocks in the UK. This pedigree also contained a moderately sized half-sib family which was analysed separately. Two QTL significant at the 5% chromosome-wide level were detected in the half-sib analysis and seven were detected in a maximum likelihood variance component analysis of the complex pedigree using identity-by-descent values estimated by Markov chain Monte Carlo methods. The estimation of QTL effects was achieved by fitting all QTL for a specific trait simultaneously, reducing the large upward bias observed in the single QTL models. Both methods of analysis detected QTL for live weight, although these mapped to different regions, and the variance components method detected QTL for ultrasonically measured fat depth. This analysis demonstrates the viability of applying a variance component analysis to large pedigrees with the presence of considerable inbreeding.