Epistatic QTL pairs associated with meat quality and carcass composition traits in a porcine Duroc × Pietrain population

Five hundred and eighty five F2 pigs from a Duroc × Pietrain resource population were genotyped using 131 genetic markers (microsatellites and SNP) spread over the 18 pig autosomes. Phenotypic information for 26 carcass composition and meat quality traits was available for all F2 animals. Linkage analysis was performed in a two-step procedure using a maximum likelihood approach implemented in the QxPak program.A number of interacting QTL was observed for different traits, leading to the identification of a variety of networks among chromosomal regions throughout the porcine genome. We distinguished 17 epistatic QTL pairs for carcass composition and 39 for meat quality traits. These interacting QTL pairs explained up to 8% of the phenotypic variance.Our findings demonstrate the significance of epistasis in pigs. We have revealed evidence for epistatic relationships between different chromosomal regions, confirmed known QTL loci and connected regions reported in other studies. Considering interactions between loci allowed us to identify several novel QTL and trait-specific relationships of loci within and across chromosomes.Until now, most QTL studies have considered additive and dominance effects and sometimes imprinting effects, but epistatic interactions between two or more loci are commonly ignored. The significance of interactions between different loci in explaining the genetic variability of traits has long been controversial.Epistatic effects can be clearly defined and verified when a combination of two mutations yields an unexpected phenotype that cannot be explained by the independent effect of each mutation [1]. For example, Steiner et al. [2] have demonstrated the effect of gene interactions for a binary expressed trait (coat color), which is influenced by two or three loci. However, the evaluation of epistasis for complex traits is much more demanding because these traits are influenced by environmental effects and large numbers of polymorphic loci [3]. F