Joint analysis of quantitative trait loci and major-effect causative mutations affecting meat quality and carcass composition traits in pigs

Large QTL effects were detected in the absence of the RYR1 and PRKGA3 mutations, accounting for 12.7% of phenotypic variation in loin colour redness CIE-a* on SSC6 and 15% of phenotypic variation in glycolytic potential on SSC1. We detected 8 significant QTLs with effects on meat quality traits and 20 significant QTLs for carcass composition and growth traits under these conditions. In control analyses including mutation carriers, RYR1 and PRKAG3 mutations were detected as QTLs, from highly significant to suggestive, and explained 53% to 5% of the phenotypic variance according to the trait.Our results suggest that part of muscle development and backfat thickness effects commonly attributed to the RYR1 mutation may be a consequence of linkage with independent QTLs affecting those traits. The proportion of variation explained by the most significant QTLs detected in this work is close to the influence of major-effect mutations on the least affected traits, but is one order of magnitude lower than effect on variance of traits primarily affected by these causative mutations. This suggests that uncovering physiological traits directly affected by genetic polymorphisms would be an appropriate approach for further characterization of QTLs.Early research into the genetics of meat quality in pigs found causative mutations associated with marked effects on pig meat value, leading to worldwide applications in the pork production chain. The RYR1 Cys615 mutation [1] alters the function of a skeletal muscle sarcoplasmic calcium release channel, changes the contraction response to stimuli and gives rise to a malignant hyperthermia syndrome (MHS) on exposure to halothane gas. Characterization of this recessive phenotype first identified homozygous mutants, and subsequently the mutation itself. This mutation increases the pH fall rate in skeletal muscle post mortem and leads to the production of pale, soft, exsudative (PSE) meat, a long-recognized meat defect associated with maligna