Combined GWAS and LDLA approaches to improve genome-wide quantitative trait loci detection affecting carcass and meat quality traits in pig

Many QTL affecting meat quality and carcass traits have been reported. However, in most of the cases these QTL have been detected in non-commercial populations. Therefore, a family structured population of 457 F2 pigs issued from an inter-cross between 2 commercial sire lines was used to detect QTL affecting meat quality and carcass traits. All animals were genotyped using the Illumina PorcineSNP60 BeadChip platform. Genome-wide association studies were used in combination with linkage disequilibrium-linkage analysis to identify QTL. A total of 32 QTL were detected. Nine of these QTL exceeded the genome-wide 5% significance threshold. We detected 18 QTL affecting carcass composition traits and 16 QTL affecting meat quality traits. Using post-QTL bioinformatics analysis we highlighted 26 functional candidate genes related to fatness, muscle development, meat color and meat pH. Finally, our results shed light on the advantage of using different QTL detection methodologies to get a global overview of the QTL present in the studied population.