QTL detection for growth and carcass quality traits thanks to a high density SNP chip in pig

Genetic improvement of carcass quality in pig implies traits measurements on related animals. In such situation, marker-assisted selection could lead to greater genetic gain than phenotypic selection. A family structured population of 454 F2 pigs was produced as an inter-cross between 2 commercial sire lines in order to detect quantitative trait loci (QTL) for growth and carcass quality traits. Animals from the 3 generations of the experimental design were genotyped using the Porcine 60k SNP Illumina Beadchip. Linkage Disequilibrium and Linkage Analyses were performed according to a maximum-likelihood interval mapping methodology using the QTLMap software. A total of 77 QTL were detected at the 5% significance chromosome-wide level. Four of these QTL exceeded the genome-wide 5% significance threshold. Thirty nine QTL influence growth or body composition traits and 34 QTL influence meat quality traits. QTL affecting the average daily gain were detected on SSC4, 6, 14 and 15. Q TL affecting carcass composition traits were detected on all chromosomes, except SSC10, 17 and 18. Finally, QTL were detected for early and ultimate pH, colour measurements (L*a*b Minolta coordinates), shear force measured on raw and cooked meat, intramuscular fat content and glycolytic potential, on all chromosomes, except SSC12 and 13. Several QTL were co-localized suggesting pleiotropic effects for some chromosomal regions. Thus, significant QTL were detected in the present study for a large scale of production traits. Additionally, a transcriptome analysis of LM and SM samples, obtained shortly after slaughter, was realized to detect expression QTL (data not shown). These data may be useful to identify causal polymorphisms of QTL and to exploit them in efficient marker-assisted selection programs.