Accurate association mapping in livestock populations is challenging, thus I tested the properties of three methods to derive 95% confidence intervals (CI) for QTL positions [Parametric Method (PM), non-parametric centered (NPC) and non-parametric non-centered (NPNC)]. The NPC failed to provide adequate coverage for the 95% CI for the true QTL position. The 95% CI obtained with NPNC and PM had similar coverage, however the PM had shorter intervals, therefore, I recommend to use PM. Furthermore, to map regions comprising SNP associated with meat quality and carcass traits I performed Genome-wide Association analysis for 948 F2 Duroc x Pietrain resource population pigs for 38 meat quality and carcass traits using 44,911 SNP. Type I error rate was controlled at a False Discovery Rate of 5%. I found nine QTL associated with 15 traits. Three of those nine QTL [one on SSC1 (tenth rib backfat thickness), one on SSC7 (dressing percentage and loin muscle area) and one on SSC11 (belly weight)] were mapped to a specific genomic segment in this study. Moreover, two novel QTL associated with tenderness were located on SSC3 and SSC5. Also, I propose the candidate genes A Kinase (PRKA) Anchor Protein 3 for the QTL on SSC5 and Carnitine O-Acetyltransferase for the QTL on SSC1. Finally, this study shows that the variants of Protein Kinase AMP-activated 3-subunit, I199V and T30N are not associated with pH 24 post mortem and related traits in this population.
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