Genome-wide association study in an F2 Duroc x Pietrain resource population for economically important meat quality and carcass traits

Meat quality is essential for consumer acceptance, it ultimately impacts pork production profitability and it is subject to genetic control. The objective of this study was to map genomic regions associated with economically important meat quality and carcass traits. We performed a genome-wide association (GWA) analysis to map regions associated with 38 meat quality and carcass traits recorded for 948 F2 pigs from the Michigan State University Duroc x Pietrain resource population. The F0, F1, and 336 F2 pigs were genotyped with the Illumina Porcine SNP60 BeadChip, while the remaining F2 pigs were genotyped with the GeneSeek Genomic Profiler for Porcine Low Desnisty (LD) chip, and imputed with high accuracy (r(2) = 0.97). Altogether the genomic dataset comprised 1,019 animals and 44,911 SNP. A Gaussian linear mixed model was fitted to estimate the breeding values and the variance components. A linear transformation was performed to estimate the marker effects and variances. Type I error rate was controlled at a False Discovery Rate of 5%. Seven putative QTL found in this study were previously reported in other studies. Two novel QTL associated with tenderness (TEN) were located on SSC3 [135.6: 137.5Mb; False Discovery rate (FDR) < 0.03] and SSC5 (67.3: 69.1Mb; FDR < 0.02). The QTL region identified on SSC15 includes Protein Kinase AMP-activated gamma 3-subunit gene (PRKAG3), which has been associated with 24-h pH (pH24), drip loss (DL) and cook yield (CY). Also, novel candidate genes were identified for TEN in the region on SSC5 [A Kinase (PRKA) Anchor Protein 3 (AKAP3)], and for tenth rib backfat thickness (BF10) [Carnitine O-Acetyltransferase (CRAT)] on SSC1. The association of PRKAG3 gene polymorphisms with pork quality traits has been reported for several pig populations. However, there are no SNP for this gene on the chip used, thus we genotyped the animals for 2 non-synonymous variants (I199V and T30N). We then performed a GWA conditioning on the genotype of both SNP and I199V was associated with pH24, DL, protein content (PRO) and CY (P < 0.004) and T30N with Juiciness, TEN, shear force, pH24, PRO, and CY (P < 0.04). Finally, we performed a GWA conditioning on the genotype of the SNP peak detected in this study, and T30N remained associated only with PRO (P < 0.02). Therefore, in this study we identified 2 novel QTL regions, suggest 2 novel candidate genes, and conclude that other SNP in PRKAG3 or nearby gene(s) explain the observed associations on SSC15 in this population.