Evaluation of Functional Variation in Candidate Genes for Pork Quality.

Considerable variation exists in pork quality traits and consumer perception of pork eating satisfaction is largely driven by tenderness and sensory juiciness scores, which are related to shear force, cooking loss and ultimate pH. Water loss from meat during postmortem storage reduces profitability and consumer appeal. Other measures of pork quality, such as color and intramuscular fat, also affect consumer satisfaction ratings and may influence purchase decisions. Because pork quality is measured only after slaughter, development of predictive markers would improve selection and management of product quality. Several genome-wide associations (GWAS) have been performed for a multitude of pork attributes and quality traits, but the causative variation for these traits has only been identified and validated for a few candidate genes. The objective of this study was to use a commercial population to evaluate potential functional variation in candidate genes identified in a GWAS for pork quality in the USMARC Swine herd. Traits measured at 14d postmortem included slice shear force (SSF), pH, purge loss % (PURGE), cooking loss (Ck_Loss), color (L*, a*, and b*) and desmin degradation (DES). Potential functional variation was identified from whole genome sequence of the USMARC founders and from public databases (http://genome.ucsc.edu/). One hundred twelve markers in 37 candidate genes were genotyped in 1536 commercial swine collected from six different slaughter plants. Data were analyzed in Golden Helix using a single-locus Mixed Linear Model (EMMAX) with sex and plant (contemporary group) as fixed effects. A genomic relationship matrix constructed from markers shared on the Illumina PorcineSNP60v2 and GeneSeek GGP beadchips was used to correct for population stratification. Markers that we previously identified in calpastatin (CAST) on the GeneSeek GGP beadchip were associated with SSF, Ck_Loss, and DES and were the most significant markers for SSF. PRKAG3 markers were associated with PURGE, Ck_Loss, pH and L*. Most of the associations were with SNPs in genes with large known effects. Novel associations included associations of markers in CAPN1 and PEPD with SSF and CAPN1 with DES. GWAS have identified associations of the region near or containing CAPN1 with pork tenderness, however this is the first report of potentially functional SNP in CAPN1 to be associated with tenderness and related traits.