Association of single nucleotide polymorphism (SNP) markers in candidate genes and QTL regions with pork quality traits in commercial pigs

Numerous reports have described genetic markers or genomic regions (QTL) associated with pork quality and/or palatability but few validation studies have been reported. Therefore, 156 SNP markers from 45 candidate genes and eight QTL regions were analyzed for association with pork quality and palatability traits from 888 pork loins. Loins were collected at three slaughter facilities and selected to represent a wide range of pork color, pH and marbling. Phenotypic data recorded included objective and subjective measures of color and marbling, purge loss, shear force, and cooking loss. Data were analyzed with SAS PROC MIXED where loin was fit as a random effect. Results indicated some of the markers tested should be useful in industry, while others are not segregating in all populations or linkage disequilibrium between markers and causative genetic variation fluctuates among populations limiting their universal utility. Genes with the largest effects on pork quality were MC4R, IGF2, CAST and PRKAG3. ► Seven of eight QTL regions for pork quality were confirmed. ► IGF2 was associated with pork color. ► MC4R was associated with pork color, pH and marbling. ► CAST was associated with shear force. ► PRKAG3 was associated pork color, pH, purge and cooking loss.