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ARS Home » Plains Area » Clay Center, Nebraska » U.S. Meat Animal Research Center » Livestock Bio-Systems » Research » Publications at this Location » Publication #262886
Title: Association of single nucleotide polymorphism (SNP) markers in candidate genes and QTL regions with pork quality traits in commercial pigs

Author
item Rohrer, Gary
item Nonneman, Danny - Dan
item MILLER, RHONDA - Texas A&M University
item ZERBY, HENRY - The Ohio State University
item MOELLER, STEVEN - The Ohio State University

Submitted to: Meat Science
Publication Type: Peer Reviewed Journal
Publication Acceptance Date: 5/18/2012
Publication Date: 12/1/2012
Citation: Rohrer, G.A., Nonneman, D.J., Miller, R.K., Zerby, H., Moeller, S.J. 2012. Association of single nucleotide polymorphism (SNP) markers in candidate genes and QTL regions with pork quality traits in commercial pigs. Meat Science. 92(4):511-518.

Interpretive Summary: Numerous reports have described genetic markers associated with pork quality and/or palatability; however, validation of these associations in other commercial populations is necessary before these markers should be used. Therefore, we selected 156 single nucleotide polymorphism (SNP) markers from published associations and analyzed them for association with pork quality and palatability traits from 888 pork loins collected at three slaughter facilities and selected to represent a wide range of pork color, pH and marbling. Objective and subjective measures of color and marbling were collected on each loin. Loins were aged 7 - 10 days, purge loss recorded and chops frozen for subsequent analyses of shear force. Chops were thawed, purge loss determined, and then cooked to 62.8, 68.3, 73.9 or 79.4 degrees C internal temperature. Cooked chops were weighed to determine cooking loss. An average of six shear force measurements was used for analyses. Data were analyzed for associations between marker genotypes and pork quality attributes. Of the candidate genes tested, IGF2 was associated with multiple objective color parameters; MC4R with color, pH and marbling; CAST with shear force and PRKAG3 with measures of color, pH, purge and cooking loss. Significant associations were identified for seven of eight quantitative trait loci (QTL) regions tested (SSC1:60-90, SSC2:0-15, SSC2:60-80, SSC5:50-65, SSC6:50-86, SSC15:44-60, SSC17:30-70). These results indicate that some of the markers tested should be quite useful in any swine population, while the rest either do not segregate in all populations or the marker genotyped was too far from the actual mutation, which will limit their utility to the industry.

Technical Abstract: Numerous reports have described genetic markers or genomic regions (QTL) associated with pork quality and/or palatability. Validation of these associations in other commercial populations is necessary before these markers should be used. Therefore, 156 SNP markers from 45 candidate genes and 8 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. About half of the loins from one facility were enhanced. Objective and subjective measures of color and marbling were collected on each loin. Loins were aged 7-10 days, purge loss recorded and chops frozen for subsequent analyses of shear force via Warner-Bratzler instrumentation. Chops were thawed, purge loss post thawing determined, and then cooked to either 62.8, 68.3, 73.9 or 79.4 degrees C internal temperature. Cooked chops were weighed to determine cooking loss. An average of six shear force measurements was used for analyses. Data were analyzed with SAS Proc GLM for measures of quality traits of fresh loins where the model fitted included fixed effects of PLANT, DATE and marker genotype. Enhancement treatment was also included for purge loss. Thaw-purge loss data was analyzed with Proc MIXED where PLANT, DATE, Enhancement and marker genotype were fitted as fixed effects and Loin within marker genotype was a random effect. Shear force and cooking loss were analyzed with the same model except cooking time, final temperature and thaw purge loss were included as covariates. Of the candidate genes tested, IGF2 was associated with multiple objective color parameters; MC4R with color, pH and marbling; CAST with shear force and PRKAG3 with measures of color, pH, purge and cooking loss. One QTL region was not confirmed (SSC1:0-15 cM for marbling), whereas significant associations were identified for all other regions tested (SSC1:60-90, SSC2:0-15, SSC2:60-80, SSC5:50-65, SSC6:50-86, SSC15:44-60, SSC17:30-70). These results indicate that some of the markers tested should be quite useful in any swine population, while the rest either do not segregate in all populations or the linkage disequilibrium between the marker and the causative genetic variation fluctuates among populations limiting their utility to the industry.