Skip to main content
ARS Home » Plains Area » Clay Center, Nebraska » U.S. Meat Animal Research Center » Livestock Bio-Systems » Research » Publications at this Location » Publication #219022
Title: Update on genetic markers for pork quality

Author
item Rohrer, Gary
item Holl, Justin
item Lindholm-Perry, Amanda
item Nonneman, Danny - Dan
item Shackelford, Steven
item Wheeler, Tommy
item Koohmaraie, Mohammad

Submitted to: Swine Improvement Federation Proceedings
Publication Type: Proceedings
Publication Acceptance Date: 12/1/2007
Publication Date: 12/7/2007
Citation: Rohrer, G.A., Holl, J.W., Lindholm-Perry, A.K., Nonneman, D.J., Shackelford, S.D., Wheeler, T.L., Koohmaraie, M. 2007. Update on genetic markers for pork quality. Conference Proc., National Swine Improvement Federation Conference & Ann. Mtg., Dec. 5-7, 2007. Kansas City, MO, NSIF Volume 32, www.nsif.com

Interpretive Summary: Genetic markers reported to be associated with pork quality traits in the literature were tested. These markers were genotyped across pigs (n = 1291) with pork quality data available from four populations. Genetic marker-phenotype associations were determined using three different statistical models typically used in marker association studies. Model G was a fixed effects model fitting slaughter group, sex and genotype as fixed effects. Model GS was similar to model G with sire also fitted. Model GA included an animal's estimated breeding value along with fixed effects of slaughter group, sex and genotype. One SNP for ASIP, DLK1, GYS1, MC4R and RYR1 were genotyped along with three SNP for CAST and four SNP for PRKAG3. The RN causing mutation of PRKAG3 was not present and RYR1 mutation (stress allele) was only present in a few animals of one population so these SNP were not analyzed. The associations that appear to be useful for industry applications are the CAST (calpastatin) markers for pork tenderness, GYS1 for pH, MC4R for purge loss and PRKAG3 for pH and water holding capacity. These associations were the most consistent across populations. The statistical model which appeared the most robust was GA. These results indicate that some of the reported associations of genetic markers with pork quality traits are useful to improve pork quality in commercial populations.

Technical Abstract: To determine the robustness of reported marker associations with pork quality traits, assay systems were developed for as many polymorphisms from the literature as possible. These assays were genotyped across pigs (n = 1,291) with pork quality data available from four populations. Genetic marker-phenotype associations were determined using three different statistical models typically used in marker association studies. Model G was a fixed effects model fitting slaughter group, sex and genotype as fixed effects. Model GS was similar to model G with sire also fitted as a fixed effect. Model GA fitted an animal model using MTDFREML software programs and included fixed effects of genotype, slaughter group and sex. One SNP for ASIP, DLK1, GYS1, MC4R and RYR1 were genotyped along with three SNP for CAST and four SNP for PRKAG3. The RN causing mutation of PRKAG3 was not present and RYR1 mutation was only present in a few animals of one population so these SNP were not analyzed. The associations that appear to be useful for industry applications are the CAST assays for pork tenderness, GYS1 for pH, MC4R for purge loss and PRKAG3 for pH and water holding capacity. These associations were the most consistent across populations. The statistical model which appeared the most robust was GA. These results indicate that some of the reported associations of genetic markers with pork quality traits are useful in a variety of populations and should be used by the industry to improve the quality of pork produced.