Implementing meta-analysis from genome-wide association studies for pork quality traits

Authors: BERNAL RUBIO, YENI - Universidad De Buenos Aires; GUALDRON DUARTE, JOSE - Universidad De Buenos Aires; BATES, RONALD - Michigan State University; ERNST, CATHERINE - Michigan State University; Nonneman, Danny - Dan; Rohrer, Gary; King, David - Andy; Shackelford, Steven; Wheeler, Tommy; CANTET, RODOLFO - Universidad De Buenos Aires; STEIBEL, JUAN - Michigan State University

Submitted to: Journal of Animal Science
Publication Type: Peer Reviewed Journal
Publication Acceptance Date: 9/16/2015
Publication Date: 12/18/2015
Publication URL: https://handle.nal.usda.gov/10113/62985
Citation: Bernal Rubio, Y.L., Gualdrón Duarte, J.L., Bates, R.O., Ernst, C.W., Nonneman, D., Rohrer, G.A., King, D.A., Shackelford, S.D., Wheeler, T.L., Cantet, R.J.C., Steibel, J.P. 2015. Implementing meta-analysis from genome-wide association studies for pork quality traits. Journal of Animal Science. 93(12):5607-5617.

Interpretive Summary: Pork quality has a large impact on consumer preference and perception of eating quality and is largely driven by tenderness and juiciness scores, which are related to shear force, cooking loss and 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 and influence purchase decisions. Factors including genetics, cooking temperature and processing procedures also affect meat quality and tenderness. While several candidate genes have been proposed for pork quality, only a few causative genes have been identified. Many QTL studies have been reported for pork quality using different breeds and crossbred populations, but limited studies have been done using dense genetic markers in commercial animals. This study was done to identify genes affecting economically important pork quality traits. A genome-wide analysis was performed for pork quality traits (intramuscular fat, slice shear force, color, purge loss, cooking loss and pH) collected from two resource populations and a commercial population for a total of 2,800 to 4,000 meat quality records using the Illumina PorcineSNP60 Beadchip and analyzed by combining the results in a meta-analysis. Associations were detected with regions of the swine genome for shear force, intramuscular fat, pH, purge loss, cooking loss and color a*. Two genomic regions near µ-calpain and calpastatin confirmed associations for shear force and associations with purge loss, cooking loss and pH were confirmed near PRKAG3. Novel associations were detected for color a*, intramuscular fat and cooking loss. Candidate genes were identified in these regions for further study. These results suggest that markers in these regions should be useful for genetic improvement of pork quality traits in commercial populations.

Technical Abstract: Pork quality plays an important role in the meat processing industry, thus different methodologies have been implemented to elucidate the genetic architecture of traits affecting meat quality. One of the most common and widely used approaches is to perform genome-wide association (GWA) studies. However, a limitation of many GWA in animal breeding is the limited power due to reduced sample sizes in animal populations. One alternative is to implement a meta-analysis of GWA (MA-GWA) combining results from independent association studies. The objective of this study was to identify significant genomic regions associated with meat quality traits, by performing MA-GWA for eight different traits in three independent pig populations. Results from MA-GWA were used to search for genes possibly associated with the set of evaluated traits. Data from three pig datasets (USMARC, Commercial and MSUPRP) were used. A MA was implemented by combining z-scores derived for each SNP in every population, and then, weighting them using the inverse of estimated variance of SNP effects. A search for annotated genes retrieved genes previously reported as candidates for shear force (CAPN1 and CAST), as well as for ultimate pH, purge loss and cooking loss (PRKAG3). In addition, novel candidate genes were identified for intramuscular fat and cooking loss (ACSF3) and for the objective measure of muscle redness, CIE a* (GYS1 and FTL). Thus, implementation of MA-GWA allowed integration of results for economically relevant traits and identified novel genes to be tested as candidates for meat quality traits in pig populations.