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

L. L. Bernal Rubio, L. L. Gualdrón Duarte, O. O. Bates, W. W. Ernst, Nonneman, A. A. Rohere, A. A. King, D. D. Shackelford, L. L. Wheeler, J. C. J. C. Cantet, P. P. Steibel
Journal of animal science 2015 v.93 no.12 pp. 5607-5617
animal breeding, calpastatin, cooking quality, data collection, ferritin, genes, genome-wide association study, glycogen (starch) synthase, intramuscular fat, long-chain-fatty-acid-CoA ligase, meat processing plants, meat quality, meta-analysis, mitochondria, muscles, pH, polypeptides, pork, protein subunits, single nucleotide polymorphism, swine, variance
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 small 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 8 different traits in 3 independent pig populations. Results from MA-GWA were used to search for genes possibly associated with the set of evaluated traits. Data from 3 pig data sets (U.S. Meat Animal Research Center, commercial, and Michigan State University Pig Resource Population) 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 (calpain-1 catalytic subunit [CAPN1] and calpastatin [CAST]), as well as for ultimate pH, purge loss, and cook loss (protein kinase, AMP-activated, γ 3 noncatalytic subunit [PRKAG3]). In addition, novel candidate genes were identified for intramuscular fat and cook loss (acyl-CoA synthetase family member 3 mitochondrial [ACSF3]) and for the objective measure of muscle redness, CIE a* (glycogen synthase 1, muscle [GYS1] and ferritin, light polypeptide [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.