title: Genome-wide association studies (GWAS) identify a QTL close to PRKAG3 affecting meat pH and colour in crossbred commercial pigs.
abstract: BACKGROUND
  Improving meat quality is a high priority for the pork industry to satisfy consumers' preferences. GWAS have become a state-of-the-art approach to genetically improve economically important traits. However, GWAS focused on pork quality are still relatively rare.
  
  
  RESULTS
  Six genomic regions were shown to affect loin pH and Minolta colour a* and b* on both loin and ham through GWAS in 1943 crossbred commercial pigs. Five of them, located on Sus scrofa chromosome (SSC) 1, SSC5, SSC9, SSC16 and SSCX, were associated with meat colour. However, the most promising region was detected on SSC15 spanning 133-134 Mb which explained 3.51% - 17.06% of genetic variance for five measurements of pH and colour. Three SNPs (ASGA0070625, MARC0083357 and MARC0039273) in very strong LD were considered most likely to account for the effects in this region. ASGA0070625 is located in intron 2 of ZNF142, and the other two markers are close to PRKAG3, STK36, TTLL7 and CDK5R2. After fitting MARC0083357 (the closest SNP to PRKAG3) as a fixed factor, six SNPs still remained significant for at least one trait. Four of them are intragenic with ARPC2, TMBIM1, NRAMP1 and VIL1, while the remaining two are close to RUFY4 and CDK5R2. The gene network constructed demonstrated strong connections of these genes with two major hubs of PRKAG3 and UBC in the super-pathways of cell-to-cell signaling and interaction, cellular function and maintenance. All these pathways play important roles in maintaining the integral architecture and functionality of muscle cells facing the dramatic changes that occur after exsanguination, which is in agreement with the GWAS results found in this study.
  
  
  CONCLUSIONS
  There may be other markers and/or genes in this region besides PRKAG3 that have an important effect on pH and colour. The potential markers and their interactions with PRKAG3 require further investigation.
authors.affiliation: Department of Agricultural, Food & Nutritional Sciences, University of Alberta, Edmonton, AB, T6G 2P5, Canada. chunyan3@ualberta.ca.
authors.forename: Chunyan
authors.initials: C
authors.lastname: Zhang
authors.affiliation: Department of Agricultural, Food & Nutritional Sciences, University of Alberta, Edmonton, AB, T6G 2P5, Canada. Zhiquan.Wang@ales.ualberta.ca.
authors.forename: Zhiquan
authors.initials: Z
authors.lastname: Wang
authors.affiliation: Department of Agricultural, Food & Nutritional Sciences, University of Alberta, Edmonton, AB, T6G 2P5, Canada. hbruce@ualberta.ca.
authors.forename: Heather
authors.initials: H
authors.lastname: Bruce
authors.affiliation: Genesus Inc, Oakville, MB, Canada. kempb@shaw.ca.
authors.forename: Robert Alan
authors.initials: RA
authors.lastname: Kemp
authors.affiliation: Hypor Inc, Regina, SK, Canada. patrick.charagu@hendrix-genetics.com.
authors.forename: Patrick
authors.initials: P
authors.lastname: Charagu
authors.affiliation: Department of Agricultural, Food & Nutritional Sciences, University of Alberta, Edmonton, AB, T6G 2P5, Canada. miar@ualberta.ca.
authors.forename: Younes
authors.initials: Y
authors.lastname: Miar
authors.affiliation: Department of Agricultural, Food & Nutritional Sciences, University of Alberta, Edmonton, AB, T6G 2P5, Canada. tianfu@ualberta.ca.
authors.forename: Tianfu
authors.initials: T
authors.lastname: Yang
authors.affiliation: Department of Agricultural, Food & Nutritional Sciences, University of Alberta, Edmonton, AB, T6G 2P5, Canada. plastow@ualberta.ca.
authors.forename: Graham
authors.initials: G
authors.lastname: Plastow
mesh_terms: D055372:AMP-Activated Protein Kinases / Q000235:genetics*; D000818:Animals; D002875:Chromosomes; D053263:Gene Regulatory Networks; D056726:Genetic Association Studies; D055106:Genome-Wide Association Study; D023281:Genomics; D006239:Haplotypes; D006824:Hybridization, Genetic; D015810:Linkage Disequilibrium; D008460:Meat; D010641:Phenotype; D020641:Polymorphism, Single Nucleotide; D040641:Quantitative Trait Loci; D019655:Quantitative Trait, Heritable; D013552:Swine
chemical_list: D055372:AMP-Activated Protein Kinases