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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    Electronic supplementary material  The online version of this article (doi:10.1186/s12863-015-0192-1) contains supplementary material, which is available to authorized users.

Genome-wide association studies (GWAS) identify a QTL close to PRKAG3 affecting meat pH and colour in crossbred commercial pigs