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Background  Color and pH of meat measured 24 h post mortem are common selection objectives in pig breeding programs. Several amino acid substitutions in  PRKAG3  have been associated with various meat quality traits. In our previous study ASGA0070625, a SNP next to  PRKAG3 , had the most significant association with meat quality traits in the Finnish Yorkshire. However, the known amino acid substitutions, including I199V, did not show any association. The aims of this study were to characterize further variation in  PRKAG3  and its promoter region, and to test the association between these variants and the pH and color of pork meat.    Results  The data comprised of 220 Finnish Landrace and 230 Finnish Yorkshire artificial insemination boars with progeny information. We sequenced the coding and promoter region of  PRKAG3  in these and in three additional wild boars. Genotypes from our previous genome-wide scans were also included in the data. Association between SNPs or haplotypes and meat quality traits (deregressed estimates of breeding values from Finnish national breeding value estimation for pH, color lightness and redness measured from loin or ham) was tested using a linear regression model. Sequencing revealed several novel amino acid substitutions in  PRKAG3 , including K24E, I41V, K131R, and P134L. Linkage disequilibrium was strong among the novel variants, SNPs in the promoter region and ASGA0070625, especially for the Yorkshire. The strongest associations were observed between ASGA0070625 and the SNPs in the promoter region and pH measured from loin in the Yorkshire and between I199V and pH measured from ham in the Landrace. In contrast, ASGA0070625 was not significantly associated with meat quality traits in the Landrace and I199V not in the Yorkshire. Haplotype analysis showed a significant association between a haplotype consisting of  199I  and  24E  alleles (or  g.-157C  or  g.-58A  alleles in the promoter region) and pH measured from loin and ham in both breeds (P-values varied from 1.72 × 10 -4  to 1.80 × 10 -8 ).    Conclusions  We conclude that haplotype  g.-157C - g.-58A - 24E - 199I  in  PRKAG3  has a positive effect on meat quality in pigs. Our results are readily applicable for marker-assisted selection in pigs.

A combination of two variants in PRKAG3 is needed for a positive effect on meat quality in pigs