SNP detection in the porcine PPARGC1A promoter region and 3'UTR, and an association analysis in a Landrace-Duroc-Yorkshire population

Meat quality is of increasing economic importance to the pork industry today, which is in contrast with the more traditional focus of pig selection for lean growth. Meat quality is however determined by many factors with a complex mutual relationship. In this regard, PPARGC1A is a very interesting candidate gene because it not only plays a crucial role in energy and fat metabolism but also has an important influence on the muscle fibre type composition. However, only little is known about the regulation of expression of this gene in the pig and its usefulness in pig selection. In order to get a better understanding of the regulation of PPARGC1A expression, 1 898 base pairs (bp) from the promoter region and the complete 3'UTR (3 826 bp) were sequenced and screened for mutations in 7 diverse pig breeds. Respectively 5 and 6 new mutations were discovered in these regions, of which several were in complete linkage disequilibrium with each other. None of the detected SNPs appeared to be located in any conserved part of the sequence when comparing different species. In an association analysis with intramuscular fat percentage, leaf fat weight or last rib backfat depth carried out in a Landrace-Duroc-Yorkshire commercial research population (n = 960), no associations were detected for the new SNPs from this study or for 2 previously described SNPs in exon 8 and 9. The results from this study provide essential information on the sequence of the promoter region and 3'UTR of porcine PPARGC1A, necessary for unravelling the complex regulation of expression and functioning of this gene in the pig. Although no association with meat quality and fat deposition parameters was found for the newly discovered SNPs in the regulatory regions, these need to be used in future studies to (further) assess their usefulness as new selection criteria for improving meat quality while maintaining the leanness of the carcass.