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SNPs in the porcine PPARGC1a gene: Interbreed differences and their phenotypic effects


Due to its function, the peroxisome proliferative activated receptor-γ, coactivator-1α (PPARGC1A) gene is a candidate in the search for genes that may affect production traits in the pig. The purpose of this study was to screen for new SNPs in exon 8 of the porcine PPARGC1A gene and to test their possible association with production traits. Altogether 736 pigs representing five breeds Polish Landrace, n=242; Polish Large White, n=192; Hampshire, n=27; Duroc, 21; Pietrain, n=12) and synthetic line 990 (n=242) were scanned via SSCP assay. Four SNPs were found; two new ones: C/G (His338Gln) and G/A Thr359Thr), and two previously reported ones: C/A (Arg369Arg) and T/A Cys430Ser). The missense T/A and C/G SNPs demonstrated pronounced interbreed variability in terms of allele frequencies, including the exclusive presence of the C/G substitution in the Hampshire breed. The tested SNPs occurred in five putative haplotypes, and their frequency also differed substantially between breeds. The association of the SNPs with production traits was tested for G/A (Thr359Thr), C/A (Arg369Arg) and T/A (Cys430Ser) substitutions in Polish Large White, Polish Landrace and line 990. The analysis revealed only breed-specific associations. The T/A (Cys430Ser) SNP was related to the feed conversion ratio in the Polish Large White (P=0.02), and the silent G/A and C/A substitutions were respectively associated with abdominal fat in line 990 and backfat thickness in Polish Landrace (P=0.04). The combined effects of the substitutions were estimated as haplotype effects. Three significant contrasts between haplotypes were calculated, but the observed associations were again only breed-specific.



abdominal fat weight


backfat thickness


feed conversion ratio


forkhead box O1


farnesoid X receptor

GR :

glucocorticoid receptor

HNF4α :

hepatic nuclear factor 4α


intramuscular fat content


longissimus dorsi

LXRα :

liver X receptor-α

MEF2 :

myocyte enhancer factor 2

NRF-1 :

nuclear respiratory factor 1

NRF-2 :

nuclear respiratory factor 2


polymerase chain reaction


Polish Landrace


Polish Large White


peroxisome proliferative activated receptor-α

PPARβ/δ :

peroxisome proliferative activated receptor-β/δ


peroxisome proliferative activated receptor-γ, coactivator-1α


quantitative trait loci


restriction fragment length polymorphism

RYR1 :

ryanodine receptor 1


single nucleotide polymorphism


Sus scrofa chromosome 8


single strand conformation polymorphism


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Correspondence to Marek Switonski.

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Stachowiak, M., Szydlowski, M., Cieslak, J. et al. SNPs in the porcine PPARGC1a gene: Interbreed differences and their phenotypic effects. Cell Mol Biol Lett 12, 231–239 (2007).

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