- Short Communication
SNPs in the porcine PPARGC1a gene: Interbreed differences and their phenotypic effects
Cellular & Molecular Biology Letters volume 12, pages 231–239 (2007)
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
feed conversion ratio
- FOXO1 :
forkhead box O1
- FXR :
farnesoid X receptor
- GR :
- HNF4α :
hepatic nuclear factor 4α
intramuscular fat content
- 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 Large White
- PPARα :
peroxisome proliferative activated receptor-α
- PPARβ/δ :
peroxisome proliferative activated receptor-β/δ
- PPARGC1A :
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
Lin, J., Handschin, C. and Spiegelman, B.M. Metabolic control through the PGC-1 family of transcription coactivators. Cell Metab. 1 (2005) 361–369.
Rohrer, G.A. and Keele, J.W. Identification of quantitative trait loci affecting carcass composition in swine: I. Fat deposition traits. J. Anim. Sci. 76 (1998) 2247–2254.
Malek, M., Dekkers, J.C.M., Lee, H.K., Baas, T.J. and Rothschild, M.F. A molecular genome scan analysis to identify chromosomal regions influencing economic traits in the pig. I. Growth and body composition. Mamm. Genome 12 (2001) 630–636.
Quintanilla, R., Milan, D. and Bidanel, J.P. A further look at quantitative trait loci affecting growth and fatness in a cross between Meishan and Large White pig populations. Genet. Sel. Evol. 34 (2002) 193–210.
Beeckmann, P., Moser, G., Bartenschlager, H., Reiner, G. and Geldermann, H. Linkage and QTL mapping for Sus scrofa chromosome 8. J. Anim. Breed. Genet. 120 (Suppl. 1) (2003) 66–73.
Hu, Z.H., Dracheva, S., Jang, W., Maglott, D., Bastiaansen, J., Rothschild, M.F. and Reecy, J.M. A QTL resource and comparison tool for pigs: PigQTLDB. Mamm. Genome 15 (2005) 792–800.
Kunej, T., Wu, X.L., Berlic, T.M., Michal, J.J., Jiang, Z. and Dovc, P. Frequency distribution of a Cys430Ser polymorphism in peroxisome proliferators-activated receptor-gamma coactivator-1 (PPARGC1) gene sequence in Chinese and Western pig breeds. J. Anim. Breed. Genet. 122 (2005) 7–11.
Jacobs, K., Rohrer, G., Van Poucke, M., Piumi, F., Yerle, M., Barthenschlager, H., Matheeuws, M., Van Zeveren, A. and Peelman, L.J. Porcine PPARGC1A (peroxisome proliferative activated receptor gamma coactivator 1A): coding sequence, genomic organization, polymorphisms and mapping. Cytogenet. Genome Res. 112 (2006) 106–113.
Michael, L.F., Wu, Z., Cheatham, R.B., Puigserver, P., Adelmant, G., Lehman, J.J., Kelly, D.P. and Spiegelman, B.M. Restoration of insulinsensitive glucose transporter (GLUT4) gene expression in muscle cells by the transcriptional coactivator PGC-1. Proc. Natl. Acad. Sci. USA 98 (2001) 3820–3825.
Betts, M.J. and Russell, R.B. Amino acid properties and consequences of substitutions. in: Bioinformatics for Geneticist (Barnes, M.R. and Gray, I.C., Eds), Wiley, 2003, 289-314.
Wu, Z., Puigserver, P., Andersson, U., Zhang, C., Adelmant, G., Mootha, V., Troy, A., Cinti, S., Lowell, B., Scarpulla, R.C. and Spiegelman B.M. Mechanisms controlling mitochondrial biogenesis and respiration through the thermogenic coactivator PGC-1. Cell 98 (1999) 115–124.
Puigserver, P., Wu, Z., Won Park, C., Graves, R., Wright, M. and Spiegelman, B.M. A cold-inducible coactivator of nuclear receptors linked to adaptive thermogenesis. Cell 92 (1998) 829–839.
Puigserver, P., Adelmant, G., Wu, Z., Fan, M., Xu, J., O’Malley B. and Spiegelman, B.M. Activation of PPAR? coactivator-1 through transcription factor docking. Science 286 (1999) 1368–1371.
About this article
Cite this article
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). https://doi.org/10.2478/s11658-006-0066-7