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

Abstract

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.

Abbreviations

AF:

abdominal fat weight

BF:

backfat thickness

FC:

feed conversion ratio

FOXO1 :

forkhead box O1

FXR :

farnesoid X receptor

GR :

glucocorticoid receptor

HNF4α :

hepatic nuclear factor 4α

IMF:

intramuscular fat content

LD:

longissimus dorsi

LXRα :

liver X receptor-α

MEF2 :

myocyte enhancer factor 2

NRF-1 :

nuclear respiratory factor 1

NRF-2 :

nuclear respiratory factor 2

PCR:

polymerase chain reaction

PL:

Polish Landrace

PLW:

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

QTL:

quantitative trait loci

RFLP:

restriction fragment length polymorphism

RYR1 :

ryanodine receptor 1

SNP:

single nucleotide polymorphism

SSC8:

Sus scrofa chromosome 8

SSCP:

single strand conformation polymorphism

References

  1. Lin, J., Handschin, C. and Spiegelman, B.M. Metabolic control through the PGC-1 family of transcription coactivators. Cell Metab. 1 (2005) 361–369.

    Article  PubMed  Google Scholar 

  2. 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.

    CAS  PubMed  Google Scholar 

  3. 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.

    Article  CAS  PubMed  Google Scholar 

  4. 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.

    Article  CAS  PubMed  Google Scholar 

  5. 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.

    Article  CAS  Google Scholar 

  6. 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.

    Article  Google Scholar 

  7. 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.

    Article  CAS  PubMed  Google Scholar 

  8. 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.

    Article  CAS  PubMed  Google Scholar 

  9. 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.

    Article  CAS  PubMed  Google Scholar 

  10. 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.

  11. 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.

    Article  CAS  PubMed  Google Scholar 

  12. 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.

    Article  CAS  PubMed  Google Scholar 

  13. 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.

    Article  CAS  PubMed  Google Scholar 

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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). https://doi.org/10.2478/s11658-006-0066-7

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  • DOI: https://doi.org/10.2478/s11658-006-0066-7

Key Words

  • Pig
  • PPARGC1A gene
  • Quantitative trait loci
  • SNP