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Open Access Research article

Haplotypes of the porcine peroxisome proliferator-activated receptor delta gene are associated with backfat thickness

Karina Meidtner1, Hermann Schwarzenbacher1, Maren Scharfe2, Simone Severitt2, Helmut Blöcker2 and Ruedi Fries1*

Author Affiliations

1 Chair of Animal Breeding, Technical University of Munich, Hochfeldweg 1, 85354 Freising - Weihenstephan, Germany

2 Department of Genome Analysis, Helmholtz Centre for Infection Research, Inhoffenstraße 7, 38124 Braunschweig, Germany

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BMC Genetics 2009, 10:76  doi:10.1186/1471-2156-10-76

Published: 30 November 2009

Abstract

Background

Peroxisome proliferator-activated receptor delta belongs to the nuclear receptor superfamily of ligand-inducible transcription factors. It is a key regulator of lipid metabolism. The peroxisome proliferator-activated receptor delta gene (PPARD) has been assigned to a region on porcine chromosome 7, which harbours a quantitative trait locus for backfat. Thus, PPARD is considered a functional and positional candidate gene for backfat thickness. The purpose of this study was to test this candidate gene hypothesis in a cross of breeds that were highly divergent in lipid deposition characteristics.

Results

Screening for genetic variation in porcine PPARD revealed only silent mutations. Nevertheless, significant associations between PPARD haplotypes and backfat thickness were observed in the F2 generation of the Mangalitsa × Piétrain cross as well as a commercial German Landrace population. Haplotype 5 is associated with increased backfat in F2 Mangalitsa × Piétrain pigs, whereas haplotype 4 is associated with lower backfat thickness in the German Landrace population. Haplotype 4 and 5 carry the same alleles at all but one SNP. Interestingly, the opposite effects of PPARD haplotypes 4 and 5 on backfat thickness are reflected by opposite effects of these two haplotypes on PPAR-δ mRNA levels. Haplotype 4 significantly increases PPAR-δ mRNA levels, whereas haplotype 5 decreases mRNA levels of PPAR-δ.

Conclusion

This study provides evidence for an association between PPARD and backfat thickness. The association is substantiated by mRNA quantification. Further studies are required to clarify, whether the observed associations are caused by PPARD or are the result of linkage disequilibrium with a causal variant in a neighbouring gene.