ARS | Publication request: Porcine NAMPT gene: search for polymorphism, mapping and association studies

Submitted to: Animal Genetics
Publication Type: Peer Reviewed Journal
Publication Acceptance Date: March 1, 2010
Publication Date: November 10, 2010
Citation: Cepica, S., Bartenschlager, H., Ovilo, C., Zrustova, J., Masopust, M., Fernandez, A., Lopez, A., Knoll, A., Rohrer, G.A., Snelling, W.M., Geldermann, H. 2010. Porcine NAMPT gene: search for polymorphism, mapping and association studies. Animal Genetics. 41:646-651.

Interpretive Summary: A gene that is produced by fat cells and is critical in energy metabolism, named NAMPT, was studied to determine if genetic variation within the gene was associated with differences in backfat among pigs. Two differences were detected. They are single nucleotide polymorphisms (SNP) 669T>C in intron 9 and 358A>G in the promoter of the gene. Genetic mapping placed the gene on the current USDA – USMARC linkage map at position 92 cM on pig chromosome 9. Association analyses were performed in a wild boar x Meishan F2 family (WxM) and in a commercial Landrace x Chinese-European (LCE) composite population. In the WxM, both SNP were associated with muscling, fat deposition, and growth traits. In the LCE population, only SNP 669T>C was useful. Associations detected in the LCE population were with color of the lean and fatty acid composition of backfat. While the SNPs studied may cause the differences in performance observed, a more likely explanation is that they are closely associated with the causative genetic differences in the populations evaluated.

Technical Abstract: NAMPT encodes for an enzyme catalysing the rate-limiting step in NAD biosynthesis. The extracellular form of the enzyme is known as adipokine visfatin. We detected SNP AM999341:g.669T>C in intron 9 and SNP FN392209:g.358A>G in the promoter of the gene. RH mapping linked the gene to microsatellite SW944. Linkage analysis placed the gene on the current USDA – USMARC linkage map at position 92 cM on SSC9. Association analyses were performed in a wild boar x Meishan F2 family (WxM) with 45 traits recorded (growth and fattening, fat deposition, muscling, meat quality, stress resistance and other traits) and in a commercial Landrace x Chinese-European (LCE) synthetic population with records for 15 traits (growth, fat deposition, muscling, intramuscular fat, meat colour and backfat fatty acid content). In the WxM, SNP 669T>C was associated with muscling, fat deposition, growth and fattening, meat quality and other traits and in the LCE with muscling, meat quality and backfat fatty acid composition. In the WxM, SNP 358A>G was associated with muscling, fat deposition, growth and other traits. After correction for multiple testing the NAMPT haplotypes were associated in the WxM in descending order with muscling (q = 0.0056), growth (q = 0.0056), fat deposition (q = 0.0109), fat-to-meat ratio (q = 0.0135), cooling losses (q = 0.0568) and longissimus pHU (q = 0.0695). The SNPs are hypothesized to be in linkage disequilibrium with a causative mutation affecting energy metabolism as a whole rather than fat metabolism alone.