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Characterization of the porcine AMPK alpha 2 catalytic subunitgene (PRKAA2): genomic structure, polymorphism detection and association study

Lin, L., Flisikowski, K., Schwarzenbacher, H., Scharfe, M., Severitt, S., Blöcker, H., Fries, R.
Animal genetics 2010 v.41 no.2 pp. 203-207
AMP-activated protein kinase, German Landrace, amino acid substitution, bacterial artificial chromosomes, energy, exons, genes, genotyping, glucose, haplotypes, homeostasis, introns, lipid metabolism, muscle development, muscles, protein subunits, protein synthesis, radiation hybrid mapping, sequence analysis, single nucleotide polymorphism, swine
AMP-activated protein kinase (AMPK), known as a key regulator of cellular energy homeostasis, plays an important role in regulation of glucose and lipid metabolism, and protein synthesis in mammals. The characterization of porcine PRKAA2 encoding the alpha 2 catalytic subunit of AMPK is reported in this study. PRKAA2 was assigned to porcine chromosome 6q by analysis of radiation hybrids (IMpRH panel), and its genomic structure was determined by BAC sequencing. PRKAA2 spans more than 62 kb and consists of nine exons and eight introns. A total of 25 polymorphisms were identified by re-sequencing approximately 7 kb, including all the exons, exon-intron boundaries and 5′ and 3′ gene flanking regions using twelve founder animals of a Mangalitsa x Piétrain intercross. Neither of two single nucleotide polymorphisms (SNPs) found in the coding region caused an amino acid substitution. Two SNPs (NM_214266.1: c.236+142A>G and NM_214266.1: c.630C>T) in PRKAA2 were genotyped in the Mangalitsa x Piétrain F₂ cross (n = 589) and two commercial populations [Piétrain (n = 1173) and German Landrace (n = 536)] and evaluated for association with traits of interest (muscle development and fat deposition). Single SNP and haplotype analyses revealed weak associations between the PRKAA2 genotypes and loin muscle area in the investigated populations.