Sequence variation of the PRKAG3 gene in two cattle breeds: a phylogenetic analysis

Thirty-three SNPs were characterized in a region of 6.8 kb of the bovine PRKAG3 gene, a member of a 5'-AMP-activated protein kinase (AMPK) family. here, we show results of haplotype and network analysis carried out in a sample of 97 Chianina and 100 Holstein-Friesian animals typed for 11 markers. Only 10 different haplotypes were present in the total sample (out of more than a thousand theoretically possible), two at high frequencies (53% and 32%), three at low frequencies (3% to 8%), and five present in a single or two instances only (p < 0.005%). Haplotype distribution was significantly different between breeds, and haplotype diversity (heterozygosity) was significantly lower in Holstein-Friesian. Based on haplotype sequence comparison, a phylogenetic network was constructed, leading to an unambiguous topology. A high frequency haplotype was located at centre, and two main branches radiated from it, connecting the more distant haplotypes through four or five sequential base substitutions. Three SNPs were associated to amino acid change; considering only these substitutions, the total sample was subdivided in four groups of 255, 126, 12 and 1 different haplotypes, respectively. This work is preliminary to the analysis of possible associations opf specific haplotypes with phenotypic traits of commercial interest.