A Comprehensive Survey for Polymorphisms in the Bovine IFN- γ Gene Reveals a Highly Polymorphic Intronic DNA Sequence Allowing Improved Genotyping of Bovinae

Abstract

This study aimed to identify interferon-γ (IFN-γ) gene variants in cattle for diagnostic purposes. Therefore, the entire bovine IFN-γ gene (BoIFNG) and 2605 bp of its promoter DNA were sequenced. The BoIFNG DNA sequence conforms to the published part of Bo-IFN-γ cDNA. Primer extension experiments show the presence of a 5′ extension of exon 1 by 42 nucleotides (nt). One SINE element (Bov-A2) is located in the 5′-region, and two SINE elements (Bov-tA, Bov-B) are contained in the 3′-region of BoIFNG. The variants were detected by comparative sequence analysis of PCR amplicons from different bovine species. Four polymorphic mononucleotide repeats are situated in the promoter and in intron 1. Four distinct series of single nucleotide polymorphisms (SNP) were found in functionally important regions of BoIFNG. The region between the two intron 1 microsatellites contains the highest density of SNPs inBos taurus breeds. One G-T transversion in the coding region of exon 1 causes a Gly₁₄ to Val₁₄ exchange in the BoIFNG signal peptide of different bovine species. A G-A transition in exon 2 encodes a Ser₁₉ to Asn₁₉ change in the mature protein of the Tibetan yak. Genotyping of randomly sampled Holstein Friesian cows at selected SNPs and of both intron 1 microsatellites revealed two dominant BoIFNG microhaplotypes. The detected SNPs improve the recently reported genotyping system of cattle.