A medium-throughput SNP assay for detecting genetic variation in coding and non-coding portions of the red fox genome
- Author(s): Sacks, Benjamin N.
- Våge, Dag Inge
- Statham, Mark J.
- et al.
Published Web Locationhttps://doi.org/10.1007/s12686-009-9106-8
SNPs are fast becoming the marker of choice in population genetics studies of model organisms. However, a lack of efficient means to assay sufficient numbers of SNPs in non-model organisms has prevented their widespread use for conservation-related applications. We established a SNP genotyping assay (including development of new SNP markers) for detection of genetic variation in coding and non-coding parts of the fox genome, using a 96-locus multiplex format. Coding SNPs were associated with Agouti and Mc1r coat-color alleles, phylogenetically basal mitochondrial mutations, sex markers, B-chromosome proto-oncogenes, and serotonin-receptor genes. Non-coding SNPs (n = 51) included 27 newly described microsatellite-linked SNPs. A panel of red foxes (n = 96) was used to characterize minor allele frequencies and Hardy–Weinberg equilibrium. Genotyping accuracy was 99% for 72 SNPs relative to sequenced and known-phenotype animals.