Skip to main content
eScholarship
Open Access Publications from the University of California

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.
Abstract

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.

Many UC-authored scholarly publications are freely available on this site because of the UC Academic Senate's Open Access Policy. Let us know how this access is important for you.

Main Content
Current View