A medium-throughput SNP assay for detecting genetic variation in coding and non-coding portions of the red fox genome

Benjamin Sacks, Dag Inge Våge, Mark J. Statham

Research output: Contribution to journalArticle

6 Scopus citations

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 protooncogenes, 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.

Original languageEnglish (US)
Pages (from-to)459-463
Number of pages5
JournalConservation Genetics Resources
Volume1
Issue number1
DOIs
StatePublished - Dec 1 2009

Keywords

  • Coat-color
  • Red fox
  • Single nucleotide polymorphisms
  • SNPs
  • Vulpes vulpes

ASJC Scopus subject areas

  • Genetics
  • Ecology, Evolution, Behavior and Systematics

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