Marker panels for genealogy-based mapping, breed demographics, and inference-of-ancestry in the Dog

Aaron K. Wong, Alison L. Ruhe, Shameek Biswas, Kathryn R. Robertson, Ammar Ali, Joshua M. Akey, Mark W. Neff

Research output: Contribution to journalArticle

1 Scopus citations

Abstract

Short tandem repeat polymorphisms (STRPs) are robust and informative markers for a range of genetic applications. STRPs are advantageous in experimental designs that derive power from sampling many individuals rather than many loci (e.g., pedigree-based studies, fine-scale mapping, and conservation genetics). STRPs have proven useful for vetting samples prior to costly high-density SNP analysis. Here we present validated STRPs (n=1,012) spanning the canine genome (2.1+/1.4Mb; 2.1+/2.1cM). Standardized design, pre-multiplexing, M13-based dye-labeling, and selection for loci amenable to semi-automated allele-scoring minimize cost and facilitate efficient genotyping. The markers are leveraged from the canine linkage map, and thus are backed by genetic data useful for parametric multipoint analysis and assessment of empiric coverage. We demonstrate several applications with different marker subsets. The complete set provides a genome scan for linkage at 5cM resolution. A subset of the markers measures molecular diversity between domestic and wild canid populations. Another subset reflects ancestry within breeds, uncovering hidden stratification and flagging genetic outliers prior to SNP genotyping. Thus, the markers described here add flexibility and cost effectiveness to several genetic applications in the dog that complement genome-wide SNP genotyping studies. Supplemental material is available for this article. Go to the publisher's online edition of Animal Biotechnology.

Original languageEnglish (US)
Pages (from-to)241-252
Number of pages12
JournalAnimal Biotechnology
Volume23
Issue number4
DOIs
StatePublished - Jan 1 2012
Externally publishedYes

All Science Journal Classification (ASJC) codes

  • Biotechnology
  • Bioengineering
  • Animal Science and Zoology

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