Development of a high-density sub-species-specific targeted SNP assay for Rocky Mountain bighorn sheep (Ovis canadensis canadensis)

Samuel Deakin; David W Coltman

doi:10.7717/peerj.16946

Development of a high-density sub-species-specific targeted SNP assay for Rocky Mountain bighorn sheep (Ovis canadensis canadensis)

PeerJ. 2024 Feb 26:12:e16946. doi: 10.7717/peerj.16946. eCollection 2024.

Authors

Samuel Deakin¹, David W Coltman^{1

2}

Affiliations

¹ Department of Biological Sciences, University of Alberta, Edmonton, Alberta, Canada.
² Department of Biology, University of Western Ontario, London, Ontario, Canada.

Abstract

Due to their abundance and relative ease of genotyping, single nucleotide polymorphisms (SNPs) are a commonly used molecular marker for contemporary population genetic and genomic studies. A high-density and cost-effective way to type SNP loci is Allegro targeted genotyping (ATG), which is a form of targeted genotyping by sequencing developed and offered by Tecan genomics. One major drawback of this technology is the need for a reference genome and information on SNP loci when designing a SNP assay. However, for some non-model species genomic information from other closely related species can be used. Here we describe our process of developing an ATG assay to target 50,000 SNPs in Rocky Mountain bighorn sheep, using a reference genome from domestic sheep and SNP resources from prior bighorn sheep studies. We successfully developed a high accuracy, high-density, and relatively low-cost SNP assay for genotyping Rocky Mountain bighorn sheep that genotyped ~45,000 SNP loci. These loci were relatively evenly distributed throughout the genome. Furthermore, the assay produced genotypes at tens of thousands of SNP loci when tested on other mountain sheep species and subspecies.

Keywords: Allegro; Bighorn; Development; Genetic; Genomic; SNP; SPET; Sheep; Tecan; Ungulate.

MeSH terms

Animals
Genome
Genomics
Genotype
Polymorphism, Single Nucleotide* / genetics
Sheep / genetics
Sheep, Bighorn* / genetics

Associated data

Dryad/10.5061/dryad.4qk81

Grants and funding

This research was funded by a Natural Sciences and Engineering Research Council of Canada discovery grants to David W. Coltman and the Canadian Mountain Network. The funders had no role in study design, data collection and analysis, decision to publish, or preparation of the manuscript.