De novo SNP discovery in the Scandinavian brown bear (Ursus arctos)

PLoS One. 2013 Nov 18;8(11):e81012. doi: 10.1371/journal.pone.0081012. eCollection 2013.

Abstract

Information about relatedness between individuals in wild populations is advantageous when studying evolutionary, behavioural and ecological processes. Genomic data can be used to determine relatedness between individuals either when no prior knowledge exists or to confirm suspected relatedness. Here we present a set of 96 SNPs suitable for inferring relatedness for brown bears (Ursus arctos) within Scandinavia. We sequenced reduced representation libraries from nine individuals throughout the geographic range. With consensus reads containing putative SNPs, we applied strict filtering criteria with the aim of finding only high-quality, highly-informative SNPs. We tested 150 putative SNPs of which 96% were validated on a panel of 68 individuals. Ninety-six of the validated SNPs with the highest minor allele frequency were selected. The final SNP panel includes four mitochondrial markers, two monomorphic Y-chromosome sex-determination markers, three X-chromosome SNPs and 87 autosomal SNPs. From our validation sample panel, we identified two previously known parent-offspring dyads with reasonable accuracy. This panel of SNPs is a promising tool for inferring relatedness in the brown bear population in Scandinavia.

Publication types

  • Research Support, Non-U.S. Gov't

MeSH terms

  • Alleles
  • Animals
  • Chromosomes, Mammalian*
  • Female
  • Gene Frequency
  • Genes, Mitochondrial*
  • High-Throughput Nucleotide Sequencing
  • Inheritance Patterns*
  • Male
  • Phylogeography
  • Polymorphism, Single Nucleotide*
  • Scandinavian and Nordic Countries
  • Sequence Analysis, DNA
  • Ursidae / genetics*

Grants and funding

Mauritz Carlgren Foundation, Fortlöpande Miljöanalys (FOMA): Genetic Monitoring. The funders had no role in study design, data collection and analysis, decision to publish, or preparation of the manuscript.