Hundreds of SNPs for the endangered pygmy hippopotamus (Choeropsis liberiensis)

Helen Senn*, Paul O'Donoghue, Ross McEwing, Rob Ogden

*Corresponding author for this work

Research output: Contribution to journalArticlepeer-review

Abstract

The pygmy hippo is an Endangered mammal endemic to West Africa, of which only 2,000-3,000 are left in the wild. Until now genetic resources to conduct monitoring of wild populations and to facilitate captive breeding have been lacking. In this study we used restriction-site associated DNA sequencing of five pygmy hippo samples to generate 1,619 high confidence candidate single nucleotide polymorphisms (SNPs) suitable for population genetic analysis. A subset of 10 of SNPs generated were validated via resequencing with 100 % success rate and through the use of KASPar DNA probes (Kbiosciences) with 90 % success rate. To facilitate future research we present the list of 1,619 SNPs ranked according to mean genotype confidence and mean coverage.

Original languageEnglish
Pages (from-to)535-538
Number of pages4
JournalConservation Genetics Resources
Volume6
Issue number3
DOIs
Publication statusPublished - 1 Jan 2014

Keywords

  • Conservation genetics
  • Pygmy hippopotamus
  • RAD sequencing
  • Sequence data
  • SNP discovery

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