Hundreds of SNPs for the Endangered pygmy hippopotamus (Choeropsis liberiensis)
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.
KeywordsRAD sequencing SNP discovery Conservation genetics Pygmy hippopotamus Sequence data
- Etter PD, Preston JL, Bassham S, Cresko WA, Johnson EA (2011) Local de novo assembly of RAD paired-end contigs using short sequencing reads. PloS One 6(4):e18561. doi:10.1371/journal.pone.0018561
- Lewison R, Oliver W, (IUCN SSC Hippo Specialist Subgroup) (2008) Choeropsis liberiensis. In: IUCN 2013. IUCN Red List of Threatened Species. Version 2013.2. http://www.iucnredlist.org/
- Mallon D, Wightman C, De Ornellas P, Ransom C (Compilers) (2011) Conservation strategy for the pygmy hippopotamus. IUCN Species Survival Commission. Gland, Switzerland and CambridgeGoogle Scholar
- Steck (2012) International Studbook for the year 2012 pygmy hippopotamus Choeropsis liberiensis Morton, Zoo Basel, Switzerland. http://www.zoobasel.ch