Identification and evaluation of novel di- and tetranucleotide microsatellite markers from the brown bear (Ursus arctos)
- 191 Downloads
We here describe 34 novel microsatellite loci from the brown bear (Ursus arctos) identified using a next-generation sequencing approach. While we found allelic variation in 30 of these, we selected 16 polymorphic microsatellites (11 di- and 5 tetranucleotide repeats) for four multiplex-PCR assays based on genetic variability, PCR performance and interpretability. Applying these assays for the 16 novel microsatellites, we screened 31 brown bears from a northern European population. The number of alleles encountered at single loci was between 4 and 10, and expected and observed heterozygosities ranged between 0.66–0.85 and 0.60–0.97, respectively. Seven of 120 pairwise locus combinations showed linkage disequilibrium and one locus deviated from Hardy–Weinberg equilibrium, while no null-alleles were detected. Our novel multiplex-PCR assays may be useful in forensics, parentage and population genetic studies.
KeywordsDi- and tetranucleotide microsatellites High-throughput sequencing Multiplex PCR Non-invasive samples Genetic variation Ursus arctos
The study was supported by “LOEWE—Landes-Offensive zur Entwicklung Wissenschaftlich-ökonomischer Exzellenz” of Hesse’s Ministry of Higher Education, Research, and the Arts.
- Andreassen R, Schregel J, Kopatz A, Tobiassen C, Knappskog PM, Hagen SB, Kleven O, Schneider M, Kojola I, Aspi J, Rykov A, Tirronen KF, Danilov PI, Eiken HG (2012) A forensic DNA profiling system for Northern European brown bears (Ursus arctos). Forensic Sci Int Genet. doi: 10.1016/j.fsigen.2012.03.002
- Eiken HG, Andreassen R, Kopatz A, Bjervamoen SG, Wartiainen I, Tobiassen C, Knappskog PM, Aspholm PE, Smith ME, Aspi J (2009) Population data for 12 STR loci in Northern European brown bear (Ursus arctos) and application of DNA profiles for forensic casework. Forensic Sci Int Genet Suppl 2:273–274CrossRefGoogle Scholar
- Kopatz A, Eiken HG, Hagen SB, Ruokonen M, Esparza-Salas R, Schregel J, Kojola I, Smith M, Wartiainen I, Aspholm PE, Wikan S, Rykov A, Makarova O, Polikarpova N, Tirronen K, Danilov P, Aspi J (2012) Connectivity and population subdivision at the fringe of a large brown bear (Ursus arctos) population in North Western Europe. Conserv Genet 1–12. doi: 10.1007/s10592-012-0317-2
- Linacre A, Gusmao L, Hecht W, Hellmann AP, Mayr WR, Parson W, Prinz M, Schneider PM, Morling N (2011) ISFG: recommendations regarding the use of non-human (animal) DNA in forensic genetic investigations. Forensic Sci Int Genet 5:501–505. doi: 10.1016/j.fsigen.2010.10.017 PubMedCrossRefGoogle Scholar
- Rozen S, Skaletsky HJ (2000) Primer3 on the WWW for general users and for biologist programmers. In: Krawetz S, Kisener S (eds) Bioinformatics methods and protocols: methods in molecular biology. Humana Press, Totawa, pp 365–386Google Scholar