Fast and cost-effective single nucleotide polymorphism (SNP) detection in the absence of a reference genome using semideep next-generation Random Amplicon Sequencing (RAMseq).

Autor: Bayerl H; Unit of Molecular Zoology, Chair of Zoology, Technische Universität München, Freising, Germany., Kraus RHS; Department of Migration and Immuno-Ecology, Max Planck Institute for Ornithology, Radolfzell, Germany.; Department of Biology, University of Konstanz, Konstanz, Germany., Nowak C; Conservation Genetics Group, Senckenberg Research Institute and Natural History Museum Frankfurt, Gelnhausen, Germany., Foerster DW; Department of Evolutionary Genetics, Leibniz-Institute for Zoo and Wildlife Research, Berlin, Germany., Fickel J; Department of Evolutionary Genetics, Leibniz-Institute for Zoo and Wildlife Research, Berlin, Germany.; Institute for Biochemistry and Biology, University of Potsdam, Potsdam, Germany., Kuehn R; Unit of Molecular Zoology, Chair of Zoology, Technische Universität München, Freising, Germany.; Department of Fish, Wildlife and Conservation Ecology, New Mexico State University, Las Cruces, NM, USA.
Jazyk: angličtina
Zdroj: Molecular ecology resources [Mol Ecol Resour] 2018 Jan; Vol. 18 (1), pp. 107-117. Date of Electronic Publication: 2017 Oct 09.
DOI: 10.1111/1755-0998.12717
Abstrakt: Biodiversity has suffered a dramatic global decline during the past decades, and monitoring tools are urgently needed providing data for the development and evaluation of conservation efforts both on a species and on a genetic level. However, in wild species, the assessment of genetic diversity is often hampered by the lack of suitable genetic markers. In this article, we present Random Amplicon Sequencing (RAMseq), a novel approach for fast and cost-effective detection of single nucleotide polymorphisms (SNPs) in nonmodel species by semideep sequencing of random amplicons. By applying RAMseq to the Eurasian otter (Lutra lutra), we identified 238 putative SNPs after quality filtering of all candidate loci and were able to validate 32 of 77 loci tested. In a second step, we evaluated the genotyping performance of these SNP loci in noninvasive samples, one of the most challenging genotyping applications, by comparing it with genotyping results of the same faecal samples at microsatellite markers. We compared (i) polymerase chain reaction (PCR) success rate, (ii) genotyping errors and (iii) Mendelian inheritance (population parameters). SNPs produced a significantly higher PCR success rate (75.5% vs. 65.1%) and lower mean allelic error rate (8.8% vs. 13.3%) than microsatellites, but showed a higher allelic dropout rate (29.7% vs. 19.8%). Genotyping results showed no deviations from Mendelian inheritance in any of the SNP loci. Hence, RAMseq appears to be a valuable tool for the detection of genetic markers in nonmodel species, which is a common challenge in conservation genetic studies.
(© 2017 John Wiley & Sons Ltd.)
Databáze: MEDLINE
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