A simple route to single-nucleotide polymorphisms in a nonmodel species:identification and characterization of SNPs in the Artic ringed seal (Pusa hispida hispida)

• Published in: Molecular Ecology Resources
• Main Authors: Olsen, Morten Tange, Volny, Veronica Hirsh, Berube, Martine, Dietz, Rune, Lydersen, Christian, Kovacs, Kit M., Dodd, Richard S., Palsboll, Per J. .
• Format: Article in Journal/Newspaper
• Language: English
• Published: 2011
• Subjects: Arctic; discovery; genomics; natural populations; single-nucleotide polymorphism; ALLELE FREQUENCY-SPECTRUM; HUMAN GENOME; POPULATION PARAMETERS; SEQUENCE VARIATION; PHOCA-HISPIDA; HAPLOTYPE RECONSTRUCTION; DEMOGRAPHIC HISTORY; REPRODUCTIVE RATES; HUDSON-BAY; MARKERS; Greenland; Hudson; Hudson Bay; Svalbard; Phoca hispida; Pusa hispida; ringed seal
• Online Access: https://hdl.handle.net/11370/11186b36-dcc5-415d-9539-7a247580c9ae; https://research.rug.nl/en/publications/11186b36-dcc5-415d-9539-7a247580c9ae; https://doi.org/10.1111/j.1755-0998.2010.02941.x

Although single-nucleotide polymorphisms (SNPs) have become the marker of choice in the field of human genetics, these markers are only slowly emerging in ecological, evolutionary and conservation genetic analyses of nonmodel species. This is partly because of difficulties associated with the discovery and characterization of SNP markers. Herein, we adopted a simple straightforward approach to identifying SNPs, based on screening of a random genomic library. In total, we identified 768 SNPs in the ringed seal, Pusa hispida hispida, in samples from Greenland and Svalbard. Using three seal samples, SNPs were discovered at a rate of one SNP per 402 bp, whereas re-sequencing of 96 seals increased the density to one SNP per 29 bp. Although applicable to any species of interest, the approach is especially well suited for SNP discovery in nonmodel organisms and is easily implemented in any standard genetics laboratory, circumventing the need for prior genomic data and use of next-generation sequencing facilities.