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Single nucleotide polymorphism (SNP) discovery in mammals: a targeted-gene approach

Authors

  • Nicola Aitken,

    1. Laboratory for Conservation Genetics, Max Planck Institute for Evolutionary Anthropology, Inselstrasse 22, D-04103, Leipzig, Germany
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      Applied Ecology Research Group, University of Canberra, ACT 2601, Australia,
  • Steven Smith,

    1. Laboratory for Conservation Genetics, Max Planck Institute for Evolutionary Anthropology, Inselstrasse 22, D-04103, Leipzig, Germany
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      †Griffith University, QLD 4111, Australia,
  • Carsten Schwarz,

    1. Laboratory for Conservation Genetics, Max Planck Institute for Evolutionary Anthropology, Inselstrasse 22, D-04103, Leipzig, Germany
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      ‡Department of Anthropology, McMaster University, Hamilton, Ontario, Canada and
  • Phillip A. Morin

    Corresponding author
    1. Laboratory for Conservation Genetics, Max Planck Institute for Evolutionary Anthropology, Inselstrasse 22, D-04103, Leipzig, Germany
      Phillip Morin. Fax: 858 546 7003; E-mail: Phillip.Morin@noaa.gov
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      §Southwest Fisheries Science Center, 8604 La Jolla Shores Dr, La Jolla, CA 92037, USA

  • *

    Current addresses: Applied Ecology Research Group, University of Canberra, ACT 2601, Australia, †Griffith University, QLD 4111, Australia, ‡Department of Anthropology, McMaster University, Hamilton, Ontario, Canada and §Southwest Fisheries Science Center, 8604 La Jolla Shores Dr, La Jolla, CA 92037, USA

Phillip Morin. Fax: 858 546 7003; E-mail: Phillip.Morin@noaa.gov

Abstract

Single nucleotide polymorphisms (SNPs) have rarely been exploited in nonhuman and nonmodel organism genetic studies. This is due partly to difficulties in finding SNPs in species where little DNA sequence data exist, as well as to a lack of robust and inexpensive genotyping methods. We have explored one SNP discovery method for molecular ecology, evolution, and conservation studies to evaluate the method and its limitations for population genetics in mammals. We made use of ‘CATS’ (or ‘EPIC’) primers to screen for novel SNPs in mammals. Most of these primer sets were designed from primates and/or rodents, for amplifying intron regions from conserved genes. We have screened 202 loci in 16 representatives of the major mammalian clades. Polymerase chain reaction (PCR) success correlated with phylogenetic distance from the human and mouse sequences used to design most primers; for example, specific PCR products from primates and the mouse amplified the most consistently and the marsupial and armadillo amplifications were least successful. Approximately 24% (opossum) to 65% (chimpanzee) of primers produced usable PCR product(s) in the mammals tested. Products produced generally high but variable levels of readable sequence and similarity to the expected genes. In a preliminary screen of chimpanzee DNA, 12 SNPs were identified from six (of 11) sequenced regions, yielding a SNP on average every 400 base pairs (bp). Given the progress in genome sequencing, and the large numbers of CATS-like primers published to date, this approach may yield sufficient SNPs per species for population and conservation genetic studies in nonmodel mammals and other organisms.

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