Show simple item record

dc.contributor.authorAitken, Nicola
dc.contributor.authorSmith, Steven
dc.contributor.authorSchwarz, Carsten
dc.contributor.authorA. Morin, Phillip
dc.contributor.editorLoren Rieseberg
dc.date.accessioned2017-05-03T16:59:10Z
dc.date.available2017-05-03T16:59:10Z
dc.date.issued2004
dc.date.modified2009-12-21T06:45:55Z
dc.identifier.issn09621083
dc.identifier.doi10.1111/j.1365-294X.2004.02159.x
dc.identifier.urihttp://hdl.handle.net/10072/27872
dc.description.abstractSingle 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.
dc.description.peerreviewedYes
dc.description.publicationstatusYes
dc.languageEnglish
dc.language.isoeng
dc.publisherWiley-Blackwell Publishing Ltd.
dc.publisher.placeUnited Kingdom
dc.publisher.urihttps://onlinelibrary.wiley.com/toc/1365294x/2004/13/6
dc.relation.ispartofpagefrom1423
dc.relation.ispartofpageto1431
dc.relation.ispartofissue6
dc.relation.ispartofjournalMolecular Ecology
dc.relation.ispartofvolume13
dc.subject.fieldofresearchPopulation, Ecological and Evolutionary Genetics
dc.subject.fieldofresearchBiological Sciences
dc.subject.fieldofresearchcode060411
dc.subject.fieldofresearchcode06
dc.titleSingle nucleotide polymorphism (SNP) discovery in mammals: a targeted-gene approach
dc.typeJournal article
dc.type.descriptionC1 - Articles
dc.type.codeC - Journal Articles
gro.date.issued2004
gro.hasfulltextNo Full Text
gro.griffith.authorSmith, Steven J.


Files in this item

FilesSizeFormatView

There are no files associated with this item.

This item appears in the following Collection(s)

  • Journal articles
    Contains articles published by Griffith authors in scholarly journals.

Show simple item record