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Nucleic Acids Research Advance Access published online on February 20, 2007
Nucleic Acids Research, doi:10.1093/nar/gkm070
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© 2007 The Author(s)
This is an Open Access article distributed under the terms of the Creative Commons Attribution Non-Commercial License (http://creativecommons.org/licenses/by-nc/2.0/uk/) which permits unrestricted non-commercial use, distribution, and reproduction in any medium, provided the original work is properly cited.

Molecular Biology

SNP discovery by mismatch-targeting of Mu transposition

Luisa Orsini1, Maria Pajunen2, Ilkka Hanski1 and Harri Savilahti2,3,*

1Metapopulation Research Group, Department of Biological and Environmental Sciences, PO Box 65, and 2Research Program in Cellular Biotechnology, Institute of Biotechnology, PO Box 56, FIN-00014, University of Helsinki, Finland and 3Division of Genetics and Physiology, Department of Biology, FIN-20014, University of Turku, Finland

*To whom correspondence should be addressed. Tel: +358 9 191 59516; Fax: +358 9 191 59366; E-mail: harri.savilahti{at}helsinki.fi

Received September 15, 2006. Revised January 18, 2007. Accepted January 23, 2007.

Single nucleotide polymorphisms (SNPs) represent a valuable resource for the mapping of human disease genes and induced mutations in model organisms. SNPs may become the markers of choice also for population ecology and evolutionary studies, but their isolation for non-model organisms with unsequenced genomes is often difficult. Here, we describe a rapid and cost-effective strategy to isolate SNPs that exploits the property of the bacteriophage Mu transposition machinery to target mismatched DNA sites and thereby to effectively detect polymorphic loci. To demonstrate the methodology, we isolated 164 SNPs from the unsequenced genome of the Glanville fritillary butterfly (Melitaea cinxia), a much-studied species in population biology, and we validated 24 of them. The strategy involves standard molecular biology techniques as well as undemanding MuA transposase-catalyzed in vitro transposition reactions, and it is applicable to any organism.


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