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• • • Part of the book series (MIMB, volume 859) Abstract Retrotransposons are a major agent of genome evolution. Various molecular marker systems have been developed that exploit the ubiquitous nature of these genetic elements and their property of stable integration into dispersed chromosomal loci that are polymorphic within species.
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The key methods, SSAP, IRAP, REMAP, RBIP, and ISBP, all detect the sites at which the retrotransposon DNA, which is conserved between families of elements, is integrated into the genome. Marker systems exploiting these methods can be easily developed and inexpensively deployed in the absence of extensive genome sequence data. They offer access to the dynamic and polymorphic, nongenic portion of the genome and thereby complement methods, such as gene-derived SNPs, that target primarily the genic fraction. Acknowledgments Development of the methods described in this chapter was funded by contracts BIO-4-CT-960508, QLK5-CT-2000-01502, and FOOD-CT-2005-513959 to the Commission of the European Communities as well as by the Academy of Finland, Grant 120810, by Project Exbardiv of the ERA-NET Plant Genomics program and by the Ministry of Education of the Czech Republic project MSM. The Butterfly Effect Imago Rapidshare Files. We are grateful to Ruslan Kalendar, Maggie Knox, and Steven Pearce for material contributions to the methods presented here.
