ORIGINAL PAPER Comparison of the utility of barley retrotransposon families for genetic analysis by molecular marker techniques Received: 18 October 2002 / Accepted: 7 April 2003 / Published online: 24 May 2003 Ó Springer-Verlag 2003 Abstract The Sequence-Specific Amplification Polymor- phism (S-SAP) method, and the related molecular marker techniques IRAP (inter-retrotransposon ampli- fied polymorphism) and REMAP (retrotransposon- microsatellite amplified polymorphism), are based on retrotransposon activity, and are increasingly widely used. However, there have been no systematic analyses of the parameters of these methods or of the utility of different retrotransposon families in producing poly- morphic, scorable fingerprints. We have generated S-SAP, IRAP, and REMAP data for three barley (Hordeum vulgare L.) varieties using primers based on sequences from six retrotransposon families ( BARE -1, BAGY-1, BAGY-2, Sabrina, Nikita and Sukkula). The effect of the number of selective bases on the S-SAP profiles has been examined and the profiles obtained with eight MseI+3 selective primers compared for all the elements. Polymorphisms detected in the insertion pattern of all the families show that each can be used for S-SAP. The uniqueness of each transposition event and differences in the historic activity of each family suggest that the use of multiple retrotransposon families for genetic analysis will find applications in mapping, fin- gerprinting, and marker-assisted selection and evolu- tionary studies, not only in barley and other Hordeum species and related taxa, but also more generally. Keywords Barley DNA fingerprinting Inter-retrotransposon amplified polymorphism (IRAP) Æ Retrotransposon-microsatellite amplified polymorphism (REMAP) Æ Retrotransposon insertional polymorphism Æ Sequence-specific amplified polymorphism (S-SAP) markers Introduction Retrotransposons are mobile genetic elements found throughout the plant kingdom (Kumar and Bennetzen 1999; Fedoroff 2000). They generally show widespread chromosomal dispersion, variable copy number and random distribution in the genome (Kumar et al. 1997; Kalendar et al. 1999). Retrotransposons move to new chromosomal locations via an RNA intermediate, and insert new cDNA copies back into the genome (Boeke et al. 1985; Boeke and Corces 1989). This mode of rep- lication increases genome size, and contributes signifi- cantly to the total DNA of higher plants; at least 50% of the maize genome is composed of retrotransposons (Shirasu et al. 2000). Retrotransposons represent one of the most ’fluid’ genomic components (Gribbon et al. 1999); large variations in retrotransposon copy number are observed over relatively short evolutionary time scales. Different retrotransposon families, each with its own lineage and structure, have the potential to have been active at distinct phases in the evolution of a species. Retrotransposons consist of a conserved domain encoding products required for transposition, bounded by direct repeats (long terminal repeats, LTRs) that contain promoters required for replication, signals for RNA processing, and motifs necessary for the integra- tion of the DNA daughter copies (Kumar and Bennet- zen 1999; Suoniemi et al. 1997). The domain order in the polyprotein encoded between the LTRs defines retro- transposons as ‘‘copia -like’’ or ‘‘gypsy -like’’, after the type elements of Drosophila melanogaster, and defines Mol Gen Genomics (2003) 269: 464–474 DOI 10.1007/s00438-003-0850-2 F. Leigh Æ R. Kalendar Æ V. Lea Æ D. Lee Æ P. Donini A. H. Schulman Communicated by M.-A. Grandbastien F. Leigh Æ V. Lea Æ D. Lee Æ P. Donini Molecular Research Group, NIAB, Huntingdon Road, Cambridge, CB3 0LE, UK R. Kalendar Æ A. H. Schulman Plant Genomics Laboratory, Institute of Biotechnology, Viikki Biocenter, University of Helsinki, Viikinkaari 4, P.O. Box 56, FIN-00014 Helsinki, Finland A. H. Schulman (&) Plant Breeding Biotechnology, MTT Agrifood Research Finland, Myllytie 10, FIN-31600 Jokioinen, Finland E-mail: alan.schulman@helsinki.fi Tel.: +358-40-7682242 Fax: +358-9-19158952