ORIGINAL PAPER N. H. Syed Æ S. Sureshsundar Æ M. J. Wilkinson B. S. Bhau Æ J. J. V. Cavalcanti Æ A. J. Flavell Ty1-copia retrotransposon-based SSAP marker development in cashew (Anacardium occidentale L.) Received: 3 September 2004 / Accepted: 1 February 2005 / Published online: 11 March 2005 Ó Springer-Verlag 2005 Abstract The most popular retrotransposon-based molecular marker system in use at the present time is the sequence-specific amplification polymorphism (SSAP) system. This system exploits the insertional polymor- phism of long terminal repeat (LTR) retrotransposons around the genome. Because the LTR sequence is used to design primers for this method, its successful appli- cation requires sequence information from the terminal region of the mobile elements . In this study, two LTR sequences were isolated from the cashew genome and used successfully to develop SSAP marker systems. These were shown to have higher levels of polymor- phism than amplified fragment length polymorphic markers for this species. Introduction The development and subsequent application of molec- ular marker systems have greatly increased the numbers of markers that can be identified between two parents and, consequently, significantly enhanced the power of genetic analysis in both plant and animal species. Molecular markers have revolutionized the genetic analysis of crop plants, where they play a vital role in linkage analysis, physical mapping, quantitative trait locus (QTL) analysis, marker-assisted selection and map-based cloning. However, the usefulness of any gi- ven marker system depends on the species under study and the chosen application. Microsatellite markers are powerful tools but require a significant input for their discovery. Therefore, for crops where there is no or little DNA sequence information, anonymous marker sys- tems such as the amplified fragment length polymor- phism (AFLP) system have been favoured. Long terminal repeat (LTR) retrotransposons are a class of mobile genetic elements that have been har- nessed for the development of molecular markers in plants (Schulman et al. 2004). LTR retrotransposons move and replicate around their host genomes via RNA intermediates. The two major groups of LTR retro- transposons are Ty1-copia and Ty3-gypsy. LTR retro- transposons are present as large heterogeneous populations in all plant genomes (Konieczny et al. 1991; Flavell et al. 1992; Pearce et al. 1997; Suoniemi et al. 1998), and they show great variations in copy number and genome localization, even between closely related species (Pearce et al. 1996a, b; Kumar et al. 1997). The sequence-specific amplification polymorphism (SSAP) approach is the most popular transposon- based molecular marker method at the present time (Waugh et al. 1997; Schulman et al. 2004). This method exploits the variation generated by retro- transposon movement and reveals higher levels of polymorphism between individuals than the AFLP marker system in barley, pea, wheat and alfalfa (Waugh et al. 1997; Ellis et al. 1998; Flavell et al. 1998; Gribbon et al. 1999; Kalendar et al. 1999; Porceddu et al. 2002; Queen et al. 2004). The trans- poson display approach, which uses another transpo- son type called miniature inverted repeat transposable Communicated by E. Guiderdoni N.H. Syed and S. Sureshsundar contributed equally to this inves- tigation. N. H. Syed Æ S. Sureshsundar Æ A. J. Flavell Plant Research Unit, University of Dundee at SCRI, Invergowrie, Dundee, DD2 5DA, UK M. J. Wilkinson Æ J. J. V. Cavalcanti School of Plant Sciences, University of Reading, Reading, Berkshire, RG6 6AS, UK N. H. Syed (&) Scottish Crop Research Institute, Dundee, DD2 5DA, UK E-mail: nsyed@scri.sari.ac.uk Tel.: +44-1382-562731 Fax: +44-1382-568587 B. S. Bhau Regional Research Laboratory-Jorhat, Jorhat, 785 006, Assam, India Theor Appl Genet (2005) 110: 1195–1202 DOI 10.1007/s00122-005-1948-1