Characterisation of RNaseH-LTR sections of Tyl-copia retrotransposons in apple and fingerprinting of four apple clones by S-SAP analysis.

Retrotransposons are the most widespread class of eukaryotic transposable elements and play an important role in genome evolution. Several of these elements have been sequenced and were found to contain different cis-regulatory elements involved in the response to different stress conditions in their long terminal repeat sequences (LTRs). Retrotransposon-based marker systems have proved useful because of their distribution, ubiquity, and prevalence in plant genomes. Here we report on the isolation and characterisation of new RNaseH-LTR sections of the Tyl-copia-like retro-elements in apple DNA. Twenty clones were identified with a variable degree of homology to the Tyl-copia RNaseH gene. Nineteen had the characteristic RNaseH gene, stop codon, polypurine tract (PPT), and putative 3'-LTR sequence elements. The RNaseH sections were aligned using ClustalV to seek potential relationships between sequences. This analysis revealed six distinct Clusters. Conserved motifs, corresponding to cis-regulatory elements, were discovered in the LTRs using plantCARE software and four were characterised. From one putative LTR fragment, we then designed a primer, which, through sequence-specific amplification polymorphism (S-SAP), could distinguish between 'Wellspur Delicious', 'Hardispur Delicious' and 'Starkrimson', and 'Starking' apple, by fingerprinting. The first three varieties originated from 'Starking' through bud mutations. Our results suggest that these bud mutations appeared to have been derived from retrotransposon insertions. [ABSTRACT FROM AUTHOR]