Retrotransposon-based Molecular Markers in Chokecherry (Prunus virginiana L.) and Their Transferability in Rosaceae Family

Retrotransposons are the largest group of transposable elements (TEs) that are ubiquitous and well dispersed in plant genomes. Retrotransposons can be classified into two groups by the presence or absence of long terminal repeats (LTR): LTR retrotransposons and non-LTR retrotransposons. Transposition/insertion of TEs on chromosomes often generates unique repeat junctions (RJs) between TEs and their flanking sequences. Long terminal repeats are well-conserved and abundant in plant genomes, which make LTR retrotransposons valuable for development of TE junction-based markers. In this study, LTR-retrotransposons and their RJs were detected from chokecherry genome sequences generated by Roche 454 sequencing. A total of 1,246 LTR-retrotransposons were identified and 338 polymerase chain reaction (PCR) primer pairs were designed. Of which, 336 were used to amplify DNA from chokecherry and other rosaceous species. An average of 283 of 336 (84.2%) LTR primers effectively amplified DNA from chokecherries. A few chokecherry LTR primers also produced amplification in other Prunus or rosaceous species. The majority of the primers (>75%) produced a single band in chokecherries and other tested species. A total of 78 of 336 (23.2%) primers amplified polymorphic bands in eight chokecherry lines. Our results suggest that using random genome sequence data to identify LTR retrotransposon markers appears to be rapid and cost-efficient. Development of LTR-based markers in chokecherry could facilitate genetic research in chokecherry and other rosaceous species.