Development and Assessment of Retrotransposon-Based Insertional Polymorphism Markers in Pyrus L

Retrotransposons are ubiquitous component of plant genomes, especially abundant in species with large genomes, we developed retrotransposon-based insertional polymorphism (RBIP) makers by using whole genome of Pyrus (Pyrus bretschneideri Rehd. cv. ‘Dangshansuli’) to differentiate pear cultivars. LTR-harvest software and RepeatMasker were used to predict and classify LTR retrotransposons, respectively. One of the copia-like retrotransposons with high distribution was selected to develop RBIP markers based on the long terminal repeat (LTR) sequences. Out of 34 sequences including 3’ LTR and flanking genome regions, twenty-four RBIP markers were developed and used for DNA profiling of 23 pear cultivars and 7 wild pears which belong to 10 species. All pear accessions could be distinguished by those markers, and ‘Dangshansuli’ could be differentiated from the others by using only two markers (Ppcr1M1 & Ppcr1M5). All pear accessions were clustered into two clades, of which one of them includes all Oriental pear except P. xerophila, and the other clade includes P. xerophila and Occidental pears. The results indicate that retrotransposon-based molecular markers are particularly valuable for plant molecular characterization.