Sequencing of active retrotransposon (Rtsp-1 and LIb) insertion site in sweet potato. Ipomoea batatas

To conduct DNA fingerprinting in sweet potato cultivars, we identified a number of insertion sites of active retrotransposon families (Rtsp-1 and LIb) using an Illumina MiSeq sequencing platform. Many families of retrotransposons have multiple copies throughout the eukaryotic genome and their integrated copies are inherited genetically. Thus, their insertion polymorphisms among cultivars are useful for DNA fingerprinting. Our results showed that the insertion sites of the active retrotransposon families were highly polymorphic among 39 sweet potato cultivars. Using the cultivar-specific insertion sites, we successfully developed sequence-characterized amplified region (SCAR) markers, which may facilitate the precise identification of cultivars. Moreover, the genotyping data related to the insertion sites can be used to determine the genetic relationships among cultivars. The sweet potato is a non-model crop species and its whole genome sequencing data are not available, but our method enables efficient genotyping based on a number of polymorphic retrotransposon insertion sites.