Isolation of an active element from a high-copy-number family of retrotransposons in the sweetpotato genome

A large number of plant retrotransposons have been characterized, but only three families (Tnt1, Tto1 and Tos17) have been demonstrated to be transpositionally competent. We have used a novel approach to identify an active member of the Ty1- copia retrotransposon family with estimated 400 copies in the sweetpotato genome. Ty1- copia reverse transcriptase (RTase) sequences from the sweetpotato genome were analyzed, and a group of retrotransposon copies that probably arose by recent transposition events was identified and analyzed further. Transcripts containing long terminal repeats (LTRs) of this group were amplified from callus cDNA by the 3′RACE technique. Patterns of sequence-specific amplification polymorphism (S-SAP) of the LTR sequences in genomic DNA were compared between a normal plant and callus lines derived from it. In this way, a callus-specific S-SAP product was identified, which apparently resulted from the insertion of the retrotransposon detected by 3′RACE during cell culture. We conclude that our approach provides an effective way to identify active elements among the members of high-copy-number retrotransposon families.