Ty1-copia retrotransposon-based S-SAP (sequence-specific amplified polymorphism) for genetic analysis of sweetpotato

RNaseH-LTR regions of the Tyl-copia retrotransposon were amplified and cloned from the sweetpotato genome using RNaseH gene-specific degenerate primers and restriction site-specific adaptor primers. Ninety clones out of the 240 sequenced were identified with a variable degree of homology to the Tyl-copia RNaseH gene. Three (Str6, Str85, Str187) of the 90 had characteristic RNaseH-gene, stop codon, polypurine track and putative 3' LTR sequence elements. Analysis of nine selected genotypes representing Africa, South and Central America, as well as Papua New Guinea, by the established S-SAP technique revealed that the majority of the Tyl-copia transposon insertions were unique (33 to 64%) and only few common bands were detected. Analysis of 177 East African varieties further supported this finding and showed that most of the copia retrotransposon locations were represented only by some genotypes. Considering that sweetpotato has been present in the East African region for only about 500 years, and the number of genotypes introduced was possibly limited, a surprisingly high level of genetic variability of the transposon insertion sites was detected. These findings may indicate the putative activity of the retrotransposon in sweetpotato in the recent past. Comparison of the copia retrotransposon insertion-based S-SAP method to AFLP and RAPD showed that the majority of the markers were more polymorphic (97-99%) in the case of S-SAP in comparison to AFLP (70-90%) and RAPD (88%). Thus demonstrating the transposon-based molecular marker system was very efficient for genotyping.