Vine-1 retrotransposon-based sequence-specific amplified polymorphism for Vitis vinifera L. genotyping

The sequence-specific amplification polymorphism (S-SAP) method, derived from the amplified fragment length polymorphism (AFLP) technique, produces amplified fragments containing retrotransposon long terminal repeat (LTR) sequence at one end and a host restriction site at the other. The development and application of this procedure to the LTR of the Vine-1 element from grapevine is reported. Two primers derived from one of the LTR sequences flanking the retrotransposon were used in combination with MseI degenerated primers on 15 grapevine accessions. S-SAP results were compared with AFLP data. The heterozygosity and gene diversity values were higher for S-SAP than for the AFLP procedure. Results show that S-SAP amplification is effective in identifying polymorphisms and defining genetic distances among cultivars, and could be used for fingerprinting and for 'Traminer' clone identification. To the contrary Vine-1 retrotransposon-based S-SAP was not able to distinguish 'Pinot' clones.