A modified S-SAP (sequence-specific amplified polymorphism) method with universal primers for retrotransposons was used to study Vitis vinifera cv. Pinot noir. Five Pinot noir clones (20Gm, 1–44Gm, 18Gm, 20–13Gm, 1–84Gm) were analyzed by 30 S-SAP primer combinations employing five MseI- and six universal retrotransposon primers. Altogether 670 markers were generated, revealing 4.8% clonal variation and four out of five Pinot noir clones could be differentiated. This S-SAP method provides an efficient tool to randomly screen for polymorphisms produced through retrotransposition processes in the Vitis genome.
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