The extent of genetic diversity among Vanilla species: comparative results for RAPD and ISSR.

Abstract Vanilla is a large genus of about 110 species in the orchid family (Orchidaceae), including the species Vanilla planifolia from which commercial vanilla flavoring is derived. Since most species of vanilla are considered rare and endangered there is an urgent need to conserve them through genetic analysis and propagation/conservation studies on this crop. The present study investigated the genetic diversity among nine leafy- and leaf-less Vanilla species employing 30 decamer RAPD primers and 10 ISSR primers. The species under study were diverse and displayed a range of variability (0–66% and 0–81% for RAPD and ISSR, respectively). A total of 154 RAPD polymorphic markers (83.24%, h  = 0.378) and 93 ISSR polymorphic markers (86.11%, h  = 0.363) were used to generate a genetic similarity matrix followed by the cluster analysis. Specific groupings were revealed by each cluster analysis with slight variation between two different markers. Among the nine species studied, V. planifolia , Vanilla aphylla and Vanilla tahitensis revealed very low level of variation within their collections, thus indicating a narrow genetic base. The large genetic distance of Vanilla andamanica from other species suggests its different origin. A close genetic affinity was observed between the pairs V. planifolia , V. tahitensis and Vanilla albida , V. aphylla . These are the first comparative results for RAPD and ISSR reporting inter-relationship among nine cultivated, wild and hybrid Vanilla species.