Seagrasses are submerged marine flowering plants belonging to four core families Cymodoceaceae, Hydrocharitaceae, Posidoniaceae and Zosteraceae of the monocot order Alismatales, which form critical habitats in the tidal and sub-tidal zones of shallow and sheltered localities of seas, backwaters, lagoons and estuaries. In the present work, the inter and intraspecies genetic diversity of six species of seagrass namely, Halophila ovalis, Halophila ovata, Halophila beccarii (Hydrocharitaceae), Halodule pinifolia, Halodule uninervis and Cymodocea serrulata (Cymodoceaceae) occurring in Chilika lagoon of Odisha coast were assessed using RAPD and ISSR molecular markers. With 10 RAPD primers, 79 loci were amplified, out of which 50 (63%) were polymorphic in nature. Similarly, 54 out of 84 bands (64%) generated with 11 ISSR primers, were found to be polymorphic. The dendrogram constructed using combined RAPD and ISSR data separated members of Cymodoceaceae (C. serrulata, H. pinifolia and H. uninervis) and Hydrocharitaceae (H. ovalis, H. ovata and H. beccarii) into two distinct clusters justifying their inclusion in distinct botanical families based on morphological traits. All the accessions of a particular species also formed distinct groups with varying levels of similarities. The present study revealed that RAPD and ISSR markers can be effectively used for species identification of seagrasses even at juvenile and non-flowering stage.
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