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In this study, genetic diversity among watermelon accessions was studied by analyzing morphological and physiological traits using Random Amplified Polymorphic DNA (RAPD). Thirty-seven morphological and physiological traits showed significant variation among the accessions. Some watermelon accessions showed typical attributes of seed characters and fruit flesh and skin color. Principle component analysis allocated the high variance percentage for fruit and seed characters. Cluster analysis of morphological and physiological characters separated Citrullus colocynthis in one independent cluster clearly. The 18 RAPD markers represented 126 polymorphic bands of 154 total bands. Cluster analysis using RAPD markers at similarity 0.54 also clarified colocynth genotypes in one separated group. Three main clusters distinguished for other accessions that were classified mainly by fruit shape and flesh color, then, by fruit skin color. The most similarity (1) was observed among three accessions in the same cluster, contrary to the different collecting areas, which may indicate that accessions were distributed in different areas from the same genetic sources. The Genetic Similarity coefficients (GS) among evaluated accessions ranged from 0.45 to 1.00, indicating that they had relatively high genetic diversity. Altogether, the high variation, especially for phenotypic traits, of watermelon accessions in Iran could be considered as a good resource for selection and breeding program.

Keywords: Genetic similarity, Principle component analysis, Random amplified polymorphic DNA.

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