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Random amplified polymorphic DNA (RAPD) has been used widely in diversity studies, including population structure and phylogenetics at all taxonomic levels. However, there is a problem in stability and repeatability of RAPD in some cases. Therefore, conversion of RAPD markers into new type of PCR-based marker to overcome low levels of repeatability of RAPD marker is needed. The aim of this study was to develop sequence-tagged site (STS) markers by designing specific primers based on RAPD marker sequences to provide the potential markers for analyzing genetic diversity of melon germplasm. Eight RAPD-STS markers were successfully converted from RAPD markers and have two polymorphism types: A20 and B99 showed different sizes of fragment; A22, A31, A57, B15, B71 and C00 showed presence/absence polymorphism in melon germsplasm. The applicability of new RAPD-STS markers has been demonstrated by comparing genotype analysis of 41 melon accessions using RAPD and RAPD-STS markers. Both of RAPD markers and RAPD-STS markers divided them into two major clusters. However, the RAPD-STS markers were more polymorphic than RAPD markers (polymorphic index content (PIC) values were 0.346 and 0.274, respectively). Mantel's test showed significant correlation (r = 0.896, P < 0.01) between RAPD-STS dendrogram and RAPD dendrogram. Furthermore, RAPD-STS markers could give more information in population structure and identify admixture individuals by using STRUCTURE software. Eight RAPD-STS markers developed in this study are useful for genetic diversity analysis and population studies in melon.

Development of RAPD-Derived STS Markers for Genetic Diversity Assessment in Melon (Cucumis melo L.)