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

Abstract

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.