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This work is licensed under a Creative Commons Attribution-NonCommercial 4.0 International License
Article
Development of RAPD-Derived STS Markers for Genetic Diversity Assessment in Melon (Cucumis melo L.)
Author(s)
Tran Phuong Dung1, Duong Thanh Thuy1, 2, Katsunori Tanaka3, Phan Thi Phuong Nhi2, Hidetaka Nishida1 and Kenji Kato1
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DOI:10.17265/2161-6256/2015.12.001
Affiliation(s)
1. Graduate School of Environmental and Life Science, Okayama University, 1-1-1 Tsushima Naka, Kita-ku, Okayama 700-8530, Japan
2. Faculty of Agronomy, College of Agriculture and Forestry, Hue University, No. 102 Phung Hung Street, Hue City 47000, Vietnam
3. Faculty of Humanities, Hirosaki University, 1 Bunkyo, Hirosaki, Aomori 036-8560, Japan
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.
KEYWORDS
RAPD, STS, Cucumis melo L., genetic diversity, marker.
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