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Int. J. Mol. Sci. 2012, 13(3), 2951-2964; doi:10.3390/ijms13032951

Characterization of Novel Di-, Tri-, and Tetranucleotide Microsatellite Primers Suitable for Genotyping Various Plant Pathogenic Fungi with Special Emphasis on Fusaria and Mycospherella graminicola

Botany and Microbiology Department, College of Science, King Saud University, P. O. Box: 2455, Riyadh 1145, Kingdom of Saudi Arabia
Agricultural Research Center, Plant Pathology Research Institute, Giza, Egypt
Institute of Phytopathology, Christian-Albrechts-University Kiel, Hermann-Rodewald-Str. 9, D-24118, Kiel, Germany
King Abdulaziz City for Science and Technology (KACST), P. O. Box 6086, Riyadh 11442, Kingdom of Saudi Arabia
Institute of Environment and Plant Protection, Chinese Academy of Tropical Agricultural Sciences, 71737 Danzhou, Hainan, China
Author to whom correspondence should be addressed.
Received: 7 November 2011 / Revised: 9 January 2012 / Accepted: 20 February 2012 / Published: 6 March 2012
(This article belongs to the Special Issue Advances in Molecular Diagnostics)
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The goals of this investigation were to identify and evaluate the use of polymorphic microsatellite marker (PMM) analysis for molecular typing of seventeen plant pathogenic fungi. Primers for di-, tri-, and tetranucleotide loci were designed directly from the recently published genomic sequence of Mycospherlla graminicola and Fusarium graminearum. A total of 20 new microsatellite primers as easy-to-score markers were developed. Microsatellite primer PCR (MP-PCR) yielded highly reproducible and complex genomic fingerprints, with several bands ranging in size from 200 to 3000 bp. Of the 20 primers tested, only (TAGG)4, (TCC)5 and (CA)7T produced a high number of polymorphic bands from either F. graminearum or F. culmorum. (ATG)5 led to successful amplifications in M. graminicola isolates collected from Germany. Percentage of polymorphic bands among Fusarium species ranged from 9 to 100%. Cluster analysis of banding patterns of the isolates corresponded well to the established species delineations based on morphology and other methods of phylogenetic analysis. The current research demonstrates that the newly designed microsatellite primers are reliable, sensitive and technically simple tools for assaying genetic variability in plant pathogenic fungi. View Full-Text
Keywords: genotyping; tetranucleotide microsatellites; SSR; fungal plant pathogen genotyping; tetranucleotide microsatellites; SSR; fungal plant pathogen

This is an open access article distributed under the Creative Commons Attribution License (CC BY 3.0).

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Bahkali, A.H.; Abd-Elsalam, K.A.; Guo, J.-R.; Khiyami, M.A.; Verreet, J.-A. Characterization of Novel Di-, Tri-, and Tetranucleotide Microsatellite Primers Suitable for Genotyping Various Plant Pathogenic Fungi with Special Emphasis on Fusaria and Mycospherella graminicola. Int. J. Mol. Sci. 2012, 13, 2951-2964.

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