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Int J Mol Sci. 2012;13(3):2951-64. doi: 10.3390/ijms13032951. Epub 2012 Mar 6.

Characterization of novel di-, tri-, and tetranucleotide microsatellite primers suitable for genotyping various plant pathogenic fungi with special emphasis on Fusaria and Mycospherella graminicola.

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Botany and Microbiology Department, College of Science, King Saud University, P. O. Box: 2455, Riyadh 1145, Kingdom of Saudi Arabia; E-Mail:


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.


SSR; fungal plant pathogen; genotyping; tetranucleotide microsatellites

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