Pectobacterium carotovorum subsp. carotovorum (Pcc) is the causal agent of soft rot of potato tubers. This study was conducted to assess the genetic variation of a collection of 32 Pcc isolates from three different potato cultivars grown in the eastern parts of Iran using subspecies- specific PCR, 16S rDNA sequencing and rep- PCR analyses and comparing these methods with each other. In initial experiments, the identity of isolates was confirmed by specific primers related to Pcc subspecies and differentiated from closely species (P. wasabiae) using restriction enzyme analysis. All isolates were also checked for phenotypic properties and pathogenicity on potato tubers. Phylogenetic analysis, using clustering methods on partial sequences of the 16S rDNA, showed that all Iranian isolates grouped with the Pcc type strain (ATCC1571) except for six isolates from Kashmar. Based on rep-PCR cluster analysis of the pairwise similarity values using UPGMA, bacterial isolates could be separated into three clusters, the third of which (Kashmar isolates) was allocated in a distinct group. The similarity coefficients among strains ranged from 0.2 to 1. Rep-PCR primers disclosed different levels of genetic heterogeneity among Pcc isolates. No clear association was found between clustering based on rep-PCR and the geographical origin of the isolates, original host plant cultivars and the year of collection.

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