Genetic diversity of Fusarium oxysporum f. sp. cumini isolates analyzed by vegetative compatibility, sequences analysis of the rDNA IGS region and iPBS retrotransposon markers

Fusarium oxysporum f. sp. cumini, the causal agent of cumin (Cuminum cyminum L.) wilt disease is a devastating fungal pathogen, limiting cumin production in Turkey. Genetic diversity among Fusarium wilt isolates of cumin was analyzed by vegetative compatibility grouping (VCG), DNA sequencing of the intergenic spacer region (IGS) of rDNA, and Inter-PBS (iPBS) amplification of LTR retrotransposons. The pathogen isolates were grouped into thirty-three VCGs by complementation tests using nitrate non utilizing mutants; most of these VCGs contained only a single isolate. Phylogenetic analysis of IGS region revealed two main clades among the pathogen isolates in the dendrogram with a bootstrap support of 99%. The unique VCGs had similar IGS sequences and grouped into the same clades with closely related other F. oxysporum formae speciales. iPBS analysis revealed high level of intraspecific diversity among the pathogen isolates and provided a similar discrimination that was consistent in the groupings based the partial IGS sequence. The results showed that F. oxysporum isolates from cumin has a polyphyletic origin, consisting of distinct clonal lineages. Also, the results of this study supported that iPBS marker system is a powerful tool for estimating intraspecific variation within the populations of F. oxysporum.