BAKANAE DISEASE OF RICE IN ITALY: SURVEY OF INCIDENCE, IDENTIFICATION OF FUSARIUM FUJIKUROI AS THE MAJOR CAUSAL AGENT AND CHARACTERIZATION OF PATHOGEN POPULATION STRUCTURE USING MICROSATELLITE MARKERS.
Aragona, M.; Spadaro, D.; Valente, M.T.; Amatulli, M.T.; Santori, A.; Garibaldi, A.; Infantino, A.; Gullino, M.L.
Proceedings of the International Workshop: “Crop Improvement in a Changing Environment: the RISINNOVA Project for sustainable rice production in Italy” Venezia , Italy -29/30 October 2012
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Fusarium fujikuroi Niremberg, belonging to Gibberella fujikuroi complex, is the causal agent of Bakanae
disease of rice, an increasing problem for rice cultivation in Italy. The objective of this study is to determine
the genetic structure within and among populations of F. fujikuroi coming from the major Italian rice areas
by using efficient Simple Sequence Repeats (SSRs). Though F. fujikuroi is the most abundant Fusarium
species found on rice, other species can also be isolated from rice. Multiple alignment of translation
elongation factor (TEF) gene sequences of different Fusarium spp. showed a deletion of six nucleotides in F.
fujikuroi sequence. This element of variability was used to develop a conventional PCR assay for diagnosis.
Primer specificity was confirmed by analysing the DNA of several strains of Fusarium spp. isolated from rice
plants and seeds in Italy. 221 fungal isolates derived from symptomatic culms, previously selected by
morphological analysis, were examined by F. fujikuroi-specific PCR and 215 isolates were confirmed as F.
fujikuroi. Despite the detection of SSRs in fungi is harder than in other organisms, they are considered the
most robust and efficient markers in population genetics. Twenty-eight SSRs, all derived from expressed
sequence tags (ESTs), were found and tested by PCR on a sub-sample of F. fujikuroi isolates. The products
were detected by polyacrylamide gel electrophoresis (PAGE): 27 SSRs gave the expected amplicon but only
3 resulted polymorphic, with an average number of alleles per locus ranging from 2 to 5. A preliminary
statistical analysis on the distribution of polymorphisms in 135 isolates belonging to 5 pathogen
populations showed 8% of molecular variance among populations and 92% within populations. Taking into
account the low number of polymorphic SSRs found in F. fujikuroi published sequences, and the need of a
larger number of markers for population structure analysis, we are planning to perform a shotgun genome
sequencing of F. fujikuroi.