Genetic variability of Fusarium fujikuroi populations associated with bakanae of rice in Italy

The heterothallic ascomycete Fusarium fujikuroi (teleomorph: Gibberella fujikuroi) is the causal agent of bakanae of rice, a disease of increasing economic importance in the major rice-producing areas in the world and a serious threat for Italian rice cultivation. A few studies have characterized F. fujikuroi isolates in America and the Philippines but no data are available on the genetic structure of Italian pathogen populations. Microsatellite SSRs are useful tools to study the intraspecific diversity at population level. In this study, 19 polymorphic SSRs have been identified and applied to characterize the genetic variation of 334 isolates of F. fujikuroi coming from eight Italian rice-growing areas. A high degree of diversity at haplotype level has emerged: in the eight populations, 107 unique haplotypes were scored. Analysis of molecular variance (AMOVA) showed that 98% of genetic variability occurred within F. fujikuroi Italian populations, as confirmed by the allelic Shannon index ranging from 0.56 to 1.06. The presence of a 1:1 ratio of mating type alleles in six out of eight of the Italian fungal populations suggests a potential for sexual reproduction in the field. However, the high fraction of clonality (43%), confirmed by neighbour-joining clustering analysis, and the high level of linkage disequilibrium observed, indicates that reproduction of F. fujikuroi is mostly clonal in Italy. All data suggest that the observed genetic variability was probably mediated by human activity and transmission by rice seeds.