Conventional and real-time PCR for the identification of Fusarium fujikuroi and Fusarium proliferatum from diseased rice tissues and seeds

Fusarium fujikuroi is a species of the Gibberella fujikuroi species complex (GFSC) and the causal agent of bakanae disease on rice. Even if F. fujikuroi is the most abundant Fusarium species found on rice, other species can also be isolated from rice, such as F. proliferatum. Multiple alignment of translation elongation factor (TEF) gene sequences of different Fusarium spp., showed a deletion of six nucleotides in F. fujikuroi sequence and a two nucleotide polymorphism in the same region of F. proliferatum sequence. These elements of variability were used to develop a conventional and Real-Time PCR assay for diagnosis. The species specific primer pairs (Fuji1F/TEF1R and Proli1F/TEF1R) gave a product of 179 and 188 bp for F. fujikuroi and F. proliferatum respectively. Primer specificity was confirmed by analyzing the DNA of the most representative species of the GFSC and 298 strains of Fusarium spp. isolated from rice plants and seeds in Italy. The specific primers were also successfully used to detect fungal presence directly from infected rice tissues and seeds, providing a rapid tool for the early detection of pathogen contamination.