BackgroundFusarium fujikuroi is the causal agent of bakanae, the most significant seed-borne disease of rice. Molecular mechanisms regulating defence responses of rice towards this fungus are not yet fully known. To identify transcriptional mechanisms underpinning rice resistance, a RNA-seq comparative transcriptome profiling was conducted on infected seedlings of selected rice genotypes at one and three weeks post germination (wpg).ResultsTwelve rice genotypes were screened against bakanae disease leading to the identification of Selenio and Dorella as the most resistant and susceptible cultivars, respectively. Transcriptional changes were more appreciable at 3 wpg, suggesting that this infection stage is essential to study the resistance mechanisms: 3,119 DEGs were found in Selenio and 5,095 in Dorella. PR1, germin-like proteins, glycoside hydrolases, MAP kinases, and WRKY transcriptional factors were up-regulated in the resistant genotype upon infection with F. fujikuroi. Up-regulation of chitinases and down-regulation of MAP kinases and WRKY transcriptional factors were observed in the susceptible genotype. Gene ontology (GO) enrichment analyses detected in Selenio GO terms specific to response to F. fujikuroi: ‘response to chitin’, ‘jasmonic acid biosynthetic process’, and ‘plant-type hypersensitive response’, while Dorella activated different mechanisms, such as ‘response to salicylic acid stimulus’ and ‘gibberellin metabolic process’, which was in agreement with the production of gibberellin A3 in Dorella plants.ConclusionsRNA-seq profiling was performed for the first time to analyse response of rice to F. fujikuroi infection. Our findings allowed the identification of genes activated in one- and three- week-old rice seedlings of two genotypes infected with F. fujikuroi. Furthermore, we found the pathways involved in bakanae resistance, such as response to chitin, JA-dependent signalling and hypersensitive response. Collectively, this provides important information to elucidate the molecular and cellular processes occurring in rice during F. fujikuroi infection and to develop bakanae resistant rice germplasm.Electronic supplementary materialThe online version of this article (doi:10.1186/s12864-016-2925-6) contains supplementary material, which is available to authorized users.

Fusarium fujikuroi, the causal agent of bakanae disease, is the main seedborne pathogen on rice. To understand the basis of rice resistance, a quantitative method to simultaneously detect phytohormones and phytoalexins was developed by using HPLC-MS/MS. With this method dynamic profiles and possible interactions of defense-related phytohormones and phytoalexins were investigated on two rice cultivars, inoculated or not with F. fujikuroi. In the resistant cultivar Selenio, the presence of pathogen induced high production of phytoalexins, mainly sakuranetin, and symptoms of bakanae were not observed. On the contrary, in the susceptible genotype Dorella, the pathogen induced the production of gibberellin and abscisic acid and inhibited jasmonic acid production, phytoalexins were very low, and bakanae symptoms were observed. The results suggested that a wide range of secondary metabolites are involved in plant defense against pathogens and phytoalexin synthesis could be an important factor for rice resistance against bakanae disease.

Bakanae disease, which is caused by the seedborne pathogen Fusarium fujikuroi, is found throughout the world on rice. A TaqMan real-time PCR has been developed on the TEF 1-α gene to detect F. fujikuroi in different rice tissues. Three primer/probe sets were tested. The selected set produced an amplicon of 84 bp and was specific for F. fujikuroi with respect to eight Fusarium species of rice and six other rice common pathogens. The assay was validated for specificity, selectivity, sensitivity, repeatability, and reproducibility. The detection limit was set at 27.5 fg of DNA, which is approximately equivalent to one haploid genome of F. fujikuroi. The developed TaqMan real-time assay was able to efficiently detect and quantify F. fujikuroi from rice culms, leaves, roots, and seeds. At 1 week post-germination (wpg), the pathogen was more diffused in the green tissues, while at 3 wpg it was uniformly spread also in the roots. The highest concentration of F. fujikuroi was measured in the M6 cultivar, which showed around 1,450 fungal cells/g. The assay was sufficiently sensitive to detect a few genomic equivalents in the rice seeds, corresponding to 9.89 F. fujikuroi cells/g. The assay permitted bakanae disease to be detected in asymptomatic tissues at the early rice development stages.

Bull’s eye rot, caused by Phlyctema vagabunda and Neofabraea species, is one of the most important postharvest diseases of apple. South Tyrol (northern Italy) holds the largest continuous apple producing area in Europe with approximately 1 million tons being produced yearly and conserved in technologically advanced storage facilities for several months. Still, studies on the pathogen species causing postharvest bull’s eye rot of apple as well as their diversity and biology are lacking for this region. Therefore, the main purpose of the present work was to identify and characterize fungal isolates obtained from decayed apple fruit with symptoms of bull’s eye rot that were collected in 2018 and 2019 in different packinghouses of South Tyrol. Among more than 1,000 fungal isolates that were obtained, 419 could be assigned to the genera Phlyctema and/or Neofabraea based on rot symptoms on apple fruit and colony morphology on Potato Dextrose Agar (PDA). A smaller subset of 101 representative isolates was further analyzed by DNA sequencing of the internal transcribed spacer region (ITS). Furthermore, partial segments of the β-tubulin gene (TUB2), the translation elongation factor 1α gene (EF-1α) and the 16S mitochondrial rRNA gene (mtSSU) were studied. The phylogenetic analyses, including sequences of reference species, showed that P. vagabunda is the dominant species associated with bull’s eye rot of apple in the study area, while N. kienholzii was found only on a small number of apple fruit samples. The combination of multi-locus sequence data revealed eleven unique genotypes that belonged to P. vagabunda and four to N. kienholzii. To the best of our knowledge, this study is the first to report N. kienholzii as a postharvest pathogen of apple in Italy. Finally, a pathogenicity test demonstrated different degrees of virulence among selected isolates of P. vagabunda and N. kienholzii on the cultivar ‘Golden Delicious’. The present study emphasizes the importance of accurate species identification, as different species may vary in in their biological and pathogenic characteristics, and consequently require distinct disease management strategies, both in the field and during the postharvest stages.

South Tyrol (northern Italy) harbors one of the largest interconnected apple farming areas in Europe that contributes approximately 10% to the apple production of the European Union. In spite of the availability of sophisticated storage facilities, postharvest diseases occur, one of which is bitter rot of apple. In Europe, this postharvest disease is mainly caused by the Colletotrichum acutatum species complex. This work aimed to characterize the Colletotrichum species isolated from decayed apple fruit collected in 2018 and 2019 in South Tyrol. The characterization of Colletotrichum species was accomplished based on multi-locus DNA sequences of four different genomic regions, actin (ACT), glyceraldehyde-3-phosphate dehydrogenase (GAPDH), histone H3 (HIS3), and the internal transcribed spacer (ITS) region as well as morphological and pathogenicity assessment. A phylogenetic analysis based on multi-locus DNA sequences showed that the isolates obtained from apples with symptoms of bitter rot belonged to the species C. godetiae and C. fioriniae, which are part of the C. acutatum species complex. A third species isolated from apple belonging to the same species complex, C. salicis, was recently described in this area. Moreover, the Colletotrichum isolates found in this study proved to be virulent on the cultivars ‘Cripps Pink’, ‘Golden Delicious’ and ‘Roho 3615’/Evelina®. To the best of our knowledge, C. godetiae and C. fioriniae have so far never been mentioned as postharvest pathogens of apple in Italy, even though the (re)-analysis of samples collected in the past indicates that these pathogens have been occurring in Italy for at least a decade. So far, bitter rot seems to play a rather minor role as a postharvest disease in South Tyrol, but it was disproportionately represented on few scab-resistant apple cultivars, which are increasingly planted in organically managed orchards. Considering that the expansion of organic apple production and the conversion to new potentially Colletotrichum-susceptible cultivars will continue, the present study represents a first important contribution towards a better understanding of bitter rot in this geographic area.