Evaluation of bakanae disease progression caused by Fusarium fujikuroi in Oryza sativa L

Map-Based Cloning and Characterization of a Major QTL Gene, FfR1, Which Confers Resistance to Rice Bakanae Disease

Bakanae disease (BD), caused by the fungal pathogen Fusarium fujikuroi, is a serious threat to rice production worldwide. Breeding elite rice varieties resistant to BD requires the identification of resistance genes. Previously, we discovered a resistant quantitative trait locus (QTL), qFfR1, in a Korean japonica rice variety, Nampyeong. In this study, we fine-mapped qFfR1 with a Junam*4/Nampyeong BC3F3 population and delimited its location to a 37.1 kb region on chromosome 1. Complementation experiments with seven candidate genes in this region revealed that OsI_02728 is the gene for qFfR1. This gene encodes a protein with a typical leucine-rich repeat (LRR) receptor-like protein structure. RNA-sequencing-based transcriptomic analysis revealed that FfR1 induces the transcription of defense genes, including lignin and terpenoid biosynthesis genes, pathogenesis-related genes, and thionin genes. These results may facilitate investigations into the molecular mechanisms underlying BD resistance, including molecular patterns of Fusarium fujikuroi interacting with FfR1 and players working in signal transduction pathways downstream of FfR1, and the breeding of new BD-resistant varieties by providing a BD resistance gene with its precise selection marker. This will contribute to efficient control of BD, which is becoming more prevalent according to temperature rises due to climate change.

Incorporation of the histone variant H2A.Z counteracts gene silencing mediated by H3K27 trimethylation in Fusarium fujikuroi

BACKGROUND

Fusarium fujikuroi is a pathogen of rice causing diverse disease symptoms such as 'bakanae' or stunting, most likely due to the production of various natural products (NPs) during infection. Fusaria have the genetic potential to synthesize a plethora of these compounds with often diverse bioactivity. The capability to synthesize NPs exceeds the number of those being produced by far, implying a gene regulatory network decisive to induce production. One such regulatory layer is the chromatin structure and chromatin-based modifications associated with it. One prominent example is the exchange of histones against histone variants such as the H2A variant H2A.Z. Though H2A.Z already is well studied in several model organisms, its regulatory functions are not well understood. Here, we used F. fujikuroi as a model to explore the role of the prominent histone variant FfH2A.Z in gene expression within euchromatin and facultative heterochromatin.

RESULTS

Through the combination of diverse '-omics' methods, we show the global distribution of FfH2A.Z and analyze putative crosstalks between the histone variant and two prominent histone marks, i.e., H3K4me3 and H3K27me3, important for active gene transcription and silencing, respectively. We demonstrate that, if FfH2A.Z is positioned at the + 1-nucleosome, it poises chromatin for gene transcription, also within facultative heterochromatin. Lastly, functional characterization of FfH2A.Z overexpression and depletion mutants revealed that FfH2A.Z is important for wild type-like fungal development and secondary metabolism.

CONCLUSION

In this study, we show that the histone variant FfH2A.Z is a mark of positive gene transcription and acts independently of the chromatin state most likely through the stabilization of the + 1-nucleosome. Furthermore, we demonstrate that FfH2A.Z depletion does not influence the establishment of both H3K27me3 and H3K4me3, thus indicating no crosstalk between FfH2A.Z and both histone marks. These results highlight the manifold functions of the histone variant FfH2A.Z in the phytopathogen F. fujikuroi, which are distinct regarding gene transcription and crosstalk with the two prominent histone marks H3K27me3 and H3K4me3, as proposed for other model organisms.

Fungal epiphytes differentially regulate salt tolerance of invasive Ipomoea cairica according to salt stress levels

Fungal symbionts can improve plant tolerance to salt stress. However, the interaction of epiphytic Fusarium oxysporum and Fusarium fujikuroi with the tolerance of the invasive plant Ipomoea cairica against saline coastal habitats is largely unknown. This study aimed to investigate the interaction of the mixture of the two epiphytic fungi with salt tolerance of I. cairica. Surface-sterilized I. cairica cuttings inoculated (E+) and non-inoculated (E-) with the fungal mixture were cultivated with 2, 3, and 5 parts per thousand (PPT) of NaCl solutions to simulate mild, moderate, and severe salt stress, respectively. The hydroponic experiment showed that the growth inhibition and peroxidation damages of E+ and E- cuttings were aggravated with salinity. Noteworthily, E+ cuttings had higher peroxidase (POD) and catalase (CAT) activities, chlorophyll content, total biomass, aboveground biomass, total shoot length and secondary shoot number, but lower root-to-shoot ratio than E- cuttings under 2 and 3 PPT NaCl conditions. Moreover, E+ had higher superoxide dismutase (SOD) activity and proline content but lower belowground biomass and malondialdehyde (MDA) content than E- cuttings under 3 PPT NaCl condition. However, lower SOD, POD, and CAT activities, and chlorophyll content, but higher MDA content occurred in E+ cuttings than in E- cuttings under 5 PPT NaCl condition. These findings suggested that the mixture of the two epiphytic fungi increased salt tolerance of I. cairica mainly through increasing its antioxidation ability and chlorophyll stability under mildly and moderately saline conditions, but decreased salt tolerance of this plant in an opposite way under severely saline conditions.

Current Studies on Bakanae Disease in Rice: Host Range, Molecular Identification, and Disease Management

The seed borne disease such as bakanae is difficult to control. Crop yield loss caused by bakanae depending on the regions and varieties grown, ranging from 3.0% to 95.4%. Bakanae is an important disease of rice worldwide and the pathogen was identified as Fusarium fujikuroi Nirenberg (teleomorph: Gibberella fujikuroi Sawada). Currently, four Fusaria (F. fujikuroi, F. proliferatum, F. verticillioides and F. andiyazi) belonging to F. fujikuroi species complex are generally known as the pathogens of bakanae. The infection occurs through both seed and soil-borne transmission. When infection occurs during the heading stage, rice seeds become contaminated. Molecular detection of pathogens of bakanae is important because identification based on morphological and biological characters could lead to incorrect species designation and time-consuming. Seed disinfection has been studied for a long time in Korea for the management of the bakanae disease of rice. As seed disinfectants have been studied to control bakanae, resistance studies to chemicals have been also conducted. Presently biological control and resistant varieties are not widely used. The detection of this pathogen is critical for seed certification and for preventing field infections. In South Korea, bakanae is designated as a regulated pathogen. To provide highly qualified rice seeds to farms, Korea Seed & Variety Service (KSVS) has been producing and distributing certified rice seeds for producing healthy rice in fields. Therefore, the objective of the study is to summarize the recent progress in molecular identification, fungicide resistance, and the management strategy of bakanae.

Genome-Wide Identification and Functional Analysis of the bZIP Transcription Factor Family in Rice Bakanae Disease Pathogen, Fusarium fujikuroi

Fungal basic leucine zipper (bZIP) proteins play a vital role in biological processes such as growth, biotic/abiotic stress responses, nutrient utilization, and invasion. In this study, genome-wide identification of bZIP genes in the fungus Fusarium fujikuroi, the pathogen of bakanae disease, was carried out. Forty-four genes encoding bZIP transcription factors (TFs) from the genome of F. fujikuroi (FfbZIP) were identified and functionally characterized. Structures, domains, and phylogenetic relationships of the sequences were analyzed by bioinformatic approaches. Based on the phylogenetic relationships with the FfbZIP proteins of eight other fungi, the bZIP genes can be divided into six groups (A–F). The additional conserved motifs have been identified and their possible functions were predicted. To analyze functions of the bZIP genes, 11 FfbZIPs were selected according to different motifs they contained and were knocked out by genetic recombination. Results of the characteristic studies revealed that these FfbZIPs were involved in oxygen stress, osmotic stress, cell wall selection pressure, cellulose utilization, cell wall penetration, and pathogenicity. In conclusion, this study enhanced understandings of the evolution and regulatory mechanism of the FfbZIPs in fungal growth, abiotic/biotic stress resistance, and pathogenicity, which could be the reference for other fungal bZIP studies.

Epiphytic fungi induced pathogen resistance of invasive plant Ipomoea cairica against Colletotrichum gloeosporioides

Background

Ipomoea cairica (L.) Sweet is a destructive invasive weed in South China but rarely infected with pathogens in nature. Its pathogen resistance mechanism is largely unknown at present. Some non-pathogenic isolates of Fusarium oxysporum and Fusarium fujikuroi are prevalent on many plant species and function as pathogen resistance inducers of host plants. The objective of the present research is to investigate whether the symbiosis between the both fungi and I. cairica is present, and thereby induces pathogen resistance of I. cairica.

Methods

Through field investigation, we explored the occurrence rates of F. oxysporum and F. fujikuroi on leaf surfaces of I. cairica plants in natural habitats and compared their abundance between healthy leaves and leaves infected with Colletotrichum gloeosporioides, a natural pathogen. With artificial inoculation, we assessed their pathogenicity to I. cairica and studied their contribution of pathogen resistance to I. cairica against C. gloeosporioides.

Results

We found that F. oxysporum and F. fujikuroi were widely epiphytic on healthy leaf surfaces of I. cairica in sunny non-saline, shady non-saline and sunny saline habitats. Their occurrence rates reached up to 100%. Moreover, we found that the abundance of F. oxysporum and F. fujikuroi on leaves infected with C. gloeosporioides were significantly lower than that of healthy leaves. With artificial inoculation, we empirically confirmed that F. oxysporum and F. fujikuroi were non-pathogenic to I. cairica. It was interesting that colonization by F. fujikuroi, F. oxysporum alone and a mixture of both fungi resulted in a reduction of C. gloeosporioides infection to I. cairica accompanied by lower lesion area to leaf surface area ratio, increased hydrogen peroxide (H₂O₂) concentration and salicylic acid (SA) level relative to the control. However, NPR1 expression, chitinase and β-1,3-glucanase activities as well as stem length and biomass of I. cairica plant only could be significantly improved by F. oxysporum and a mixture of both fungi but not by F. fujikuroi. In addition, as compared to colonization by F. oxysporum and a mixture of both fungi, F. fujikuroi induced significantly higher jasmonic acid (JA) level but significantly lower β-1,3-glucanase activity in leaves of I. cairica plants. Thus, our findings indicated the symbiosis of epiphytic fungiF. fujikuroi and F. oxysporum induced systemic resistance of I. cairica against C. gloeosporioides. F. oxysporum played a dominant role in inducing pathogen resistance of I. cairica. Its presence alleviated the antagonism of the JA signaling on SA-dependent β-1,3-glucanase activity and enabled I. cairica plants to maintain relatively higher level of resistance against C. gloeosporioides.

Comparative genomics of geographically distant Fusarium fujikuroi isolates revealed two distinct pathotypes correlating with secondary metabolite profiles

Fusarium fujikuroi causes bakanae ("foolish seedling") disease of rice which is characterized by hyper-elongation of seedlings resulting from production of gibberellic acids (GAs) by the fungus. This plant pathogen is also known for production of harmful mycotoxins, such as fusarins, fusaric acid, apicidin F and beauvericin. Recently, we generated the first de novo genome sequence of F. fujikuroi strain IMI 58289 combined with extensive transcriptional, epigenetic, proteomic and chemical product analyses. GA production was shown to provide a selective advantage during infection of the preferred host plant rice. Here, we provide genome sequences of eight additional F. fujikuroi isolates from distant geographic regions. The isolates differ in the size of chromosomes, most likely due to variability of subtelomeric regions, the type of asexual spores (microconidia and/or macroconidia), and the number and expression of secondary metabolite gene clusters. Whilst most of the isolates caused the typical bakanae symptoms, one isolate, B14, caused stunting and early withering of infected seedlings. In contrast to the other isolates, B14 produced no GAs but high amounts of fumonisins during infection on rice. Furthermore, it differed from the other isolates by the presence of three additional polyketide synthase (PKS) genes (PKS40, PKS43, PKS51) and the absence of the F. fujikuroi-specific apicidin F (NRPS31) gene cluster. Analysis of additional field isolates confirmed the strong correlation between the pathotype (bakanae or stunting/withering), and the ability to produce either GAs or fumonisins. Deletion of the fumonisin and fusaric acid-specific PKS genes in B14 reduced the stunting/withering symptoms, whereas deletion of the PKS51 gene resulted in elevated symptom development. Phylogenetic analyses revealed two subclades of F. fujikuroi strains according to their pathotype and secondary metabolite profiles.

Development and Validation of a TaqMan Real-Time PCR Assay for the Specific Detection and Quantification of Fusarium fujikuroi in Rice Plants and Seeds

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.

The Genetic Structure, Virulence, and Fungicide Sensitivity of Fusarium fujikuroi in Taiwan

The rice disease bakanae, caused by Fusarium fujikuroi Nirenberg, has been present in Taiwan for over a century. To better understand the genetic diversity and structure of F. fujikuroi, a set of 16 polymorphic simple sequence repeat (SSR) markers were newly developed and used to analyze 637 F. fujikuroi isolates collected in 14 cities or counties around Taiwan from 1996 to 2013. On the basis of Bayesian clustering, the isolates were classified into four highly differentiated clusters: cluster B likely derived from the more widespread and genetically diversified clusters A or C, and cluster D was restricted to four cities or counties and may have been introduced from unknown sources genetically distinct from clusters A, B, and C. The coexistence of both mating types (MAT1-1:MAT1-2 = 1:1.88) and the highly diversified vegetative compatibility groups (VCG) (16 VCG among the 21 assessed isolates) suggest the likelihood of sexual reproduction in the field. However, the biased mating type ratios and linkage disequilibrium in the population suggest nonrandom mating between individuals. A significant pattern of isolation by distance was also detected, which implies a geographical restricted gene flow and low dissemination ability of F. fujikuroi. Evaluation of 24 representative isolates on eight rice varieties revealed differential levels of virulence, however no clear pattern of specific variety x isolate interaction was observed. Investigations of the differences in virulence and fungicide sensitivity between 8 early isolates (1998 and 2002) and 52 recent isolates (2012) indicate the evolution of increased resistance to the fungicide prochloraz in F. fujikuroi in Taiwan.

Multi-Homologous Recombination-Based Gene Manipulation in the Rice Pathogen Fusarium fujikuroi

Gene disruption by homologous recombination is widely used to investigate and analyze the function of genes in Fusarium fujikuroi, a fungus that causes bakanae disease and root rot symptoms in rice. To generate gene deletion constructs, the use of conventional cloning methods, which rely on restriction enzymes and ligases, has had limited success due to a lack of unique restriction enzyme sites. Although strategies that avoid the use of restriction enzymes have been employed to overcome this issue, these methods require complicated PCR steps or are frequently inefficient. Here, we introduce a cloning system that utilizes multi-fragment assembly by In-Fusion to generate a gene disruption construct. This method utilizes DNA fragment fusion and requires only one PCR step and one reaction for construction. Using this strategy, a gene disruption construct for Fusarium cyclin C1 (FCC1 ), which is associated with fumonisin B1 biosynthesis, was successfully created and used for fungal transformation. In vivo and in vitro experiments using confirmed fcc1 mutants suggest that fumonisin production is closely related to disease symptoms exhibited by F. fujikuroi strain B14. Taken together, this multi-fragment assembly method represents a simpler and a more convenient process for targeted gene disruption in fungi.

Comparison of the Antimicrobial Properties of Chitosan Oligosaccharides (COS) and EDTA against Fusarium fujikuroi Causing Rice Bakanae Disease

Bakanae disease is a destructive rice disease in South Korea caused by Fusarium fujikuroi infection. Chemical fungicides have been used to manage the disease, but the emergence of fungicide-resistant strains has gradually increased. Two chelating agents, chitosan oligosaccharides (COS) and ethylenediaminetetraacetatic acid (EDTA), are well known as biosafe and biocompatible antimicrobial agents. In this study, we compared the actions of COS and EDTA to gain a better understanding of the underlying antimicrobial activities and to evaluate them as eco-friendly fungicides against F. fujikuroi. While COS exhibited a rapid fungicidal effect on hyphal growing cells within 5 min, EDTA had a fungistatic effect on reversible growth inhibition. Scanning electron microscopy revealed that COS treatment resulted in pore-formation and cellular leakage along the growing hyphae, whereas EDTA caused no significant morphological changes. COS activity was greatly suppressed by the addition of Ca(2+) to the medium, and EDTA action was largely suppressed by Mn(2+) and slightly by Ca(2+), respectively. Taken together, these results indicated that two chelating agents, COS and EDTA, have different modes of antimicrobial action on F. fujikuroi. Thus, the combination of chelating agents having different modes of action might be an effective disease management strategy to prevent or delay the development of fungicide-resistant strains.

Jasmonic Acid, Abscisic Acid, and Salicylic Acid Are Involved in the Phytoalexin Responses of Rice to Fusarium fujikuroi, a High Gibberellin Producer Pathogen

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.