Survey of Fusarium spp. Causing Wheat Crown Rot in Major Winter Wheat Growing Regions of China

The critical roles of the Zn2Cys6 transcription factor Fp487 in the development and virulence of Fusarium pseudograminearum: A potential target for Fusarium crown rot control

Fusarium crown rot (FCR) caused by Fusarium pseudograminearum poses a significant threat to wheat production in the Huang-Huai-Hai region of China. However, the pathogenic mechanism of F. pseudograminearum is still poorly understood. Zn2Cys6 transcription factors, which are exclusive to fungi, play pivotal roles in regulating fungal development, drug resistance, pathogenicity, and secondary metabolism. In this study, we present the functional characterization of a Zn2Cys6 transcription factor F. pseudograminearum, designated Fp487. In F. pseudograminearum, Fp487 is shown to be required for mycelial growth through gene knockout and phenotypic analyses. Compared with wild-type CF14047, the ∆Fp487 mutant displayed a slight reduction in growth rate but a significant decrease in conidiogenesis, pathogenicity and 3-acetyl-deoxynivalenol (3AcDON) production. Moreover, the mutant exhibited heightened sensitivity to oxidative and cytomembrane stress. Furthermore, we synthesized dsRNA from the Fp487 gene in vitro, resulting in a reduction in the growth rate of F. pseudograminearum and its virulence on barley leaves through spray-induced gene silencing (SIGS). Notably, this study makes the first instance of inducing the expression of abundant dsRNA from F. pseudograminearum by engineering the Escherichia coli strain HT115 (DE3) and utilizing the SIGS technique to evaluate the virulence effect of dsRNA on F. pseudograminearum. In conclusion, our findings revealed the crucial role of Fp487 in regulating pathogenicity, stress responses, DON production, and conidiogenesis in F. pseudograminearum. Furthermore, Fp487 is a potential RNAi-based target for FCR control.

The G143S mutation in cytochrome b confers high resistance to pyraclostrobin in Fusarium pseudograminearum

BACKGROUND

Wheat crown rot (WCR), primarily caused by Fusarium pseudograminearum has become more and more prevalent in winter wheat areas in China. However, limited fungicides have been registered for the control of WCR in China so far. Pyraclostrobin is a representative quinone outside inhibitor (QoI) with excellent activity against Fusarium spp. There is currently limited research on the resistance risk and resistance mechanism of F. pseudograminearum to pyraclostrobin.

RESULTS

Here, we determined the activity of pyraclostrobin against F. pseudograminearum. The EC50 values ranged from 0.022 to 0.172 μg mL-1 with an average EC50 value of 0.071 ± 0.030 μg mL-1. Four highly pyraclostrobin-resistant mutants were obtained from two sensitive strains by ultraviolet (UV) mutagenesis in the laboratory. The mutants showed decreased mycelial growth rate and virulence as compared with the corresponding wild-type strains, indicating that pyraclostrobin resistance suffered a fitness penalty in F. pseudograminearum. It was found that the high resistance of four mutants was caused by the G143S mutation in Cytb. Molecular docking analysis also further confirms that the G143S mutation in Cytb decreased the binding affinity between pyraclostrobin and Cytb.

CONCLUSION

The resistance risk of F. pseudograminearum to pyraclostrobin could be low to medium. Although a mutation at the G143S position of Cytb could potentially occur, this mutation decreases the fitness of the mutant, which may reduce its survival in the environment. Therefore, the negative consequences of a possible mutation are lower. This makes pyraclostrobin a good candidate for controlling crown rot in wheat. © 2024 Society of Chemical Industry.

Genome Analyses Reveal the Secondary Metabolites that Potentially Influence the Geographical Distribution of Fusarium pseudograminearum Populations

Fusarium crown rot (FCR), caused by Fusarium pseudograminearum, significantly impacts wheat yield and quality in China's Huanghuai region. The rapid F. pseudograminearum epidemic and FCR outbreak within a decade remain unexplained. In this study, two high-quality, chromosome-level genomes of F. pseudograminearum strains producing 3-acetyl-deoxynivalenol (3AcDON) and 15-acetyl-deoxynivalenol (15AcDON) toxins were assembled. Additionally, 38 related strains were resequenced. Genomic differences such as single nucleotide polymorphisms (SNPs), insertions/deletions (indels), and structural variations (SVs) among F. pseudograminearum strains were analyzed. The whole-genome SNP locus-based population classification mirrored the toxin chemotype (3AcDON and 15AcDON)-based classification, indicating the presence of genes associated with the trichothecene toxin gene cluster. Further analysis of differential SNP, indel, and SV loci between the 3AcDON and 15AcDON populations revealed a predominant connection to secondary metabolite synthesis genes. Notably, the majority of the secondary metabolite biosynthesis gene cluster loci were located in SNP-dense genomic regions, suggesting high mutability and a possible contribution to F. pseudograminearum population structure and environmental adaptability. This study provides insightful perspectives on the distribution and evolution of F. pseudograminearum and for forecasting the spread of wheat FCR, thereby aiding in the development of preventive measures and control strategies.

Isolation, characterization, and pathogenicity of Fusarium species causing crown rot of wheat

Fusarium crown rot (FCR) is one of the most important soilborne diseases affecting wheat production. To investigate the diversity of the pathogens causing this disease, 199 diseased wheat samples were collected from 13 cities in Shandong province. In total, 468 isolates were obtained, and from these isolates, 11 Fusarium species were identified based on phylogenetic analyses with the translation elongation factor-1α (TEF-1α), RNA polymerase II largest subunit (RPB1), and RNA polymerase II second largest subunit (RPB2) gene sequences. Of these Fusarium isolates, 283 were identified as Fusarium pseudograminearum and the remaining isolates were identified as Fusarium graminearum (n = 113), Fusarium sinensis (n = 28), Fusarium acuminatum (n = 18), Fusarium incarnatum (n = 13), Fusarium ipomoeae (n = 5), Fusarium flocciferum (n = 3), Fusarium proliferatum (n = 2), Fusarium asiaticum (n = 1), Fusarium culmorum (n = 1), and Fusarium oxysporum (n = 1), suggesting that F. pseudograminearum is the dominant pathogen of FCR of wheat in Shandong province. Pathogenicity tests demonstrated that all 11 Fusarium species could cause typical symptoms of FCR on wheat seedlings. The results of the study indicate that a greater diversity of Fusarium species can cause FCR of wheat in Shandong province than that has been previously reported. This is the first report in the world of Fusarium incarnatum, Fusarium ipomoeae, and Fusarium flocciferum as pathogens causing FCR in wheat.

Genomics Analysis Reveals the Potential Biocontrol Mechanism of Pseudomonas aeruginosa QY43 against Fusarium pseudograminearum

Fusarium crown rot (FCR) in wheat is a prevalent soil-borne disease worldwide and poses a significant threat to the production of wheat (Triticum aestivum) in China, with F. pseudograminearum being the dominant pathogen. Currently, there is a shortage of biocontrol resources to control FCR induced by F. pseudograminearum, along with biocontrol mechanisms. In this study, we have identified 37 strains of biocontrol bacteria displaying antagonistic effects against F. pseudograminearum from over 8000 single colonies isolated from soil samples with a high incidence of FCR. Among them, QY43 exhibited remarkable efficacy in controlling FCR. Further analysis identified the isolate QY43 as Pseudomonas aeruginosa, based on its colony morphology and molecular biology. In vitro, QY43 significantly inhibited the growth, conidial germination, and the pathogenicity of F. pseudograminearum. In addition, QY43 exhibited a broad spectrum of antagonistic activities against several plant pathogens. The genomics analysis revealed that there are genes encoding potential biocontrol factors in the genome of QY43. The experimental results confirmed that QY43 secretes biocontrol factor siderophores and pyocyanin. In summary, QY43 exhibits a broad spectrum of antagonistic activities and the capacity to produce diverse biocontrol factors, thereby showing substantial potential for biocontrol applications to plant disease.

Inhibitory activity to Fusarium spp. and control potential for wheat Fusarium crown rot of a novel succinate dehydrogenase inhibitor cyclobutrifluram

BACKGROUND

Wheat Fusarium crown rot (FCR) is a serious problem primarily caused by Fusarium pseudograminearum, a pathogenic agent known to produce mycotoxins, including deoxynivalenol (DON). Cyclobutrifluram, a novel succinate dehydrogenase inhibitor devised by Syngenta, has immense potential to control both nematodes and Fusarium diseases. However, its efficacy in combating Fusarium species, its ability to prevent and reverse the detrimental effects of FCR, and its impact on the production of DON by F. pseudograminearum are yet to be fully ascertained.

RESULTS

Cyclobutrifluram exhibited substantial inhibitory activity against Fusarium species, with half-maximal effective concentration values ranging from 0.0021-0.0647 μg mL-1 . It demonstrated significant inhibitory activity toward three developmental stages of F. pseudograminearum, F. graminearum and F. asiaticum. Furthermore, cyclobutrifluram showed both protective and curative activities against FCR and was rapidly absorbed by roots and transported to wheat stems and leaves. Cyclobutrifluram could also decrease DON production by F. pseudograminearum.

CONCLUSION

This investigation has revealed the potential of cyclobutrifluram as a formidable candidate fungicide, particularly in its ability to effectively combat FCR and other Fusarium-related ailments. This novel compound has exceptional pathogen-fighting capabilities, coupled with remarkable systemic translocation properties and a notable ability to reduce the production of DON. © 2023 Society of Chemical Industry.

Population Genetic Analyses and Trichothecene Genotype Profiling of Fusarium pseudograminearum Causing Wheat Crown Rot in Henan, China

In China, Fusarium pseudograminearum has emerged as a major pathogen causing Fusarium crown rot (FCR) and caused significant losses. Studies on the pathogen's properties, especially its mating type and trichothecene chemotypes, are critical with respect to disease epidemiology and food/feed safety. There are currently few available reports on these issues. This study investigated the species composition, mating type idiomorphs, and trichothecene genotypes of Fusarium spp. causing FCR in Henan, China. A significant shift in F. pseudograminearum-induced FCR was found in the present study. Of the 144 purified strains, 143 were F. pseudograminearum, whereas only 1 Fusarium graminearum was identified. Moreover, a significant trichothecene-producing capability of F. pseudograminearum strains from Henan was observed in this work. Among the 143 F. pseudograminearum strains identified, F. pseudograminearum with a 15ADON genotype was found to be predominant (133 isolates), accounting for 92.36% of all strains, followed by F. pseudograminearum with a 3ADON genotype, whereas only one NIV genotype strain was detected. Overall, a relatively well-balanced 1:1 ratio of the F. pseudograminearum population was found in Henan. To the best of our knowledge, this is the first study that has examined the Fusarium populations responsible for FCR across the Henan wheat-growing region.

A novel QTL conferring Fusarium crown rot resistance on chromosome 2A in a wheat EMS mutant

KEY MESSAGE

A novel QTL on chromosome 2A for Fusarium crown rot resistance was identified and validated in wheat. Fusarium crown rot (FCR) is a fungal disease that causes significant yield losses in many cereal growing regions in the world. In this study, genetic analysis was conducted for a wheat EMS mutant C549 which showed stable resistance to FCR at seedling stage. A total of 10 QTL were detected on chromosomes 1A, 2A, 3B, 4A, 6B, and 7B using a population of 138 F7 recombinant inbred lines (RILs) derived from a cross between C549 and a Chinese germplasm 3642. A novel locus Qfcr.cau-2A, which accounted for up to 24.42% of the phenotypic variation with a LOD value of 12.78, was consistently detected across all six trials conducted. Furthermore, possible effects of heading date (HD) and plant height on FCR severity were also investigated in the mapping population. While plant height had no effects on FCR resistance, a weak and negative association between FCR resistance and HD was observed. A QTL for HD (Qhd.cau-2A.2) was coincident with Qfcr.cau-2A. Conditional QTL mapping indicated that although Qfcr.cau-2A and Qhd.cau-2A.2 had significant interactions, Qfcr.cau-2A remained significant after the effects of HD was removed. It is unlikely that genes underlying these two loci are same. Nevertheless, the stable expression of Qfcr.cau-2A in the validation population of 148 F7 RILs developed between C549 and its wild parent Chuannong 16 demonstrated the potential value of this locus in FCR resistance breeding programs.

Dissecting the genetic basis of Fusarium crown rot resistance in wheat by genome wide association study

KEY MESSAGE

A locus conferring Fusarium crown rot resistance was identified on chromosome arm 3DL through genome wide association study and further validated in two recombinant inbred lines populations. Fusarium crown rot (FCR) is a severe soil borne disease in many wheat growing regions of the world. In this study, we attempted to detect loci conferring FCR resistance through a new seedling inoculation assay. A total of 223 wheat accessions from different geography origins were used to assemble an association panel for GWAS analysis. Four genotypes including Heng 4332, Luwanmai, Pingan 998 and Yannong 24 showed stable resistance to FCR. A total of 54 SNPs associated with FCR resistance were identified. Among the 10 putative QTLs represented by these SNPs, seven QTLs on chromosome 2B, 3A, 3D, 4A, 7A and 7B were novel and were consistently detected in at least two of the three trials conducted. Qfcr.cau.3D-3, which was targeted by 38 SNPs clustered within a genomic region of approximately 5.57 Mb (609.12-614.69 Mb) on chromosome arm 3DL, was consistently detected in all the three trials. The effects of Qfcr.cau.3D-3 were further validated in two recombinant inbred line populations. The presence of this locus reduced FCR severity up to 21.55%. Interestingly, the collinear positions of sequences containing the four SNPs associated with two FCR loci (Qfcr.cau.3A and Qfcr.cau.3B) were within the regions of Qfcr.cau.3D-3, suggesting that genes underlying these three loci may be homologous. Our results provide useful information for improving FCR resistance in wheat.

Efficacy of cyclobutrifluram in controlling Fusarium crown rot of wheat and resistance risk of three Fusarium species to cyclobutrifluram

Cyclobutrifluram (TYMIRIUM® technology), a new succinate dehydrogenase inhibitor (SDHI) fungicide, is currently being registered by SYNGENTA for controlling Fusarium crown rot (FCR) of wheat in China. The application of 15 or 30 g of active ingredient/100 kg seed of cyclobutrifluram significantly reduced pre-emergence damping-off, discoloration on the stem base and formation of whiteheads caused by FCR. The EC50 values of cyclobutrifluram for 60 isolates of F. pseudograminearum, 30 isolates of F. asiaticum and 30 isolates of F. graminearum ranged from 0.016 to 0.142 mg L-1, 0.010 to 0.041 mg L-1 and 0.012 to 0.059 mg L-1, respectively. One hundred and seven cyclobutrifluram-resistant (CR) mutants were obtained from three Fusarium species isolates, with ten types of mutations identified in Sdh genes. Three Fusarium species isolates exhibited similar resistance mechanisms, with the most prevalent mutations, SdhC1A83V and SdhC1R86K, accounting for 61.68% of mutants. The CR mutants possessed comparable or slightly impaired fitness compared to the corresponding parental isolates. The CR mutants carrying FpSdhBH248Y/Q/D exhibited increased sensitivity to fluopyram. An overall moderate risk of resistance development in three Fusarium species was recommended for cyclobutrifluram.

Resistant risk and resistance-related point mutation in SdhC1 of pydiflumetofen in Fusarium pseudograminearum

BACKGROUND

Fusarium pseudograminearum is one of the dominant pathogens of Fusarium crown rot (FCR) worldwide. Unfortunately, no fungicides have yet been registered for the control of FCR in wheat in China. Pydiflumetofen, a new-generation succinate dehydrogenase inhibitor, exhibits excellent inhibitory activity to Fusarium spp. A resistance risk assessment of F. pseudograminearum to pydiflumetofen and the resistance mechanism involved have not yet been investigated.

RESULTS

The median effective concentration (EC50 ) value of 103 F. pseudograminearum isolates to pydiflumetofen was 0.0162 μg mL-1 , and the sensitivity exhibited a unimodal distribution. Four resistant mutants were generated by fungicide adaption, which possessed similar or impaired fitness compared to corresponding parental isolates based on the results of mycelial growth, conidiation, conidium germination rate, and virulence determination. Pydiflumetofen showed strong positive cross-resistance with cyclobutrifluram and fluopyram but no cross-resistance with carbendazim, phenamacril, tebuconazole, fludioxonil, or pyraclostrobin. Sequence alignment revealed that pydiflumetofen-resistant F. pseudograminearum mutants had two single-point mutations of A83V or R86K in FpSdhC1 . Molecular docking further confirmed that point mutation of A83V or R86K in FpSdhC1 could confer resistance of F. pseudograminearum to pydiflumetofen.

CONCLUSION

Fusarium pseudograminearum shows an overall moderate risk of developing resistance to pydiflumetofen, and point mutation FpSdhC1 A83V or FpSdhC1 R86K could confer pydiflumetofen resistance in F. pseudograminearum. This study provided vital data for monitoring the emergence of resistance and developing resistance management strategies for pydiflumetofen. © 2023 Society of Chemical Industry.

Occurrence and Chemical Control Strategy of Wheat Brown Foot Rot Caused by Microdochium majus

Wheat brown foot rot (WBFR), caused by a variety of phytopathogenic fungi, is an important soilborne and seedborne disease of wheat. WBFR causes wheat lodging and seedling dieback, which seriously affect the yield and quality of wheat. In this study, 64 isolates of WBFR were isolated from different wheat fields in Yancheng city, Jiangsu Province, China. The internal transcribed spacer, elongation factor 1α, and RNA polymerase II subunit were amplified and the sequencing results of the fragments were analyzed with BLAST in NCBI. Through morphological and molecular identification, all of the isolates were identified as Microdochium majus. Verification by Koch's postulates confirmed that M. majus was the pathogen causing WBFR. The antifungal activities of fludioxonil and prochloraz against 64 isolates of M. majus were determined based on mycelial growth inhibition method. The results showed that fludioxonil and prochloraz had good antifungal activity against M. majus. The mean 50% effective concentration values of fludioxonil and prochloraz against M. majus were 0.2956 ± 0.1285 μg/ml and 0.0422 ± 0.0157 μg/ml, respectively. Control efficacy for seed-coating treatments conducted in a greenhouse indicated that M. majus severely damaged the normal growth of wheat, while seed coating with fludioxonil or prochloraz significantly reduced the disease incidence and improved the seedling survival rates. At fludioxonil doses of 7.5 g per 100 kg and prochloraz doses of 15 g per 100 kg, the incidence was reduced by 22.26 and 25.33%, seedling survival rates increased by 25.37 and 22.66%, and control efficacy reached 70.02 and 72.30%, respectively. These findings provide vital information for the accurate diagnosis and effective management of WBFR.

Improved quantification of Fusarium pseudograminearum (Fusarium crown rot) using qPCR measurement of infection in multi-species winter cereal experiments

Fusarium crown rot (FCR) causes significant grain yield loss in winter cereals around the world. Breeding for resistance and/or tolerance to FCR has been slow with relatively limited success. In this study, multi-species experiments were used to demonstrate an improved method to quantify FCR infection levels at plant maturity using quantitative PCR (qPCR), as well as the genotype yield retention using residual regression deviation. Using qPCR to measure FCR infection allowed a higher degree of resolution between genotypes than traditional visual stem basal browning assessments. The results were consistent across three environments with different levels of disease expression. The improved measure of FCR infection along with genotype yield retention allows for partitioning of both tolerance and partial resistance. Together these methods offer new insights into FCR partial resistance and its relative importance to tolerance in bread wheat and barley. This new approach offers a more robust, unbiased way to select for both FCR traits within breeding programs. Key message: Genetic gain for tolerance and partial resistance against Fusarium crown rot (FCR) in winter cereals has been impeded by laborious and variable visual measures of infection severity. This paper presents results of an improved method to quantify FCR infection that are strongly correlated to yield loss and reveal previously unrecognised partial resistance in barley and wheat varieties.

Baseline Pydiflumetofen Sensitivity of Fusarium pseudograminearum Isolates Collected from Henan, China, and Potential Resistance Mechanisms

Fusarium crown rot (FCR), caused by Fusarium pseudograminearum, is one of the most important diseases impacting wheat production in the Huanghuai region, the most important wheat-growing region of China. The current study found that the SDHI fungicide pydiflumetofen, which was recently developed by Syngenta Crop Protection, provided effective control of 67 wild-type F. pseudograminearum isolates in potato dextrose agar, with an average EC50 value of 0.060 ± 0.0098 μg/ml (SE). Further investigation revealed that the risk of fungicide resistance in pydiflumetofen was medium to high. Four F. pseudograminearum mutants generated by repeated exposure to pydiflumetofen under laboratory conditions indicated that pydiflumetofen resistance was associated with fitness penalties. Mutants exhibited significantly (P < 0.05) reduced sporulation in mung bean broth and significantly (P < 0.05) reduced pathogenicity in wheat seedlings. Sequence analysis indicated that the observed pydiflumetofen resistance of the mutants was likely associated with amino acid changes in the different subunits of the succinate dehydrogenase target protein, including R18L and V160M substitutions in the FpSdhA sequence; D69V, D147G, and C257R in FpSdhB; and W78R in FpSdhC. This study found no evidence of cross-resistance between pydiflumetofen and the alternative fungicides tebuconazole, fludioxonil, carbendazim, or fluazinam, which all have distinct modes of action and could therefore be used in combination or rotation with pydiflumetofen to reduce the risk of resistance emerging in the field. Taken together, these results indicate that pydiflumetofen has potential as a novel fungicide for the control of FCR caused by F. pseudograminearum and could therefore be of great significance in ensuring high and stable wheat yields in China.

Genome-wide association analysis of Fusarium crown rot resistance in Chinese wheat landraces

KEY MESSAGE

A novel locus for Fusarium crown rot (FCR) resistance was identified on chromosome 1B at 641.36-645.13 Mb using GWAS and could averagely increase 39.66% of FCR resistance in a biparental population. Fusarium crown rot can cause considerable yield losses. Developing and growing resistance cultivars is one of the most effective approaches for controlling this disease. In this study, 361 Chinese wheat landraces were evaluated for FCR resistance, and 27 with the disease index lower than 30.00 showed potential in wheat breeding programs. Using a genome-wide association study approach, putative quantitative trait loci (QTL) for FCR resistance was identified. A total of 21 putative loci on chromosomes 1A, 1B, 2B, 2D, 3B, 3D, 4B, 5A, 5B, 7A, and 7B were significantly associated with FCR resistance. Among these, a major locus Qfcr.sicau.1B-4 was consistently identified among all the trials on chromosome 1B with the physical regions from 641.36 to 645.13 Mb. A polymorphism kompetitive allele-specific polymerase (KASP) marker was developed and used to validate its effect in an F_2:3 population consisting of 136 lines. The results showed the presence of this resistance allele could explain up to 39.66% of phenotypic variance compared to its counterparts. In addition, quantitative real-time polymerase chain reaction showed that two candidate genes of Qfcr.sicau.1B-4 were differently expressed after inoculation. Our study provided useful information for improving FCR resistance in wheat.

Host Specificity of Soilborne Pathogens in Hordeum Species and Their Relatives

Soilborne pathogens destabilize the yields of Triticeae crops, including barley (Hordeum vulgare L.) and wheat (Triticum aestivum L.). Although genetic resistance derived from relatives of these species has been utilized to prevent rust diseases (i.e., in the wheat-rye 1BL-1RS translocation line), research on resistance against soilborne pathogens remains limited. Here, we performed field trials using 76 genotypes representing 28 Hordeum, six Triticum, and two Aegilops species to examine resistance against three soilborne bymoviruses: barley yellow mosaic virus (BaYMV), barley mild mosaic virus (BaMMV), and wheat yellow mosaic virus (WYMV). We also performed greenhouse tests using the soilborne fungal pathogen Fusarium pseudograminearum, which causes Fusarium crown rot (FCR). Using RT-PCR, we detected BaMMV and BaYMV in several Hordeum species, whereas WYMV induced systemic infection in the Triticum and Aegilops species. The identification of FCR susceptibility in all species examined suggests that F. pseudograminearum is a facultative fungal pathogen in Triticeae. Intraspecies variation in FCR disease severity was observed for several species, pointing to the possibility of exploring host resistance mechanisms. Therefore, by unlocking the host specificity of four soilborne pathogens in Hordeum species and their relatives, we obtained insights for the further exploration of wild sources of soilborne pathogen resistance for future wheat and barley improvement programs.

Resistance risk assessment of Fusarium pseudograminearum from wheat to prothioconazole

Fusarium crown rot (FCR), primarily caused by Fusarium pseudograminearum, poses significant threats to cereal crops worldwide. Prothioconazole is a demethylation inhibitor (DMI) fungicide used to control FCR. However, the risk of resistance in F. pseudograminearum to prothioconazole has not yet been evaluated. In this study, the sensitivity of a total of 255 F. pseudograminearum strains obtained from Henan Province, China to prothioconazole were determined by the mycelial growth inhibition. The results showed that the effective concentration to 50% growth inhibition (EC₅₀) of these strains ranged from 0.4228 μg/mL to 2.5284 μg/mL, with a mean EC₅₀ value of 1.0692 ± 0.4527 μg/mL (mean ± SD). Thirty prothioconazole-resistant mutants were obtained out of six selected sensitive parental strains by means of fungicide taming. The resistant mutants exhibited defects in vegetative growth, conidia production, and pathogenicity on wheat seedlings compared to their parental strains. Under ion, cell wall, and temperature stress conditions but not osmotic stress, all the mutants exhibited decreased growth rates compared with their parental strains, which was consistent with the control treatment. Cross-resistance test showed that there was a cross-resistance relationship between prothioconazole and four DMI fungicides, including prochloraz, metconazole, tebuconazole and hexaconazole, but no cross-resistance was observed between prothioconazole and carbendazim, phenamacril, fludioxonil, or azoxystrobin. Although no site mutation occurred on Cyp51a and Cyp51b genes, the constitutive expression level of the Cyp51a gene was significantly increased in all mutants. After being treated with prothioconazole, the Cyp51a and Cyp51b genes were significantly increased in both the resistant mutants and their parents. These results suggested that the resistance to prothioconazole of the mutants may be attributed to the changes of the relative expression level of Cyp51a and Cyp51b genes. Taken together, these results could provide a theoretical basis for the scientific use of prothioconazole in the field and fungicide resistance management strategies.

A cell wall invertase modulates resistance to fusarium crown rot and sharp eyespot in common wheat

Fusarium crown rot (FCR) and sharp eyespot (SE) are serious soil-borne diseases in wheat and its relatives that have been reported to cause wheat yield losses in many areas. In this study, the expression of a cell wall invertase gene, TaCWI-B1, was identified to be associated with FCR resistance through a combination of bulk segregant RNA sequencing and genome resequencing in a recombinant inbred line population. Two bi-parental populations were developed to further verify TaCWI-B1 association with FCR resistance. Overexpression lines and ethyl methanesulfonate (EMS) mutants revealed TaCWI-B1 positively regulating FCR resistance. Determination of cell wall thickness and components showed that the TaCWI-B1-overexpression lines exhibited considerably increased thickness and pectin and cellulose contents. Furthermore, we found that TaCWI-B1 directly interacted with an alpha-galactosidase (TaGAL). EMS mutants showed that TaGAL negatively modulated FCR resistance. The expression of TaGAL is negatively correlated with TaCWI-B1 levels, thus may reduce mannan degradation in the cell wall, consequently leading to thickening of the cell wall. Additionally, TaCWI-B1-overexpression lines and TaGAL mutants showed higher resistance to SE; however, TaCWI-B1 mutants were more susceptible to SE than controls. This study provides insights into a FCR and SE resistance gene to combat soil-borne diseases in common wheat.

Antifungal activities of metconazole against the emerging wheat pathogen Fusarium pseudograminearum

Fusarium crown rot of wheat is a serious fungal disease that occurs worldwide. The disease has been emerging in the major wheat-growing areas in China since 2010. Fusarium pseudogramineaum is the predominant causative pathogen of crown rot of wheat in China. The 14α-demethylation inhibitor (DMI) fungicide metconazole has been shown to be effective against Fusarium spp., but little is known about its specific activity against F. pseudogramineaum. Metconazole exhibited strong antifungal activities against all thirty-nine F. pseudogramineaum strains collected from the major wheat-growing areas in China. Metconazole inhibited mycelial growth and conidial germ tube elongation of F. pseudograminearum. Metconazole treatment significantly reduced the production of major toxins and the expression levels of toxin biosynthesis genes. Genome-wide transcriptional profiling of F. pseudograminearum in response to metconazole indicated that the expression of genes involved in ergosterol biosynthesis, including fungicide target genes (cyp51 genes), was significantly induced by metconazole. Nine ATP-binding cassette (ABC) transporter-encoding genes were significantly expressed in response to metconazole treatment. Reduced ergosterol production and antioxidant enzyme activities were observed after metconazole treatment. Greenhouse experiments indicated a significant reduction in crown rot occurrence in wheat after seed treatment with metconazole. This study evaluated the potential of metconazole to manage wheat crown rot and provides information to understand its antifungal activities and mechanism of action against F. pseudograminearum.

Resistance Risk and Resistance-Related Point Mutation in SdhB and SdhC1 of Cyclobutrifluram in Fusarium pseudograminearum

Cyclobutrifluram is a novel succinate dehydrogenase inhibitor (SDHI) developed by Syngenta and helps to inhibit Fusarium pseudograminearum. Here, the potential for cyclobutrifluram resistance in F. pseudograminearum and the resistance mechanism involved were evaluated. Baseline sensitivity of F. pseudograminearum to cyclobutrifluram was determined with a mean EC₅₀ value of 0.0248 μg/mL. Fungicide adaption generated five resistant mutants, which possess a comparable or a slightly impaired fitness compared to corresponding parental isolates. This indicates that the resistance risk of F. pseudograminearum to cyclobutrifluram might be moderate. Cyclobutrifluram-resistant isolates also demonstrated resistance to pydiflumetofen but sensitivity to carbendazim, phenamacril, tebuconazole, fludioxonil, or pyraclostrobin. Additionally, point mutations H248Y in FpSdhB and A83V or R86K in FpSdhC₁ were found in cyclobutrifluram-resistant F. pseudograminearum mutants. Molecular docking and overexpression transformation assay revealed that FpSdhB^H248Y and FpSdhC₁^A83V or FpSdhC₁^R86K confer the resistance of F. pseudograminearum to cyclobutrifluram.

Detection of fungicide resistance to fludioxonil and tebuconazole in Fusarium pseudograminearum, the causal agent of Fusarium crown rot in wheat

Fusarium crown rot (FCR) on wheat is a soil-borne disease that affects the yield and quality of the produce. In 2020, 297 Fusarium pseudograminearum isolates were isolated from diseased FCR wheat samples from eight regional areas across Hebei Province in China. Baseline sensitivity of F. pseudograminearum to fludioxonil (0.0613 ± 0.0347 μg/mL) and tebuconazole (0.2328 ± 0.0840 μg/mL) were constructed based on the in vitro tests of 71 and 83 isolates, respectively. The resistance index analysis showed no resistance isolate to fludioxonil but two low-resistance isolates to tebuconazole in 2020. There was an increased frequency of resistant isolates from 2021 to 2022 based on the baseline sensitivity for tebuconazole. There was no cross-resistance between fludioxonil and tebuconazole. This study provides a significant theoretical and practical basis for monitoring the resistance of F. pseudograminearum to fungicides, especially the control of FCR.

Antagonistic Effect of Trichoderma longibrachiatum (TL6 and TL13) on Fusarium solani and Fusarium avenaceum Causing Root Rot on Snow Pea Plants

Snow pea root rot in China is caused by Fusarium solani (FSH) and Fusarium avenaceum (FAH), which affect snow pea production. The chemical control methods used against FSH and FAH are toxic to the environment and resistance may be developed in persistence applications. Therefore, an alternative approach is needed to control these pathogens. This study focuses on Trichoderma longibrachiatum strains (TL6 and TL13), mycoparasitic mechanisms of FSH and FAH, as well as growth-promoting potentials on snow pea seedlings under FSH and FAH stress at the physiological, biochemical, and molecular levels. The average inhibitory rates of TL6 against FSH and FAH were 54.58% and 69.16%, respectively, on day 7. Similarly, TL13 average inhibitory rates against FSH and FAH were 59.06% and 71.27%, respectively, on day 7. The combined TL13 and TL6 with FSH and FAH reduced disease severity by 86.6, 81.6, 57.60, and 60.90%, respectively, in comparison to the controls. The snow pea plants inoculated with FSH and FAH without TL6 and TL13 increased malondialdehyde (MDA) and hydrogen peroxide (H2O2) contents in the leaves by 64.8, 66.0, 64.4 and 65.9%, respectively, compared to the control. However, the combined FSH and FAH with TL6 and TL13 decreased the MDA and H2O2 content by 75.6, 76.8, 70.0, and 76.4%, respectively, in comparison to the controls. In addition, the combined TL6 + FSH and TL6 + FAH increased the activity of superoxide dismutase (SOD), peroxidase (POD), and catalase (CAT) by 60.5, 64.7, and 60.3%, respectively, and 60.0, 64.9, and 56.6%, respectively, compared to the controls. Again, compared to the controls, the combined TL13 + FSH and TL13 + FAH increased the activity of SOD, POD, and CAT by 69.7, 68.6, and 65.6%, respectively, and 70.10, 69.5, and 65.8%, respectively. Our results suggest that the pretreatment of snow pea seeds with TL6 and TL13 increases snow pea seedling growth, controls FSH and FAH root rot, increases antioxidant enzyme activity, and activates plant defense mechanisms. The TL13 strain had the greatest performance in terms of pathogen inhibition and snow pea growth promotion compared to the TL6 strain.

Source Identification and Genome-Wide Association Analysis of Crown Rot Resistance in Wheat

Crown rot (CR) is a soil-borne disease of wheat in arid and semiarid areas of the world. The incidence rate and severity of CR are increasing with each passing year, which seriously threatens the safety of world wheat production. Here, 522 wheat varieties/lines representing genetic diversity were used to identify and evaluate the resistance source to CR disease. Six varieties, including Zimai 12, Xinong 509, Mazhamai, Sifangmai, and Dawson, were classified as resistant ® to CR. Seventy-nine varieties were classified as moderately resistant (MR) to CR, accounting for 15.13% of the tested varieties. The wheat 660 K SNP array was used to identify resistance loci by genome-wide association analysis (GWAS). A total of 33 SNPs, located on chromosomes 1A, 1B, 1D, 4A, and 4D, were significantly correlated with seedling resistance to CR in two years. Among them, one SNP on chromosome 1A and nine SNPs on chromosome 1B showed most significant resistance to disease, phenotypic variance explained (PVE) by these SNPs were more than 8.45%. Except that significant locus AX-110436287 and AX109621209 on chromosome 1B and AX-94692276 on 1D are close to the already reported QTL, other SNPs are newly discovered resistance loci. These results could lay a strong theoretical foundation for the genetic improvement and breeding for CR resistance in wheat.

Trichoderma atroviride seed dressing influenced the fungal community and pathogenic fungi in the wheat rhizosphere

Fusarium crown rot and wheat sharp eyespot are major soil-borne diseases of wheat, causing serious losses to wheat yield in China. We applied high-throughput sequencing combined with qPCR to determine the effect of winter wheat seed dressing, with either Trichoderma atroviride HB20111 spore suspension or a chemical fungicide consisting of 6% tebuconazole, on the fungal community composition and absolute content of pathogens Fusarium pseudograminearum and Rhizoctonia cerealis in the rhizosphere at 180 days after planting. The results showed that the Trichoderma and chemical fungicide significantly reduced the amount of F. pseudograminearum in the rhizosphere soil (p < 0.05), and also changed the composition and structure of the fungal community. In addition, field disease investigation and yield measurement showed that T. atroviride HB20111 treatment reduced the whiteheads with an average control effect of 60.1%, 14.9% higher than the chemical treatment; T. atroviride HB20111 increased yield by 7.7%, which was slightly more than the chemical treatment. Therefore, T. atroviride HB20111 was found to have the potential to replace chemical fungicides to control an extended range of soil-borne diseases of wheat and to improve wheat yield.

Antagonistic Activity of Fungal Strains against Fusarium Crown Rot

The crown rot of wheat is a destructive soil-borne pathogen that severely reduces the yield and quality of wheat. This study aimed to screen and identify the antagonistic strains against Fusarium pseudograminearum (Fp), which is the dominant pathogen associated with the crown rot of wheat in China, and evaluate their biosynthetic potential. The antagonistic strains were screened via a dual-culture antagonism assay, and then identified by combining the morphological characteristics and internal transcribed spacer gene sequencing. The polyketide synthases (PKS-I and PKS-II) and non-ribosomal peptide synthetase (NRPS) genes in the antagonistic strains were detected via specific amplification of chromosomal DNA. Eleven out of 157 fungal strains, including six strains with matrix competition and five strains with antibiosis, were obtained. The eleven antagonistic strains belonged to the following four genera: Alternaria, Botryosphaeria, Phoma and Talaromyces. The inhibition rate of six strains with matrix competition was greater than 50%, with B. dothidea S2-22 demonstrating the highest at 80.3%. The width of the inhibition zone of T. trachyspermus R-17 among the five strains with antibiosis was the widest at 11 mm. Among the eleven antagonistic strains, three strains of A. alternata and the strain P. moricola only contained the PKS-II gene, the strain A. tenuissima contained PKS-I and PKS-II genes, three strains of B. dothidea contained PKS-II and NRPS genes, while three strains of T. trachyspermus did not contain any genes. These results demonstrated potential strains for the biocontrol of the crown rot of wheat. In particular, T. trachyspermus R-17 can be investigated further as a promising agent, and the active substances secreted by antagonistic strains may be synthesized by other pathways.

Trichoderma longibrachiatum (TG1) Enhances Wheat Seedlings Tolerance to Salt Stress and Resistance to Fusarium pseudograminearum

Salinity is abiotic stress that inhibits seed germination and suppresses plant growth and root development in a dose-dependent manner. Fusarium pseudograminearum (Fg) is a plant pathogen that causes wheat crown rot. Chemical control methods against Fg are toxic to the environment and resistance has been observed in wheat crops. Therefore, an alternative approach is needed to manage this devastating disease and the effects of salinity. Our research focused on the mycoparasitic mechanisms of Trichoderma longibrachiatum (TG1) on Fg and the induction of defenses in wheat seedlings under salt and Fg stress at physiological, biochemical and molecular levels. The average inhibition rate of TG1 against Fg was 33.86%, 36.32%, 44.59%, and 46.62%, respectively, in the four NaCl treatments (0, 50, 100, and 150 mM). The mycoparasitic mechanisms of TG1 against Fg were coiling, penetration, and wrapping of Fg hyphae. In response to inoculation of TG1 with Fg, significant upregulation of cell wall degrading enzymes (CWDEs) was observed. The expression of β-1, 6-glucan synthase (PP4), endochitinase precursor (PH-1), and chitinase (chi18-15) increased by 1. 6, 1. 9, and 1.3-fold on day 14 compared with day 3. Wheat seedlings with combined TG1 + Fg treatments under different NaCl stress levels decreased disease index by an average of 51.89%; increased the superoxide dismutase (SOD), peroxidase (POD), and catalase (CAT) activity by an average of 38%, 61%, and 24.96%, respectively; and decreased malondialdehyde (MDA) and hydrogen peroxide (H2O2) content by an average of 44.07% and 41.75% respectively, compared with Fg treated seedlings. The combined TG1 + Fg treatment induced the transcription level of plant defense-related genes resulting in an increase in tyrosin-protein kinase (PR2), chitinase class I (CHIA1), and pathogenesis-related protein (PR1-2) by an average of 1.15, 1.35, and 1.37-fold, respectively compared to Fg treatment. However, the expression levels of phenylalanine ammonia-lyase (PAL) increased 3.40-fold under various NaCl stresses. Our results suggest that TG1 enhances wheat seedling growth and controls wheat crown rot disease by strengthening the plant defense system and upregulating the expression of pathogenesis-related genes under both Fg and salt stress.

Contamination and Translocation of Deoxynivalenol and Its Derivatives Associated with Fusarium Crown Rot of Wheat in Northern China

Fusarium crown rot (FCR) is one of the most important wheat diseases in northern China. The main causal agent of FCR, Fusarium pseudograminearum, can produce mycotoxins such as type B trichothecenes. Therefore, FCR could be an additional source of mycotoxin contamination during wheat production. Field inoculation experiments demonstrated that FCR disease severity strongly impacts the distribution pattern of trichothecenes in different wheat tissues. Mycotoxins were mainly observed in lower internodes, and a low amount was detected in the upper parts above the fourth internode. However, high levels of trichothecene accumulation were detected in the upper segments of wheat plants under field conditions, which would threaten the feed production. The variation of mycotoxin content among sampling sites indicated that besides disease severity, other factors like climate, irrigation, and fungicide application may influence the mycotoxin accumulation in wheat. A comprehensive survey of deoxynivalenol (DON) and its derivatives in wheat heads with FCR symptoms in natural fields was conducted at 80 sites in seven provinces in northern China. Much higher levels of mycotoxin were observed compared with inoculation experiments. The mycotoxin content varied greatly among sampling sites, but no significant differences were observed if compared at province level, which indicated the variation is mainly caused by local conditions. Trace amounts of mycotoxin appeared to be translocated to grains, which revealed that FCR infection in natural fields poses a relatively small threat to contamination of grains but a larger one to plant parts that may be used as animal feed. To our knowledge, this is the first report of trichothecene accumulation in wheat stems and heads, as well as grains after FCR infection in natural field conditions. These investigations provide novel insights into food and feed safety risk caused by FCR in northern China.

Simultaneous quantitation of 3ADON and 15ADON chemotypes of DON-producing Fusarium species in Chinese wheat based on duplex droplet digital PCR assay

Pathogens within Fusarium species are the primary agents of Fusarium head blight (FHB) of wheat, which bring about yield reduction and deoxynivalenol (DON) contamination and are of great concern worldwide. DON-producing Fusarium species can be classified into 3-acetyldeoxynivalenol (3ADON) and 15-acetyldeoxynivalenol (15ADON) chemotypes according to the trichothecene metabolites they produce. The detection of these two chemotypes of pathogens is paramount to the successful implementation of disease management strategies and pathogen-related DON forecasting models. In this study, a duplex droplet digital PCR (duplex ddPCR) assay was developed that allowed for the simultaneous quantitation of 3ADON and 15ADON chemotypes of DON-producing Fusarium species. The assay specificity was tested against 30 isolates of target Fusarium species and several non-target Fusarium species that are frequently isolated from wheat in China. Analyzing 90 wheat samples collected from the North China plain and Yangtze River plain demonstrated that the duplex ddPCR assay coupled with magnetic bead-based DNA extraction was competent for investigating composition of 3ADON and 15ADON chemotypes in Chinese wheat. This assay will be useful for monitoring the epidemic and geographic distribution of 3ADON and 15ADON chemotypes of FHB pathogens, which will help with the disease control and DON management.

Functional Characterization of Calcineurin-Responsive Transcription Factors Fg01341 and Fg01350 in Fusarium graminearum

Ca^{2 +}/calmodulin-dependent phosphatase calcineurin is one of the important regulators of intracellular calcium homeostasis and has been investigated extensively in Saccharomyces cerevisiae. However, only a few reports have explored the function of the Crz1 homolog in filamentous fungi, especially in Fusarium graminearum. In this study, we identified Fg01341 as a potential ortholog of yeast Crz1. Fg01341 could interact with calcineurin and initiate nuclear transport in a calcineurin-dependent manner. The ΔFg01341 mutant exhibited normal hyphal growth on basic medium and conidia formation, but sexual reproduction was partially blocked. Pathogenicity assays showed that the virulence of the ΔFg01341 mutant in flowering wheat heads and corn silks dramatically decreased and was thus consistent with the reduction in deoxynivalenol production. Unexpectedly, the sensitivity to osmotic stress of the deletion mutant and that of the wild-type strain did not present any differences. The deletion mutant showed higher sensitivity to tebuconazole than the wild-type strain. Results also showed that the transcription factor Fg01350 might be the calcineurin target and was independent of Crz1. Furthermore, ΔFg01350 showed defects in hyphal growth, sexual production, virulence, and deoxynivalenol production. Collectively, the results indicate that these two proteins functionally redundant and that the calcineurin-Crz1-independent pathway is particularly important in F. graminearum.

Identification of a novel genomic region associated with resistance to Fusarium crown rot in wheat

Genome-wide association study (GWAS) on 358 Chinese wheat germplasms and validation in a biparental population identified a novel significant genomic region on 5DL for FCR resistance. Fusarium crown rot (FCR) is a chronic and severe disease in many dryland wheat-producing areas worldwide. In the last few years, the incidence and severity of FCR progressively increased in China, and the disease has currently become a new threat to local wheat crops. Here, we report a genome-wide association study (GWAS) on a set of 358 Chinese germplasms with the wheat 55 K SNP array. A total of 104 SNPs on chromosomes 1BS, 1DS, 2AL, 5AL, 5DS, 5DL, 6BS and 7BL were significantly associated with seedling resistance to FCR in the association panel. Of these SNPs, a novel 13.78 Mb region targeted by five SNPs on chromosome arm 5DL was continually detected in all three trials. The effects of this region on FCR resistance was confirmed in biparental population. qRT-PCR showed that within this 5DL region, several genes encoding TIR-NBS-LRR proteins and proteins related to mycotoxins deoxynivalenol (DON) detoxification increased rapidly in the disease-resistant variety 04 Zhong 36 than the susceptible variety Xinmai 26 after inoculation. Our study provides new insights into gene discovery and creation of new cultivars with desirable alleles for improving FCR resistance in wheat.

Identification of New Sources of Resistance to Crown Rot and Fusarium Head Blight in Wheat

Crown rot (CR) and Fusarium head blight (FHB) are two serious wheat diseases caused by Fusarium pathogens in China. To identify new resistant sources for CR and FHB, 205 Chinese wheat cultivars collected from Huang-Huai wheat-growing region in China were screened for resistance. Cunmai633, LS4607, Pubing01, and Hongyun2 showed seedling resistance to CR with disease index (DI) less than 0.25. Sixteen cultivars showed adult-plant resistance to CR with DI lower than 0.10. Twenty-six cultivars showed moderate resistance to CR at seedling stage with DI from 0.26 to 0.35, and 63 cultivars showed moderate adult-plant resistance with DI from 0.11 to 0.20. Among them, Cunmai633, LS4607, Pubing01, Xinong916, Zhengda161, Xumai14017, Zhengpinmai30, Bainong8822, Jimai216, Huacheng865, Fengyumai5, and Tianmin319 showed resistance or moderate resistance to CR at both seedling and adult plant stages, with Cunmai633 showing the best resistance. Most of the cultivars (>76%) were susceptible to FHB in both the 2017 and 2018 experiments with DI > 0.40. However, some cultivars demonstrated excellent FHB resistance. For example, Zhongyu1526, Tianminxiaoyan369, and Yangao168 were resistant (DI ≤ 0.25) in 2017 and moderately resistant (0.26 ≤ DI ≤ 0.40) in 2018; Zhongwo9 was moderately resistant in 2017 (DI = 0.38) and resistant in 2018 (DI = 0.25). Eight cultivars (Cunmai608, Zhengmai162, Minfeng266, Junda159, LS4607, Deyan1603, Pumai1165, and Fengmai12) showed moderate FHB resistance with DI lower than 0.40 in both experiments. LS4607 showed moderate resistance to both diseases. The resistant cultivars identified in this study can be used for mapping the resistance genes and improving resistance to CR and/or FHB.

Novel positive-sense single-stranded RNA virus related to alphavirus-like viruses from Fusarium graminearum

A putative novel positive-sense (+) RNA virus was detected in isolate CF16158 of the fungus Fusarium graminearum, the causal agent of Fusarium head blight and crown rot in wheat in China. The full genome of this virus was sequenced and characterized. The complete cDNA sequence is 7,051 nt long and contains four open reading frames (ORFs). ORF2 is predicted to encode helicase (Hel) and RNA-dependent RNA polymerase (RdRp) domains that are conserved among the alphavirus-like viruses. Pairwise comparisons and phylogenetic analysis of the deduced amino acid sequences of Hel and RdRp indicated that this (+) RNA mycovirus is a novel member of a new, yet to be established family of alphavirus-like viruses. Therefore, we named this virus "Fusarium graminearum alphavirus-like virus 1" (FgALV1). This is the first report of a full-length genomic sequence of a putative alphavirus-like virus in F. graminearum.

Effects of Lysobacter antibioticus HS124, an effective biocontrol agent against Fusarium graminearum, on crown rot disease and growth promotion of wheat

Lysobacter antibioticus HS124 inhibited mycelial growth of Fusarium graminearum (74.66%) under the dual culture method. Microscopic investigation clearly showed that amendment with different concentrations (10%, 30%, and 50%) of HS124 bacterial culture filtrate on potato dextrose agar plates caused abnormal hyphal structures, including swelling and distortion. Its inhibition toward mycelial growth of F. graminearum was increased with increasing concentration of n-butanol crude extract of HS124. The highest inhibition (43.14%) was detected at a crude concentration of 10 mg/disc, whereas the lowest inhibition (21.57%) was observed at 2 mg/disc. Although mycelial growth of F. graminearum was promoted by volatile organic compounds (VOCs) produced by HS124 as compared with the control, these VOCs clearly decreased fungal pigmentation resulting in a reduction of fungal sporulation. Microscopic investigation revealed hyphal deformation of F. graminearum due to VOCs. These compounds also had a negative effect on spore germination of F. graminearum. In vivo evaluations demonstrated that HS124 inoculation of wheat plants reduced crown rot disease incidence by 73.70% as compared with the control. HS124 inoculation of wheat plants also promoted most of the growth characteristics compared with the control or fungicide-treated plants. Our results provide strong evidence that HS124 could control F. graminearum infections and promote growth of wheat plants as part of management strategies for crown rot disease.

Investigation and genome-wide association study for Fusarium crown rot resistance in Chinese common wheat

BACKGROUND

Fusarium crown rot (FCR) is a severe and chronic disease in common wheat and is able to cause serious yield loss and health problems to human and livestock.

RESULTS

Here, 234 Chinese wheat cultivars were evaluated in four greenhouse experiments for FCR resistance and genome-wide association studies (GWAS) were performed using the wheat 660 K genotyping assay. The results indicated that most cultivars evaluated showed FCR disease index (DI) of 40-60, while some cultivars showed stably good FCR resistance (DI < 30). GWAS identified 286 SNPs to be significantly associated with FCR resistance, of which 266, 6 and 8 were distributed on chromosomes 6A, 6B and 6D, respectively. The significant SNPs on 6A were located in a 7.0-Mb region containing 51 annotated genes. On the other hand, QTL mapping using a bi-parental population derived from UC1110 and PI610750 detected three QTLs on chromosomes 6A (explaining 7.77-10.17% of phenotypic variation), 2D (7.15-9.29%) and 2A (5.24-6.92%). The 6A QTL in the UC1110/PI610750 population falls into the same chromosomal region as those detected from GWAS, demonstrating its importance in Chinese materials for FCR resistance.

CONCLUSION

This study could provide useful information for utilization of FCR-resistant wheat germplasm and further understanding of molecular and genetics basis of FCR resistance in common wheat.

Diversity of the Fusarium pathogens associated with crown rot in the Huanghuai wheat-growing region of China

To investigate the distribution and diversity of the pathogens associated with Fusarium crown rot in the Huanghuai wheat-growing region (HHWGR) of China, we collected wheat samples with symptomatic stem bases from seven provinces in the HHWGR between 2013 and 2016. A total of 1196 isolates obtained from 222 locations were identified as 9 Fusarium species based on morphological and molecular identification. Of these pathogen species, F. pseudograminearum was the dominant species. Furthermore, F. sinensis was isolated from the disease specimens and tested for virulence to wheat. The result of the pathogenicity revealed that an intraspecific differentiation existed in F. pseudograminearum; sequence analysis of the EF-1α gene showed that 194 F. pseudograminearum isolates were differentiated into two distinct clades which closed to the strains from Australia and China respectively, but neither pathogenicity nor EF-1α sequence was related to the geographic origins of these isolates. However, universal rice primers-polymerase chain reaction showed a correlation with the geographical origins of the 194 isolates, which were divided into eight subclusters, the level of genetic diversity was higher within a geographical population than among the different populations. The results of these analyses can be directly used to facilitate disease monitoring and development of control strategies.

Development of tightly linked markers and identification of candidate genes for Fusarium crown rot resistance in barley by exploiting a near-isogenic line-derived population

This study demonstrates the feasibility of developing co-segregating markers and identifying candidate genes for Fusarium crown rot resistance in barley based on the generation and exploitation of a near-isogenic line-derived large population. Fusarium crown rot (FCR) is a chronic and severe disease in cereals in semi-arid regions worldwide. Previous studies showed that FCR assessment could be affected by many factors including plant height, growth rate as well as drought stress. Thus, accurate assessment, which is essential for detailed mapping of any locus conferring FCR resistance, is difficult. Targeting one of the resistance loci reported earlier, we developed a near-isogenic line-derived population consisting of 1820 F9 lines. By analysing this population, the Qcrs.cpi-4H locus was mapped to an interval of 0.09 cM covering a physical distance of about 637 kb and 13 markers co-segregating with the targeted locus were developed. Candidate genes underlying the resistance locus were identified by analysing the expression and sequence variation of genes in the targeted interval. The accurate localization and the development of co-segregating markers should facilitate the incorporation of this large-effect QTL into breeding programmes as well as the cloning of gene(s) underlying the locus.

Molecular Characterization, Fitness, and Mycotoxin Production of Fusarium asiaticum Strains Resistant to Fludioxonil

Fludioxonil is used in seedborne disease management of various fungal pathogens, including Fusarium asiaticum, the predominant causal agent of Fusarium head blight in China. In this study, we screened resistant strains from a large number of F. asiaticum strains collected from 2012 to 2016 and found that 4 of 1,000 field strains were highly resistant to fludioxonil. The 50% effective concentration values of the resistant strains and induced mutants ranged from 80 to >400 μg/ml. Compared with field-sensitive strains, all field-collected and laboratory-induced resistant strains exhibited fitness defects in traits including mycelial growth, conidial production, pathogenicity, and sensitivity to osmotic conditions. In the presence of fludioxonil, significantly higher glycerol accumulation was found in sensitive strains but not in resistant individuals. The fludioxonil-resistant strains produced lower amounts of glycerol in liquid culture and lower amounts of trichothecene mycotoxins in rice culture and inoculated wheat spikelets than the fludioxonil-sensitive strains. Sequence analyses of the key genes of the two-component histidine kinase signaling pathway showed various amino acid substitutions in the Os1, Os4, and Os5 genes between field-sensitive and resistant strains or mutants. The results of this study suggest a potential risk of fludioxonil resistance development and a possible influence of resistance mutations on fitness parameters and toxin production in F. asiaticum.

Fusarium crown rot caused by Fusarium pseudograminearum in cereal crops: recent progress and future prospects

Diseases caused by Fusarium pathogens inflict major yield and quality losses on many economically important plant species worldwide, including cereals. Fusarium crown rot (FCR), caused by Fusarium pseudograminearum, is a cereal disease that occurs in many arid and semi-arid cropping regions of the world. In recent years, this disease has become more prevalent, in part as a result of the adoption of moisture-preserving cultural practices, such as minimum tillage and stubble retention. In this pathogen profile, we present a brief overview of recent research efforts that have not only advanced our understanding of the interactions between F. pseudograminearum and cereal hosts, but have also provided new disease management options. For instance, significant progress has been made in the genetic characterization of pathogen populations, the development of new tools for disease prediction, and the identification and pyramiding of loci that confer quantitative resistance to FCR in wheat and barley. In addition, transcriptome analyses have revealed new insights into the processes involved in host defence. Significant progress has also been made in understanding the mechanistic details of the F. pseudograminearum infection process. The sequencing and comparative analyses of the F. pseudograminearum genome have revealed novel virulence factors, possibly acquired through horizontal gene transfer. In addition, a conserved pathogen gene cluster involved in the degradation of wheat defence compounds has been identified, and a role for the trichothecene toxin deoxynivalenol (DON) in pathogen virulence has been reported. Overall, a better understanding of cereal host-F. pseudograminearum interactions will lead to the development of new control options for this increasingly important disease problem. Taxonomy: Fusarium pseudograminearum O'Donnell & Aoki; Kingdom Fungi; Phylum Ascomycota; Subphylum Pezizomycotina; Class Sordariomycetes; Subclass Hypocreomycetidae; Order Hypocreales; Family Nectriaceae; Genus Fusarium. Disease symptoms: Fusarium crown rot caused by F. pseudograminearum is also known as crown rot, foot rot and root rot. Infected seedlings can die before or after emergence. If infected seedlings survive, typical disease symptoms are browning of the coleoptile, subcrown internode, lower leaf sheaths and adjacent stems and nodal tissues; this browning can become evident within a few weeks after planting or throughout plant development. Infected plants may develop white heads with no or shrivelled grains. Disease symptoms are exacerbated under water limitation. Identification and detection: Fusarium pseudograminearum macroconidia usually contain three to five septa (22-60.5 × 2.5-5.5 μm). On potato dextrose agar (PDA), aerial mycelia appear floccose and reddish white, with red or reddish-brown reverse pigmentation. Diagnostic polymerase chain reaction (PCR) tests based on the amplification of the gene encoding translation elongation factor-1a (TEF-1a) have been developed for molecular identification. Host range: All major winter cereals can be colonized by F. pseudograminearum. However, the main impact of this pathogen is on bread (Triticum aestivum L.) and durum (Triticum turgidum L. spp. durum (Dest.)) wheat and barley (Hordeum vulgare L.). Oats (Avena sativa L.) can be infected, but show little or no disease symptoms. In addition, the pathogen has been isolated from various other grass genera, such as Phalaris, Agropyron and Bromus, which may occur as common weeds. Useful websites: https://nt.ars-grin.gov/fungaldatabases/; http://plantpath.psu.edu/facilities/fusarium-research-center; https://nt.ars-grin.gov/fungaldatabases/; http://www.speciesfungorum.org/Names/Names.asp.

Spatial Distribution of Root and Crown Rot Fungi Associated With Winter Wheat in the North China Plain and Its Relationship With Climate Variables

The distribution frequency of pathogenic fungi associated with root and crown rot of winter wheat (Triticum aestivum) from 104 fields in the North China Plain was determined during the period from 2013 to 2016. The four most important species identified were Bipolaris sorokiniana (24.0% from roots; 33.7% from stems), Fusarium pseudograminearum (14.9% from roots; 27.8% from stems), Rhizoctonia cerealis (1.7% from roots; 4.4% from stems), and Gaeumannomyces graminis var. tritici (9.8% from roots; 4.4% from stems). We observed that the recovered species varied with the agronomic zone. Fusarium pseudograminearum was predominant in regions 1 and 3, whereas F. graminearum, F. acuminatum, and R. cerealis were predominant in regions 2 and 4. The incidence of F. pseudograminearum and R. cerealis was significantly different between regions 1 and 4, while no significant association was found in the distribution of the other species and the agronomic zones. A negative correlation between the frequency of occurrence of F. pseudograminearum and mean annual precipitation during 2013-2016 (r = -0.71; P < 0.01) in the North China Plain and a positive correlation between the mean annual precipitation during 2013-2016 and the frequency of occurrence of F. asiaticum (r = 0.74; P < 0.01) were observed. Several Fusarium species were also found with low frequencies of ~2.1%-3.4 % (F. graminearum, F. acuminatum, and F. sinensis) and ~0.1%-1.3% (F. equiseti, F. oxysporum, F. proliferatum, F. culmorum, F. avenaceum, and F. asiaticum). In more than 93% of the fields, from the root and crown tissues of wheat, two or more root and crown rot species were isolated. The coexistence of Fusarium spp. and B. sorokiniana in one field (65.4%) or in individual plants (11.6%) was more common than for the other species combinations. Moreover, this is the first report on the association between F. sinensis and root and crown rot of wheat. Our results would be useful in the framing guidelines for the management of root and crown rot fungi in wheat in different agronomic zones of the North China Plain.

Long-term no-till: A major driver of fungal communities in dryland wheat cropping systems

In the dryland Pacific Northwest wheat cropping systems, no-till is becoming more prevalent as a way to reduce soil erosion and fuel inputs. Tillage can have a profound effect on microbial communities and soilborne fungal pathogens, such as Rhizoctonia. We compared the fungal communities in long-term no-till (NT) plots adjacent to conventionally tilled (CT) plots, over three years at two locations in Washington state and one location in Idaho, US. We used pyrosequencing of the fungal ITS gene and identified 422 OTUs after rarefication. Fungal richness was higher in NT compared to CT, in two of the locations. Humicola nigrescens, Cryptococcus terreus, Cadophora spp. Hydnodontaceae spp., and Exophiala spp. were more abundant in NT, while species of Glarea, Coniochaetales, Mycosphaerella tassiana, Cryptococcus bhutanensis, Chaetomium perlucidum, and Ulocladium chartarum were more abundant in CT in most locations. Other abundant groups that did not show any trends were Fusarium, Mortierella, Penicillium, Aspergillus, and Macroventuria. Plant pathogens such as Rhizoctonia (Ceratobasidiaceae) were not abundant enough to see tillage differences, but Microdochium bolleyi, a weak root pathogen, was more abundant in NT. Our results suggest that NT fungi are better adapted at utilizing intact, decaying roots as a food source and may exist as root endophytes. CT fungi can utilize mature plant residues that are turned into the soil with tillage as pioneer colonizers, and then produce large numbers of conidia. But a larger proportion of the fungal community is not affected by tillage and may be niche generalists.

Fitness of three chemotypes of Fusarium graminearum species complex in major winter wheat-producing areas of China

In China, Fusarium head blight is caused mainly by the Fusarium graminearum species complex (FGSC), which produces trichothecene toxins. The FGSC is divided into three chemotypes: 3-acetyldeoxynivalenol (3-ADON), 15-acetyldeoxynivalenol (15-ADON), and nivalenol (NIV). In order to predict the geographical changes in the distribution of these chemotype populations in major winter wheat-producing areas in China, the biological characteristics of twenty randomly selected isolates from each of the three chemotypes were studied. No significant difference was exhibited in the growth rate of 3-ADON, 15-ADON, and NIV isolates at 15°C. At 20°C and 25°C, the growth rate of 15-ADON isolates was the highest. At 30°C, the growth rate of NIV and 3-ADON isolates was significantly higher than that of 15-ADON isolates. The 15-ADON isolates produced the highest quantities of perithecia and two to three days earlier than the other two populations at each temperature, and released more ascospores at 18°C. The aggressiveness test on wheat seedlings and ears indicated there was no significant difference between the 3-ADON and 15-ADON isolates. However, the aggressiveness of NIV isolates was significantly lower than that of the 3-ADON and 15-ADON isolates. The DON content in grains from heads inoculated with the 3-ADON isolates was higher than the content of 15-ADON and NIV isolates. The results showed that 15-ADON population had the advantage in perithecia formation and ascospore release, and the 3-ADON population produced more DON in wheat grains. We suggested that distribution of these three chemotype populations may be related to these biological characteristics.