Candidate Genes for Aggressiveness in a Natural Fusarium culmorum Population Greatly Differ between Wheat and Rye Head Blight

Genome-Wide Association Study of Fungicide Sensitivity in a Fusarium graminearum Population Collected from North Dakota

Fusarium head blight is a destructive disease of small grains. The disease is predominantly caused by the haploid ascomycete fungus Fusarium graminearum in North America. To understand the genetics of quantitative traits for sensitivity to fungicides in this fungal pathogen, we conducted a genome-wide association study of sensitivity to two demethylation inhibition class fungicides, tebuconazole and prothioconazole, using an F. graminearum population of 183 isolates collected between 1981 and 2013 from North Dakota. Baseline sensitivity to tebuconazole and prothioconazole was established using 21 isolates collected between 1981 and 1994. Most fungal isolates were sensitive to both tebuconazole and prothioconazole; however, five isolates showed significantly reduced sensitivity to prothioconazole. The genome-wide association study identified one significant marker-trait association on chromosome 3 for tebuconazole resistance, whereas six significant marker-trait associations, one on chromosome 1, three on chromosome 2, and two on chromosome 4, were detected for prothioconazole resistance. Functional annotation of the marker-trait association for tebuconazole revealed a candidate gene encoding a basic helix-loop-helix domain-containing protein that reinforces sterol in the fungal membrane. Putative genes for prothioconazole resistance were also identified, which are involved in RNA interference, the detoxification by ubiquitin-proteasome pathway, and membrane integrity reinforcement. Considering the potential of the pathogen toward overcoming chemical control, continued monitoring of fungal sensitivities to commercially applied fungicides, especially those containing prothioconazole, is warranted to reduce risks of fungicide resistance in the pathogen populations.

Fusarium culmorum Produces NX-2 Toxin Simultaneously with Deoxynivalenol and 3-Acetyl-Deoxynivalenol or Nivalenol

Fusarium culmorum is a major pathogen of grain crops. Infected plants accumulate deoxynivalenol (DON), 3-acetyl-deoxynivalenol (3-ADON), or nivalenol (NIV), which are mycotoxins of the trichothecene B group. These toxins are also produced by F. graminearum species complex. New trichothecenes structurally similar to trichothecenes B but lacking the carbonyl group on C-8, designated NX toxins, were recently discovered in atypical isolates of F. graminearum from North America. Only these isolates and a few strains of a yet to be characterized Fusarium species from South Africa are known to produce NX-2 and other NX toxins. Here, we report that among 20 F. culmorum strains isolated from maize, wheat, and oat in Europe and Asia over a period of 70 years, 18 strains produced NX-2 simultaneously with 3-ADON and DON or NIV. Rice cultures of strains producing 3-ADON accumulated NX-2 in amounts corresponding to 2−8% of 3-ADON (1.2−36 mg/kg). A strain producing NIV accumulated NX-2 and NIV at comparable amounts (13.6 and 10.3 mg/kg, respectively). In F. graminearum, producers of NX-2 possess a special variant of cytochrome P450 monooxygenase encoded by TRI1 that is unable to oxidize C-8. In F. culmorum, producers and nonproducers of NX-2 possess identical TRI1; the reason for the production of NX-2 is unknown. Our results indicate that the production of NX-2 simultaneously with trichothecenes B is a common feature of F. culmorum.

Genome-wide association study for deoxynivalenol production and aggressiveness in wheat and rye head blight by resequencing 92 isolates of Fusarium culmorum

Background

Fusarium culmorum is an important pathogen causing head blight of cereals in Europe. This disease is of worldwide importance leading to reduced yield, grain quality, and contamination by mycotoxins. These mycotoxins are harmful for livestock and humans; therefore, many countries have strict regulatory limits for raw materials and processed food. Extensive genetic diversity is described among field populations of F. culmorum isolates for aggressiveness and production of the trichothecene mycotoxin deoxynivalenol (DON). However, the causes for this quantitative variation are not clear, yet. We analyzed 92 isolates sampled from different field populations in Germany, Russia, and Syria together with an international collection for aggressiveness and DON production in replicated field experiments at two locations in two years with two hosts, wheat and rye. The 30x coverage whole-genome resequencing of all isolates resulted in the identification of 130,389 high quality single nucleotide polymorphisms (SNPs) that were used for the first genome-wide association study in this phytopathogenic fungus.

Results

In wheat, 20 and 27 SNPs were detected for aggressiveness and DON content, respectively, of which 10 overlapped. Additionally, two different SNPs were significantly associated with aggressiveness in rye that were among those SNPs being associated with DON production in wheat. Most of the SNPs explained only a small proportion of genotypic variance (p_G), however, four SNPs were associated with major quantitative trait loci (QTLs) with p_G ranging from 12 to 48%. The QTL with the highest p_G was involved in DON production and associated with a SNP most probably located within the Tri4 gene.

Conclusions

The diversity of 92 isolates of F. culmorum were captured using a heuristic approach. Key phenotypic traits, SNPs, and candidate genes underlying aggressiveness and DON production were identified. Clearly, many QTLs are responsible for aggressiveness and DON content in wheat, both traits following a quantitative inheritance. Several SNPs involved in DON metabolism, among them the Tri4 gene of the trichothecene pathway, were inferred as important source of variation in fungal aggressiveness. Using this information underlying the phenotypic variation will be of paramount importance in evaluating strategies for successful resistance breeding.

Supplementary Information

The online version contains supplementary material available at 10.1186/s12864-021-07931-5.

Cereal Root Interactions with Soilborne Pathogens—From Trait to Gene and Back

Realizing the yield potential of crop plants in the presence of shifting pathogen populations, soil quality, rainfall, and other agro-environmental variables remains a challenge for growers and breeders worldwide. In this review, we discuss current approaches for combatting the soilborne phytopathogenic nematodes, Pratylenchus and Heterodera of wheat and barley, and Meloidogyne graminicola Golden and Birchfield, 1965 of rice. The necrotrophic fungal pathogens, Rhizoctonia solani Kühn 1858 AG-8 and Fusarium spp. of wheat and barley, also are discussed. These pathogens constitute major causes of yield loss in small-grain cereals of the Pacific Northwest, USA and throughout the world. Current topics include new sources of genetic resistance, molecular leads from whole genome sequencing and genome-wide patterns of hosts, nematode or fungal gene expression during root-pathogen interactions, host-induced gene silencing, and building a molecular toolbox of genes and regulatory sequences for deployment of resistance genes. In conclusion, improvement of wheat, barley, and rice will require multiple approaches.

Antifungal, Antibacterial, and Antioxidant Activities of Acacia Saligna (Labill.) H. L. Wendl. Flower Extract: HPLC Analysis of Phenolic and Flavonoid Compounds

In this study, for the environmental development, the antifungal, antibacterial, and antioxidant activities of a water extract of flowers from Acacia saligna (Labill.) H. L. Wendl. were evaluated. The extract concentrations were prepared by dissolving them in 10% DMSO. Wood samples of Melia azedarach were treated with water extract, and the antifungal activity was examined at concentrations of 0%, 1%, 2%, and 3% against three mold fungi; Fusarium culmorum MH352452, Rhizoctonia solani MH352450, and Penicillium chrysogenum MH352451 that cause root rot, cankers, and green fruit rot, respectively, isolated from infected Citrus sinensis L. Antibacterial evaluation of the extract was assayed against four phytopathogenic bacteria, including Agrobacterium tumefaciens, Enterobacter cloacae, Erwinia amylovora, and Pectobacterium carotovorum subsp. carotovorum, using the micro-dilution method to determine the minimum inhibitory concentrations (MICs). Further, the antioxidant capacity of the water extract was measured via 2,2'-diphenylpicrylhydrazyl (DPPH). Phenolic and flavonoid compounds in the water extract were analyzed using HPLC: benzoic acid, caffeine, and o-coumaric acid were the most abundant phenolic compounds; while the flavonoid compounds naringenin, quercetin, and kaempferol were identified compared with the standard flavonoid compounds. The antioxidant activity of the water extract in terms of IC₅₀ was considered weak (463.71 μg/mL) compared to the standard used, butylated hydroxytoluene (BHT) (6.26 μg/mL). The MIC values were 200, 300, 300, and 100 µg/mL against the growth of A. tumefaciens, E. cloacae, E. amylovora, and P. carotovorum subsp. carotovorum, respectively, which were lower than the positive control used (Tobramycin 10 μg/disc). By increasing the extract concentration, the percentage inhibition of fungal mycelial was significantly increased compared to the control treatment, especially against P. chrysogenum, suggesting that the use of A. saligna flower extract as an environmentally friendly wood bio-preservative inhibited the growth of molds that cause discoloration of wood and wood products.

Alternaria and Fusarium Fungi: Differences in Distribution and Spore Deposition in a Topographically Heterogeneous Wheat Field

Fusarium spp. and Alternaria spp., two genera of filamentous fungi, are common colonizers of the wheat phyllosphere. Both can be pathogenic and produce mycotoxins that are harmful to consumers. Their in-field infection dynamics have been a focus for the development of new control strategies. We analysed the abundance on plant ears and spore deposition patterns of Fusarium spp. and Alternaria spp. in a topographically heterogeneous field. Abundances were assessed genetically, using qPCR-based techniques, and passive spore traps were installed for quantifying the spore deposition at different plant heights. Data loggers were placed to measure the differences in microclimate across the field. Results indicate different distribution and spore deposition patterns for the two fungi. Fusarium spp. spore and genetic abundances were higher in spots with a more humid and colder under-canopy microclimate. Alternaria spp. showed the opposite trend for genetic abundance, while its spore deposition was not correlated to any of the microclimatic conditions and was more uniform across the field. Our study extends the knowledge on the dispersal and in-field infection dynamics of Fusarium spp. and Alternaria spp., important for a better understanding of the epidemiology of these wheat pathogens. It also illustrates that topographically heterogeneous fields are a suitable environment for studying the ecology of phyllosphere-colonizing fungi.

Special Issue: Genomic Data in Pathogenic Fungi

This special issue, "Genomic Data in Pathogenic Fungi," focuses on the genomics of human and plant pathogens. Efforts like this are important because so little information about these organisms is available.[...].