A global pangenome for the wheat fungal pathogen Pyrenophora tritici-repentis and prediction of effector protein structural homology.

The adaptive potential of plant fungal pathogens is largely governed by the gene content of a species, consisting of core and accessory genes across the pathogen isolate repertoire. To approximate the complete gene repertoire of a globally significant crop fungal pathogen, a pan genomic analysis was undertaken for Pyrenophora tritici-repentis (Ptr), the causal agent of tan (or yellow) spot disease in wheat. In this study, 15 new Ptr genomes were sequenced, assembled and annotated, including isolates from three races not previously sequenced. Together with 11 previously published Ptr genomes, a pangenome for 26 Ptr isolates from Australia, Europe, North Africa and America, representing nearly all known races, revealed a conserved core-gene content of 57 % and presents a new Ptr resource for searching natural homologues (orthologues not acquired by horizontal transfer from another species) using remote protein structural homology. Here, we identify for the first time a non-synonymous mutation in the Ptr necrotrophic effector gene ToxB, multiple copies of the inactive toxb within an isolate, a distant natural Pyrenophora homologue of a known Parastagonopora nodorum necrotrophic effector (SnTox3), and clear genomic break points for the ToxA effector horizontal transfer region. This comprehensive genomic analysis of Ptr races includes nine isolates sequenced via long read technologies. Accordingly, these resources provide a more complete representation of the species, and serve as a resource to monitor variations potentially involved in pathogenicity.

Spatio-temporal distribution of DMI and SDHI fungicide resistance of Zymoseptoria tritici throughout Europe based on frequencies of key target-site alterations.

BACKGROUND: Over the past decade, demethylation inhibitor (DMI) and succinate dehydrogenase inhibitor (SDHI) fungicides have been extensively used to control to septoria tritici blotch, caused by Zymoseptoria tritici on wheat. This has led to the development and selection of alterations in the target-site enzymes (CYP51 and SDH, respectively). RESULTS: Taking advantage of newly and previously developed qPCR assays, the frequency of key alterations associated with DMI (CYP51-S524T) and SDHI (SDHC-T79N/I, C-N86S and C-H152R) resistance was assessed in Z. tritici-infected wheat leaf samples collected from commercial crops (n = 140) across 14 European countries prior to fungicide application in the spring of 2019. This revealed the presence of a West to East gradient in the frequencies of the most common key alterations conferring azole (S524T) and SDHI resistance (T79N and N86S), with the highest frequencies measured in Ireland and Great Britain. These observations were corroborated by sequencing (CYP51 and SDH subunits) and sensitivity phenotyping (prothioconazole-desthio and fluxapyroxad) of Z. tritici isolates collected from a selection of field samples. Additional sampling made at the end of the 2019 season confirmed the continued increase in frequency of the targeted alterations. Investigations on historical leaf DNA samples originating from different European countries revealed that the frequency of all key alterations (except C-T79I) has been gradually increasing over the past decade. CONCLUSION: Whilst these alterations are quickly becoming dominant in Ireland and Great Britain, scope still exists to delay their selection throughout the wider European population, emphasizing the need for the implementation of fungicide antiresistance measures. © 2021 Society of Chemical Industry.

Spatiotemporal Variation and Networks in the Mycobiome of the Wheat Canopy.

The phyllosphere is an important habitat for a diverse microbiome and an important entry point for many pathogens. Factors that shape the phyllosphere microbiome and also the co-existence among members and how they affect disease development are largely understudied. In this study we examined the wheat mycobiome by using metabarcoding of the fungal ITS1 region. Leaf samples were taken from four cultivars grown at two locations in Denmark. Samples were taken from the three uppermost leaves and at three growth stages to better understand spatiotemporal variation of the mycobiome. Analysis of read abundances showed that geographical location had a major effect in shaping the mycobiome in the total dataset, but also leaf position, growth stage and cultivar were important drivers of fungal communities. Cultivar was most important in explaining variation in older leaves whereas location better explained the variation in younger leaves, suggesting that communities are shaped over time by the leaf environment. Network analysis revealed negative co-existence between Zymoseptoria tritici and the yeasts Sporobolomyces, Dioszegia, and Cystofilobasidiaceae. The relative abundance of Z. tritici and the yeasts was relatively constant between individual samples, suggesting that fast growing fungi rapidly occupy empty space in the phyllosphere.

Targeting Fungicide Inputs According to Need.

Fungicides should be used to the extent required to minimize economic costs of disease in a given field in a given season. The maximum number of treatments and maximum dose per treatment are set by fungicide manufacturers and regulators at a level that provides effective control under high disease pressure. Lower doses are economically optimal under low or moderate disease pressure, or where other control measures such as resistant cultivars constrain epidemics. Farmers in many countries often apply reduced doses, although they may still apply higher doses than the optimum to insure against losses in high disease seasons. Evidence supports reducing the number of treatments and reducing the applied dose to slow the evolution of fungicide resistance. The continuing research challenge is to improve prediction of future disease damage and account for the combined effect of integrated control measures to estimate the optimum number of treatments and the optimum dose needed to minimize economic costs. The theory for optimizing dose is well developed but requires translation into decision tools because the current basis for farmers' dose decisions is unclear.

Disease Impact on Wheat Yield Potential and Prospects of Genetic Control.

Wheat is grown worldwide in diverse geographical regions, environments, and production systems. Although many diseases and pests are known to reduce grain yield potential and quality, the three rusts and powdery mildew fungi have historically caused major crop losses and continue to remain economically important despite the widespread use of host resistance and fungicides. The evolution and fast spread of virulent and more aggressive race lineages of rust fungi have only worsened the situation. Fusarium head blight, leaf spotting diseases, and, more recently, wheat blast (in South America and Bangladesh) have become diseases of major importance in recent years largely because of intensive production systems, the expansion of conservation agriculture, undesirable crop rotations, or increased dependency on fungicides. High genetic diversity for race-specific and quantitative resistance is known for most diseases; their selection through phenotyping reinforced with molecular strategies offers great promise in achieving more durable resistance and enhancing global wheat productivity.

Correlation of Deoxynivalenol Accumulation in Fusarium-Infected Winter and Spring Wheat Cultivars with Secondary Metabolites at Different Growth Stages.

Fusarium infection in wheat causes Fusarium head blight, resulting in yield losses and contamination of grains with trichothecenes. Some plant secondary metabolites inhibit accumulation of trichothecenes. Eighteen Fusarium infected wheat cultivars were harvested at five time points and analyzed for the trichothecene deoxynivalenol (DON) and 38 wheat secondary metabolites (benzoxazinoids, phenolic acids, carotenoids, and flavonoids). Multivariate analysis showed that harvest time strongly impacted the content of secondary metabolites, more distinctly for winter wheat than spring wheat. The benzoxazinoid 2-ß-glucopyranoside-2,4-dihydroxy-7-methoxy-1,4-benzoxazin-3-one (DIMBOA-glc), α-tocopherol, and the flavonoids homoorientin and orientin were identified as potential inhibitors of DON accumulation. Several phenolic acids, lutein and ß-carotene also affected DON accumulation, but the effect varied for the two wheat types. The results could form a basis for choosing wheat cultivars using metabolite profiling as a marker for selecting wheat cultivars with improved resistance against Fusarium head blight and accumulation of trichothecene toxins in wheat heads.

Synthesis and quantitation of six phenolic amides in Amaranthus spp.

Cinnamoylphenethylamines are phenolic amides in which cinnamic acid provides the acid moiety and phenethylamine the amine moiety. Single ion monitoring (SIM) in LC-MS was performed on amaranth leaf extracts. Masses corresponding to sets of regioisomers, including previously reported compounds, were examined. Six peaks were detected and their corresponding standards synthesized for a quantitative LC-MS/MS investigation of cinnamoylphenethylamines in amaranth. Four cinnamoylphenethylamines (caffeoyltyramine, feruloyldopamine, sinapoyltyramine, and p-coumaroyltyramine) are reported in the Amaranthaceae for the first time; also, one rare compound, feruloyl-4-O-methyldopamine, appeared to be quite common in the genus Amaranthus. Feruloyldopamine showed moderate antifungal activity toward an isolate of Fusarium culmorum. Our LC-MS approach, in conjunction with the straightforward synthesis, provides a simple, reliable way of quantitatively investigating cinnamoylphenethylamines in plants. Concentrations of cinnamoylphenethylamines vary widely: feruloyltyramine was present in quantities of 5.26 to 114.31 microg/g and feruloyldopamine in quantities of 0.16 to 10.27 microg/g, depending on the plant sample.