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.

SummaryThe phyllosphere mycobiome in cereals is an important determinant of crop health. However, an understanding of the factors shaping this community is lacking.Fungal diversity in leaves from a range of cultivars of winter wheat (Triticum aestivum), winter and spring barley (Hordeum vulgare) and a smaller number of samples from oat (Avena sativa), rye (Secale cereale) and triticale (Triticum 9 Secale) was studied using next-generation sequencing. The effects of host genotype, fungicide treatment and location on fungal communities were explored.In total, 635 251 fungal internal transcribed spacer (ITS) reads were obtained from 210 leaf samples. Visual disease assessments and relative read abundance of Zymoseptoria tritici and Ramularia collo-cygni were strongly positively related. Crop genotype at the species level explained 43% of the variance in the total dataset, followed by fungicide treatment (13%) and location (4%). Indicator species, including plant pathogens, responding to factors such as crop species, location and treatment were identified.Host genotype at both the species and cultivar level is important in shaping phyllosphere fungal communities, whereas fungicide treatment and location have minor effects. We found many host-specific fungal pathogens, but also a large diversity of fungi that were relatively insensitive to host genetic background, indicating that host-specific pathogens live in a 'sea' of nonspecific fungi.

Quantitative real-time polymerase chain reaction differentiating 10 Fusarium spp. and Microdochium nivale or M. majus was applied to a total of 396 grain samples of wheat, barley, triticale, oat, and rye sampled across Denmark from 2003 to 2007, along with selected samples of wheat and barley from 1957 to 2000, to determine incidence and abundance of individual Fusarium spp. The mycotoxins deoxynivalenol (DON), nivalenol, zearalenone, T-2, and HT-2 were quantified using liquid chromatography-double mass spectrometry. Major differences in the Fusarium species complex among the five cereals as well as great yearly variation were seen. Fusarium graminearum, F. culmorum, and F. avenaceum were dominant in wheat, with DON as the dominant mycotoxin. F. langsethiae, F. culmorum, and F. avenaceum were dominant in barley and oat, leading to relatively high levels of the mycotoxins T-2 and HT-2. F. graminearum, F. culmorum, and F. avenaceum dominated in triticale and rye. The nontoxigenic M. nivale/majus were present in significant amounts in all cereal species. Wheat and barley samples from 1957 to 1996 exhibited no or very low amounts of F. graminearum, indicating a recent increase of this pathogen. Biomass and mycotoxin data exhibited good correlations between Fusarium spp. and their corresponding mycotoxins under field conditions.

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