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Fusarium head blight (FHB) of Triticum spp. is caused by diverse, mycotoxigenic members of the genus Fusarium. In New York, United States, Fusarium graminearum is considered the primary FHB incitant on common wheat (Triticum aestivum), but there is no record of the Fusarium spp. colonizing wheat crops marketed as high value ‘ancient grains’ (T. dicoccum, T. spelta, and T. monococcum). The incidence and severity of FHB on these crops was recorded at variety trials in 2017 and 2018, and a brief survey of the Fusarium flora associated with symptomatic spikes was conducted at these trials and an additional research site in 2018. A significant difference in mean incidence and severity was observed between crop varieties in 2017, suggesting that partial varietal resistance will contribute to successful FHB management in New York ‘ancient grain’ crops. The survey of Fusarium flora associated with symptomatic tissue recorded seven species or species complexes, based on colony morphology and DNA sequence homology. Fusarium acuminatum, F. avenaceum, the F. graminearum species complex, the F. incarnatum-equiseti species complex, F. poae and F. sporotrichioides have been linked previously to FHB in wheat, while F. armeniacum had not been associated with FHB symptomatic wheat spikes prior to this study. The diversity of Fusarium species recovered raises the concern that mycotoxins which are not routinely tested for may be found in high-value Triticum crops grown in New York.

The crop pathogen Fusarium graminearum often colonizes non-cultivated grasses, but the phenotypic variation found in isolates recovered from these hosts has not been thoroughly investigated or compared to that observed in isolates collected from crop hosts. Fusarium graminearum growth, perithecia formation, and virulence on crops (maize seedlings, wheat seedlings, wheat spikes) were measured in laboratory and greenhouse experiments using isolates (n = 24) recovered from three non-cultivated grasses (Bromus inermis, Dactylis glomerata, and Phalaris arundinacea) and winter wheat (Triticum aestivum) found at a single research farm in northeastern New York. While individual isolates varied significantly for all phenotypes measured, grass and wheat derived isolates displayed a comparable range of phenotypic values. Trichothecene genotypes were determined from the TRI12 and TRI1 loci, and mycotoxin production was quantified in mature wheat spikes. Trichothecene genotype and phenotype were largely concordant and were not related to isolate source. These findings support consideration of non-cultivated hosts as sources of diverse pathogen inoculum that may cause crop disease.

Research was undertaken to clarify the taxonomic identity of leaf rust (Pucciniales) fungi on bioenergy switchgrass in the Eastern and Central U.S. We integrated internal transcribed spacer 2 (ITS2) and partial 28S ribosomal RNA gene sequence data from collections taken from cultivated switchgrass and herbarium specimens, including purported aecial and telial states of Puccinia graminicola and Puccinia pammelii. Maximum likelihood and Bayesian analyses revealed four monophyletic clades: Puccinia emaculata sensu stricto (s.s.), P. pammelii, P. graminicola, and Puccinia novopanici. Results also indicated that P. emaculata s.s. was not affecting cultivated, bioenergy switchgrass. Aecidium pammelii and P. pammelii were distinct phylogenetically from P. emaculata s.s. and grouped within a well-supported clade, demonstrating aecial-telial host alternation for P. pammelii between Euphorbia corollata and switchgrass. Aecidium stillingiae on queen’s delight (Stillingia sylvatica)—a purported aecial state host for P. graminicola—shared identical sequences with the recently described species Puccinia pascua. The latter fungus, however, was recovered within a subclade of P. graminicola. Hence, queen’s delight likely is not an aecial host to P. graminicola s.s. Additional molecular studies are warranted to determine species boundaries within the P. graminicola complex. The majority of contemporary collections from cultivated switchgrass were recognized as P. novopanici. Collectively, bioenergy switchgrass is host to at least three phylogenetically distinct species, presenting a significant challenge to the future selection and breeding of switchgrass with improved rust resistance.

Key message Genome-wide association mapping in conjunction with population sequencing map and Ensembl plants was used to identify markers/candidate genes linked to leaf rust, stripe rust and tan spot resistance in wheat. Abstract Leaf rust (LR), stripe rust (YR) and tan spot (TS) are some of the important foliar diseases in wheat (Triticum aestivum L.). To identify candidate resistance genes for these diseases in CIMMYT’s (International Maize and Wheat Improvement Center) International bread wheat screening nurseries, we used genome-wide association studies (GWAS) in conjunction with information from the population sequencing map and Ensembl plants. Wheat entries were genotyped using genotyping-by-sequencing and phenotyped in replicated trials. Using a mixed linear model, we observed that seedling resistance to LR was associated with 12 markers on chromosomes 1DS, 2AS, 2BL, 3B, 4AL, 6AS and 6AL, and seedling resistance to TS was associated with 14 markers on chromosomes 1AS, 2AL, 2BL, 3AS, 3AL, 3B, 6AS and 6AL. Seedling and adult plant resistance (APR) to YR were associated with several markers at the distal end of chromosome 2AS. In addition, YR APR was also associated with markers on chromosomes 2DL, 3B and 7DS. The potential candidate genes for these diseases included several resistance genes, receptor-like serine/threonine-protein kinases and defense-related enzymes. However, extensive LD in wheat that decays at about 5 × 107 bps, poses a huge challenge for delineating candidate gene intervals and candidates should be further mapped, functionally characterized and validated. We also explored a segment on chromosome 2AS associated with multiple disease resistance and identified seventeen disease resistance linked genes. We conclude that identifying candidate genes linked to significant markers in GWAS is feasible in wheat, thus creating opportunities for accelerating molecular breeding. Electronic supplementary material The online version of this article (10.1007/s00122-018-3086-6) contains supplementary material, which is available to authorized users.

Current knowledge of the aerobiology of Fusarium graminearum sensu lato is based on decades of published research documenting the processes of spore discharge, atmospheric transport, and deposition in this important pathogen of cereal crops worldwide. Spores from both local and more distant sources have been shown to cause infection in susceptible cereal crops when environmental conditions are favorable. Susceptible crops may be exposed throughout a growing season to airborne spores deposited in rain events and in night-time hours through gravitational settling. Given that spores deposited on cereal florets originate from distant as well as local sources, disease risk forecasts, based currently on weather favoring local spore production during the days before peak infection (i.e., initiation of crop flowering), might be improved by placing greater emphasis on local weather directly favoring infection at and following the time of flowering. Also, considering the genetic diversity of fungal spores introduced to local agricultural fields following atmospheric transport, crop breeders should select resistant varieties based on screening against a set of fungal isolates that represent the range of virulence observed in fungal populations across a broader geographic region. An increased understanding of the aerobiology of F. graminearum contributes to the overall knowledge of plant pathogen transport in the atmosphere.

Phaeosphaeria avenaria, one of the causal agents of stagonospora leaf blotch diseases in cereals, is composed of two subspecies, P. avenaria f. sp. triticea (Pat) and P. avenaria f. sp. avenaria (Paa). The Pat subspecies was grouped into Pat1-Pat3, based on restriction fragment length polymorphism (RFLP) and ribosomal DNA (rDNA) internal transcribed spacer (ITS) sequences in previous studies. Mating-type genes and their potential use in phylogeny and molecular classification were studied by DNA hybridization and PCR amplification. The majority of Pat1 isolates reported to be homothallic and producing sexual reproduction structures on cultural media had only the MAT1-1 gene. Minor sequence variations were found in the conserved region of MAT1-1 gene in Pat1 isolates. However, both mating-type genes, MAT1-1 and MAT1-2, were identified in P. avenaria isolates represented by ATCC12277 from oats (Paa) and the Pat2 isolates from foxtail barley ( Hordeum jubatum L.). Cluster analyses based on mating-type gene conserved regions revealed that cereal Phaeosphaeria is not phylogenetically closely related to other ascomycetes, including Mycosphaerella graminicola (anamorph Septoria tritici). The sequence diversity of mating-type genes in Pat and Paa supports our previous phylogenetic relationship and molecular classification based on RFLP fingerprinting and rDNA ITS sequences.

The dynamics of wheat spindle streak mosaic bymovirus in winter wheat were studied during two crop cycles in a field site with a history of high virus incidence. Individual plants of two susceptible cultivars were sampled from autumn to spring and the presence of virus antigen in roots and leaves was determined by ELISA. Virus incidence was higher in cv. Frankenmuth than in cv. Augusta. During year one, incidence of viral antigen in roots remained very low for four months after sowing, and did not reach maximum levels until the following spring. During year two, incidence of viral antigen in roots rose to maximum levels in autumn, only three months after sowing. These results strongly suggested that root infection occurred in spring as well as in autumn. In both cultivars and in both years, we detected the virus in roots one month prior to its detection in leaves, suggesting that virus moves slowly from roots into leaves. Maximum incidence of virus in leaves occurred in spring of both years, coinciding with the period of symptom development. Typical symptoms (yellow streaks, spindles, and mosaic) were observed in year two, whereas only mild mosaic was observed in year one. Virus antigen was detected in nonsymptomatic leaves from two months after sowing through crop senescence. Because antigen could be detected in roots throughout the crop cycle, and zoosporangia and cystosori of the fungal vector could be detected one and two months, respectively, after sowing, it is possible that wheat spindle streak mosaic bymovirus is acquired and/or spread by the vector during the majority of the crop cycle.

Seed transmission ofPyrenophora tritici-repentis, a common foliar pathogen of wheat, was investigated in soft white winter wheat cv. Frankenmuth and found to be non-systemic; the emerging coleoptile was infected externally by hyphal growth from the infected pericarp. Hyphae from the infected coleoptile then infected the first and second seedling leaves as they emerged. Coleoptile symptoms ranged from tiny brown streaks or spots to large, brown necrotic areas accompanied by cracking and distortion of the coleoptile. Small brown spots sometimes occurred on the first and rarely on the second seedling leaves, often accompanied by leaf distortion. Pseudothecial initials of the fungus were present within or on the seed remnants. Seed transmission efficiency was as high as 92%in vitro and 60% in potting soil outdoors. Seed infection did not affect germinationin vitro, but slightly reduced emergence in potting soil. Seedling weight and height were reduced significantly. In potting soil, seed infection also resulted in delayed plant growth and increased tan spot severity at later stages of plant development. Under controlled conditions, seed transmission efficiency and incidence of pseudothecia on seed were negatively correlated with seed germination temperature in the range of 9 to 21 °C, whereas frequency of recovery of the fungus from symptomatic coleoptiles and leaves was positively correlated with seed germination temperature. These results suggest that infected seed may serve as a source of inoculum for tan spot epidemics and for dispersal of strains of the fungus to new areas.

Background The discovery and development of novel plant cell wall degrading enzymes is a key step towards more efficient depolymerization of polysaccharides to fermentable sugars for the production of liquid transportation biofuels and other bioproducts. The industrial fungus Trichoderma reesei is known to be highly cellulolytic and is a major industrial microbial source for commercial cellulases, xylanases and other cell wall degrading enzymes. However, enzyme-prospecting research continues to identify opportunities to enhance the activity of T. reesei enzyme preparations by supplementing with enzymatic diversity from other microbes. The goal of this study was to evaluate the enzymatic potential of a broad range of plant pathogenic and non-pathogenic fungi for their ability to degrade plant biomass and isolated polysaccharides. Results Large-scale screening identified a range of hydrolytic activities among 348 unique isolates representing 156 species of plant pathogenic and non-pathogenic fungi. Hierarchical clustering was used to identify groups of species with similar hydrolytic profiles. Among moderately and highly active species, plant pathogenic species were found to be more active than non-pathogens on six of eight substrates tested, with no significant difference seen on the other two substrates. Among the pathogenic fungi, greater hydrolysis was seen when they were tested on biomass and hemicellulose derived from their host plants (commelinoid monocot or dicot). Although T. reesei has a hydrolytic profile that is highly active on cellulose and pretreated biomass, it was less active than some natural isolates of fungi when tested on xylans and untreated biomass. Conclusions Several highly active isolates of plant pathogenic fungi were identified, particularly when tested on xylans and untreated biomass. There were statistically significant preferences for biomass type reflecting the monocot or dicot host preference of the pathogen tested. These highly active fungi are promising targets for identification and characterization of novel cell wall degrading enzymes for industrial applications.

Cochliobolus heterostrophus was transformed with a plasmid (pH1S) containing a bacterial gene (hygB), which confers resistance to the antibiotic hygromycin B when under control of an 838-bp fragment of promoter 1 from C. heterostrophus. The plasmid integrated at either homologous (52% single copy, 33% tandemly repeated copies) or ectopic (4% single copy, 11% tandemly repeated copies) sites on different chromosomes, resulting in four distinct configurations of integrated DNA. All four configurations were highly stable during mitotic growth; virtually no loss of integrated DNA was detected after five subcultures on nonselective medium or after seven cycles of pathogenesis on maize, the normal host of this fungus. However, deletion of integrated DNA was detected after eight or more disease cycles. The frequency of deletion depended on the configuration of the recombinant chromosome. A single copy of pH1S integrated at an homologous site was flanked by direct repeats of the target sequence and was least stable; up to 50% of the population lacked integrated DNA after 12 disease cycles. A single copy integrated at an ectopic site had no repeated DNA directly associated with it and was the most stable; no deletions were detected after 12 disease cycles. Tandemly repeated copies of pH1S integrated at either homologous or ectopic sites appeared to have intermediate stability; 2–18% of each population lost at least one copy after 12 disease cycles, although in no case were all copies deleted. Cytosine residues of integrated DNA were methylated during mitotic growth, but this had no apparent effect on the expression of hygB.