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Perennial grain crops are emerging as a promising addition to sustainable agricultural systems because of their low-input requirements and delivery of ecosystem services. However, adoption of these crops is expected to bring novel management challenges, including those related to plant diseases. In New York, fungal pathogens of annual grains have a significant impact on crop yield and value and are generally controlled through a combination of host resistances, cultural practices and chemical fungicides. Without the availability of crop rotation and soil tillage practices, disease control in perennial grain systems may be problematic, and little is known about perennial grain crop susceptibility to local plant pathogen populations. During 2017 and 2018, ongoing field trials of two perennial grain crops recently introduced in New York, intermediate wheatgrass (IWG; Thinopyrum intermedium) and perennial cereal rye (PCR; Secale cereale), were assessed for the presence of putative fungal pathogens on actively growing plants, overwintered crop residue and harvested grain. A total of nine potential host–pathogen combinations were recorded based on symptomology, pathogen morphology and DNA sequences. Common annual crop pathogens were recovered most frequently, but, at one site, Phyllachora graminis, causal fungus of tar spot and a pathogen not previously reported on crops in New York, was found on IWG. Residue colonization by an important toxigenic pathogen (Fusarium graminearum) was high in both crops, though mycotoxin levels in associated grain were low, indicating either the hosts or environment were unsuitable for disease development. Seed-borne fungal communities differed across crops and locations, and black point, a condition caused by Alternaria and Bipolaris fungi and indicative of compromised grain quality, was prevalent in PCR under some conditions. Growing PCR with intercropped red clover (Trifolium pratense L.) resulted in less Stagonospora colonization of stem residue, and PCR grown with an oat (Avena sativa L.) nurse crop had a reduced incidence of black point. These alternative cultural practices may prove useful for managing disease in perennial grains. Our results suggest that the incorporation of perennial crops into the agricultural landscape will lead to familiar plant disease problems requiring new solutions as well as new problems that may require significant research investments.

Isolates representing 14 Alternaria section Infectoriae species collected from diverse hosts and locations were shotgun sequenced. These genome assemblies and annotations will improve the study of taxonomy and biology in this group of ubiquitous fungi.

Isolates representing 14

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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.

International audience; Scientific communication is facilitated by a data-driven, scientifically sound taxonomy that considers the end-user's needs and established successful practice. Previously (Geiser et al. 2013; Phytopathology 103:400-408. 2013), the Fusarium community voiced near unanimous support for a concept of Fusarium that represented a clade comprising all agriculturally and clinically important Fusarium species, including the F. solani Species Complex (FSSC). Subsequently, this concept was challenged by one research group (Lombard et al. 2015 Studies in Mycology 80: 189-245) who proposed dividing Fusarium into seven genera, including the FSSC as the genus Neocosmospora, with subsequent justification based on claims that the Geiser et al. (2013) concept of Fusarium is polyphyletic (Sandoval-Denis et al. 2018; Persoonia 41:109-129). Here we test this claim, and provide a phylogeny based on exonic nucleotide sequences of 19 orthologous protein-coding genes that strongly support the monophyly of Fusarium including the FSSC. We reassert the practical and scientific argument in support of a Fusarium that includes the FSSC and several other basal lineages, consistent with the longstanding use of this name among plant pathologists, medical mycologists, quarantine officials, regulatory agencies, students and researchers with a stake in its taxonomy. In recognition of this monophyly, 40 species recently described as Neocosmospora were recombined in Fusarium, and nine others were renamed Fusarium. Here the global Fusarium community voices strong support for the inclusion of the FSSC in Fusarium, as it remains the best scientific, nomenclatural and practical taxonomic option available.

Soybean (Glycine max [L.] Merrill) yield losses as a result of plant diseases were estimated by university and government plant pathologists in 29 soybean producing states in the United States and in Ontario, Canada, from 2015 through 2019. In general, the estimated losses that resulted from each of 28 plant diseases or pathogens varied by state or province as well as year. Soybean cyst nematode (SCN) (Heterodera glycines Ichinohe) caused more than twice as much loss as any other disease during the survey period. Seedling diseases (caused by various pathogens), Sclerotinia stem rot (white mold) (caused by Sclerotinia sclerotiorum [Lib.] de Bary), and sudden death syndrome (caused by Fusarium virguliforme O’Donnell & T. Aoki) caused the next greatest yield losses, in descending order. Following SCN, the most damaging diseases in the northern United States and Ontario differed from those in the southern United States. The estimated mean economic loss from all soybean diseases, averaged across the United States and Ontario, Canada was US$45 per acre (US$111 per hectare). The outcome from the current survey will provide pertinent information regarding the important soybean diseases and their overall severity in the soybean crop and help guide future research and Extension efforts on managing soybean diseases.

The movement of plant pathogens between cultivated and natural host communities can result in lost agricultural production and altered microbial or plant biodiversity. Fusarium graminearum incidence was studied in wild grass hosts for 3 years to better understand the ecology of this plant pathogen at the interface of crop fields and nonagricultural environments. Research sites (n = 23) were spread between regions of high and low agricultural production and included both agricultural and nonagricultural fields. Pathogen incidence in living grass spikes and senesced, overwintered stems varied between regions of New York and was lowest in a region with sparser agricultural production (P = 0.001). However, pathogen incidence within regions was similar at both agricultural and nonagricultural sites. The groundcover of crop and wild hosts within 1 km of sample sites were equally effective predictors of pathogen incidence, indicating either host group may drive pathogen spread. Rainfall in the 8 weeks preceding sample collection was strongly correlated with F. graminearum incidence in grasses, as well as an increased prevalence of F. graminearum in Fusarium spp. communities (P = 0.001). Grass species diversity was not associated with a reduction in pathogen incidence, and F. graminearum incidence did not vary among the most well-sampled grasses. These results indicate the pathogen colonizes and spreads in noncultivated grasses in a manner consistent with existing concepts of pathogen epidemiology in cereal crops. Increasing host acreage, whether cultivated or not, could drive the colonization of grasses in remote or protected environments, potentially altering their microbial communities.

The structure and diversity of wild grass spike-inhabiting Fusarium communities are not well understood. Fifteen common, non-cultivated grasses were surveyed across two years, regions, and land use...

Crown rust is the principal disease of spring oat in New York. Management with resistance genes is effective but contingent on understanding varietal responses to local pathogen populations. Field studies were conducted from 2015 to 2018 to assess the crown rust susceptibility of commercial cultivars and public breeding lines under natural conditions in New York. Three of the 10 commercial varieties trialed were determined to be resistant, and breeding lines from five different states also exhibited resistance. On average, yield was reduced by 34.56 kg/ha for every 1% increase in crown rust severity, whereas the impact on test weight was negligible. A race differential panel was deployed in 2018 at a central screening nursery to determine the range of pathogen virulence present. Susceptible interactions were observed on only five crown rust differentials, and virulence on all five has been recorded at high levels across the country. Crown rust may be a limiting factor to oat production in New York, but yield potential and crop value can be preserved by planting an appropriately resistant variety.

Annual reductions in corn (Zea mays L.) yield caused by diseases were estimated by university Extension-affiliated plant pathologists in 26 corn-producing states in the United States and in Ontario, Canada, from 2016 through 2019. Estimated loss from each disease varied greatly by state or province and year. Gray leaf spot (caused by Cercospora zeae-maydis Tehon & E.Y. Daniels) caused the greatest estimated yield loss in parts of the northern United States and Ontario in all years except 2019, and Fusarium stalk rot (caused by Fusarium spp.) also greatly reduced yield. Tar spot (caused by Phyllachora maydis Maubl.), a relatively new disease in the United States, was estimated to cause substantial yield loss in 2018 and 2019 in several northern states. Gray leaf spot and southern rust (caused by Puccinia polysora Underw.) caused the most estimated yield losses in the southern United States. Unfavorable wet and delayed harvest conditions in 2018 resulted in an estimated 2.5 billion bushels (63.5 million metric tons) of grain contaminated with mycotoxins. The estimated mean economic loss due to reduced yield caused by corn diseases in the United States and Ontario from 2016 to 2019 was US$55.90 per acre (US$138.13 per hectare). Results from this survey provide scientists, corn breeders, government agencies, and educators with data to help inform and prioritize research, policy, and educational efforts in corn pathology and disease management.

Fusarium head blight (FHB) caused primarily by Fusarium graminearum, is a major disease of wheat in the United States. FHB is managed in part by applications of demethylation inhibitor (DMI) triazole fungicides during anthesis. The objective of this study was to examine the sensitivity of U.S. populations of F. graminearum to the DMI triazole fungicides metconazole and tebuconazole. Isolates of F. graminearum collected from wheat between 1981 and 2014 were tested for fungicide sensitivity using mycelial growth assays to determine the effective concentration at which 50% of fungal growth was inhibited (EC50). A total of 45 isolates were tested for metconazole sensitivity and 47 for sensitivity to tebuconazole. Isolates were analyzed in groups based on collection date. Groupings consisted of isolates collected prior to widespread fungicide use in wheat (designated as year 2000) or after fungicides became available for use in wheat. The mean EC50 for isolates collected prior to 2000 was 0.0240 µg/ml for metconazole and 0.1610 µg/ml for tebuconazole. For both fungicides, isolates collected between 2000 and 2014 had significantly higher (P = 0.05) mean EC50 values (mean EC50 = 0.0405 and 0.3311 µg/ml for metconazole and tebuconazole, respectively) compared with isolates collected prior to 2000. Isolate, year, and state of collection all affected the mean EC50 values of isolates collected between 2000 and 2014. A single isolate collected from Illinois in 2012 exhibited EC50 values of 0.1734 µg/ml for metconazole and 1.7339 µg/ml for tebuconazole, indicating reduced sensitivity compared with the mean EC50 of other isolates collected between 2000 and 2014. This study is the first step toward developing a fungicide sensitivity monitoring program for F. graminearum in the United States.

Fusarium graminearum is primarily understood as an agricultural pathogen affecting cereal crops, but its host range also includes diverse, noncultivated grasses ubiquitous across agricultural and natural environments. Wild grasses may select for the production of diverse toxin variants (chemotypes) and serve as reservoirs of genetic diversity or sources of disease-inciting inoculum. Populations at the intersection of wheat and wild grass communities were described using 909 isolates collected from wheat spikes, wild grass spikes, and overwintered wild grass stems found at natural and agricultural sites in regions of high and low crop production. Trichothecene (TRI) genotypes correlated to pathogen chemotype were predicted from two loci, and multilocus genotypes (MLGs) were determined using eight microsatellite loci. The genetic diversity of wild grass and wheat-derived populations was comparable, and their differentiation was low. Duplicate MLGs were rare even in samples collected from a single square meter, although they could be found in multiple hosts, environments, regions, and years. TRI genotype frequencies differed between region and land use. Admixture between TRI genotype-defined populations, which correspond to three previously described sympatric North American populations, was detected and was highest in a region with remote host communities and little agricultural production. Nonagricultural environments may maintain different pathogen TRI genotypes than wheat fields and provide an opportunity for recombination between isolates from different F. graminearum populations. A lack of structural barriers suggests that pathogen gene flow is uninhibited between wheat and wild grass communities, and the recovery of putative clones from multiple hosts and environments provides initial evidence that noncultivated grasses are a source of local and regional inoculum.

Switchgrass (Panicum virgatum L.) is a biomass candidate crop which has been improved for yield, but disease resistance development has largely been ignored. Bipolaris oryzae (Breda de Haan) Shoemaker can cause Bipolaris seed rot, reducing seedling establishment, and Bipolaris leaf spot, reducing biomass yield. In order to initiate a breeding program, heritability based on half-sib progenies of the disease resistance were conducted in 47 half-sib progenies of lowland ‘Kanlow’ and upland ‘Cave-in-Rock’. Test crosses of progenies from resistant and susceptible parents in upland ‘Shelter’ and Cave-in-Rock were conducted to determine genetic control of resistance to Bipolaris leaf spot. To breed for resistance to two diseases, two cycles of recurrent phenotypic selection were done separately in Shelter and Cave-in-Rock at 10% selection intensity. As a result, resistance to Bipolaris seed rot showed moderate to high heritability (0.33 ± 0.16 to 0.83 ± 0.09) in both individual- and half-sib-based computations, reflecting actual genetic gain (44.5–125.3%) from two cycles of selections. However, resistance to Bipolaris leaf spot showed non-significant heritability (0.02 ± 0.06 to 0.19 ± 0.19) and non-significant progress of selection for the trait. Results from test crosses suggested that the resistance was not controlled by R genes but possibly was quantitatively inherited by many alleles with small effects. Such a difference in the gains resulted in non-significant correlation between two resistances. Due to high progress in selection resistance to Bipolaris seed rot, the screening method for resistance can be integrated to existing breeding programs.

In addition to causing disease in wheat and other grain crops, Fusarium graminearum is associated with a wide range of forage, weedy and non-cultivated gramineous species.. The nature of these asso...

Fusarium graminearum is ranked among the five most destructive fungal pathogens that affect agroecosystems. It causes floral diseases in small grain cereals including wheat, barley, and oats, as well as maize and rice. We conducted a systematic review of peer-reviewed studies reporting species within the F. graminearum species complex (FGSC) and created two main data tables. The first contained summarized data from the articles including bibliographic, geographic, methodological (ID methods), host of origin and species, while the second data table contains information about the described strains such as publication, isolate code(s), host/substrate, year of isolation, geographical coordinates, species and trichothecene genotype. Analyses of the bibliographic data obtained from 123 publications from 2000 to 2021 by 498 unique authors and published in 40 journals are summarized. We describe the frequency of species and chemotypes for 16,274 strains for which geographical information was available, either provided as raw data or extracted from the publications, and sampled across six continents and 32 countries. The database and interactive interface are publicly available, allowing for searches, summarization, and mapping of strains according to several criteria including article, country, host, species and trichothecene genotype. The database will be updated as new articles are published and should be useful for guiding future surveys and exploring factors associated with species distribution such as climate and land use. Authors are encouraged to submit data at the strain level to the database, which is accessible at https://fgsc.netlify.app .

Many of the major stem rust resistance genes deployed in commercial wheat (Triticum spp.) cultivars and breeding lines become ineffective over time because of the continuous emergence of virulent races. A genome‐wide association study (GWAS) was conducted using 26,439 single nucleotide polymorphism (SNP) markers and 280 durum wheat [Triticum turgidum L. subsp. Durum (Desf.) Husnot] lines from CIMMYT to identify genomic regions associated with seedling resistance to races TTKSK, TKTTF, JRCQC, and TTRTF and field resistance to TKTTF and JRCQC. The phenotypic data analysis across environments revealed 61–91 and 59–77% of phenotypic variation was explained by the genotypic component for seedling and adult plant response of lines, respectively. For seedling resistance, mixed linear model (MLM) identified eight novel and nine previously reported quantitative trait loci (QTL) while a fixed and random model circulating probability unification (FarmCPU) detected 12 novel and eight previously reported QTL. For field resistance, MLM identified 12 novel and seven previously reported loci while FarmCPU identified seven novel and nine previously reported loci. The regions of Sr7a, Sr8155B1, Sr11, alleles of Sr13, Sr17, Sr22/Sr25, and Sr49 were identified. Novel loci on chromosomes 3B, 4A, 6A, 6B, 7A, and 7B could be used as sources of resistance to the races virulent on durum wheat. Two large‐effect markers on chromosome 6A could potentially be used to differentiate resistant haplotypes of Sr13 (R1 and R3). Allelism tests for Sr13, breaking the deleterious effect associated with Sr22/Sr25 and retaining the resistance allele at the Sr49 locus, are needed to protect future varieties from emerging races.

Scientific communication is facilitated by a data-driven, scientifically sound taxonomy that considers the end-user's needs and established successful practice. In 2013, the

Pathogens play an important role in the evolution of plant populations, but genetic mechanisms underlying disease resistance may differ greatly between geographic areas as well as over time. Local adaptation is thought to be an important step in plant evolution, and may be impacted by differential pathogen pressures in concert with abiotic factors. This study uses locally adapted ecotypes of the native perennial switchgrass (Panicum virgatum) to examine the temporal and spatial variation in the genetic architecture of resistance to fungal pathogens, namely switchgrass leaf rust (Puccinia novopanici). To identify loci underlying variation in pathogen resistance in switchgrass, we scored rust damage across an outcrossed mapping population at eight locations across the central United States from southern Texas to Michigan. We followed rust progression at these sites for three years and mapped quantitative trait loci (QTLs) using function-valued transformations of rust progression curves. Overall, we mapped 51 QTLs that varied in presence and strength over the three-year period. Two large-effect QTLs were consistently associated with variation in rust progression in multiple sites and years, and are therefore potentially the result of the same underlying resistance genes. Interestingly, these two large-effect QTLs were almost exclusively detected in northern sites. This pattern could be caused by geographic difference in genetic architecture. The distribution of rust strains or variation in climatic conditions across the field sites could result in genotype-by-environment interactions in efficacy of rust resistance loci. Beyond reducing rust damage by 34%, the beneficial alleles at the two loci also increased biomass by 44%, suggesting a direct benefit by pleiotropy or indirect benefit through genetic linkage. Our results suggest an important role for fungal pathogens in the local adaptation of switchgrass and illustrate an influential geographic component of the genetic architecture of plant disease resistance.

The main techniques for minimizing Fusarium head blight (FHB, or scab) and deoxynivalenol in wheat and barley are well established and generally available: planting of moderately FHB-resistant cultivars, risk monitoring, and timely use of the most effective fungicides. Yet the adoption of these techniques remains uneven across the FHB-prone portions of the U.S. cereal production area. A national survey was undertaken by the U.S. Wheat and Barley Scab Initiative in 17 states where six market classes of wheat and barley are grown. In 2014, 5,107 usable responses were obtained. The highest percentages reporting losses attributable to FHB in the previous 5 years were in North Dakota, Maryland, Kentucky, and states bordering the Great Lakes but across all states, ≥75% of respondents reported no FHB-related losses in the previous 5 years. Adoption of cultivar resistance was uneven by state and market class and was low except among hard red spring wheat growers. In 13 states, a majority of respondents had not applied an FHB-targeted fungicide in the previous 5 years. Although the primary FHB information source varied by state, crop consultants were considered to be an important source or their primary source of information on risk or management of FHB by the largest percentage of respondents. Use of an FHB risk forecasting website was about twice as high in North Dakota as the 17-state average of 6%. The most frequently cited barriers to adopting FHB management practices were weather or logistics preventing timely fungicide application, difficulty in determining flowering timing for fungicide applications, and the impracticality of FHB-reducing rotations. The results highlight the challenges of managing an episodically damaging crop disease and point to specific areas for improvement.

Field trials were conducted in 17 U.S. states to evaluate the effects of quinone outside inhibitor (QoI) and demethylation inhibitor (DMI) fungicide programs on Fusarium head blight index (IND) and deoxynivalenol (DON) toxin in wheat. Four DMI-only treatments applied at Feekes 10.5.1, five QoI-only treatments applied between Feekes 9 or Feekes 10.5, three QoI+DMI mixtures applied at Feekes 10.5, and three treatments consisting of a QoI at Feekes 9 followed by a DMI at Feekes 10.5.1 were evaluated. Network meta-analytical models were fitted to log-transformed mean IND and DON data and estimated contrasts of log means were used to obtain estimates of mean percent controls relative to the nontreated check as measures of efficacy. Results from the meta-analyses were also used to assess the risk of DON increase in future trials. DMI at Feekes 10.5.1 were the most effective programs against IND and DON and the least likely to increase DON in future trials. QoI-only programs increased mean DON over the nontreated checks and were the most likely to do so in future trials, particularly when applied at Feekes 10.5. The effects of QoI+DMI combinations depended on the active ingredients and whether the two were applied as a mixture at heading or sequentially. Following a Feekes 9 QoI application with a Feekes 10.5.1 application of a DMI reduced the negative effect of the QoI on DON but was not sufficient to achieve the efficacy of the Feekes 10.5.1 DMI-only treatments. Our results suggest that one must be prudent when using QoI treatments under moderate to high risk of FHB, particularly where the QoI is used without an effective DMI applied in combination or in sequence.

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.

Seed of soft white winter wheat collected from New York regional cultivar trials in 1995 and 1996 were assayed on an agar medium selective for Stagonospora nodorum. Incidence of seed infection varied with production environment. Relative incidence of seed infection differed significantly among cultivars and was consistent across environments. The flag leaves and ears of 12 cultivars were inoculated quantitatively at flowering in a glasshouse. Cultivars did not differ significantly in disease on the flag leaves. Incidence of seed infection for all cultivars was above 60%, but was significantly lower in Delaware and Houser than in other cultivars. Results confirm that wheat cultivars differ in their relative susceptibility to seed infection by S. nodorum. Resistance in wheat to seed infection by S. nodorum may be a useful mechanism for reducing initial inoculum in areas where infected seed is considered the primary inoculum source for Stagonospora nodorum blotch.

Soilborne wheat mosaic virus (SBWMV) was detected in New York in 1998 for the first time and has been associated with yield loss where identified. We assessed 115 regionally adapted small grains genotypes for resistance to SBWMV over four growing seasons. Resistance to SBWMV reduces the percentage of plants that develop detectable viral titer and symptoms. Logistic regression was used to analyze disease incidence data and was compared with a general linear model for categorizing relative resistance to SBWMV. Logistic regression facilitated assessment of the effects of small sample size, low disease incidence, and nonuniform disease distribution. By increasing sample size from 20 to 30 stems per replicate, the number of resistance categories was increased through improved resolution of intermediate resistance classes. In environments with low disease incidence, the number of genotypes categorized as susceptible decreased while intermediate genotypes appeared to be resistant in the analysis. Inclusion of disease distribution data as covariates in a spatially balanced experiment did not increase the power of the logistic analysis. No genotype assessed in multiple years was immune to infection. However, 41 of the regionally adapted genotypes tested repeatedly expressed strong resistance to SBWMV, providing growers a choice of cultivars resistant to SBWMV.

We report brown root rot (BRR) of alfalfa, caused by the fungal pathogen Phoma sclerotioides, for the first time in the eastern United States. Alfalfa production fields in New York, Vermont, and New Hampshire were sampled in spring 2005, and soil characteristics were related to variability in BRR incidence and severity in two New York fields sampled extensively. BRR was detected in 8 of 10 fields sampled in New York, 6 of 7 fields sampled in Vermont, and 5 of 6 fields sampled in New Hampshire. Lesions on both roots and crowns were common in all three states, and most BRR lesions extended into the cortical tissues. Diagnostic polymerase chain reaction (PCR) of P. sclerotioides isolates produced a single amplicon of the expected size. In vivo conidia and pycnidia morphology of northeastern isolates was consistent with published descriptions of P. sclerotioides, and P. sclerotioides was reisolated from symptomatic lesions after pathogenicity testing. In two New York fields sampled extensively, BRR severity varied with soil strength, soil texture, soil saturation, and alfalfa stand density. The spatial pattern of BRR within fields suggests the pathogen was not recently introduced. The results suggest BRR is widespread in alfalfa production fields in New York, Vermont, and New Hampshire.

Brown root rot (BRR), caused by the fungal pathogen Phoma sclerotioides G. Preuss ex Sacc. (synonym Plenodomus meliloti Dearn. & G.B. Sanford), is associated with winterkill, slow emergence from winter dormancy, and yield loss of alfalfa (Medicago sativa L.) (1,2). BRR is a problem in regions with severe winters and is common in Alaska and Alberta, Saskatchewan and Manitoba, Canada. It was first observed in the continental United States in Wyoming during 1996 (2) and has subsequently been found in Idaho, Minnesota, Montana, New Hampshire, New York, Vermont, and Wisconsin. In the intermountain valleys of northern New Mexico and western Colorado, winters can be severe; alfalfa winterkill events occur periodically, but it is unknown if BRR is present. In May 2006, alfalfa plants were collected from production fields in Huerfano, Otero, and Rio Grande counties in Colorado and Rio Arriba and Taos counties in New Mexico and assessed for BRR. Two to three fields were sampled per county and 20 or 40 plants were collected per field. All fields existed for at least two winters. Fields sampled in Rio Grande County exhibited severe winterkill, with most plants completely girdled by crown lesions. Plants from other fields exhibited a range of root and crown rots. Isolation of P. sclerotioides was attempted from all plants with a previously described protocol (4). The pathogen was isolated from crown lesions of one alfalfa plant each from Rio Grande and Taos counties. Both lesions extended into the cortex. On potato dextrose agar and water agar with barley (4), single-conidium cultures of each isolate produced large pycnidia (0.35 to 0.80 mm in diameter) with multiple beaks, white cirri darkening to yellow with age, and unicellular, hyaline, ovoid conidia 5 to 7 μm long by 2 μm wide. Diagnostic PCR of the cultures using P. sclerotioides-specific primers (3) resulted in a single amplicon of expected size (500 bp). The internal transcribed spacer (ITS) 1, 5.8S, and ITS2 of the rDNA were amplified and sequenced using primers ITS1 and ITS4. The ITS sequences (GenBank Accession Nos. EU265669 and EU265670) were >98% identical to P. sclerotioides ATCC isolate 56515 over 503 bp of aligned sequence. Potted ‘Vernal’ alfalfa was inoculated 4 months after seeding, kept at 4°C for 5.5 weeks, 0 to –2°C for 12 weeks, and 4°C for 3 weeks. Of the 14 plants inoculated with the Colorado isolate, 11 developed cortical lesions and 8 winterkilled. Of the 23 plants inoculated with the New Mexico isolate, 22 developed cortical lesions and 16 winterkilled. Lesions were light to very dark brown, sometimes with a darker border and often containing abundant pycnidia. Winterkill was associated with lesions girdling the crown. P. sclerotioides was isolated from the lesions. To our knowledge, this is the southernmost report of BRR in North America and the first report of BRR in New Mexico and Colorado. The incidence and severity of BRR in the region surveyed appear to be considerably lower than in the more northern regions. References: (1) B. Berkenkamp et al. Can. J. Plant Sci. 71:211, 1991. (2) C. R. Hollingsworth et al. Can. J. Plant Pathol. 25:215, 2003. (3) R. C. Larsen et al. Plant Dis. 86:928, 2002. (4) M. J. Wunsch et al. Plant Dis. 91:1293, 2007.

Knowledge of the movement of Gibberella zeae (Fusarium graminearum) from a local source of inoculum in infested cereal debris is critical to the management of Fusarium head blight (FHB) of wheat. Previous spatial dissemination and infection studies were unable to completely distinguish the contributions of released inocula from those of background inocula. Clones of G. zeae were released and recaptured in five wheat fields in New York and Virginia in 2007 and 2008. Amplified fragment length polymorphisms were used to track and unambiguously identify the released clones in heterogeneous populations of the fungus recovered from infected wheat spikes collected at 0, 3, 6, and ≥24 m from small-area sources of infested corn residues. The percent recovery of the released clones decreased significantly at fairly short distances from the inoculum sources. Isolates of G. zeae recovered at 0, 3, 6, and ≥24 m from the center of source areas shared 65, 19, 13, and 5% of the genotypes of the released clones, respectively. More importantly, the incidence of spike infection attributable to released clones averaged 15, 2, 1, and

Indiangrass or yellow indiangrass (Sorghastrum nutans L.) is a warm-season, perennial grass grown for livestock forage, erosion control, wildlife food and cover, landscaping, and more recently, as a biofuel crop. In August of 2007, foliar lesions were observed on plants within mature stands of a number of cultivars and populations of indiangrass at the USDA-NRCS Plant Materials Center in Big Flats (Chemung County), NY. In subsequent years, similar lesions were observed in both mature and immature (less than 3 years old) stands of indiangrass in Chemung and Tompkins counties. Lesions were elliptical to irregular with distinct or diffuse purple margins often surrounded by tan-to-maroon halos and were sometimes observed on the leaf sheath and stem. Lesions were generally less than 2 cm long, approximately 2 mm wide, and often coalesced when disease was severe. Centers became necrotic and often developed numerous acervuli with black setae. After 2 to 5 days of incubation in moist chambers, symptomatic leaf tissue developed acervuli containing masses of cream-colored spores. Spores streaked onto potato dextrose agar containing streptomycin gave rise to cultures with gray mycelium often accompanied by sporulating avervuli. The fungus was identified as Colletotrichum caudatum (Peck ex Sacc.) Peck on the basis of cultural characteristics and conidial morphology (2). Conidia were one celled, hyaline, fusiform, and falcate with a filiform, caudate appendage. Conidial length averaged 28 μm (21 to 45 μm), width averaged 5 μm (4 to 6 μm), and the appendage averaged 15 μm (5 to 29 μm) long. The sequence of the rDNA internal transcribed spacer (ITS) regions of an isolate from ‘Rumsey’ indiangrass in Chemung County, NY (Cc004NY07, GenBank Accession No. JF437056) exhibited 98% nucleotide identity to C. caudatum isolates (GenBank Accession Nos. AB042304 and AB042305) collected from bentgrass (Agrostis sp. L.) and cogongrass (Imperata cylindrica L.) in Japan (1). Colletotrichum species from grasses are not discriminated solely on ITS sequence, but the unique caudate appendage is diagnostic of C. caudatum. Pathogenicity of the sequenced isolate plus a second isolate from ‘Rumsey’ indiangrass (Cc006NY07) was evaluated in greenhouse experiments. Eight-week-old plants of indiangrass population ‘PA Ecotype’ (Ernst Conservation Seeds, Meadville, PA) were inoculated with conidial suspensions (2 × 106 conidia/ml) of C. caudatum. Twelve plants were sprayed with either inoculum or sterile water (as the control treatment) until runoff with a spray bottle. After inoculum had dried, plants were placed in a mist chamber for 48 h. Plants were then returned to the greenhouse and observed for disease development, which occurred within 1 week of inoculation. No symptoms developed on the control plants. Foliar lesions closely resembled those observed in the field. C. caudatum was reisolated consistently from symptomatic tissue collected from greenhouse experiments. To our knowledge, this is the first report of C. caudatum causing anthracnose on indiangrass in New York, though it has been reported in the adjoining states of New Jersey (2) and Pennsylvania (3). Indiangrass cultivars should be assessed for susceptibility to regional isolates of C. caudatum prior to expanded regional production of indiangrass as a biofuel crop. References: (1) J. Moriwaki et al. J. Gen. Plant Pathol. 68:307, 2002. (2) T. R. Nag Raj. Can. J. Bot. 51:2463, 1973. (3) K. E. Zeiders. Plant Dis. 71:348, 1987.

Switchgrass (Panicum virgatum L.) is a perennial grass with biofuel potential. From 2007 to 2010, foliar lesions were observed on first year and mature stands of switchgrass in various locations in New York. Foliar lesions were purple, elliptical (up to 1 cm) with either distinct or diffuse margins, and occasionally with yellow halos and/or white necrotic centers. After 2 to 5 days of moist chamber incubation, surface-sterilized, symptomatic leaf tissue produced conidia that when streaked onto potato dextrose agar containing 0.3 g of streptomycin per liter gave rise to cultures with gray-to-black mycelium that developed brown conidia. The fungus was identified as Bipolaris oryzae (Breda de Haan) Shoemaker on the basis of conidial morphology (1,2). Conidiophores were brown, straight, cylindrical, and multiseptate. Conidia were brown, curved, ellipsoidal tapering to rounded ends, with 3 to 14 septa. Conidia averaged 105 μm (54 to 160 μm) long and 16 μm (12 to 20 μm) wide. Sequences of the glyceraldehyde-3-phosphate dehydrogenase (GDP) gene of three isolates from Tompkins County (Cornell Accession and corresponding GenBank Nos.: Bo005NY07 [cv. Cave-in-Rock], JF521648; Bo006NY07 [cv. Kanlow], JF521649; and Bo038NY07 [cv. Shawnee], JF521650) exhibited 100% nucleotide identity to B. oryzae isolates (GenBank Nos. AY277282–AY277285) collected from switchgrass in North Dakota (1). Sequences of the rDNA internal transcribed spacer (ITS) regions of the isolates (Cornell Accession and corresponding GenBank Nos.: Bo005NY07, JF693908; Bo006NY07, JF693909; and Bo038NY07, JF693910) exhibited 100% nucleotide identity to B. oryzae isolates (GenBank Nos. GU222690–GU222693) collected from switchgrass in Mississippi (3). Pathogenicity of two of the sequenced isolates (Bo006NY07 and Bo038NY07) along with one other isolate (Bo116NY09 from ‘Cave-in-Rock’ in Cayuga County) was evaluated in the greenhouse. Six- to eight-week-old switchgrass plants were inoculated with conidial suspensions (40,000 conidia/ml) of B. oryzae. Inoculum or sterilized water was applied until runoff. There were three plants per treatment of each of ‘Blackwell’, ‘Carthage’, ‘Cave-in-Rock’, ‘Kanlow’, ‘Shawnee’, ‘Shelter’, and ‘Sunburst’. After inoculum had dried, plants were placed in a mist chamber for 24 h and then returned to the greenhouse. Symptoms developed 2 to 4 days after inoculation for all cultivars. No symptoms developed on the control plants. Foliar lesions closely resembled those observed in the field. B. oryzae was consistently reisolated from symptomatic tissue collected from greenhouse experiments. B. oryzae was first reported as a pathogen of switchgrass in North Dakota (1) and more recently in Mississippi (3). To our knowledge, this is the first report of B. oryzae causing a leaf spot on switchgrass in New York. Observation of severe leaf spot in several field plots suggests that switchgrass populations should be screened for their reaction to regional isolates of B. oryzae prior to expanded production of switchgrass as a biofuel crop. References: (1) J. M. Krupinsky et al. Can. J. Plant Pathol. 26:371 2004. (2) R. A. Shoemaker. Can. J. Bot. 37:883, 1959. (3) M. Tomaso-Peterson and C. J. Balbalian. Plant Dis. 94:643 2010.

Switchgrass (Panicum virgatum L.) is a native perennial grass with potential as a biofuel crop. The smut fungus, Tilletia maclaganii (Berk.) Clint., is associated with significant biomass reduction in switchgrass in the Midwest (4), but has not been reported in the northeast United States in more than 60 years (New York in 1890 and Pennsylvania in 1946) (2,3). From 2007 to 2010, smutted panicles were observed on the majority of plants in stands of several switchgrass cultivars at the USDA-NRCS Plant Materials Center in Big Flats (Chemung County), NY; in production fields of several switchgrass cultivars near Meadville (Crawford County), PA; and in an ornamental bed of switchgrass in Ithaca (Tompkins County), NY. Smutted panicles emerged 3 to 4 weeks prior to healthy panicles, had a compact, club-shaped appearance, and enlarged florets with swollen ovaries that readily released a powdery mass of odorless, rusty orange-to-dark brown teliospores when pinched. The entire caryopsis of every floret within a panicle was smutted and the infected plants appeared stunted, indicative of systemic infection. The fungus from each location was identified as T. maclaganii based on host, habit, and teliospore morphology (3). Teliospores were pale yellowish brown to reddish brown, varied from globose to slightly irregular in shape, and averaged 21 μm (18 to 25 μm) in diameter. The exospore was thick (2 to 3 μm), finely verrucose, and no sheath was present. True sterile cells, pale yellow and 10 to 18 μm in diameter, were sparsely present. Teliospores germinated and formed large (40 to 60 × 3 to 6 μm), nonconjugating basidiospores within 20 h on 2% water agar (WA). Occasionally, we also found the floret-infecting species T. pulcherrima (1) on switchgrass at very low incidence in Big Flats, NY, but it was easily distinguished from T. maclaganii. Stratified seeds (3 g) of ‘Shelter’, washed and found to be free of teliospores, were dusted with 0.04 g of teliospores of T. maclaganii isolate Tm001NY09 (Cornell Plant Pathology Herbarium Accession CUP-67931) harvested from infected ‘Shelter’ in Big Flats, NY in 2009. Inoculated and noninoculated seeds were sown in seedling trays, transplanted, and evaluated at panicle emergence. There were no symptoms on plants from noninoculated seeds. Symptoms on inoculated plants were consistent with field observations and teliospores were reisolated from infected panicles and cultured on 2% WA. Teliospores harvested from a single panicle infected with Tm001NY09 were used for culturing and DNA extraction. The fully annotated sequence of the rDNA internal transcribed spacer and 5.8S regions of this isolate were deposited in GenBank (Accession No. JF745116). Smut outbreaks in New York and Pennsylvania suggest that T. maclaganii must be managed effectively if switchgrass production is to be sustainable in the Northeast. References: (1) L. M. Carris et al. Plant Dis. 92:1707, 2008. (2) R. Durán and G. W. Fischer. The Genus Tilletia. Washington State University, Pullman, WA, 1961. (3) D. F. Farr and A. Y. Rossman. Fungal Databases. Systematic Mycology and Microbiology Laboratory, ARS, USDA. Retrieved from http://nt.ars-grin.gov/fungaldatabases/ , May 3, 2011 (4) P. M. Thomsen et al. Online publication. doi:10.1094/PHP-2008-0317-01-RS. Plant Health Progress, 2008.

Switchgrass (Panicum virgatum L.) is a perennial grass with significant potential as a biofuel crop. From 2007 to 2010, foliar lesions were observed in new and mature stands of switchgrass in various locations in New York. Lesions were elliptical with purple margins and white necrotic centers, generally 20-year-old naturalized stand of switchgrass in Steuben County), JF437053; Cn080NY08 (from ‘Pathfinder’ in Chemung County), JF437054; and Cn101NY09 (from ‘Blackwell’ in Chemung County), JF437055) exhibited 100% nucleotide identity to the type isolate of C. nativas (GenBank No. GQ919068) collected from switchgrass selection ‘Brooklyn’ in New Jersey (1). Pathogenicity of the sequenced isolates along with seven other isolates (Cn105NY09 from ‘Sunburst’ in Tompkins County; Cn107NY09 from ‘Trailblazer’ in Tompkins County; Cn109NY09 from ‘Forestburg’ in Tompkins County; Cn111NY09 and Cn112NY09 from ‘Shelter’ in Tompkins County; and Cn122NY09 and Cn123NY09 from ‘Cave-in-Rock’ in Genesee County) was evaluated in greenhouse experiments. Seven- to eight-week-old switchgrass plants were inoculated with conidial suspensions (1 × 106 conidia/ml) of C. nativas. Inoculum or sterilized water was sprayed until runoff. Three plants of each of ‘Cave-in-Rock’ and ‘Kanlow’ were sprayed per treatment and the experiment was repeated for 3 of the 10 isolates. Inoculated plants were placed in a mist chamber for 48 h before they were returned to the greenhouse and observed for disease development, which occurred within 1 week of inoculation for both cultivars. No symptoms developed on the control plants. Foliar lesions closely resembled those observed in the field. C. nativas was consistently reisolated from symptomatic tissue collected from greenhouse experiments. Switchgrass anthracnose associated with C. graminicola sensu lata has been reported in many U.S. states (2). On the basis of molecular phylogenetics and distinguishing morphological characters, Crouch et al. erected C. navitas as a novel species distinct from C. graminicola sensu stricto, a taxon restricted to the corn anthracnose pathogen (1). C. nativas was first documented on switchgrass in New Jersey (1) and appears to be the same pathogen causing anthracnose of switchgrass in the adjoining state of Pennsylvania (1,3). To our knowledge, this is the first report of C. nativas causing anthracnose of switchgrass in New York. References: (1) J. A. Crouch et al. Mycol. Res. 113:1411, 2009. (2) D. F. Farr and A. Y. Rossman. Fungal Databases, Systematic Mycology and Microbiology Laboratory, ARS, USDA. Retrieved from http://nt.ars-grin.gov/fungaldatabases/ , May 5, 2011. (3) M. A. Sanderson et al. Agron. J. 100:510, 2008.

Wheat and barley are critical food and feed crops around the world. Wheat is grown on more land area worldwide than any other crop. In the United States, production of wheat and barley contributes to domestic food and feed use, and contributes to the export market and balance of trade. Fifteen years ago, Plant Disease published a feature article titled “Scab of wheat and barley: A re-emerging disease of devastating impact”. That article described the series of severe Fusarium head blight (FHB) epidemics that occurred in the United States and Canada, primarily from 1991 through 1996, with emphasis on the unparalleled economic and sociological impacts caused by the 1993 FHB epidemic in spring grains in the Northern Great Plains region. Earlier publications had dealt with the scope and damage caused by this disease in the United States, Canada, Europe, and China. Reviews published after 1997 further described this disease and its impact on North American grain production in the 1990s. This article reviews the disease and documents the information on U.S. FHB epidemics since 1997. The primary goal of this article is to summarize a sustained, coordinated, and collaborative research program that was put in place shortly after the 1993 epidemic, a program intended to quickly lead to improved management strategies and outreach implementation. This program serves as a model to deal with other emerging plant disease threats.