Cochliobolus sativus, the causal agent of spot blotch, poses a major challenge for barley producers in western Canada, causing significant yield losses under favourable conditions. Spot blotch management in this region increasingly relies on fungicides to protect grain yield and quality; however, repeated use can increase the risk of developing insensitivity. In this study, single-spore isolates of C. sativus collected from barley leaf samples in Alberta, Saskatchewan, and Manitoba between 2018-2021 were evaluated for sensitivity to propiconazole, fluxapyroxad, and pyraclostrobin. The mean concentrations required to inhibit fungal growth by 50% (EC50) were determined to be 0.5 mg L-1 for propiconazole, 0.08 mg L-1 for fluxapyroxad, and 0.003 mg L-1 for pyraclostrobin. The sensitivity of 105, 103, and 101 isolates to propiconazole, fluxapyroxad, and pyraclostrobin, respectively, was then evaluated using discriminatory doses. Growth inhibition ranged from 71.7-98.1% for propiconazole, 58.0-100% for fluxapyroxad, and 73.6-100% for pyraclostrobin. Although none of the isolates exhibited complete insensitivity to any of the fungicides tested, 6% displayed intermediate sensitivity (30-70% growth inhibition) to fluxapyroxad. However, those isolates showed clear dose-dependent inhibition at higher fluxapyroxad concentrations, confirming that they remained largely sensitive. Overall, the data provide no evidence of a consistent, population-wide shift in the sensitivity of C. sativus isolates to the fungicides evaluated during the study period. In addition, this study represents the first systematic assessment of sensitivity to propiconazole, fluxapyroxad, and pyraclostrobin in the current western Canadian C. sativus population, providing valuable baseline data for future monitoring and fungicide stewardship.

Spot blotch, caused by Cochliobolus sativus, is a major disease of barley in western Canada. Understanding the virulence diversity of C. sativus is essential for deployment of host resistance. In this study, 49 C. sativus isolates were evaluated on 12 barley differential host genotypes and classified into nine virulence groups (VGs) based on host responses. The three most prevalent VGs (0.0.0.0, 5.7.0.0 and 5.7.0.4) accounted for 67% of the isolates, and five novel VGs were identified. Classification using the North Dakota differential system revealed a high prevalence of pathotype 1 (50%) and the emergence of pathotype 3 (28%), consistent with increased cultivation of two-row, 'Bowman'-derived barley cultivars that are more susceptible to this pathotype. No correlation was observed between isolate virulence and geographic origin. Hierarchical clustering supported the VG classifications, revealing four major clusters aligned with infection response (IR) patterns and host genotype specificity. Virulence groups causing severe spot blotch exhibited high regression coefficients, reflecting a greater increase in IR on susceptible hosts, whereas VG 0.0.0.0 consistently showed low coefficients and caused only mild symptoms across all hosts. Regression analyses indicated that several six-row (e.g. ND B112, 'Robust', 'Stander') and some two-row genotypes (TR 251) maintained relatively durable resistance, whereas other two-row genotypes, including 'Bowman' and its derivatives, exhibited greater variability in susceptibility. These findings suggest that host selection pressure may be contributing to shifts in the distribution of virulence phenotypes within the C. sativus population, underscoring the importance of ongoing pathogen monitoring and strategic resistance gene deployment.

Abstract Puccinia triticina Eriks. (Pt) is a basidiomycete fungal pathogen causing wheat leaf rust, a significant global threat to wheat production, leading to substantial yield losses in susceptible cultivars. Traditional management strategies, including planting resistant cultivars and deploying fungicides, are increasingly challenged by this pathogen’s rapid evolution and emergence of new virulent races. Recent interest has focused on mycoviruses, viruses that infect fungi, for their potential roles in biological control and influencing fungal population dynamics. This study investigates the virome of 117 Pt isolates collected across Canada when inoculated onto the susceptible wheat cultivar Thatcher. The total RNA was isolated from infected leaf tissues and metatranscriptome analysis followed by manual filtering steps revealed 37 unique viral species at the amino-acid (AA) level with the identity ranging from 30.4% to 100% across 6 viral families and unclassified viruses. High-throughput sequencing and RT-PCR amplification from germinated urediniospores mats confirmed the presence of putative mycoviruses, which could provide insights into their impact on the biology and epidemiology of Pt. Additionally, among the 37 viral species, we describe 17 novel viruses with high divergence based on the amino acid similarity from known viral species. This study reveals a diverse virome associated with P. triticina across Canada, highlighting the potential influence of mycoviruses on the pathogen’s biology, evolution, and epidemiology. This represents the first step toward opening new avenues for innovative management strategies against wheat leaf rust.

Fusarium poae has emerged as a predominant Fusarium species affecting barley and oats in Canada. Despite its widespread occurrence and ability to produce multiple mycotoxins, its population genetics remain poorly understood. In this study, we used restriction site-associated DNA sequencing (RADseq) to characterize the population structure and genomic diversity of F. poae isolates collected from four regions of Canada. A total of 1059 high-quality single-nucleotide polymorphisms (SNPs) were generated. Principal coordinate and phylogenetic analyses revealed a hierarchical population structure consisting of two major genetic groups (Group I and Group II), with Group II further divided into two subgroups (IIa and IIb). Subgroup IIa represented a distinct lineage marked by reduced nucleotide diversity, negative Tajima's D values and elevated genome-wide linkage disequilibrium. Analysis of molecular variance showed that most genetic variation (63%) occurs within genetic groups, with 37% attributable to differences among groups. In contrast, when populations were partitioned by geographic region, only 3% of the variation was explained by differences among regions. Although regional differentiation was weak, it was statistically significant, reflecting shifts in the relative frequencies of genetic groups across regions. All genetic groups and regions exhibited significant multilocus linkage disequilibrium, indicating predominantly clonal reproduction in the field. Together, these findings reveal substantial genomic diversity of F. poae and highlight the emergence of a genetically distinct lineage within Group II. This study provides a genomic foundation for future investigations into the pathogenicity and mycotoxin production associated with F. poae in Canadian cereal production.

Fusarium head blight is a limitation to grain production and can be caused by several different Fusarium species. We evaluated the ability of matrix-assisted laser desorption/ionization time of flight mass spectrometry (MALDI-TOF MS) to perform species identifications. The method generates a unique peptide mass fingerprint (PMF) for each sample that can be matched to a reference library. We first created a reference library of PMF profiles for Fusarium species from across Canada. Then, we tested the library to perform identifications using two validation panels. The first panel consisted of 820 fungal isolates from wheat (2021-2023 harvest years) and the second was 74 fungal isolates from oat and barley (2022 harvest year). The species identity of samples from the validation panels was confirmed with high-throughput quantitative PCR using species-specific DNA markers. The first validation panel was mostly F. graminearum and there was 95% overlap between the MALDI-TOF MS and DNA-based identifications. The second panel was mostly F. poae and the identifications from the two methods had 86% overlap. Our findings indicate that MALDI-TOF MS biotyping is sensitive enough to identify Fusarium strains to their species complexes and certain Fusarium strains to the species level.

Genome mining of fungal plant pathogens has uncovered biosynthetic gene clusters encoded on lineage-specific accessory chromosomes, revealing untapped potential for novel natural product discovery by metabolomic assessment of fungal populations. In Fusarium poae, a species contributing to Fusarium head blight on cereals, whole-genome sequencing and comparative metabolomics identified an accessory chromosome-associated biosynthetic gene cluster responsible for the production of a novel family of secondary metabolites, the fusadapamides. These linear tripeptides contain l-2,3-diaminopropionic acid (l-Dap), a rare nonproteinogenic amino acid not previously reported in fungi. Biochemical and genetic analyses revealed that F. poae synthesizes l-Dap via an accessory chromosome-encoded two-gene module that uniquely utilizes l-alanine as a substrate, diverging from known bacterial and plant l-Dap biosynthesis pathways. While fusadapamide production appears limited within Fusarium, homologous l-Dap biosynthetic modules were identified across diverse ascomycetes, suggesting a broader role in fungal secondary metabolism. This study highlights the power of using untargeted metabolomics at population-scale to uncover accessory chromosome-linked biosynthetic innovations and expands our understanding of fungal natural product biosynthesis.

Most soybeans’ (Glycine max L.) yield losses around the world are attributable to soil-borne diseases caused by pathogenic fungal species such as those from the genus Fusarium. When studying infection processes of soil-borne plant pathogens, maintaining consistency and effectiveness of disease assessment based on the visual estimation of host resistance is often challenging. To standardize the inoculation protocol, we studied Fusarium root rot (FRR) infection on soybean plants using three Fusarium species (F. graminearum, F. avenaceum and F. poae) and four different inoculation methods (i) root dipping, (ii) soil-conidia, (iii) cornmeal-soil, and (iv) mycelial plugs. The most efficient method to infect soybean plant roots with the tested Fusarium species and to observe the infection process was by using the cornmeal-soil method. After inoculation, seedlings were assessed at the V3 stage for root rot symptoms as well as for the effects of infection on root length, root weight, and shoot height. In parallel, Fusarium colonization was monitored using polymerase chain reaction (PCR). A significant difference in final disease ratings was observed when comparing the tested methods. The cornmeal-soil-conidia method was the most efficient in inducing soybean root rot disease in response to inoculation with the three tested Fusarium species. This optimized inoculation protocol will allow more consistency for soybean-pathogen interaction studies, such as early plant responses to soil-borne fungi, which will also contribute to more standardized methods aimed at developing new management strategies for soil-borne diseases of soybean.

AAC Malcolm is a hulless, six-row spring barley (Hordeum vulgare L.) cultivar adapted to the growing conditions of eastern Canada. It was evaluated in the Ontario Barley Orthogonal Test (2018–2020) before being registered in Canada in 2023. AAC Malcolm is high-yielding and good lodging resistance. AAC Malcolm is recommended for commercial production in eastern Canada.

Abstract The obligate fungal pathogen Puccinia triticina causes leaf rust symptoms on wheat worldwide. Epidemics of leaf rust occur during periods of mild weather with high relative humidity. The pathogen infects leaves, causing orange to red pustules, containing millions of urediniospores, reducing the photosynthetic area and causing desiccation and yield loss. Wind-borne urediniospores are produced in continuous asexual cycles on wheat plants. Genetic resistance is the primary control strategy. There are over 80 known leaf rust ( Lr ) resistance genes, and most are race-specific and are active from the seedling stage to maturity. A few Lr genes are nonrace-specific and confer partial resistance to leaf rust and other diseases at the adult plant stage. Combining Lr genes that confer seedling and adult plant resistance has been particularly successful and durable. Pathogen populations are genetically diverse, and races evolve continuously to evade recognition by Lr genes. This results in boom-and-bust cycles when new cultivars with race-specific Lr genes are resistant for some years, but become susceptible, due to evolution of the P. triticina population. Surveillance of P. triticina for the evolution of races helps to develop wheat cultivars with Lr genes that will be resistant to the most prevalent races. Information © The Authors 2024

AAC Stockton is a hulled two-row spring general purpose barley (Hordeum vulgare L.) cultivar widely adapted to western Canada. It was developed from the cross TR11219/CDC Kindersley made in 2012, and it was evaluated in the Western Cooperative Two-row Barley Registration Test (2020–2021) before being registered in 2023. AAC Stockton will offer a good production choice for barley growers across the Prairies due to its grain yield potential, lodging resistance, and improved Fusarium head blight resistance.

AAC Lariat is a hulled, two-row, spring, general purpose barley ( Hordeum vulgare L.) cultivar widely adapted to western Canada. It was developed from the cross AAC Synergy/TR09398 made in 2010 and it was evaluated in the Western Cooperative Tworow Barley Registration Test (2019-2020) before being registered in 2022. With its high yield, good standability, and disease resistance, AAC Lariat will offer a good production choice for feed growers across the Prairies.

Puccinia triticina, the causal agent of wheat leaf rust, is a dynamic pathogen causing significant yield losses worldwide. In this study, we analysed the virulence and genetic structure of 98 P. triticina isolates collected in Canada between 2018 and 2020. Isolates from Manitoba and Saskatchewan were found to be highly related for virulence, as were isolates from Quebec and Ontario. Isolates from Alberta had a virulence profile more similar to those from Manitoba and Saskatchewan than to Ontario and Quebec. To study the genetic structure of P. triticina populations, we used the restriction site-associated DNA (RAD) genotyping-by-sequencing method to identify single-nucleotide polymorphisms (SNPs). The Puccinia DNA sequences were aligned against the reference genome of P. triticina race BBBD and 1898 SNPs were identified. The phylogenetic analysis using SNP markers grouped these P. triticina into three genetic clades. The separation of P. triticina into three genetic clades was also supported by principal component analysis. Isolates from Clade 1 and Clade 2 were found throughout Canada, whereas Clade 3 isolates were only found in Ontario and Quebec. There were differences in virulence profiles among P. triticina isolates from the three genetic clades and a general correlation between virulence phenotypes and SNP genotypes was observed. These results indicate that the SNPs derived from RAD genotyping-by-sequencing could be useful in tracking the genetic and virulence dynamics of this pathogen in Canadian wheat.

Barley is the third most important cereal crop in terms of production in Canada, and Fusarium head blight (FHB) is one of the main fungal diseases of barley. FHB is caused by a species complex of Fusaria, of which Fusarium graminearum Schwabe is the main causal species of FHB epidemics in Canada. Field surveys show that two or more Fusarium species often co-exist within the same field or grain sample, and F. poae is reported as another important species in barley. This study aimed to determine the pathogenicity of F. graminearum, F. poae, and a co-inoculation of both species causing FHB in barley. Two susceptible barley cultivars were spray-inoculated at 10 to 14 days after heading. Phenotypic disease severity was rated on a scale of 0–9 at 4, 7, 14, 21, and 28 days after inoculation. There was a significant difference in FHB severity between F. graminearum and F. poae, where infection with F. graminearum produced more severe disease ratings. F. poae generated lower disease ratings and was not statistically different from the control. When heads were co-inoculated with both Fusarium species, the resulting FHB severity was unchanged relative to heads inoculated with F. graminearum only. The ratio of F. graminearum to F. poae genomic DNA was also no different than when heads were inoculated with F. graminearum alone, as quantified with ddPCR using markers specific to each species. The metabolomic analysis of sample extracts showed that F. graminearum-associated metabolites dominated the mycotoxin profile of co-inoculated samples, which corroborated our other findings where F. graminearum appeared to outcompete F. poae in barley. No significant effect on visual FHB disease ratings or fungal DNA detection was observed between the cultivars tested. However, there were some metabolome differences between cultivars in response to the challenge by both F. graminearum and F. poae.

AAC Douglas is a white-hulled spring oat (Avena sativa L.) cultivar, with superior grain-yield potential in the western Canadian oat production areas, yielding 3.5% higher than Summit. AAC Douglas was registered for commercial production in Canada (Reg. No. 8950) on 21 February 2020. AAC Douglas has high protein (5% higher significantly (P = 0.05) than AC Morgan) and beta-glucan content (10.6% higher than the nearest check, Summit), making it attractive for milling purposes. AAC Douglas is resistant to loose smut and covered smut, with moderately resistant to intermediate reactions to other diseases encountered in western Canada.

Aims Current understanding of how cropping sequence affects pathogen-suppressive microbiomes in soil is limited. We investigated the effects of several cropping sequences from the 2020–2021 growing seasons, including cereals, pulses, and an oilseed, on microbial communities in rhizosphere and bulk soils in two western Canadian field locations. Methods The fungi and bacteria were characterized by Internal Transcribed Spacer (ITS) and 16S rRNA gene sequencing, respectively. The QIIME 2™ bioinformatic pipeline was used to measure the diversity and abundance of microbial species. Additionally, the concentration of the soil mineral chemicals, including macro and micro nutrients, was determined by colorimetric analysis. Results Ascomycota (62.5%) was the most common fungal phylum, followed by Glomeromycota (11.1%), Mucoromycota (8.9%), and Basidiomycota (6.8%). Pseudomonadota (35.0%), Actinomycetota (21.1%), and Bacillota (10.1%) were the three most common bacterial phyla. Fungal OTU richness and phylogenetic diversity were highest in the cereal-pulse cropping sequencing, and bacterial OTU richness was highest in the pulse-oilseed sequences. Fusarium was the fungal genus most commonly associated with cereal-cereal monoculture and least common in the oilseed-pulse cropping sequences. The fungi ( Mortierella , Funneliformis , and Diversispora ) and bacteria ( Rhizobium , Bradyrhizobium , Flavobacterium , and Candidatus ) were higher in the cropping sequences involving pulses. The most prevalent bacteria were Streptomyces in cereal-related sequences and Solirubrobacter and Pseudomonas in oilseed-related sequences. Among soil mineral chemicals, nitrate-nitrogen, copper, calcium, potassium, and chlorine were associated with a number of beneficial fungal and bacterial genera but not with pathogenic fungal genera. Conclusions The results highlight the consequences of crop species selection in cropping sequences and the management of agrochemicals in the agricultural production system.

Gene editing in polyploid crops still suffers from low efficiency, and further improvement is needed for its routine implementation in the modern breeding practice. Here we examined factors that affect the CRISPR/Cas9-mediated gene editing efficiency in allohexaploid wheat plants. We selected three guide RNAs (gRNAs) and evaluated the potential of using heat shock at the seedlings stage to increase editing efficiency in transgenic plants. Only one out of three gRNAs demonstrated significantly increased editing efficiency following heat shock treatment. We also examined the expression of DNA repair and replication gene orthologues in response to heat shock in wheat leaves. Misregulation of the chromatin remodelers following the heat shock treatment could potentially be involved in the increase of editing efficiency in wheat. Overall, the editing efficiency of gRNAs observed in our study correlated with predictive scores from the gRNA design tools. The editing rate of the top-ranked gRNAs could potentially be increased using heat treatment of the transgenic plants.

Fusarium head blight (FHB) is one of the most important diseases of barley in Manitoba province (western Canada), and other major barley producing regions of the world. Little is known about the Fusarium species and mycotoxin spectra associated with FHB of barley in Manitoba. Hence, barley grain samples were collected from 149 commercial fields from 2017 to 2019, along with information on respective cropping history, and analyzed with respect to Fusarium species spectra, abundance, chemotype composition, and mycotoxin profiles. Fusarium poae was the predominant Fusarium species associated with FHB of barley in Manitoba, followed by F. graminearum, and F. sporotrichioides; F. equiseti and F. avenaceum were also detected but at low levels. F. poae strains with the nivalenol (NIV) chemotype and F. graminearum strains with 3-acetyl deoxynivalenol (3-ADON) and 15-acetyl deoxynivalenol (15-ADON) chemotypes were commonly detected in the barley grain samples. Nivalenol (597.7, 219.1, and 412.4 µg kg−1) and deoxynivalenol (DON) (264.7, 56.7, and 65.3 µg kg−1) were the two most prevalent mycotoxins contaminating Manitoba barley in 2017, 2018 and 2019, respectively. A substantially higher DON content was detected in grain samples from barley fields with cereals as a preceding crop compared to canola and flax. Furthermore, F. poae proved less sensitive to four triazole fungicides (metconazole, prothioconazole+tebuconazole, tebuconazole, and prothioconazole) than F. graminearum. Findings from this research will assist barley producers with improved understanding of FHB threat levels and optimizing practices for the best management of FHB in barley.

AAC Kongsore is a white-hulled spring oat ( Avena sativa L.) cultivar selected and developed under organic management. AAC Kongsore had high yields under organic and conventional production systems, compared to check cultivars (AAC Oravena, Leggett, AC Morgan and CDC Dancer). AAC Kongsore has good physical and milling quality traits.

Fusarium head blight (FHB) can lead to dramatic yield losses and mycotoxin contamination in small grain cereals in Canada. To assess the extent and severity of FHB in oat, samples collected from 168 commercial oat fields in the province of Manitoba, Canada, during 2016–2018 were analyzed for the occurrence of Fusarium head blight and associated mycotoxins. Through morphological and molecular analysis, F. poae was found to be the predominant Fusarium species affecting oat, followed by F. graminearum, F. sporotrichioides, F. avenaceum, and F. culmorum. Deoxynivalenol (DON) and nivalenol (NIV), type B trichothecenes, were the two most abundant Fusarium mycotoxins detected in oat. Beauvericin (BEA) was also frequently detected, though at lower concentrations. Close clustering of F. poae and NIV/BEA, F. graminearum and DON, and F. sporotrichioides and HT2/T2 (type A trichothecenes) was detected in the principal component analysis. Sampling location and crop rotation significantly impacted the concentrations of Fusarium mycotoxins in oat. A phylogenetic analysis of 95 F. poae strains from Manitoba was conducted using the concatenated nucleotide sequences of Tef-1α, Tri1, and Tri8 genes. The results indicated that all F. poae strains belong to a monophyletic lineage. Four subgroups of F. poae strains were identified; however, no correlations were observed between the grouping of F. poae strains and sample locations/crop rotations.

Fusarium head blight (FHB) is a major disease in wheat causing severe economic losses globally by reducing yield and contaminating grain with mycotoxins. In Canada, Fusarium graminearum is the principal etiological agent of FHB in wheat, producing mainly the trichothecene mycotoxin, deoxynivalenol (DON) and its acetyl derivatives (15-acetyl deoxynivalenol (15ADON) and 3-acetyl deoxynivalenol (3ADON)). Understanding the population biology of F. graminearum such as the genetic variability, as well as mycotoxin chemotype diversity among isolates is important in developing sustainable disease management tools. In this study, 570 F. graminearum isolates collected from commercial wheat crops in five geographic regions in three provinces in Canada in 2018 and 2019 were analyzed for population diversity and structure using 10 variable number of tandem repeats (VNTR) markers. A subset of isolates collected from the north-eastern United States was also included for comparative analysis. About 75% of the isolates collected in the Canadian provinces of Saskatchewan and Manitoba were 3ADON indicating a 6-fold increase in Saskatchewan and a 2.5-fold increase in Manitoba within the past 15 years. All isolates from Ontario and those collected from the United States were 15ADON and isolates had a similar population structure. There was high gene diversity (H = 0.803–0.893) in the F. graminearum populations in all regions. Gene flow was high between Saskatchewan and Manitoba (Nm = 4.971–21.750), indicating no genetic differentiation between these regions. In contrast, less gene flow was observed among the western provinces and Ontario (Nm = 3.829–9.756) and USA isolates ((Nm = 2.803–6.150). However, Bayesian clustering model analyses of trichothecene chemotype subpopulations divided the populations into two clusters, which was correlated with trichothecene types. Additionally, population cluster analysis revealed there was more admixture of isolates among isolates of the 3ADON chemotypes than among the 15ADON chemotype, an observation that could play a role in the increased virulence of F. graminearum. Understanding the population genetic structure and mycotoxin chemotype variations of the pathogen will assist in developing FHB resistant wheat cultivars and in mycotoxin risk assessment in Canada.