Cereal Disease Laboratory

Abstract The fungi causing diseases of cereal crops and other grasses, known as the brown leaf rusts, have historically been classified in the Puccinia recondita (sensu lato) species complex. Despite a long history of taxonomic effort, the recognition of the many included discrete taxa has been challenged due to overlapping morphological characters and primary grass hosts. More recent studies employing DNA sequence analyses identified multiple phylogenetic lineages in the complex, with two corresponding to species important to agricultural production, Puccinia triticina and P. recondita sensu stricto, on wheat and rye respectively. In this study, a second wheat-associated species, Puccinia tritici-duri , as yet known only from the Mediterranean region, and a new species recently discovered in the Golan Heights on wild emmer wheat, were examined and compared with P. triticina . We conducted detailed morphological examinations of telial and uredinial stages, DNA sequence analyses of the ribosomal DNA internal transcribed spacer region and elongation factor 1-α, and greenhouse inoculation experiments using a broad selection of Triticum and Aegilops telial hosts. The results demonstrated that the three wheat-associated species are distinct, placed in three unrelated lineages within the P. recondita complex. They confirm an overlap in host associations, which varied depending on species or cultivar. Based on the combined evidence, we formally propose the new species as Puccinia tritici-golanensis and provide comprehensive notes for the other two species, supported by descriptions and illustrations.

Eukaryotic microorganisms are an important, but understudied, component of freshwater aquatic ecosystems, and are significant sources of mortality in early life stages of fishes in natural and aquaculture systems. The eukaryotic microbiome colonizing egg surfaces of the lake sturgeon (Acipenser fulvescens) was characterized from eggs collected in natural stream habitats and a streamside hatchery in the Cheboygan River watershed in MI, USA. The taxonomic diversity of members of the Kingdoms Fungi and Stramenopile associated with infections of lake sturgeon eggs during spawning is contributing to lake sturgeon mortality in the hatchery. Characterization of the microbial communities from deposited eggs demonstrated heavy influence of spawning location on the diversity of Pythium, an Oomycete predominating in the microbiome. The Ascomycota also had a strong and distinguishing presence, with members of the Dothidiales found only on eggs from the streamside hatchery. Aureobasidium pullulans, a ubiquitous pigmented yeast, was present in the greatest numbers of egg samples, and Helotiales were found only on samples from the Black River. Independent isolates were collected from egg surfaces and tested for chemical sensitivity to the oomicides ethaboxam and mefenoxam, which are used for control of Oomycete agricultural pathogens. Ethaboxam inhibited mycelial growth almost completely for all Saprolegnia strains tested, while mefenoxam, at 20 × strength, was largely ineffective. Water prevents the natural inactivation of mefenoxam by light, thus is not advisable in aquatic systems, where it could accumulate. Alternatively, ethaboxam may be a nonpersistent, welcome control option for these fish pathogens.

As Ethiopia pushes toward self-sufficiency in wheat production, it has escaped large outbreaks of Fusarium head blight (FHB), a disease that threatens wheat production globally. However, in 2022, FHB incidences in Ethiopia rose to 80%, with some areas experiencing 100% disease severity. Here we provide insights into the etiology of this disease outbreak and point toward future directions to mitigate the emerging threat of FHB on a global scale. Although most wheat samples from 2022 exhibited low trichothecene levels, 26% exceeded recommended thresholds and several contained multiple trichothecene variants. We obtained 64 isolates from the outbreak and identified diverse members of the Fusarium graminearum species complex (FGSC) and many Epicoccum species. The FGSC species contributing to the outbreak are rare on a global scale. Genomic analyses reveal that Fusarium aethiopicum has persisted in Ethiopia for decades and shares ancient ancestry with a newly emerged novel species in the FGSC that we formally described as Fusarium kistleri. Single-nucleotide polymorphism-based analyses suggest high clonal fraction among FGSC isolates in Ethiopia, raising questions about a recent population expansion. Our findings reveal that although Epicoccum alone causes minimal disease on wheat, its presence can have a small but synergistic impact on disease symptoms when F. graminearum has already infected. The unique diversity and species composition of the 2022 Ethiopian outbreak underscores the importance of addressing emerging threats in a globalized agricultural economy to secure food safety, food security, and global food equity.

Developing disease-resistant crops is a critical strategy for reducing chemical treatments and mitigating plant disease outbreaks, particularly amid global environmental changes. Fusarium head blight (FHB), caused by a complex of Fusarium species, is one of the most devastating cereal diseases, leading to significant economic losses and contamination of grain with harmful mycotoxins that threaten global cereal production and human health. The high variability in virulence within the complex of Fusarium spp and the lack of efficient high-throughput screening methods have impeded the development of resistant cultivars and made large-scale virulence testing labor-intensive and time-consuming. This study evaluates the efficacy of detached leaf, coleoptile, and seedling assays as high-throughput alternatives to the standard head infection assay for assessing the virulence of Fusarium species and differentiating wheat genotypes by resistance or susceptibility. Two near-isogenic wheat lines, one carrying FHB resistance loci and the other without, were used to assess the virulence of four Fusarium species. The seedling and coleoptile assays showed strong concordance with the traditional head infection assay, accurately reflecting differences in disease severity across Fusarium species and between wheat lines. Conversely, the detached leaf assay provided some differentiation among species but was inconsistent in identifying differences between plant genotypes. Across all assays, F. graminearum consistently exhibited the highest virulence, causing severe disease in leaves, stems, seedlings, and heads, while F. poae was the least virulent. Interestingly, F. culmorum and F. avenaceum displayed tissue-specific variability. These findings establish the coleoptile and seedling assays as rapid, high-throughput alternatives for breeding programs, accelerating the identification of FHB-resistant genotypes and reducing the reliance on the labor-intensive head assay.Supplementary InformationThe online version contains supplementary material available at 10.1186/s13007-025-01402-8.

Barley malt quality analysis is essential for craft malt houses, commercial producers, and barley breeding programs, yet traditional methods are resource-intensive and time-consuming. We combined attenuated total reflectance-Fourier transform infrared (ATR-FTIR) spectroscopy with automated multivariate regression models to predict eight malt quality traits. Using super partial least-squares (sPLS) and super support vector regression (sSVR), quality metrics were evaluated using 460 barley lines from three U.S. locations. External validation coefficients of determination (Rv2) were the highest for barley protein (BP), soluble protein/total protein (S/T), and malt extract (ME). These values were respectively 0.946, 0.907, and 0.880 for sSVR and 0.942, 0.901, and 0.867 for sPLS. Average validation errors for ME, BP, and S/T were 1.3%, 4.6%, and 6.3%, respectively, for sSVR and 1.4%, 4.7%, and 6.5% for sPLS, respectively. Variable selection methods─binning, wavelet, and variance feature ranking (VFR)─were compared, with binning and wavelet techniques retaining information effectively even when measurements were reduced by 95%. The ratio of performance to deviation (RPD) values of BP, S/T, and ME models for sPLS to sSVR were 4.2 to 4.3, 3.2 to 3.3, and 2.7 to 2.9, respectively. These models provide an efficient, nondestructive alternative for rapid barley malt quality analysis, offering scalable tools for research and industry applications in barley breeding and malt production.

Abstract‘Avalon’ (Reg. no. CV‐383, PI 700308) is the first two‐row, winter malt barley (Hordeum vulgare L.) cultivar developed by the Virginia Agricultural Experimental Station. Avalon was released in May 2020. Prior to being named, Avalon was tested under the experimental designation VA16M‐81. Avalon was evaluated from 2018 to 2023 in the Eastern Malt Barley Trials (EMBT) at one to three locations in three states and in the Winter Malt Barley Trial (WMBT) from 2020 to 2023 in six to 15 states. In the EMBT in Virginia, mean grain yield (5604 kg ha−1) of Avalon was higher to cultivar ‘Violetta’, but lower than those of ‘Flavia’, ‘Calypso’, and ‘Thoroughbred’. Average grain volume weight of Avalon (64.9 kg hL−1) was significantly (P ≤ 0.05) higher than the check cultivars, except Violetta. Head emergence of Avalon was 3 days earlier than Flavia and Calypso and 1 to 2 days later than Violetta and Thoroughbred, respectively. Avalon was developed primarily as a malt barley cultivar. On the basis of malting evaluations, Avalon has acceptable quality profiles with specific quality traits including high extract, low protein content, and low beta‐glucan for the years tested. Avalon provides malt barley producers and end users in the eastern United States with excellent malt quality and a unique and distinct flavor profile having good to moderate resistance to all diseases prevalent in the eastern United States. It is moderately susceptible to Fusarium head blight but has moderately low deoxynivalenol accumulation in the grain.

Puccinia coronata f. sp. avenae (Pca) is an important foliar pathogen of oat which causes crown rust disease. The virulence profile of 48 Pca isolates derived from different locations in Australia was characterized using a collection of oat lines often utilized in rust surveys in the United States and Australia. This analysis indicates that Pca populations in Eastern Australia are broadly virulent, which contrasts with the population in Western Australia (WA). Several oat lines/Pc genes are effective against all rust samples collected from WA, suggesting they may provide useful resistance in this region if deployed in combination. We identified 19 lines from the United States oat differential set that display disease resistance to Pca in WA, with some in agreement with previous rust survey reports. We adopted the 10-letter nomenclature system to define oat crown rust races in Australia and compare the frequency of those virulence traits to published data from the United States. Based on this nomenclature, 42 unique races were detected among the 48 isolates, reflecting the high diversity of virulence phenotypes for Pca in Australia. Nevertheless, the Pca population in the United States is substantially more broadly virulent than that of Australia. Close examination of resistance profiles for the oat differential set lines after infection with Pca supports hypotheses of allelism or redundancy among Pc genes or the presence of several resistance genes in some oat differential lines. These findings illustrate the need to deconvolute the oat differential set using molecular tools.[Formula: see text] Copyright © 2024 The Author(s). This is an open access article distributed under the CC BY-NC-ND 4.0 International license.

Pulmonary hypertension (PH)due to interstitial lung disease (ILD),a commonly encountered complication of fibrotic ILDs, is associated with significant morbidity and mortality. Until recently, the studies of pulmonary vasodilator therapy in PH-ILDhave been largely disappointing, with some even demonstrating the potential for harm. This paper is part of a series of Consensus Statements from the Pulmonary Vascular Research Institute's Innovative Drug Development Initiative for Group 3 Pulmonary Hypertension, with prior publications covering pathogenesis, prevalence, clinical features, phenotyping, clinical trials, and impact of PH-ILD.It offers a comprehensive review of and a holistic approach to treatment of PH-ILD,including the management of underlying interstitial lung diseases, importance of treating the comorbidities, emphasis on importance of exercise and palliation of dyspnea, and review of the most up-to-date guidelines for referral for potential lung transplant work up. It also summarizes the prior, ongoing, and possibly future studies in treatment of the vascular derangement of this morbid condition.

Barley leaf rust, caused by Puccinia hordei, is an important disease of barley worldwide. The pathogen can develop new races that overcome resistance genes, emphasizing the need for monitoring its virulence. This study characterized 519 P. hordei isolates collected in the United States from the 1989 to 2000 and 2010 to 2020 survey periods on 15 Rph (Reaction to Puccinia hordei) genes. We analyzed linearized infection type data to detect virulence patterns across the United States and in five geographical regions: Pacific/West (PW), Southwest (SW), Midwest (MW), Northeast (NE), and Southeast (SE). Over 32 years, we observed high mean infection scores for Rph1.a, Rph4.d, and Rph8.h; intermediate scores for Rph2.b, Rph9.i, Rph10.o, Rph11.p, and Rph13.x; and low scores for Rph3.c, Rph5.e, Rph5.f, Rph7.g, Rph9.z, Rph14.ab, and Rph15.ad. Virulence for Rph2.b, Rph3.c, Rph5.e, Rph9.z, Rph10.o, Rph11.p, and Rph13.x significantly differed between the two survey periods. From 1989 to 2020, regional patterns of virulence were found for Rph5.e, Rph5.f, Rph7.g, and Rph14.ab, while regionalities of virulence for Rph3.c, Rph9.i, Rph9.z were only observed in the 2010 to 2020 survey period. Virulence associations were also detected in the P. hordei population. Notably, isolates that were virulent to Rph5.e and Rph6.f were more likely to be avirulent to Rph7.g and Rph13.x, and vice versa. In decreasing order of effectiveness, Rph15.ad, Rph5.e, Rph3.c, Rph9.z, Rph7.g, Rph5.f, and Rph14.ab were the most effective Rph genes in the United States from 1989 to 2020. Pyramiding Rph15.ad with other widely effective Rph and adult plant resistance genes may provide long-lasting resistance against P. hordei.

Six quantitative trait loci (QTL) for adult plant resistance (APR) against oat crown rust (Puccinia coronata f. sp. avenae) were identified from mapping three recombinant inbred populations (RILs). Using genotyping-by-sequencing with markers called against the OT3098 v1 reference genome, the QTL were mapped on six different chromosomes, namely: Chr1D, Chr4D, Chr5A, Chr5D, Chr7A, and Chr7C. Composite interval mapping with marker cofactor selection showed that the phenotypic variance explained by all identified QTL for coefficient of infection range from 12.2 to 46.9%, while heritability estimates ranged from 0.11 to 0.38. The significant regions were narrowed down to intervals of 3.9 to 25 cM, equivalent to physical distances of 11 to 133 Mb. At least two flanking SNP markers were identified within 10 cM of each QTL that could be used in marker-assisted introgression, pyramiding, and selection. The additive effects of the QTL in each population were determined using SNP haplotype data, which showed significantly lower coefficient of infection (CI) in lines homozygous for the resistant alleles. Analysis of pairwise linkage disequilibrium also revealed high correlation of markers and presence of linkage blocks in the significant regions. To further facilitate marker-assisted breeding, Polymerase Chain Reaction Allelic Competitive Extension (PACE) markers for the APR loci were developed. Putative candidate genes were also identified in each of the significant regions, which include resistance gene analogs that encode for kinases, ligases, and predicted receptors of avirulence proteins from pathogens.