Rhizoctonia root and crown rot (RRCR) is one of the major soilborne diseases of sugar beet that causes significant yield loss and exacerbates postharvest losses in the storage piles. To investigate the soil fungal communities (mycobiomes) influencing Rhizoctonia root rot (RRR), we used Illumina sequencing of the ITS rRNA gene to analyze field soils collected over three years (2016-2018) representing different levels of disease severity. Our analysis revealed that overall fungal diversity (alpha-diversity) and community composition (beta-diversity) did not correlate significantly with disease severity. This suggests that disease management strategies focused solely on broad-spectrum shifts in fungal diversity are unlikely to be effective. The soil mycobiome was consistently dominated by the phyla Ascomycota (mean relative abundance: 57.1%) and Basidiomycota (mean relative abundance: 21.1%), with Mrakia and Mortierella among the most prevalent genera. While the pathogen Rhizoctonia was ubiquitous, its relative abundance was generally low (similar to 2%). The RRR suppressiveness was associated with high abundance and significant expression of biocontrol and symbiotrophic fungal taxa. The current study provides in depth understanding of soil mycobiomes and functions that might be important indicators of Rhizoctonia suppressiveness in sugar beet. Future studies should focus on isolating and characterizing the specific biocontrol (e.g., Cladorrhinum, Chaetomium, and Cladorrhinum spp.) and symbiotrophic fungal taxa identified in this study to test their efficacy against R. solani AG 2-2. Further research is needed to determine the optimal conditions for inoculating sugar beet fields with these candidate microbes, and to assess their impact on RRR severity under field conditions.

Cercospora leaf spot (CLS), caused by Cercospora beticola, is the most devastating foliar diseases of sugar beet in Minnesota and North Dakota. CLS symptoms develop first on older leaves as small, circular, tan to brown spots that become large necrotic lesions as the infections become severe, leading to reduced root and sugar yield. In this study, we evaluated the efficacy of demethylation inhibitor (DMI) fungicides within a four-spray fungicide program for management of CLS. The trial was conducted at the Northwest Research and Outreach Center in Crookston, MN, on a moderately susceptible sugar beet variety ( Beta vulgaris ‘Crystal 912RR’). Results from this trial will help sugar beet growers make informed decisions on selecting a suitable DMI fungicide for managing CLS.

Seedling damping-off and root and crown rot, caused by the soilborne fungus Rhizoctonia solani AG 2-2, are the most common root diseases of sugar beet in Minnesota, North Dakota, and Michigan. Early season infection leads to poor stands, while mid-to-late season infection of plants results in root rot with dark-brown to black lesions on the surface, leading to chlorotic and wilting foliage and plant death under severe infection. In this study, 15 sugar beet ( Beta vulgaris subsp. vulgaris) breeding lines were screened for resistance to Rhizoctonia root and crown rot (RRCR). The nonirrigated trial was conducted at the University of Minnesota, Northwest Research and Outreach Center in Crookston, MN. Results from this trial will aid in breeding efforts to improve resistance to Rhizoctonia diseases in sugar beet.

Cercospora leaf spot (CLS), caused by Cercospora beticola Sacc., remains a major foliar disease of sugar beet (Beta vulgaris subsp. vulgaris L.) worldwide. Increasing prevalence of resistance to demethylation inhibitor (DMI) fungicides also constrain effective management practices. The efficacy of commercially available DMI fungicides (prothioconazole, tetraconazole, difenoconazole plus propiconazole, and mefentrifluconazole) was evaluated when tank-mixed with broad-spectrum partners including mancozeb, copper, sulfur, potassium phosphite, sodium bicarbonate, and Bacillus subtilis. Field trials were conducted in 2020 and 2021 in Northwest Minnesota. All DMI fungicides suppressed CLS relative to the nontreated control, and mixtures with select partners significantly enhanced disease control and sucrose yield. Notably, mancozeb and copper consistently improved outcomes when combined across multiple DMIs, whereas sulfur, phosphite, and B. subtilis exhibited improved outcomes in specific pairings. Fungicide efficacy varied by combination, emphasizing the importance of tank-mix partner selection. These findings demonstrate that strategic tank mixes can enhance CLS disease suppression and improve sucrose yield outcomes in sugar beet.

Cercospora beticola, the causal agent of Cercospora leaf spot (CLS) in sugar beet, is a major pathogen that significantly impacts crop productivity. The emergence and spread of resistance to demethylation inhibitor (DMI) fungicides further complicate effective disease management. Current methods for monitoring DMI sensitivity, such as radial growth and molecular assays, are limited by low throughput or binary detection of known resistance alleles, respectively. In this study, we developed and validated a high-throughput microplate-based assay to determine DMI fungicide sensitivity in C. beticola using optical density (OD) measurements. The assay was optimized for media type, inoculum preparation, wavelength, fungicide concentration gradients, and incubation time. Relative effective fungicide concentrations that inhibit 50% of growth (EC 50 ) were determined to provide quantitative assessment of fungicide sensitivity to tetraconazole, prothioconazole, difenoconazole, and mefentrifluconazole. The assay demonstrated consistency across two microplate brands and strong correlation with CbCyp51 haplotypes associated with DMI resistance. Our results show that the microplate assay is an efficient tool for monitoring quantitative fungicide sensitivity in C. beticola, offering improved throughput compared to the conventional Petri plate method.

In this study, meta-transcriptome sequencing was conducted on a total of 18 sugarbeet (Beta vulgaris L. subsp. vulgaris) sample libraries to profile the virome of field-grown sugarbeet to identify the occurrence and distribution of known and potentially new viruses from five different states in the United States. Sugarbeet roots with symptoms resembling rhizomania caused by beet necrotic yellow vein virus (BNYVV), or leaves exhibiting leaf-curling, yellowing to browning, or green mosaic were collected from the sugarbeet growing areas of California, Colorado, Idaho, Minnesota, and North Dakota. In silico analysis of de novo assembled contigs revealed the presence of nearly full-length genomes of BNYVV, beet soil-borne virus (BSBV), and beet soil-borne mosaic virus (BSBMV), which represent known sugarbeet-infecting viruses. Among those, BNYVV was widespread across the locations, whereas BSBV was prevalent in Minnesota and Idaho, and BSBMV was only detected in Minnesota. In addition, two recently reported Beta vulgaris satellite virus isoforms (BvSatV-1A and BvSatV-1B) were detected in new locations, indicating the geographical expansion of this known virus. Besides these known sugarbeet-infecting viruses, the bioinformatic analysis identified the widespread occurrence of a new uncharacterized Erysiphe necator-associated abispo virus (En_abispoV), a fungus-related virus that was identified in all 14 libraries. En_abispoV contains two RNA components, and nearly complete sequences of both RNA1 and RNA2 were obtained from RNASeq and were further confirmed by primer-walking RT-PCR and Sanger sequencing. Phylogenetic comparison of En_abispoV isolates obtained in this study showed varying levels of genetic diversity within RNA1 and RNA2 compared to previously reported isolates. The undertaken meta-transcriptomic approach revealed the widespread nature of coexisting viruses associated with field-grown sugarbeet exhibiting virus disease-like symptoms in the United States.

Epigenetics has emerged as a potent field of study for understanding the factors influencing the effectiveness of human disease treatments and for identifying alternations induced by pathogens in host plants. However, there has been a paucity of research on the epigenetic control of the proliferation and pathogenicity of fungal plant pathogens. Fungal plant pathogens such as Magnaporthe oryzae, a significant threat to global rice production, provide an important model for exploring how epigenetic mechanisms govern fungal proliferation and virulence. In M. oryzae, epigenetic alterations, such as DNA methylation, histone modification, and non-coding RNAs, regulate gene expression patterns that influence the pathogen’s ability to infect its host. These modifications can enhance fungal adaptability, allowing the pathogen to survive in diverse environments and evade host immune responses. Our primary objective is to provide a comprehensive review of the existing epigenetic research on M. oryzae and shed light on how these changes influence the pathogen’s lifecycle, its ability to invade host tissues, and the overall severity of the disease. We begin by examining the epigenetic alterations occurring in M. oryzae and their contributions to the virulence and proliferation of the fungus. To advance our understanding of epigenetic mechanisms in M. oryzae and similar plant diseases, we emphasize the need to address unanswered questions and explore future research directions. This information is crucial for developing new antifungal treatments that target epigenetic pathways, which could lead to improved disease management.

Cercospora leaf spot (CLS) is one of the most yield-limiting foliar disease of sugar beet in the United States. Standard practices to control this disease include selection of tolerant varieties, crop rotations, and reliance on fungicides. However, genetic resistance still requires some fungicides for acceptable control under high disease pressure, and there are only a limited number of fungicides registered for control of this disease. Regev® is a newly registered hybrid fungicide for sugar beet disease control that contains eight biological active ingredients from tea tree oil (TTO) and one active ingredient from the synthetic fungicide, difenoconazole. Tea tree oil provides a new and unique mode of activity against both fungal and bacterial plant pathogens, and it has a low resistance risk. Eight trials were conducted to evaluate Regev for efficacy against Cercospora leafspot, and sugar beet yield and quality benefits in Minnesota and Michigan. Five of the trials had slightly different treatments with the primary goal of allowing trialists to conduct trials with treatments that were appropriate for their locations. However, one of the trials at the Northwest Research and Outreach Center (NWROC) of the University of Minnesota in Crookston, Minnesota, was conducted three times over the years 2021, 2022, and 2023. Across the eight trials, spray programs that included Regev provided control of Cercospora leaf spot equal to standard fungicide programs.

Aphanomyces cochlioides , the causal agent of seedling damping-off and Aphanomyces root rot (ARR) of sugar beet, causes yield losses in major sugar beet growing regions. Currently, a 4-week soil bioassay and a 2-day culture-based assay are used to diagnose presence of A. cochlioides. However, these assays can be time-consuming and lack sensitivity. In this study we developed a sensitive, specific, and rapid assay to detect and quantify DNA of A. cochlioides . We developed a TaqMan qPCR assay targeting a region of the mitochondrial genome of A. cochlioides representing a unique gene order for Aphanomyces with genus-specific primers and a species-specific probe. The qPCR assay detected A. cochlioides in 12 naturally infested field soil samples with disease severity index (DSI) values of 48-100, in sugar beet seedlings 5-7 days after planting, and with as little as 1 fg of pure A. cochlioides DNA. Adult sugar beet roots with ARR symptoms were sampled to further validate this qPCR assay. Aphanomyces cochlioides was detected in 95% of these samples using this qPCR assay, while only 23% of the same samples were positive using a culture-based assay. This shows the improved sensitivity of this qPCR assay for disease diagnosis and could provide growers with ARR risk of a field, which would help them make informed disease management decisions. However, further research is required to translate the results of this study to growers’ fields to quantify A. cochlioides with a high degree of accuracy. ### Competing Interest Statement The authors have declared no competing interest.

ABSTRACTAphanomyces cochlioides, the causal agent of damping-off and root rot of sugar beet (Beta vulgaris L.), is a soil-dwelling oomycete responsible for yield losses in all major sugar beet growing regions. Currently, genomic resources for A. cochlioides are limited. Here we report a de novo genome assembly using a combination of long-read MinION (Oxford Nanopore Technologies) and short-read Illumina sequence data for A. cochlioides isolate 103-1, from Breckenridge, MN. The assembled genome was 76.3 Mb, with a contig N50 of 2.6 Mb. The reference assembly was annotated and was composed of 32.1% repetitive elements and 20,274 gene models. This high-quality genome assembly of A. cochlioides will be a valuable resource for understanding genetic variation, virulence factors, and comparative genomics of this important sugar beet pathogen.

This protocol was used to extract high molecular weight (HMW) DNA from Aphanomyces cochlioides for MinION (Oxford Nanopore) long-read sequencing, which was used for de novo genome assembly. A gel electrophoresis analysis showed that there was a band around 48 kb, a band above 48 kb, and a band in the gel well. With the modified genomic-tips procedure we describe here, each 1 gram sample of A. cochlioides mycelium yielded approximately 6 - 11 micrograms of DNA.

Rhizoctonia crown and root rot (RCRR), caused by Rhizoctonia solani AG 2-2, is becoming more frequent and widespread in the sugarbeet-growing regions of Minnesota and North Dakota. In this region, symptoms of RCRR typically begin at about 8 weeks after planting and continue to develop until harvest. Infected plants occur sporadically or in large portions of the field. Advances in remote sensors and vehicle platforms have regenerated interest in withinseason aerial mapping/detection of RCRR.

Rhizoctonia solani causes root and stem diseases on soybean and sugar beet, and fungicides are commonly used to manage these diseases. Quinone outside inhibitor (QoI) fungicides (pyraclostrobin and azoxystrobin) have been used for in-furrow and postemergence application since 2000. Succinate dehydrogenase inhibitor (SDHI) fungicides (sedaxane, penthiopyrad, and fluxapyroxad) became popular seed treatments after their registration in Minnesota and North Dakota between 2012 and 2016. Periodic monitoring of sensitivity to these fungicides in R. solani anastomosis group (AG) 2-2 is important to detect potential shifts in sensitivity over time. R. solani AG 2-2 isolates (n = 35) collected from soybean and sugar beet in Minnesota and North Dakota were evaluated in vitro for sensitivity. Isolates were considered as baseline or nonbaseline for the above-mentioned fungicides based on previous potential exposure. The effective concentration (EC50) required to suppress radial fungal growth by 50% was determined. The mean EC50 values for sedaxane, penthiopyrad, fluxapyroxad, and pyraclostrobin were 0.1, 0.15, 0.16, and 0.25 (µg ml−1), respectively. The mean EC50 value for azoxystrobin for 22 isolates was 0.76 to 1.56 µg ml−1; and EC50 could not be determined for 13 isolates because of <50% inhibition at the highest concentrations used. The EC50 values for the QoI fungicides did not differ significantly between baseline and nonbaseline isolates. EC50 values for SDHI fungicides were significantly higher for isolates collected from soybean than from sugar beet, and isolates collected from both crops had similar EC50 values for pyraclostrobin. All SDHI fungicides and pyraclostrobin effectively suppressed R. solani isolates from soybean and sugar beet at low concentrations in vitro.