Infection of Soybean Seed by Fusarium graminearum and Effect of Seed Treatments on Disease Under Controlled Conditions

Wheat Rhizosphere-Derived Bacteria Protect Soybean from Soilborne Diseases

Soybean (Glycine max [L.] Merr.) is an important oilseed crop with a high economic value. However, three damaging soybean diseases, soybean cyst nematode (SCN; Heterodera glycines Ichinohe), Sclerotinia stem rot caused by the fungus Sclerotinia sclerotiorum (Lid.) de Bary, and soybean root rot caused by Fusarium spp., are major constraints to soybean production in the Great Plains. Current disease management options, including resistant or tolerant varieties, fungicides, nematicides, and agricultural practices (crop rotation and tillage), have limited efficacy for these pathogens or have adverse effects on the ecosystem. Microbes with antagonistic activity are a promising option to control soybean diseases with the advantage of being environmentally friendly and sustainable. In this study, 61 bacterial strains isolated from wheat rhizospheres were used to examine their antagonistic abilities against three soybean pathogens. Six bacterial strains significantly inhibited the growth of Fusarium graminearum in the dual-culture assay. These bacterial strains were identified as Chryseobacterium ginsengisoli, C. indologenes, Pseudomonas poae, two Pseudomonas spp., and Delftia acidovorans by 16S rRNA gene sequencing. Moreover, C. ginsengisoli, C. indologenes, and P. poae significantly increased the mortality of SCN second-stage juveniles (J2), and two Pseudomonas spp. inhibited the growth of S. sclerotiorum in vitro. Further growth chamber tests found that C. ginsengisoli and C. indologenes reduced soybean Fusarium root rot disease. C. ginsengisoli and P. poae dramatically decreased SCN egg number on SCN-susceptible soybean 'Williams 82'. Two Pseudomonas spp. protected soybean plants from leaf damage and collapse after being infected by S. sclerotiorum. These bacteria exhibit versatile antagonistic potential. This work lays the foundation for further research on the field control of soybean pathogens.

Select Cover Crop Residue and Soil Microbiomes Contribute to Suppression of Fusarium Root and Crown Rot in Barley and Soybean

Fusarium root and crown rot (FRCR) negatively impact several economically important plant species. Cover crops host different soil and residue microbiomes, thereby potentially influencing pathogen load and disease severity. The carryover effect of cover crops on FRCR in barley and soybean was investigated. Field trials were conducted in Prince Edward Island, Canada. Two cover crops from each plant group, including forbs, brassicas, legumes, and grasses, were grown in a randomized complete block design with barley and soybean planted in split plots the following year. Barley and soybean roots were assessed for FRCR through visual disease rating and Fusarium spp. were isolated from diseased tissue. Fungal and bacterial communities in cover crop residues were quantified using amplicon sequencing. The disease-suppressive effects of soil were tested in greenhouse studies. The results indicated that sorghum-sudangrass-associated microbiomes suppress Fusarium spp., leading to reduced FRCR in both barley and soybean. The oilseed radish microbiome had the opposite effect, consequently increasing FRCR incidence in barley and soybean. The results from this study indicate that cover crop residue and the associated soil microbiome influence the incidence and severity of FRCR in subsequent crops. This information can be used to determine cover cropping strategies in barley and soybean production systems.

Using Mass Spectrometry Imaging to Visualize Pesticide Accumulation and Time-Dependent Distribution in Fungicide-Coated Seeds

Pesticide seed treatment provides efficient crop protection in the early season and enables a reduction in the quantity of fungicides used later. Hence, it has been a practical application for crop protection in major crop sectors such as corn, soybean, wheat, and cotton. The chemicals on pesticide-treated seeds may show different distributions depending on the structure of the seeds and the physical properties of the chemicals, but they have not been well studied because of a lack of versatile analytical tools. Here, we used mass spectrometry imaging to visualize the distribution of a fungicide (ethaboxam) in corn and soybean seeds coated with it. Contrasting distribution patterns were noted, which are likely dependent on the seed structure. We also obtained information on fungicide distribution after the seedings, which will contribute to a better understanding of the fungicide delivery pathway within plants. Using this new analytical method, we were able to obtain hitherto unavailable time-dependent, dynamic information on the ethaboxam. We expect that this method will be a useful tool with widespread applications in pesticide development and use. Copyright © 2023 Shuichi Shimma, Hiromi Saito, Takuya Inoue, and Fukumatsu Iwahashi. This is an open-access article distributed under the terms of Creative Commons Attribution Non-Commercial 4.0 International License, which permits use, distribution, and reproduction in any medium, provided the original work is properly cited and is not used for commercial purposes.

Identification and Pathogenicity of Fusarium Isolated from Soybean in Poland

Fungi belonging to the Fusarium genus are commonly isolated from soybean plants and seeds but not all of them are pathogenic. The aim of this study was to compare the pathogenicity among different Fusarium isolates obtained from soybean plants with disease symptoms originating from an experimental field located in the southeast of Poland. Nineteen fungal isolates were selected for the pathogenicity assay, including eight isolates of F. oxysporum, six isolates of F. graminearum, four isolates of F. culmorum and one isolate of F. redolens. Species identification of these isolates was carried out using microscopic methods and sequencing of two genes: translation elongation factor 1-alpha (TEF1) and RNA polymerase second largest subunit (RPB2). To our knowledge, this is the first report of F. redolens being isolated from soybean in Europe. The pathogenicity test was set up by fungal inoculation of healthy soybean seeds of three cultivars: Abelina, Atlanta and Mavka. Symptoms were assessed seven days after inoculation. Disease area percentage of Fusarium inoculated seeds was significantly higher compared to uninoculated control. Nineteen isolates differed in their aggressiveness as the median disease area percentage ranged between 5.0 and 88.0% depending on isolate. The obtained isolates of four Fusarium species may be used in the future screening of soybean cultivars for resistance to these pathogens.

Characterization of the Virulence and Yield Impact of Fusarium Species on Canola (Brassica napus)

Multiple species of Fusarium can contribute to the development of root rot in canola (Brassica napus), making disease management difficult. We conducted field and greenhouse experiments to investigate the impacts of Fusarium avenaceum and Fusarium proliferatum, and the interaction between Fusarium oxysporum and F. proliferatum on root rot severity and canola yields. Inoculation with any of the three Fusarium spp. resulted in significant disease severity and reduced seedling emergence compared with non-inoculated controls, leading to yield reductions of up to 35%. Notably, there was a strong correlation (r = 0.93) between root rot severity at the seedling stage and at maturity. Regression analysis indicated a linear decline in seedling emergence with increasing disease severity. Furthermore, disease severity at maturity adversely affected the pod number per plant and the seed weight per plant, with both parameters ultimately approaching zero at a severity of 4.0 on a 0-4 scale. Co-inoculation with F. oxysporum and F. proliferatum induced more severe root rot than inoculation with each species on its own, suggesting synergistic interactions between these fungi. Knowledge of these interactions and the relative virulence of Fusarium spp. will contribute to the improved management of root rot in canola.

Production status and research advancement on root rot disease of faba bean (Vicia faba L.) in China

China is the largest producer of faba bean with a total harvested area of 8.11×10⁵ ha and a total production of 1.69 ×10⁶ tons (dry beans) in 2020, accounting for 30% of the world production. Faba bean is grown in China for both fresh pods and dry seed. East China cultivates large seed cultivars for food processing and fresh vegetables, while northwestern and southwestern China grow cultivars for dry seeds, with an increased production of fresh green pods. Most of the faba bean is consumed domestically, with limited exports. The absence of unified quality control measures and simple traditional cultivation practices contributes to the lower competitiveness of the faba bean industry in international markets. Recently, new cultivation methods have emerged with improved weed control, as well as better water and drainage management, resulting in higher quality and income for producers. Root rot disease in faba bean is caused by multiple pathogens, including Fusarium spp., Rhizoctonia spp., and Pythium spp. Fusarium spp. is the most prevalent species causing root rot in faba bean crops and is responsible for severe yield loss, with different species causing the disease in different regions in China. The yield loss ranges from 5% to 30%, up to 100% in severely infected fields. The management of faba bean root rot disease in China involves a combination of physical, chemical, and bio-control methods, including intercropping with non-host crops, applying rational nitrogen, and treating seeds with chemical or bio-seed treatments. However, the effectiveness of these methods is limited due to the high cost, the broad host range of the pathogens, and potential negative impacts on the environment and non-targeted soil organisms. Intercropping is the most widely utilized and economically friendly control method to date. This review provides an overview of the current status of faba bean production in China, the challenges faced by the industry due to root rot disease, and the progress in identifying and managing this disease. This information is critical for developing integrated management strategies to effectively control root rot in faba bean cultivation and facilitating the high-quality development of the faba bean industry.

Identification of New Fusarium sulawense Strains Causing Soybean Pod Blight in China and Their Control Using Carbendazim, Dipicolinic Acid and Kojic Acid

Soybean plants are highly susceptible to Fusarium species, which significantly reduce soybean production and quality. Several Fusarium species have been reported to synthesize mycotoxins, such as trichothecene, which have been related to major human diseases. In November 2021, soybean pods in Nantong municipality, China, showed black necrotic lesions during the harvest stage. The disease incidence reached 69%. The pathogen was identified as Fusarium sulawense via morphological analysis and sequencing of ITS, EF1-α and RPB2 genes. A PCR assay with primers targeting the trichothecene biosynthesis genes suggested that the three isolates could synthesize trichothecenes. The effectiveness of fungicide carbendazim and natural metabolites dipicolinic acid and kojic acid was screened for the management of F. sulawense on postharvest soybean pods. The highest efficacy was obtained when combining 3.8 mg/mL carbendazim and 0.84 mg/mL dipicolinic acid (curative efficacy: 49.1% lesion length inhibition; preventive efficacy: 82.7% lesion length inhibition), or 1.9 mg/mL carbendazim and 0.71 mg/mL kojic acid (preventive efficacy: 84.9% lesion length inhibition). Collectively, this report will lead to a better understanding of the safety hazards found in soybean products in China and reveals the application of dipicolinic and kojic acids to reduce the use of carbendazim.

β-Glucan-Functionalized Mesoporous Silica Nanoparticles for Smart Control of Fungicide Release and Translocation in Plants

In this work, an enzyme-responsive nanovehicle for improving captan (CAP) contact fungicide bioactivity and translocation in plant tissues was synthesized (CAP-MSNs-β-glucan) by attaching β-glucan to the outer surface of mesoporous silica nanoparticles. CAP-MSNs-β-glucan properties were tested by FTIR, ζ-potential, DLS, XRD, TGA, FE-SEM, and HR-TEM. Cargo protection ability of CAP-MSNs-β-glucan from photolysis and hydrolysis was examined in comparison to CAP commercial formulation (CAP-CF). CAP-MSNs-β-glucan distribution in plant tissues, bioactivity against Fusarium graminearum, and biotoxicity toward zebrafish (Danio rerio) were tested and compared with that of CAP-CF. CAP-MSNs-β-glucan results showed good loading efficacy reaching 18.39% and enzymatic-release dependency up to 83.8% of the total cargo after 20 days of β-glucan unsealing. CAP-MSNs-β-glucan showed significant release protection under pH changes. MSNs-β-glucan showed excellent CAP protection from UV. CAP-MSNs-β-glucan showed better distribution in corn tissues and 1.28 more inhibiting potency to Fusarium graminearum than CAP-CF. CAP-MSNs-β-glucan showed 1.88 times lower toxicity than CAP-CF to zebrafish after 96 h of treatment. We recommend using such formulations to overcome shortcomings of contact fungicides and achieve better and sustainable farming.

Logistic Models Derived via LASSO Methods for Quantifying the Risk of Natural Contamination of Maize Grain with Deoxynivalenol

Models were developed to quantify the risk of deoxynivalenol (DON) contamination of maize grain based on weather, cultural practices, hybrid resistance, and Gibberella ear rot (GER) intensity. Data on natural DON contamination of 15 to 16 hybrids and weather were collected from 10 Ohio locations over 4 years. Logistic regression with 10-fold cross-validation was used to develop models to predict the risk of DON ≥1 ppm. The presence and severity of GER predicted DON risk with an accuracy of 0.81 and 0.87, respectively. Temperature, relative humidity, surface wetness, and rainfall were used to generate 37 weather-based predictor variables summarized over each of six 15-day windows relative to maize silking (R1). With these variables, least absolute shrinkage and selection operator (LASSO) followed by all-subsets variable selection and logistic regression with 10-fold cross-validation were used to build single-window weather-based models, from which 11 with one or two predictors were selected based on performance metrics and simplicity. LASSO logistic regression was also used to build more complex multiwindow models with up to 22 predictors. The performance of the best single-window models was comparable to that of the best multiwindow models, with accuracy ranging from 0.81 to 0.83 for the former and 0.83 to 0.87 for the latter group of models. These results indicated that the risk of DON ≥1 ppm can be accurately predicted with simple models built using temperature- and moisture-based predictors from a single window. These models will be the foundation for developing tools to predict the risk of DON contamination of maize grain.

Characterization of Current Fusarium oxysporum f. sp. vasinfectum Isolates from Cotton in the San Joaquin Valley of California and Lower Valley El Paso, Texas

Fusarium oxysporum f. sp. vasinfectum race 4 is a causal agent of Fusarium wilt of cotton (Gossypium spp.). This study aimed to characterize the existing distribution and frequency of current field populations of F. oxysporum f. sp. vasinfectum race 4 genotypes in the San Joaquin Valley (SJV) of California and Lower Valley El Paso, TX and examine representative isolates for aggressiveness during different stages of seedling development. A survey was conducted from 2017 to 2019 across 13 locations in the SJV and one location in El Paso, TX during 2018. From the SJV, isolates identified as the F. oxysporum f. sp. vasinfectum race 4 T genotype were dispersed across the SJV, whereas isolates identified as the F. oxysporum f. sp. vasinfectum race 4 N genotype were most frequently isolated from cotton fields in the northern county of Merced. The F. oxysporum f. sp. vasinfectum race 4 isolates from the Texas location were identified as the MT genotype. A selection of representative isolates was evaluated using three inoculation assays (rolled-towel, F. oxysporum f. sp. vasinfectum-infested oat seed, and root-dip inoculation) to test the isolates' abilities to produce symptoms during seedling stages of cotton development. All isolates tested were capable of producing symptoms on cotton; however, isolate aggressiveness varied within and across inoculation assays. In all assays, higher levels of disease development were observed in the moderately susceptible Pima (Gossypium barbadense L.) cultivars (DP-340 or PHY-830) when compared with the moderately tolerant Upland (G. hirsutum L.) cultivar (FM-2334). However, no correlation was found among the different response variables for the rolled-towel assay when compared with the root-dip and infested oat seed assays. These results suggest that different genes are involved in the resistance response during the early seedling development stage measured in the rolled-towel assay compared with the later seedling development stages measured during the root-dip inoculation and infested oat seed assays, revealing the complexity of the Fusarium wilt disease and host-plant resistance mechanisms.

Evaluation of Pyraclostrobin as an Ingredient for Soybean Seed Treatment by Analyzing its Accumulation-Dissipation Kinetics, Plant-Growth Activation, and Protection Against Phytophthora sojae

Seed treatment with fungicides has been regarded as a principal, effective, and economic technique for soybean [Glycine max (L.) Merr.] against pathogenic microorganisms during seed germination and seedling growth. Investigation of the characteristics of seed-treatment reagents is an indispensable basis for their application. The aim of the present work is to evaluate the use of pyraclostrobin as an ingredient for soybean seed treatment by investigating its accumulation-dissipation kinetics in plants, plant-growth activation, and protection against Phytophthora sojae. The results showed that the pyraclostrobin stimulated the visible growth (root and shoot length) of soybean plants, increased the chlorophyll level and root activity, and lowered the malonaldehyde (MDA) level. The peak level and bioavailability of pyraclostrobin in soybean roots were 19.9- and 33.2-fold those in leaves, respectively, indicating that pyraclostrobin was mainly accumulated in roots. Pyraclostrobin had a continuous positive effect on the flavonoid levels and the phenylalanine ammonialyase (PAL) activity in roots and leaves, which could enhance the plant defense system. Pyraclostrobin showed in vitro toxicity to P. sojae with a half-inhibition concentration (EC50) of 1.59 and 1.24 μg/mL for pyraclostrobin and pyraclostrobin plus salicylhydroxamic acid (SHAM, an inhibitor of the alternative pathway of respiration), respectively. Seed treatment with pyraclostrobin significantly reduced the severity of Phytophthora root rot, with a control efficacy of 60.7%. To the best of our knowledge, this is the first report on the characteristics of pyraclostrobin used in soybean seed treatment and its efficacy against Phytophthora root rot.

Soybean seed treatment: how do fungicides translocate in plants?

BACKGROUND

Soybean seed treatment with fungicides is a well-established disease management strategy. However, the movement of these fungicides within seedlings is not always well characterized. Thus, the objectives of this study were to determine the pattern of translocation of three fungicides with different modes of action applied as a seed treatment, and the effect of soil type on translocation.

RESULTS

Most of the absorbed radioactivity was concentrated in the cotyledons and the maximum sum of the rates of absorption by roots, stems, and leaves of the plants was 15%. In most cases, absorption by roots, stems, and leaves were lower than 5% for 14 C-pyraclostrobin and 14 C-metalaxyl, and 1.6% for 14 C-carbendazim. Fungicides absorbed by the roots and the whole seedlings were higher when plants were grown in soil with lower organic matter content. Fungicides in the cotyledons are unlikely to be redistributed and are lost when cotyledons fall off the plants.

CONCLUSION

Cotyledons are the part of the plant where fungicides are most absorbed, regardless of the fungicide. Soil type affects the absorption of fungicides, and in this study it was most likely caused by soil organic matter. These data improve knowledge of the movement of seed treatment fungicides in soybean seedlings and may help the development of seed treatment chemistry to manage seed and soilborne pathogens.

A Genome-Wide Association Study To Understand the Effect of Fusarium verticillioides Infection on Seedlings of a Maize Diversity Panel

Fusarium verticillioides, which causes ear, kernel and stem rots, has been reported as the most prevalent species on maize worldwide. Kernel infection by F. verticillioides results in reduced seed yield and quality as well as fumonisin contamination, and may affect seedling traits like germination rate, entire plant seedling length and weight. Maize resistance to Fusarium is a quantitative and complex trait controlled by numerous genes with small effects. In the present work, a Genome Wide Association Study (GWAS) of traits related to Fusarium seedling rot was carried out in 230 lines of a maize association population using 226,446 SNP markers. Phenotypes were scored on artificially infected kernels applying the rolled towel assay screening method and three traits related to disease response were measured in inoculated and not-inoculated seedlings: plant seedling length (PL), plant seedling weight (PW) and germination rate (GERM). Overall, GWAS resulted in 42 SNPs significantly associated with the examined traits. Two and eleven SNPs were associated with PL in inoculated and not-inoculated samples, respectively. Additionally, six and one SNPs were associated with PW and GERM traits in not-inoculated kernels, and further nine and thirteen SNPs were associated to the same traits in inoculated kernels. Five genes containing the significant SNPs or physically closed to them were proposed for Fusarium resistance, and 18 out of 25 genes containing or adjacent to significant SNPs identified by GWAS in the current research co-localized within QTL regions previously reported for resistance to Fusarium seed rot, Fusarium ear rot and fumonisin accumulation. Furthermore, linkage disequilibrium analysis revealed an additional gene not directly observed by GWAS analysis. These findings could aid to better understand the complex interaction between maize and F. verticillioides.

Specific Detection and Identification of Fusarium graminearum Sensu Stricto Using a PCR-RFLP Tool and Specific Primers Targeting the Translational Elongation Factor 1α Gene

Fusarium graminearum is a toxigenic plant pathogen that causes Fusarium head blight (FHB) disease on cereal crops. It has recently shown to have cross-pathogenicity on noncereals (i.e., Fusarium root rot [FRR] on soybean) in Canada and elsewhere. Specific detection and differentiation of this potent toxigenic, trichothecene-producing pathogen among other closely related species is extremely important for disease control and mycotoxin monitoring. Here, we designed a PCR restriction fragment length polymorphism protocol based on the DNA sequence of the translational elongation factor 1α (TEF1α) gene. A unique restriction site to the enzyme HpaII is only found in F. graminearum sensu stricto strains among different Fusarium strains in the F. graminearum species complex (FGSC) and other Fusarium spp. associated with FHB in cereals and FRR in soybean. Partial amplification of the TEF1α gene with newly designed primers mh1/mh2 generated a 459-bp PCR fragment. Restriction digestion of the generated fragments with the HpaII enzyme generated a unique restriction pattern that can rapidly and accurately differentiate F. graminearum sensu stricto among all other Fusarium spp. A primer pair (FgssF/FgssR) specific to F. graminearum sensu stricto also was designed and can distinguish F. graminearum sensu stricto from all other Fusarium spp. in the FGSC and other closely related Fusarium spp. involved in FHB and FRR. This finding will be very useful for the specific detection of F. graminearum sensu stricto for diagnostic purposes as well as for the accurate detection of this pathogen in breeding and other research purposes.

Effects of Temperature and pH on Fusarium oxysporum and Soybean Seedling Disease

Fusarium oxysporum (Fo) is an important pathogen that reduces soybean yield by causing seedling disease and root rot. This study assessed the effects of pH and temperature on Fo fungal growth and seedling disease. In an in vitro assay, 14 Fo isolates collected from symptomatic soybean roots across Iowa in 2007 were grown on artificial culture media at five pH levels (4, 5, 6, 7, and 8) and incubated at four temperatures (15, 20, 25, or 30°C). In a rolled-towel assay, soybean seeds from Fo-susceptible cultivar Jack were inoculated with a suspension of a pathogenic or a nonpathogenic Fo isolate; both isolates were previously designated for their relative aggressiveness in causing root rot at 25°C. The seeds were placed in rolled germination paper, and the rolls were incubated in all combinations of buffer solutions at four pH levels (4, 5, 6, and 7), and four temperatures (15, 20, 25, or 30°C). There was a significant interaction between temperature and pH (P < 0.05) for in vitro radial growth and root rot severity. Isolates showed the most in vitro radial growth after incubation at pH 6 and 25°C. For the rolled-towel assay, the pathogenic isolate caused the most severe root rot at pH 6 and 30°C. Gaussian regression analysis estimates for optimal conditions were pH 6.3 at 27.1°C for maximal fungal growth and pH 5.9 at 30°C for maximal root rot severity. These results indicate that optimal pH and temperature conditions are similar for Fo growth and disease in soybean seedlings and suggest that Fo may be a more important seedling pathogen when soybeans are planted under warm conditions in moderately acidic soils.

Characterization and Pathogenicity of Fusarium Species Associated with Soybean Pods in Maize/Soybean Strip Intercropping

Intercropping has been considered as a kind of a sustainable agricultural cropping system. In southwest China, maize/soybean strip intercropping has commonly been practised under local limited agricultural land resources. However, heavy rainfall in combination with high humidity and low temperatures cause severe pod and seed deterioration in the maturity and pre-harvesting stages of intercropped soybean. Numerous Fusarium species have been reported as the dominant pathogens of soybean root rot, seedling blight, as well as pod field mold in this area. However, the diversity and pathogenicity of Fusarium species on soybean pods remain unclear. In the current study, diseased soybean pods were collected during the cropping season of 2018 from five different intercropped soybean producing areas. A total of 83 Fusarium isolates were isolated and identified as F. fujikuroi, F. graminearum, F. proliferatum, and F. incarnatum-equiseti species complex based on morphological characteristics and phylogenetic analysis of the nucleotide sequence of EF1-α and RPB2 genes. Pathogenicity tests demonstrated that all Fusarium species were pathogenic to seeds of the intercropped soybean cultivar Nandou12. Fusarium fujikuroi had the maximum disease severity, with a significant reduction of seed germination rate, root length, and seed weight, followed by F. equiseti, F. graminearum, F. proliferatum, and F. incarnatum. Additionally, the diversity of Fusarium species on soybean pods was also considerably distinct according to the geographical origin and soybean varieties. Thus, the findings of the current study will be helpful for the management and resistance breeding of soybean pod decay in the maize/soybean intercropping system.

A Genome Wide Association Study Reveals Markers and Genes Associated with Resistance to Fusarium verticillioides Infection of Seedlings in a Maize Diversity Panel

Fusarium verticillioides infects maize, causing ear rot, yield loss and contamination by fumonisin mycotoxins. The fungus can be transmitted via kernels and cause systemic infection in maize. Maize resistance to the fungus may occur at different developmental stages, from seedling to maturity. Resistance during kernel germination is part of the plant-pathogen interaction and so far this aspect has not been investigated. In the present study, a genome wide association study (GWAS) of resistance to Fusarium during the seedling developmental stage was conducted in a maize diversity panel using 226,446 SNP markers. Seedling germination and disease phenotypes were scored on artificially inoculated kernels using the rolled towel assay. GWAS identified 164 SNPs significantly associated with the traits examined. Four SNPs were associated with disease severity score after inoculation, 153 were associated with severity in asymptomatic kernels and 7 with the difference between the severity ratings in inoculated and non-inoculated seeds. A set of genes containing or physically near the significant SNPs were identified as candidates for Fusarium resistance at the seedling stage. Functional analysis revealed that many of these genes are directly involved in plant defense against pathogens and stress responses, including transcription factors, chitinase, cytochrome P450, and ubiquitination proteins. In addition, 25 genes were found in high linkage disequilibrium with the associated SNPs identified by GWAS and four of them directly involved in disease resistance. These findings contribute to understanding the complex system of maize-F. verticillioides and may improve genomic selection for Fusarium resistance at the seedling stage.

Loci and candidate genes in soybean that confer resistance to Fusarium graminearum

KEY MESSAGE

Association analysis techniques were used to identify and verify twelve single nucleotide polymorphisms (SNPs) associated with Fusarium graminearum resistance. Two novel candidate genes were obtained. Fusarium graminearum causes seed and root rot and seedling damping-off of soybean, leading to severe yield loss. Presently, the genetic basis of resistance to F. graminearum is elucidated in only four soybean accessions, which is not sufficient for resistance improvement. The objective of the present study was to identify the genome-wide genetic architecture of resistance to F. graminearum in landraces and cultivated soybeans based on a growth room evaluation. The resistance levels of 314 diverse accessions were tested, and 22,888 single nucleotide polymorphisms (SNPs) with a minor allele frequency of > 0.05 were developed using the specific-locus amplified fragment sequencing (SLAF-seq) approach. Twelve SNPs were identified as associated with F. graminearum resistance, and these SNPs were located at 12 genomic regions on eight chromosomes (Chr.) and could explain 5.53-14.71% of the observed phenotypic variation. One SNP, rs9479021, located on Chr.6, overlapped with qRfg_Gm06, the known QTL for resistance to F. graminearum. The other SNPs were novel and associated with resistance to F. graminearum. Nine novel candidate genes were predicted to contribute to resistance to F. graminearum according to the haplotype and transcript abundance analysis of the candidate genes. The identified markers and resistant cultivars are valuable for the improvement of resistance to F. graminearum.

In Vitro and in Field Response of Different Fungicides against Aspergillus flavus and Fusarium Species Causing Ear Rot Disease of Maize

Aspergillus flavus, the main aflatoxin B₁ producing fungal species, Fusarium graminearum, a deoxynivalenol producer, and the fumonisin-producing species F. proliferatum and F. verticillioides are the main toxigenic fungi (TF) that colonize maize. Several strategies are available to control TF and related mycotoxins, such as chemical control. However, there is poor knowledge on the efficacy of fungicides on maize plants since few molecules are registered. The sensitivity of F. graminearum, F. proliferatum, F. verticillioides, and A. flavus to eleven fungicides, selected based on their different modes of action, was evaluated in both in vitro assays and, after selection, in the field. In vitro, demethylation inhibitors (DMI) showed excellent performances, followed by thiophanate-methyl and folpet. Among the succinate dehydrogenase inhibitors (SDHI), isopyrazam showed a higher effectiveness against Fusarium species than boscalid, which was ineffective against Fusarium, like the phenyl-pyrrole fludioxonil. Furthermore, both SDHIs and fludioxonil were more active against A. flavus than Fusarium species. In field trials, prothioconazole and thiophanate-methyl were confirmed to be effective to reduce F. graminearum (52% and 48%) and F. proliferatum contamination (44% and 27%). On the other hand, prothioconazole and boscalid could reduce A. flavus contamination at values of 75% and 56%, respectively.

Aflatoxin B1 and zearalenone in soybeans: occurrence and distribution in whole and defective kernels

Few studies have addressed the distribution of mycotoxins in soybean and/or their processing fractions. In this study, samples from commercial lots were collected in four Brazilian states. The distribution of mycotoxins in soybean fractions, according to their commercial grading system, namely whole kernels (WK), split, broken and crushed kernels (SBCK), damaged kernels (DK), heat damaged and burned kernels (HDBK), moldy kernels (MK), greenish kernels (GK), foreign material + impurities (FMI), were analyzed using HPLC-FLD. AFB1 and ZEN tested positive in 43.3 and 80%, respectively. The incidence of AFB1 was higher in MK (50%), followed by HDBK (30.4%) and FMI (26.0%). ZEA incidence ranged from 69% (SBCK) to 100% (HDBK). Co-occurrence (53.3%) in at least one fraction was also detected. Brazil is the second world producer of soybeans, which places the country in a very important position. Therefore, the information provided is crucial and timely relevant for the industry and policymakers.

Effect of water activity and temperature on growth and trichothecene production by Fusarium meridionale

Fusarium meridionale has been frequently isolated from soybean in Argentina and showed similar pathogenicity as F. graminearum sensu stricto. However, no data on their growth and mycotoxin production under different environmental conditions are yet available. The aims of this study were: to determine the effect of temperature, water activity (aW) and strain on growth of F. meridionale and to evaluate deoxynivalenol (DON) and nivalenol (NIV) production in a soybean based medium. The results showed that optimal conditions for F. meridionale growth were at 25 °C and 0.98-0.99 aW. Deoxynivalenol production was favored at 25 °C and 0.96 aW while NIV production was strain-dependent, being 30 °C and 0.98 aW optimal conditions for F. meridionale B2300 strain and 20 °C and 0.98 aW for F. meridionale F5043 and F. meridionale 5048 strains. These conditions are similar to those observed at pre-harvest stage in soybean crop, thus control strategies need to be considered to reduce the risk of the occurrence of DON and NIV in harvested grains.

The Effect of Cold Stress on Damping-Off of Soybean Caused by Pythium sylvaticum

To improve our understanding of the timing of cold stress and its effect on Pythium damping-off, we performed a factorial experiment with two cold stress temperatures (4 and 10°C); exposure to 96 h of cold stress at 0, 1, 2, 4, 6, and 8 days after planting; and inoculation with Pythium sylvaticum-infested millet or control. Increased susceptibility to damping-off resulting in reduced emergence was found in inoculated plants when the cold stress period began 2 or 4 days after planting. In the noninoculated controls, no effect of cold stress on emergence was observed. Slower seedling growth was observed during the cold stress period and in inoculated plants after exposure to cold stress. Seed exudation, mycelial growth, and sporangia germination of P. sylvaticum was evaluated at 4, 10, and 18°C. The greatest seed exudation was observed at 4°C. Low temperatures delayed mycelial growth of P. sylvaticum, although the pathogen was still able to grow at 4°C. Sporangia incubated for 3 h at 18°C in the presence of seed exudates had higher germination in comparison with sporangia incubated at 10 or 4°C. Moreover, more sporangia germinated in response to seed exudates that were previously collected from seed imbibed for 24 h at low temperatures (4°C). These results suggest that cold stress 2 to 4 days after planting increases soybean susceptibility to damping-off, presumably because of increased seed exudation and delayed seedling growth.

Isolate-Cultivar Interactions, In Vitro Growth, and Fungicide Sensitivity of Fusarium oxysporum Isolates Causing Seedling Disease on Soybean

Fusarium oxysporum is frequently associated with soybean root rot in the United States. Information about pathogenicity and other phenotypic characteristics of F. oxysporum populations is limited. The objective of the research described herein was to assess phenotypic characteristics of F. oxysporum isolates from soybean, including the interaction between isolates and soybean cultivars, fungal growth characteristics in culture, and sensitivity to fungicides commonly used as seed treatment products. The pathogenicity of 14 isolates was evaluated in rolled-towel and Petri-dish assays using 11 soybean cultivars. In the rolled-towel assay, seed were inoculated with a conidial suspension and disease severity was observed. In the Petri-dish assay, F. oxysporum isolates were grown on 2% water agar and seed were placed on the F. oxysporum colony to observe the symptoms that developed. Cultivars differed in susceptibility to F. oxysporum, and significant (P = 0.0140) isolate-cultivar interactions were observed. F. oxysporum isolates differed in radial growth on potato dextrose agar at 25°C. Pyraclostrobin and trifloxystrobin reduced conidial germination with average 50% effective concentration (EC50) of 0.15 and 0.20 µg active ingredient (a.i.)/ml, respectively. Ipconazole reduced fungal growth with average EC50 of 0.23 µg a.i./ml, whereas fludioxonil was ineffective. Our results illustrate soybean F. oxysporum isolate variability and the potential for their management through cultivar selection or seed treatment.

Pathogenicity of Fumonisin-producing and Nonproducing Strains of Aspergillus Species in Section Nigri to Maize Ears and Seedlings

Species of Aspergillus section Nigri are commonly associated with maize kernels, and some strains can produce fumonisin mycotoxins. However, there is little information about the extent to which these fungi contribute to fumonisin contamination in grain, the damage they cause to maize ears, or their effects on maize seed germination and seedling health. We compared fumonisin-producing and nonproducing strains of A. niger, A. welwitschiae, A. phoenicis, A. tubingensis, and A. carbonarius from the United States and Italy in laboratory and field studies to assess their ability to contribute to fumonisin contamination, to cause maize ear rot, and to affect seed germination and seedling growth. In laboratory experiments, some strains of each Aspergillus species reduced germination or seedling growth, but there was high variability among strains within species. There were no consistent differences between fumonisin-producing and nonproducing strains. In field studies in Iowa and Illinois, strains were variable in their ability to cause ear rot symptoms, but this was independent of the ability of the Aspergillus strains to produce fumonisins. Contamination of grain with fumonisins was not consistently increased by inoculation with Aspergillus strains compared with the control, and was much greater in F. verticillioides-inoculated treatments than in Aspergillus-inoculated treatments. However, the ratio of the FB analogs FB₂ and FB₁ was altered by inoculation with some Aspergillus strains, indicating that FB₂ production by Aspergillus strains occurred in the field. These results demonstrate the pathogenic capabilities of strains of Aspergillus in section Nigri, but suggest that their effects on maize ears and seedlings are not related to their ability to produce fumonisins, and that fumonisin contamination of grain caused by Aspergillus spp. is not as significant as that caused by Fusarium spp.

Molecular Basis of Resistance to Fusarium Ear Rot in Maize

The impact of climate change has been identified as an emerging issue for food security and safety, and the increased incidence of mycotoxin contamination in maize over the last two decades is considered a potential emerging hazard. Disease control by chemical and agronomic approaches is often ineffective and increases the cost of production; for this reason the exploitation of genetic resistance is the most sustainable method for reducing contamination. The review focuses on the significant advances that have been made in the development of transcriptomic, genetic and genomic information for maize, Fusarium verticillioides molds, and their interactions, over recent years. Findings from transcriptomic studies have been used to outline a specific model for the intracellular signaling cascade occurring in maize cells against F. verticillioides infection. Several recognition receptors, such as receptor-like kinases and R genes, are involved in pathogen perception, and trigger down-stream signaling networks mediated by mitogen-associated protein kinases. These signals could be orchestrated primarily by hormones, including salicylic acid, auxin, abscisic acid, ethylene, and jasmonic acid, in association with calcium signaling, targeting multiple transcription factors that in turn promote the down-stream activation of defensive response genes, such as those related to detoxification processes, phenylpropanoid, and oxylipin metabolic pathways. At the genetic and genomic levels, several quantitative trait loci (QTL) and single-nucleotide polymorphism markers for resistance to Fusarium ear rot deriving from QTL mapping and genome-wide association studies are described, indicating the complexity of this polygenic trait. All these findings will contribute to identifying candidate genes for resistance and to applying genomic technologies for selecting resistant maize genotypes and speeding up a strategy of breeding to contrast disease, through plants resistant to mycotoxin-producing pathogens.

Genetic mapping and haplotype analysis of a locus for quantitative resistance to Fusarium graminearum in soybean accession PI 567516C

KEY MESSAGE

A major novel quantitative disease resistance locus, qRfg_Gm06, for Fusarium graminearum was genetically mapped to chromosome 6. Genomic-assisted haplotype analysis within this region identified three putative candidate genes. Fusarium graminearum causes seed, root rot, and seedling damping-off in soybean which contributes to reduced stands and yield. A cultivar Magellan and PI 567516C were identified with low and high levels of partial resistance to F. graminearum, respectively. Quantitative disease resistance loci (QDRL) were mapped with 241 F7:8 recombinant inbred lines (RILs) derived from a cross of Magellan × PI 567516C. Phenotypic evaluation for resistance to F. graminearum used the rolled towel assay in a randomized incomplete block design. The genetic map was constructed from 927 polymorphic single nucleotide polymorphism (SNP) and simple sequence repeat (SSR) markers. One major QDRL qRfg_Gm06 was detected and mapped to chromosome 6 with a LOD score of 20.3 explaining 40.2% of the total phenotypic variation. This QDRL was mapped to a ~400 kb genomic region of the Williams 82 reference genome. Genome mining of this region identified 14 putative candidate disease resistance genes. Haplotype analysis of this locus using whole genome re-sequencing (WGRS) of 106 diverse soybean lines narrowed the list to three genes. A SNP genotyping Kompetitive allele-specific PCR (KASP) assay was designed for one of the genes and was validated in a subset of the RILs and all 106 diverse lines.

Fungicide and Cultivar Effects on Sudden Death Syndrome and Yield of Soybean

The effect of fungicides on severity of sudden death syndrome (SDS; caused by Fusarium virguliforme), plant establishment, and soybean yield was evaluated in 12 field experiments conducted in Illinois, Indiana, Iowa, Michigan, and Ontario in 2013 and 2014. Two soybean cultivars that differed in susceptibility to SDS were planted in fields with a history of SDS or with artificial augmentation of F. virguliforme. Efficacy of seed, in-furrow, and foliar-applied fungicides was assessed. SDS levels varied across locations and years. Fluopyram applied on the seed or in-furrow reduced foliar disease index maximum up to 95% in 5 of the 12 experiments. In three experiments with significant (P < 0.10) treatment effect, fluopyram seed treatment improved yields up to 11% compared with the base seed treatment comprising prothioconazole + penflufen + metalaxyl and clothianidin + Bacillus firmus. Meta-analysis also indicated that the fluopyram seed treatment and in-furrow application were effective at reducing SDS and increasing yield relative to the control; however, the baseline disease influenced the yield and disease response to fungicide treatments. Treatment effect was not significant when disease pressure was low. The concentration of F. virguliforme DNA in soybean roots, measured by a specific real-time quantitative polymerase chain reaction assay, was not different among fungicide treatments in 9 of 10 experiments. Moderately resistant cultivars had less disease than susceptible cultivars, indicating that resistant cultivars in combination with fluopyram seed treatment or in-furrow application could provide effective management of SDS.

Transcriptome profiling of soybean (Glycine max) roots challenged with pathogenic and non-pathogenic isolates of Fusarium oxysporum

BACKGROUND

Fusarium oxysporum is one of the most common fungal pathogens causing soybean root rot and seedling blight in U.S.A. In a recent study, significant variation in aggressiveness was observed among isolates of F. oxysporum collected from roots in Iowa, ranging from highly pathogenic to weakly or non-pathogenic isolates.

RESULTS

We used RNA-seq analysis to investigate the molecular aspects of the interactions of a partially resistant soybean genotype with non-pathogenic/pathogenic isolates of F. oxysporum at 72 and 96 h post inoculation (hpi). Markedly different gene expression profiles were observed in response to the two isolates. A peak of highly differentially expressed genes (HDEGs) was triggered at 72 hpi in soybean roots and the number of HDEGs was about eight times higher in response to the pathogenic isolate compared to the non-pathogenic one (1,659 vs. 203 HDEGs, respectively). Furthermore, the magnitude of induction was much greater in response to the pathogenic isolate. This response included a stronger activation of defense-related genes, transcription factors, and genes involved in ethylene biosynthesis, secondary and sugar metabolism.

CONCLUSIONS

The obtained data provide an important insight into the transcriptional responses of soybean-F. oxysporum interactions and illustrate the more drastic changes in the host transcriptome in response to the pathogenic isolate. These results may be useful in the developing new methods of broadening resistance of soybean to F. oxysporum, including the over-expression of key soybean genes.

Identification and mapping of quantitative trait loci (QTL) conferring resistance to Fusarium graminearum from soybean PI 567301B

KEY MESSAGE

A major novel QTL was identified in a recombinant inbred line population derived from a cross of 'Wyandot' × PI 567301B for Fusarium graminearum, a seed and seedling pathogen of soybean. Fusarium graminearum is now recognized as a primary pathogen of soybean, causing root, seed rot and seedling damping-off in North America. In a preliminary screen, 'Wyandot' and PI 567301B were identified with medium and high levels of partial resistance to F. graminearum, respectively. The objective of this study was to characterise resistance towards F. graminearum using 184 recombinant inbred lines (RILs) derived from a cross of 'Wyandot' × PI 567301B. The parents and the RILs of the mapping population were evaluated for resistance towards F. graminearum using the rolled towel assay in a randomized incomplete block design. A genetic map was constructed from 2545 SNP markers and 2 SSR markers by composite interval mapping. One major and one minor QTL were identified on chromosomes 8 and 6, respectively, which explained 38.5 and 8.1 % of the phenotypic variance. The major QTL on chromosome 8 was mapped to a 300 kb size genomic region of the Williams 82 sequence. Annotation of this region indicates that there are 39 genes including the Rhg4 locus for soybean cyst nematode (SCN) resistance. Based on previous screens, PI 567301B is susceptible to SCN. Fine mapping of this locus will assist in cloning these candidate genes as well as identifying DNA markers flanking the QTL that can be used in marker-assisted breeding to develop cultivars with high levels of resistance to F. graminearum.

Genotypic and Phenotypic Characterization of Fungi in the Fusarium oxysporum Species Complex from Soybean Roots

Isolates in the Fusarium oxysporum species complex (FOSC) from soybean range from nonpathogenic to aggressive pathogens causing seedling damping-off, wilt, and root rot. The objective of this research was to characterize the genotype and phenotype of isolates within the FOSC recovered predominantly from soybean roots and seedlings. Sequence analyses of the translation elongation factor (tef1α) gene and the mitochondrial small subunit (mtSSU), polymerase chain reaction restriction fragment length polymorphism (PCR-RFLP) analysis of the intergenic spacer (IGS) region, and identification of the mating type loci were conducted for 170 isolates. Vegetative compatibility (VC) tests were conducted for 114 isolates. Isolate aggressiveness was tested using a rolled towel assay for 159 isolates. Phylogenetic analysis of the tef1α and mtSSU and PCR-RFLP analysis of the IGS region separated the FOSC isolates into five clades, including F. commune. Both mating type loci, MAT1-1 or MAT1-2, were present in isolates from all clades. The VC tests were not informative, because most VC groups consisted of a single isolate. Isolate aggressiveness varied within and among clades; isolates in clade 2 were significantly less aggressive (P < 0.0001) when compared with isolates from the other clades and F. commune. The results from this study demonstrate the high levels of genotypic and phenotypic diversity within the FOSC from soybean but further work is needed to identify characteristics associated with pathogenic capabilities.

Fusarium graminearum Possesses Virulence Factors Common to Fusarium Head Blight of Wheat and Seedling Rot of Soybean but Differing in Their Impact on Disease Severity

Fusarium graminearum is a toxigenic fungal pathogen that causes Fusarium head blight (FHB) and crown rot on cereal crops worldwide. This fungus also causes damping-off and crown and root rots at the early stage of crop development in soybean cultivated in North and South America. Several F. graminearum genes were investigated for their contribution to FHB in cereals but no inherent study is reported for the dicotyledonous soybean host. In this study we determined the disease severity on soybean seedlings of five single gene disrupted mutants of F. graminearum, previously characterized in wheat spike infection. Three of these mutants are impaired on a specific function as the production of deoxynivalenol (DON, Δtri5), lipase (ΔFgl1), and xylanase (Δxyl03624), while the remaining two are MAP kinase mutants (ΔFgOS-2, Δgpmk1), which are altered in signaling pathways. The mutants that were reduced in virulence (Δtri5, ΔFgl1, and ΔFgOS-2) or are avirulent (Δgpmk1) on wheat were correspondently less virulent or avirulent in soybean seedlings, as shown by the extension of lesions and seedling lengths. The Δxyl03624 mutant was as virulent as the wild type mirroring the behavior observed in wheat. However, a different ranking of symptom severity occurred in the two hosts: the ΔFgOS-2 mutant, that infects wheat spikelets similarly to Δtri5 and ΔFgl1 mutants, provided much reduced symptoms in soybean. Differently from the other mutants, we observed that the ΔFgOS-2 mutant was several fold more sensitive to the glyceollin phytoalexin suggesting that its reduced virulence may be due to its hypersensitivity to this phytoalexin. In conclusion, lipase and DON seem important for full disease symptom development in soybean seedlings, OS-2 and Gpmk1 MAP kinases are essential for virulence, and OS-2 is involved in conferring resistance to the soybean phytoalexin.

Adsorption-desorption and leaching of pyraclostrobin in Indian soils

Pyraclostrobin is a new broad-spectrum foliar applied and seed protectant fungicide of the strobilurin group. In this paper, adsorption-desorption of pyraclostrobin has been investigated in three different soils viz. Inceptisol (sandy loam, Delhi), Vertisol (sandy clay, Hyderabad) and Ultisol (sandy clay loam, Thrissur). Effect of organic matter and clay content on sorption was also studied in Inceptisol of Delhi. Leaching potential of pyraclostrobin as influenced by rainfall was studied in intact soil columns to confirm the results of adsorption-desorption studies. The adsorption studies were carried out at initial concentrations of 0.05, 0.1, 0.5, 1 and 1.5 μg mL(-1). The distribution coefficient (Kd) values in three test soils ranged from 4.91 to 18.26 indicating moderate to high adsorption. Among the three test soils, adsorption was the highest in Ultisol (Kd 18.26), followed by Vertisol (Kd 9.87) and Inceptisol (Kd 4.91). KF value was also highest for Ultisol soil (66.21), followed by Vertisol (40.88) and Inceptisol (8.59). S-type adsorption isotherms were observed in all the three test soils. Kd values in organic carbon-removed soil and clay-removed soil were 3.57 and 2.83 respectively, indicating lower adsorption than normal Inceptisol. Desorption studies were carried out at initial concentrations of 0.5, 1 and 1.5 μg mL(-1). Desorption was the greatest in Inceptisol, followed by Vertisol and Ultisol. Amounts of pyraclostrobin desorbed in three desorption cycles for different concentrations were 23.1-25.3%, 9.4-20.7% and 8.1-13.6% in Inceptisol, Vertisol and Ultisol respectively. Desorption was higher in clay fraction-removed and organic carbonremoved soils than normal Inceptisol. Desorption was slower than adsorption in all the test soils, indicating hysteresis effect (with hysteresis coefficient values varying from 0.05 to 0.20). Low values of hysteresis coefficient suggest high hysteresis effect indicating easy and strong adsorption, and slow desorption, of pyraclostrobin in soils. Higher hysteresis coefficient values in organic carbon removed soil (0.25-0.30) and clay fraction removed soil (0.28-0.36) as compared to normal Inceptisol soil suggest relatively weak adsorption and easy desorption of pyraclostrobin. Results of regression analysis suggest that the organic matter and pH of the soil play a major role in adsorption of pyraclostrobin. Leaching studies were carried out in intact soil columns in Inceptisol. The columns were leached with different amounts of water simulating different amounts of rainfall. The results suggest that most of the pyraclostrobin residues will remain present in the top soil layers even under high rainfall conditions and chances of pyraclostrobin moving to lower soil depth are almost negligible.