scholarly journals Diagnostic qPCR Assay to Detect Fusarium brasiliense, a Causal Agent of Soybean Sudden Death Syndrome and Root Rot of Dry Bean

Plant Disease ◽  
2020 ◽  
Vol 104 (1) ◽  
pp. 246-254
Author(s):  
Mitchell G. Roth ◽  
Kjersten A. Oudman ◽  
Amanda Griffin ◽  
Janette L. Jacobs ◽  
Hyunkyu Sang ◽  
...  

Species within clade 2 of the Fusarium solani species complex (FSSC) are significant pathogens of dry bean (Phaseolus vulgaris) and soybean (Glycine max), causing root rot and/or sudden death syndrome (SDS). These species are morphologically difficult to distinguish and often require molecular tools for proper diagnosis to a species level. Here, a TaqMan probe-based quantitative PCR (qPCR) assay was developed to distinguish Fusarium brasiliense from other closely related species within clade 2 of the FSSC. The assay displays high specificity against close relatives and high sensitivity, with a detection limit of 100 fg. This assay was able to detect F. brasiliense from purified mycelia, infected dry bean roots, and soil samples throughout Michigan. When multiplexed with an existing qPCR assay specific to Fusarium virguliforme, accurate quantification of both F. brasiliense and F. virguliforme was obtained, which can facilitate accurate diagnoses and identify coinfections with a single reaction. The assay is compatible with multiple qPCR thermal cycling platforms and will be helpful in providing accurate detection of F. brasiliense. Management of root rot and SDS pathogens in clade 2 of the FSSC is challenging and must be done proactively, because no midseason management strategies currently exist. However, accurate detection can facilitate management decisions for subsequent growing seasons to successfully manage these pathogens.

Plant Disease ◽  
2019 ◽  
Vol 103 (6) ◽  
pp. 1234-1243 ◽  
Author(s):  
Jie Wang ◽  
Hyunkyu Sang ◽  
Janette L. Jacobs ◽  
Kjersten A. Oudman ◽  
Linda E. Hanson ◽  
...  

Sudden death syndrome (SDS), caused by members of Fusarium solani species complex (FSSC) clade 2, is a major and economically important disease in soybean worldwide. The primary causal agent of SDS isolated to date in North America has been F. virguliforme. In 2014 and 2016, SDS symptoms were found in two soybean fields located on the same farm in Michigan. Seventy Fusarium strains were isolated from roots of the SDS-symptomatic soybeans in two fields. Phylogenetic analysis of partial sequences of elongation factor-1α, the nuclear ribosomal DNA intergenic spacer region, and the RNA polymerase II beta subunit revealed that the primary FSSC species isolated was F. brasiliense (58 and 36% in each field) and the remaining Fusarium strains were identified as F. cuneirostrum, F. phaseoli, an undescribed Fusarium sp. from FSSC clade 2, and strains in FSSC clade 5 and FSSC clade 11. Molecular identification was supported with morphological analysis and a pathogenicity assay. The soybean seedling pathogenicity assay indicated that F. brasiliense was capable of causing typical foliar SDS symptoms. Both root rot and foliar disease severity were variable by strain, just as they are in F. virguliforme. Both FSSC 5 and FSSC 11 strains were also capable of causing root rot, but SDS foliar symptoms were not detected. To our knowledge, this is the first report of F. brasiliense causing SDS in soybean in the United States and the first report of F. cuneirostrum, F. phaseoli, an as-yet-unnamed Fusarium sp., and strains in FSSC clade 5 and FSSC clade 11 associated with or causing root rot of soybean in Michigan.


Plant Disease ◽  
2017 ◽  
Vol 101 (3) ◽  
pp. 434-441 ◽  
Author(s):  
Gretchen M. Freed ◽  
Crystal M. Floyd ◽  
Dean K. Malvick

Sudden death syndrome (SDS) of soybean, caused by Fusarium virguliforme, is a significant disease of soybean. The suite of factors that influence disease development is incompletely understood. The goal of this study was to determine the effects of pathogen population levels, crop residues, seed exudates, and their interactions on development of SDS and growth of F. virguliforme. Studies were conducted in a greenhouse with cultivars susceptible and partially resistant to SDS, four pathogen population levels, and six crop residue treatments (none; ground corn seed, stalks, and roots; ground soybean stems; and sorghum seed). Root rot was assessed 15 and 50 days after inoculation (dai) and foliar disease and plant biomass were assessed 50 dai. Population level increases and crop residues had significant interacting effects on increasing foliar disease severity and root rot and on biomass reduction. Disease severity was positively correlated with population and biomass was negatively correlated. Plants grown with no crop residues exhibited low or no root rot or foliar disease 15 dai, and severity was greatest with corn and sorghum seed. In vitro studies were conducted to test the effects of exudates collected from germinating soybean and corn seed on growth of F. virguliforme and F. solani. Growth of these fungi was greater in exudates than in water. More growth occurred in exudates collected during soybean radicle emergence than those sampled at other times during germination. These studies show that pathogen population levels and crop-derived nutrients in soil interact and influence severity of SDS. Results have implications for gaging disease risk and managing SDS.


Plant Disease ◽  
2011 ◽  
Vol 95 (4) ◽  
pp. 436-440 ◽  
Author(s):  
C. C. Gongora-Canul ◽  
L. F. S. Leandro

Sudden death syndrome (SDS) of soybean is favored by planting in cool soil but epidemics can be severe even when planting occurs later in the season into warmer soil. Our objective was to determine how soil temperature affects susceptibility of plants exposed to Fusarium virguliforme at different ages. Soybean plants were grown in rhizotrons in water baths at 17, 23, and 29°C. Subsets of plants were inoculated 0, 3, 7, and 13 days after planting (DAP) by drenching soil with a conidial suspension. Root rot developed in all inoculated plants but severity decreased with increasing temperature and plant age at inoculation. Severity of foliar symptoms also decreased with increasing plant age. Whereas plants inoculated 0 DAP developed severe foliar symptoms at all temperatures, plants inoculated 3 and 7 DAP developed symptoms only at 17 and 23°C, and those inoculated 13 DAP never developed foliar symptoms at any temperature. Root length at inoculation was negatively correlated with disease severity. Our findings suggest that roots are most susceptible to infection during the first days after seed germination and that accelerated root growth in warmer temperatures reduces susceptibility to root infection conducive to foliar symptoms. However, soil temperature may not affect infections that occur as soon as seeds germinate.


Plant Disease ◽  
2010 ◽  
Vol 94 (9) ◽  
pp. 1164-1164 ◽  
Author(s):  
M. I. Chilvers ◽  
D. E. Brown-Rytlewski

Leaf lesions and root rot symptoms typical of soybean sudden death syndrome (SDS) caused by Fusarium virguliforme O'Donnell & T. Aoki were observed in commercial soybeans (Glycine max (L.) Merr.) in southern Michigan. Leaf symptoms ranged from chlorotic spots to severe interveinal chlorosis and necrosis, no foliar pathogens were noted. In 2008, isolates were collected from Berrien and St. Joseph counties. In 2009, isolates were collected from Cass, St. Joseph, Van Buren, Allegan, and Monroe counties. Pieces of roots with root rot symptoms were washed prior to surface disinfestation with 70% ethanol for 30 s and 0.5% NaOCl for 1 min and incubated on water agar (WA) in petri plates amended with 50 μg/ml of chloramphenicol for the production of sporodochia. Alternatively, spores were collected directly from nondisinfested roots expressing blue sporodochia. Single-spore cultures were derived by streaking macroconidia with a bacterial loop onto 3% WA + chloramphenicol and incubated overnight. With a dissecting microscope, single germinated macroconidia were collected with a sterile 0.2-mm-diameter insect pin and transferred to potato dextrose agar (PDA). Cultures on PDA grew slowly and developed blue-to-purple masses of sporodochia typical of F. virguliforme descriptions and similar to a representative isolate, Mont-1, grown alongside (1,2). Size of macroconidia from the six representative isolates, one from each county (including isolates derived from surface-disinfested and nondisinfested roots), and Mont-1 were determined to be within the range for F. virguliforme (42 to 56 × 5 to 6 μm), with an average of four septa per macroconidia. Identity of the representative isolates was confirmed by partial DNA sequencing of both strands of the internal transcribed spacer (ITS) region of the ribosomal RNA gene, translation elongation factor 1-α, and β-tubulin loci. All six representative isolates were identical in each of the three loci and matched with 100% similarity F. virguliforme accessions in GenBank and Fusarium-ID database searches, except for the β-tubulin locus in which a single nucleotide insertion was noted (Accession Nos. HM453328–HM453330). Sequences were 98 to 99% similar to other SDS Fusarium spp. not yet recorded in the United States. Koch's postulates were performed in the greenhouse according to Malvick and Bussey (3). Infested sorghum seed (~20 g) was placed 2 cm below soybean seed of susceptible cv. Williams 82 in plastic pots. Noninfested sorghum seed was used as a negative control and sorghum infested with Mont-1 as a positive control. Chlorotic spots developed 2 weeks after establishing the trial, and 3 to 4 weeks postinoculation, severe SDS symptoms of foliar interveinal chlorosis and necrosis and severe root rot developed. Koch's postulates were completed by reisolating F. virguliforme from a subset of infected plants. In addition, an isolate of F. virguliforme collected in 2008 was used to inoculate a 2009 field trial in East Lansing, MI with no history of SDS. Typical SDS symptoms developed in the field trial and F. virguliforme was isolated from a symptomatic plant that was identified as described above. Despite being reported across the majority of soybean-producing states, to our knowledge, this is the first confirmation and distribution report for SDS in Michigan. References: (1) T. Aoki et al. Mycoscience 46:162, 2005. (2) G. L. Hartman et al. Plant Dis. 81:515, 1997. (3) D. K. Malvick and K. E. Bussey. Can. J. Plant Pathol. 30:467, 2008.


Mycologia ◽  
2014 ◽  
Vol 106 (4) ◽  
pp. 686-697 ◽  
Author(s):  
Teresa J. Hughes ◽  
Kerry O’Donnell ◽  
Stacy Sink ◽  
Alejandro P. Rooney ◽  
María Mercedes Scandiani ◽  
...  

2019 ◽  
Vol 109 (10) ◽  
pp. 1710-1719 ◽  
Author(s):  
Mitchell G. Roth ◽  
Zachary A. Noel ◽  
Jie Wang ◽  
Fred Warner ◽  
Adam M. Byrne ◽  
...  

In the United States, sudden death syndrome (SDS) of soybean is caused by the fungal pathogen Fusarium virguliforme and is responsible for important yield losses each year. Understanding the risk of SDS development and subsequent yield loss could provide growers with valuable information for management of this challenging disease. Current management strategies for F. virguliforme use partially resistant cultivars, fungicide seed treatments, and extended crop rotations with diverse crops. The aim of this study was to develop models to predict SDS severity and soybean yield loss using at-planting risk factors to integrate with current SDS management strategies. In 2014 and 2015, field studies were conducted in adjacent fields in Decatur, MI, which were intensively monitored for F. virguliforme and nematode quantities at-planting, plant health throughout the growing season, end-of-season SDS severity, and yield using an unbiased grid sampling scheme. In both years, F. virguliforme and soybean cyst nematode (SCN) quantities were unevenly distributed throughout the field. The distribution of F. virguliforme at-planting had a significant correlation with end-of-season SDS severity in 2015, and a significant correlation to yield in 2014 (P < 0.05). SCN distributions at-planting were significantly correlated with end-of-season SDS severity and yield in 2015 (P < 0.05). Prediction models developed through multiple linear regression showed that F. virguliforme abundance (P < 0.001), SCN egg quantity (P < 0.001), and year (P < 0.01) explained the most variation in end-of-season SDS (R2 = 0.32), whereas end-of-season SDS (P < 0.001) and end-of-season root dry weight (P < 0.001) explained the most variation in soybean yield (R2 = 0.53). Further, multivariate analyses support a synergistic relationship between F. virguliforme and SCN, enhancing the severity of foliar SDS. These models indicate that it is possible to predict patches of SDS severity using at-planting risk factors. Verifying these models and incorporating additional data types may help improve SDS management and forecast soybean markets in response to SDS threats.


Plant Disease ◽  
2011 ◽  
Vol 95 (3) ◽  
pp. 242-247 ◽  
Author(s):  
C. C. Gongora-Canul ◽  
L. F. S. Leandro

Soybean sudden death syndrome is characterized by root rot followed by the development of foliar symptoms. However, it is not known how time of infection affects disease severity. Soybean plants were inoculated at 0, 4, 7, 14, 21, 28, and 35 days after planting (DAP) by drenching potting media with conidia of Fusarium virguliforme, then incubating in growth chambers at 17°C for 7 days followed by 24°C for 31 days. Root rot and severity of foliar symptoms were assessed 18 and 38 days after inoculation (DAI). Root rot developed on plants inoculated at all ages but plants inoculated at seed stage (0 DAP) had the highest (P < 0.01) root rot severity (>90%). At 38 DAI, foliar symptoms were severe (>80%) on plants inoculated at 0 DAP but did not develop on plants inoculated at all other ages. Xylem colonization by F. virguliforme was more frequent in plants inoculated at 0 DAP than on plants inoculated at later stages. The results of this study suggest that soybean roots become less susceptible to xylem colonization and the subsequent development of foliar symptoms as plants mature. Therefore, practices aimed at protecting seed and seedling roots from infection may improve soybean sudden death management.


2019 ◽  
Vol 20 (1) ◽  
pp. 29-34 ◽  
Author(s):  
Yuba R. Kandel ◽  
Leonor F. S. Leandro ◽  
Daren S. Mueller

Conservation tillage has become a common practice of soybean farming in the Midwestern United States owing to the benefits of soil and moisture conservation. Field trials were established in a field with a history of sudden death syndrome (SDS; caused by Fusarium virguliforme) in Iowa in 2011 and evaluated for five consecutive years to determine the impact of tillage on SDS and yield. The experiment was laid out in a split-split-plot design with four replicates. The main plot factor was tillage (no-till both crops, no-till corn and chisel plow soybean, and disc corn and chisel plow soybean), and each main plot was divided into subplots of corn or soybeans (in a 2-year rotation). Each subplot was again divided into two subsubplots, in which two soybean cultivars, moderately susceptible (MS) and moderately resistant (MR) to SDS, were planted each year. Root rot and SDS disease index (FDX) differed among years, because some years were more favorable for the disease than the others. However, tillage did not affect any parameters, including yield, in any year (P > 0.05). Cultivar effect was significant for each parameter occasionally. When significant, the MR cultivar had lower root rot and FDX and greater yield than the MS cultivar. These data suggest planting resistant cultivars can be an effective management tactic, but tillage does not help for SDS management.


2015 ◽  
Vol 105 (3) ◽  
pp. 378-387 ◽  
Author(s):  
Jie Wang ◽  
Janette L. Jacobs ◽  
Jan M. Byrne ◽  
Martin I. Chilvers

Fusarium virguliforme (syn. F. solani f. sp. glycines) is the primary causal pathogen responsible for soybean sudden death syndrome (SDS) in North America. Diagnosis of SDS is difficult because symptoms can be inconsistent or similar to several soybean diseases and disorders. Additionally, quantification and identification of F. virguliforme by traditional dilution plating of soil or ground plant tissue is problematic due to the slow growth rate and plastic morphology of F. virguliforme. Although several real-time quantitative polymerase chain reaction (qPCR)-based assays have been developed for F. virguliforme, the performance of those assays does not allow for accurate quantification of F. virguliforme due to the reclassification of the F. solani species complex. In this study, we developed a TaqMan qPCR assay based on the ribosomal DNA (rDNA) intergenic spacer (IGS) region of F. virguliforme. Specificity of the assay was demonstrated by challenging it with genomic DNA of closely related Fusarium spp. and commonly encountered soilborne fungal pathogens. The detection limit of this assay was determined to be 100 fg of pure F. virguliforme genomic DNA or 100 macroconidia in 0.5 g of soil. An exogenous control was multiplexed with the assay to evaluate for PCR inhibition. Target locus copy number variation had minimal impact, with a range of rDNA copy number from 138 to 233 copies per haploid genome, resulting in a minor variation of up to 0.76 cycle threshold values between strains. The qPCR assay is transferable across platforms, as validated on the primary real-time PCR platform used in the Northcentral region of the National Plant Diagnostic Network. A conventional PCR assay for F. virguliforme detection was also developed and validated for use in situations where qPCR is not possible.


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