Life Sciences Commons^™

Chromatin Immunoprecipitation (Chip) Assay For Detecting Direct And Indirect Protein -Dna Interactions In Magnaporthe Oryzae, Gang Li, Margarita Marroquin-Guzman, Richard A. Wilson

Department of Plant Pathology: Faculty Publications

Chromatin immunoprecipitation (ChIP) is a powerful technology for analyzing protein-DNA interactions in cells. Robust ChIP procedures have been established for investigating direct interactions between protein and DNA. However, detecting indirect protein-DNA interactions in vivo is challenging. Recently, we used ChIP to analyze an indirect protein-DNA interaction between a putative histone demethylase, MoJmjC, and the promoter of the superoxide dismutase 1-encoding gene MoSOD1 in the rice blast fungus Magnaporthe oryzae (M. oryzae) (Fernandez et al., 2014). We tagged MoJmjC with the 3x FLAG epitope (Fernandez et al., 2014), instead of the larger and more commonly used GFP epitope, to mitigate …

Transgenic Soybean Plants Expressing Asoybean Homolog Of Glycine-Rich Protein 7 (Grp7) And Exhibiting Improved Innate Immunity, James R. Alfano, Anna Joe, Thomas E. Clemente, Zhengqing Fu, Ming Guo, Byeong-Ryool Jeong, Thomas Elthon

Department of Plant Pathology: Faculty Publications

This disclosure provides for transgenic Soybean plants expressing a soybean homolog of glycine-rich protein 7 (GRP7) and exhibiting improved innate immunity and meth ods of making Such plants.

The Khmer Software Package: Enabling Efficient Nucleotide Sequence Analysis [Version 1; Referees: 2 Approved, 1 Approved With Reservations], Michael R. Crusoe, Hussien F. Alameldin, Sherine Awad, Elmar Boucher, Adam Caldwell, Reed Cartwright, Amanda Charbonneau, Bede Constantinides, Greg Edvenson, Scott Fay, Jacob Fenton, Thomas Fenzl, Jordan Fish, Leonor Garcia-Gutierrez, Phillip Garland, Jonathan Gluck, Iván González, Sarah Guermond, Jiarong Guo, Aditi Gupta, Joshua R. Herr, Adina Howe, Alex Hyer, Andreas Härpfer, Luiz Irber, Rhys Kidd, David Lin, Justin Lippi, Tamer Mansour, Pamela Mca'nulty, Eric Mcdonald, Jessica Mizzi, Kevin D. Murray, Joshua R. Nahum, Kaben Nanlohy, Alexander Johan Nederbragt, Humberto Ortiz-Zuazaga, Jeramia Ory, Jason Pell, Charles Pepe-Ranney, Zachary N. Russ, Camille Scott, Josiah Seaman, Scott Sievert 38, Jared Simpson, Connor T. Skennerton, James Spencer, Ramakrishnan Srinivasan, Daniel Standage, James A. Stapleton, Susan R. Steinman, Joe Stein, Benjamin Taylor, Will Trimble, Heather L. Wiencko, Michael Wright, Brian Wyss, Qingpeng Zhang, En Zyme, C. Titus Brown, Erich Schwarz

Department of Plant Pathology: Faculty Publications

The khmer package is a freely available software library for working efficiently with fixed length DNA words, or k-mers. khmer provides implementations of a probabilistic k-mer counting data structure, a compressible De Bruijn graph representation, De Bruijn graph partitioning, and digital normalization. khmer is implemented in C++ and Python, and is freely available under the BSD license at https://github.com/dib-lab/khmer/.

A Unique 5' Translation Element Discovered In Triticum Mosaic Virus, Robyn Roberts, Jincan Zhang, Laura K. Mayberry, Satyanarayana Tatineni, Karen S. Browning, Aurelie M. Rakotondrafara

Department of Plant Pathology: Faculty Publications

Several plant viruses encode elements at the 5' end of their RNAs, which, unlike most cellular mRNAs, can initiate translation in the absence of a 5' m7GpppG cap. Here, we describe an exceptionally long (739-nucleotide [nt]) leader sequence in triticum mosaic virus (TriMV), a recently emerged wheat pathogen that belongs to the Potyviridae family of positive-strand RNA viruses. We demonstrate that the TriMV 5' leader drives strong cap-independent translation in both wheat germ extract and oat protoplasts through a novel, noncanonical translation mechanism. Translation preferentially initiates at the 13th start codon within the leader sequence independently of eIF4E but involves …

Gata-Dependent Glutaminolysis Drives Appressorium Formation In Magnaporthe Oryzae By Suppressing Tor Inhibition Of Camp/Pka Signaling, Margarita Marroquin-Guzman, Richard A. Wilson

Department of Plant Pathology: Faculty Publications

Fungal plant pathogens are persistent and global food security threats. To invade their hosts they often form highly specialized infection structures, known as appressoria. The cAMP/ PKA- and MAP kinase-signaling cascades have been functionally delineated as positive-acting pathways required for appressorium development. Negative-acting regulatory pathways that block appressorial development are not known. Here, we present the first detailed evidence that the conserved Target of Rapamycin (TOR) signaling pathway is a powerful inhibitor of appressorium formation by the rice blast fungus Magnaporthe oryzae. We determined TOR signaling was activated in an M. oryzae mutant strain lacking a functional copy of …

Recommendations Of Generic Names In Diaporthales Competing For Protection Or Use, Amy Y. Rossman, Gerard C. Adams, Paul F. Cannon, Lisa A. Castlebury, Pedro W. Crous, Marieka Gryzenhout, Walter M. Jaklitsch, Luis C. Mejia, Dmitar Stoykov, Dhanushka Udayanga, Hermann Voglmayr, Donald M. Walker

Department of Plant Pathology: Faculty Publications

In advancing to one name for fungi, this paper treats generic names competing for use in the order Diaporthales (Ascomycota, Sordariomycetes) and makes a recommendation for the use or protection of one generic name among synonymous names that may be either sexually or asexually typified. A table is presented that summarizes these recommendations. Among the genera most commonly encountered in this order, Cytospora is recommended over Valsa and Diaporthe over Phomopsis. New combinations are introduced for the oldest epithet of important species in the recommended genus. These include Amphiporthe tiliae, Coryneum lanciforme, Cytospora brevispora, C. ceratosperma, C. …

From Select Agent To An Established Pathogen: The Response To Phakopsora Pachyrhizi (Soybean Rust) In North America, Heather Y. Kelly, Nicholas S. Dufault, David R. Walker, Scott A. Isard, Raymond W. Schneider, Loren J. Giesler, David L. Wright, James J. Marois, Glen L. Hartman

Department of Plant Pathology: Faculty Publications

The pathogen causing soybean rust, Phakopsora pachyrhizi, was first described in Japan in 1902. The disease was important in the Eastern Hemisphere for many decades before the fungus was reported in Hawaii in 1994, which was followed by reports from countries in Africa and South America. In 2004, P. pachyrhizi was confirmed in Louisiana, making it the first report in the continental United States. Based on yield losses from countries in Asia, Africa, and South America, it was clear that this pathogen could have a major economic impact on the yield of 30 million ha of soybean in the …

Pilg Is Involved In The Regulation Of Twitching Motility And Antifungal Antibiotic Biosynthesis In The Biological Control Agent Lysobacter Enzymogenes, Xue Zhou, Guoliang Qian, Yuan Chen, Liangcheng Du, Fengquan Liu, Gary Y. Yuen

Department of Plant Pathology: Faculty Publications

Lysobacter enzymogenes strain C3 is a gliding bacterium which produces the antifungal secondary metabolite heat-stable antifungal factor (HSAF) and type IV pilus (T4P) as important mechanisms in biological control activity against fungal pathogens. To date, the regulators that control HSAF biosynthesis and T4P-dependent twitching motility in L. enzymogenes are poorly explored. In the present study, we addressed the role of pilG in the regulation of these two traits in L. enzymogenes. PilG of L. enzymogenes was found to be a response regulator, commonly known as a component of a two-component transduction system. Mutation of pilG in strain C3 abolished its …

Fine-Scale Genetic Structure Of Monilinia Fructicola During Brown Rot Epidemics Within Individual Peach Tree Canopies, Sydney E. Everhart, H. Scherm

Department of Plant Pathology: Faculty Publications

The purpose of this study was to determine the fine-scale genetic structure of populations of the brown rot pathogen Monilinia fructicola within individual peach tree canopies to better understand within-tree plant pathogen diversity and to complement previous work on spatiotemporal development of brown rot disease at the canopy level. Across 3 years in a total of six trees, we monitored disease development, collected isolates from every M. fructicola symptom during the course of the season, and created high-resolution three-dimensional maps of all symptom and isolate locations within individual canopies using an electromagnetic digitizer. Each canopy population (65 to 173 isolates …

Fungicide And Herbicide Effects On Gray Leaf Spot In Nebraska Field Corn, 2014, J. D. Harbour, T. A. Jackson-Ziems

Department of Plant Pathology: Faculty Publications

The objective of the trial was to compare fungicide and herbicide treatments for gray leaf spot (GLS) efficacy. Corn was grown under normal, irrigated agronomic practices at the South Central Ag Lab near Clay Center, NE. Soils were a silt loam with 6.7 pH and 1.8% organic matter and the previous crop was corn. Reduced tillage was performed prior to planting. Corn (DKC 64-83 RIB, moderately susceptible to GLS) was planted at approximately 34,000 seed/A on 2 May. Seven treatments were arranged in a randomized complete block design with six replications. . . . Treatments applied at V8 or R1 …

Foliar Fungicide Comparisons For Gray Leaf Spot Management And Lodging In Nebraska Field Corn, 2014, J. D. Harbour, T. A. Jackson-Ziems

Department of Plant Pathology: Faculty Publications

The objective of the trial was to compare foliar fungicides with other fungicide programs for gray leaf spot (GLS) efficacy. Corn was grown under normal, irrigated agronomic practices at the South Central Ag Lab near Clay Center, NE. Soils were a silt loam with 6.7 pH and 1.8 % organic matter, and the previous crop was corn. Reduced tillage was performed to the field prior to planting. Corn (DKC 64-83 RIB, moderately susceptible to GLS) was planted at approximately 34,000 seed/A on 20 May. Eleven treatments were arranged in a randomized complete block design with six replications. . . . …

What’S New In Plant Pathology, Tamra A. Jackson-Ziems, Loren Giesler, Robert M. Harveson, Stephen N. Wegulo, Kevin A. Korus, Tony O. Adesemoye

Department of Plant Pathology: Faculty Publications

Extension Plant Pathology Team Update

Changes to the Plant Disease Management Section of the 2015 Weed Guide

During the past year, several new products have become available for disease management. These products and additional products have been added to the Plant Disease Management Section of the 2015 Weed Guide. Products added to the Weed Guide have been summarized in Tables 1-3.

Table 1. Foliar Products

Table 2. Seed Treatment Products

Table 3. Seed Treatment Nematicides

Differentiating Chemical And Disease Symptoms In The Field, Kevin A. Korus, Loren J. Giesler, Robert M. Harveson, Tamra A. Jackson-Ziems, Lowell Sandell, Stephen Wegulo

Department of Plant Pathology: Faculty Publications

In years with conditions favorable for seedling disease and other disease there are typically concerns and inquiries about the cause(s) of symptoms in agronomic plants. Many of the questions focus on differentiating between plant injuries potentially caused by recent herbicide applications versus symptoms caused by plant pathogens. Chemical injury in row crops is caused by chemicals such as herbicides, fertilizers, fungicides, insecticides, growth regulators, and crop oils when they are applied individually, as a mixture, or together with adjuvants. If chemicals are applied incorrectly, plants may be damaged at any point during the growing season. Chemical injury can result from …

Effect Of Waxy (Low Amylose) On Fungal Infection Of Sorghum Grain, Deanna L. Funnell-Harris, Scott E. Sattler, Patrick M. O'Neill, Kent M. Eskridge, Jeffrey F. Pedersen

Department of Plant Pathology: Faculty Publications

Loss of function mutations in waxy, encoding granule bound starch synthase (GBSS) that synthesizes amylose, results in starch granules containing mostly amylopectin. Low amylose grain with altered starch properties has increased usability for feed, food, and grain-based ethanol. In sorghum, two classes of waxy (wx) alleles had been characterized for absence or presence of GBSS: wx^a (GBSS^-) and wx^b (GBSS+, with reduced activity). Field-grown grain of wild-type; waxy, GBSS^-; and waxy, GBSS⁺ plant introduction accessions were screened for fungal infection. Overall, results showed that waxy grains were not more susceptible than …

Multi-Year Pathogen Survey Of Biofuel Switchgrass Breeding Plots Reveals High Prevalence Of Infections By Panicum Mosaic Virus And Its Satellite Virus, Catherine L. Stewart, Jesse D. Pyle, Charlene C. Jochum, Kenneth P. Vogel, Gary Y. Yuen, Karen-Beth G. Scholthof

Department of Plant Pathology: Faculty Publications

Switchgrass (Panicum virgatum) cultivars are currently under development as lignocellulosic feedstock. Here we present a survey of three established switchgrass experimental nurseries in Nebraska in which we identified Panicum mosaic virus (PMV) as the most prevalent virus. In 2012, 72% of 139 symptomatic plants tested positive for PMV. Of the PMV-positive samples, 19% were coinfected with its satellite virus (SPMV). Less than 14% of all sampled plants in 2012 were positive for four additional viruses known to infect switchgrass. In 2013, randomized sampling of switchgrass individuals from the same 2012 breeding plots revealed that infection by PMV or PMV+SPMV …

The Effects Of Fungicides And Regalia Tank Mixtures On Fray Leaf Spot In Nebraska Field Corn, 2014, J. D. Harbour, T. A. Jackson-Ziems

Department of Plant Pathology: Faculty Publications

The objective of the trial was to compare industry fungicide programs with the microbial Regalia Rx plus fungicide tank mixtures for gray leaf spot (GLS) efficacy. Corn was grown under normal, irrigated agronomic practices at the South Central Ag Lab near Clay Center, NE. Soils were a silt loam with 6.7 pH and 1.8 % organic matter. Reduced tillage was performed to the field prior to planting. Corn (DKC 64-83 RIB, moderately susceptible to GLS) was planted at approximately 34,000 seed/A on 20 May. Seven treatments were arranged in a randomized complete block design with six replications. . . . …

Corn Disease Update, Tamra A. Jackson-Ziems

Department of Plant Pathology: Faculty Publications

The harsh growing conditions during 2014 contributed to several disease problems in corn, in spite of the overall high yields across the state. The extended cold and wet conditions early in the season led to development of seedling diseases and crop stress. Then, in many parts of the state, repeated and unprecedented strong storms battered and wounded crops with multiple and widespread hail events, high winds, very heavy rain, and devastating tornadoes. Many fields were planted late or replanted, some more than once, further delaying the crop. Cool summer and fall conditions delayed maturity and led to early frost events …

Characterizing The Agronomic Benefits Of Solatenol Fungicide Tank-Mixture Applications In Nebraska Field Corn, 2014, J. D. Harbour, T. A. Jackson-Ziems

Department of Plant Pathology: Faculty Publications

The objective of the trial was characterize Solatenol fungicide tank mix programs and compare performance to Quilt Xcel for gray leaf spot (GLS) efficacy. Corn was grown under normal, irrigated agronomic practices at the South Central Ag Lab near Clay Center, NE. Soils were a silt loam with 6.7 pH and 1.8 % organic matter. Reduced tillage was performed to the field prior to planting. Corn (G11U58-3111 susceptible to GLS) was planted at approximately 34,000 seed/A on 20 May. Eight treatments were arranged in a randomized complete block design with six replications. . . . Fungicides applied at V5, R1, …

Effect Of Y-Trellis And Vertical Shoot Positioning Training Systems On Downy Mildew And Botrytis Bunch Rot Of Grape In Highlands Of Southern Brazil, Betina Pereira De Bem, Amauri Bogo, Sydney Everhart, Ricardo Trezzi Casa, Mayra Juline Gonçalves, José Luiz Marcon Filho, Isabel Cristina Da Cunha

Department of Plant Pathology: Faculty Publications

Downy mildew (Plasmopara viticola) and botrytis bunch rot (Botrytis cinerea) are important diseases in the highlands of Santa Catarina State, a relatively new wine-growing region in Brazil. Although it is known that training systems can affect microclimate and subsequent disease development, this has not been examined in the highlands of Brazil. Thus, the purpose of this study was to evaluate the influence of Y-trellis (YT) and vertical shoot positioning (VSP) training system on downy mildew and botrytis bunch rot disease development in “Cabernet Sauvignon” cultivar. Experiments were carried out in commercial vineyards in São Joaquim, SC …

In Vitro Transcripts Of Wild-Type And Fluorescent Protein-Tagged Triticum Mosaic Virus (Family Potyviridae) Are Biologically Active In Wheat, Satyanarayana Tatineni, Anthony J. Mcmechan, Melissa Bartels, Gary L. Hein, Robert A. Graybosch

Department of Plant Pathology: Faculty Publications

Triticum mosaic virus (TriMV) (genus Poacevirus, family Potyviridae) is a recently described eriophyid mite-transmitted wheat virus. In vitro RNA transcripts generated from full-length cDNA clones of TriMV proved infectious on wheat. Wheat seedlings inoculated with in vitro transcripts elicited mosaic and mottling symptoms similar to the wildtype virus, and the progeny virus was efficiently transmitted by wheat curl mites, indicating that the cloned virus retained pathogenicity, movement, and wheat curl mite transmission characteristics. A series of TriMV-based expression vectors was constructed by engineering a green fluorescent protein (GFP) or red fluorescent protein (RFP) open reading frame with homologous …

Roles And Programming Of Arabidopsis Argonaute Proteins During Turnip Mosaic Virus Infection, Hernan Garcia-Ruiz, Alberto Carbonell, J. Steen Hoyer, Noah Fahlgren, Kerrigan B. Gilbert, Atsushi Takeda, Annalisa Giampetruzzi, Mayra T. Garcia Ruiz, Michaela G. Mcginn, Nicholas Lowery, Maria T. Martinez Baladejo, James C. Carrington

Department of Plant Pathology: Faculty Publications

In eukaryotes, ARGONAUTE proteins (AGOs) associate with microRNAs (miRNAs), short interfering RNAs (siRNAs), and other classes of small RNAs to regulate target RNA or target loci. Viral infection in plants induces a potent and highly specific antiviral RNA silencing response characterized by the formation of virus-derived siRNAs. Arabidopsis thaliana has ten AGO genes of which AGO1, AGO2, and AGO7 have been shown to play roles in antiviral defense. A genetic analysis was used to identify and characterize the roles of AGO proteins in antiviral defense against Turnip mosaic virus (TuMV) in Arabidopsis. AGO1, AGO2 and AGO10 promoted anti-TuMV defense …

Fungicide-Induced Transposon Movement In Monilinia Fructicola, Fengping Chen, Sydney E. Everhart, P. Karen Bryson, Chaoxi Luo, Xi Song, Xili Liu, Guido Schnabel

Department of Plant Pathology: Faculty Publications

Repeated applications of fungicides with a single mode of action are believed to select for pre-existing resistant strains in a pathogen population, while the impact of sub-lethal doses of such fungicides on sensitive members of the population is unknown. In this study, in vitro evidence is presented that continuous exposure of Monilinia fructicola mycelium to some fungicides can induce genetic change in form of transposon transposition. Three fungicide-sensitive M. fructicola isolates were exposed in 12 weekly transfers of mycelia to a dose gradient of demethylation inhibitor fungicide (DMI) SYP-Z048 and quinone outside inhibitor fungicide (QoI) azoxystrobin in solo or mixture …

A Spectrum Of Hrt-Dependent Hypersensitive Responses Elicited By The 52 Amino Acid N-Terminus Of Turnip Crinkle Virus Capsid Protein And Its Mutants, Sung-Hwan Kang, Feng Qu, Thomas Jack Morris

Department of Plant Pathology: Faculty Publications

The capsid protein (CP) of turnip crinkle virus (TCV) is the elicitor of hypersensitive response (HR) and resistance mediated by the resistance protein HRT in the Di-17 ecotype of Arabidopsis. Here we identified the N-terminal 52-amino-acid R domain of TCV CP as the elicitor of HRT-dependent HR in Nicotiana benthamiana. Mutating this domain at position 6 (R6A), but not at positions 8 (R8A) or 14 (G14A), abolished HR in N. benthamiana. However, on Di-17 Arabidopsis leaves only R8A R domain elicited visible epidermal HR. When incorporated in infectious TCV RNAs, R8A and G14A mutations exerted dramatically different effects …

Weather Variability And Disease Management Strategies, Kevin Korus, Tony O. Adesemoye, Loren Giesler, Robert M. Harveson, Tamra A. Jackson-Ziems, Stephen N. Wegulo

Department of Plant Pathology: Faculty Publications

This year’s title of “weather variability and disease management strategies” was chosen because we need to remember how weather conditions this year have impacted crop productivity and disease development. This will enable us to look forward and develop better management decisions for future growing seasons. Agricultural production is dependent on many climatic factors such as rain, humidity, temperature, and sunlight. These climate conditions have direct effects on yield as well as other indirect effects. One specific indirect effect of extreme weather events is increased pressure from pathogens and pests. Plant pathogens are commonly favored by very specific, and sometimes extreme, …