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Smrt Sequencing Of Paramecium Bursaria Chlorella Virus-1 Reveals Diverse Methylation Stability In Adenines Targeted By Restriction Modification Systems, Samantha R. Coy, Eric R. Gann, Spiridon E. Papoulis, Michael E. Holder, Nadim J. Ajami, Joseph F. Petrosino, Erik R. Zinser, James L. Van Etten, Steven W. Wilhelm 2020 University of Tennessee, Knoxville & Rice University

Smrt Sequencing Of Paramecium Bursaria Chlorella Virus-1 Reveals Diverse Methylation Stability In Adenines Targeted By Restriction Modification Systems, Samantha R. Coy, Eric R. Gann, Spiridon E. Papoulis, Michael E. Holder, Nadim J. Ajami, Joseph F. Petrosino, Erik R. Zinser, James L. Van Etten, Steven W. Wilhelm

James Van Etten Publications

Chloroviruses (family Phycodnaviridae) infect eukaryotic, freshwater, unicellular green algae. A unique feature of these viruses is an abundance of DNA methyltransferases, with isolates dedicating up to 4.5% of their protein coding potential to these genes. This diversity highlights just one of the long-standing values of the chlorovirus model system; where group-wide epigenomic characterization might begin to elucidate the function(s) of DNA methylation in large dsDNA viruses. We characterized DNA modifications in the prototype chlorovirus, PBCV-1, using single-molecule real time (SMRT) sequencing (aka PacBio). Results were compared to total available sites predicted in silico based on DNA sequence alone ...


Fungicide Sensitivity Of Sclerotinia Sclerotiorum Isolates From Five States With Different Fungicide Treatments, Cristian Wulkop Gil, Edgar Nieto-Lopez, Sydney Everhart 2020 University of Nebraska-Lincoln

Fungicide Sensitivity Of Sclerotinia Sclerotiorum Isolates From Five States With Different Fungicide Treatments, Cristian Wulkop Gil, Edgar Nieto-Lopez, Sydney Everhart

UCARE Research Products

Sclerotinia sclerotiorum is a plant pathogenic fungus that causes a disease called white mold that can infect more than 450 plant species including soybeans, dry beans, green beans, canola, and sunflower. This pathogen is capable of up to $252M in losses every year (U.S. Canola Association, 2014). Fungicides are widely used in developed agricultural systems to control disease. However, resistance to the most effective fungicides has emerged and spread in pathogen populations and there have been multiple reports of S. sclerotiorum isolates becoming resistant to certain fungicides. Since different fields in different states use different fungicide treatments on plants ...


Mechanisms Of Silencing Suppression By A Polerovirus P0 Protein, Natalie Holste, Hernan Garcia-Ruiz 2020 University of Nebraska - Lincoln

Mechanisms Of Silencing Suppression By A Polerovirus P0 Protein, Natalie Holste, Hernan Garcia-Ruiz

Posters & Presentations in Biological Sciences

Maize lethal necrosis is an intense viral disease spreading across sub-Saharan Africa. Maize is the staple crop grown in sub-Saharan Africa, but most crops infected with maize lethal necrosis will not survive to harvest. This causes immense economic hardship and starvation within the population. Maize lethal necrosis consists of a combination of two viruses, Maize chlorotic mottle virus (MCMV) and a virus from the genus potyvirus. In a recent study, a Maize yellow dwarf virus-RMV (MYDV-RMV)-like polerovirus, was repeatedly detected in plants with maize lethal necrosis. Poleroviruses have a silencing suppressor, P0 protein, and the mechanism of suppression is ...


Mapping Quantitative Trait Loci Associated With Leaf Rust Resistance In Five Spring Wheat Populations Using Single Nucleotide Polymorphism Markers, Firdissa E. Bokore, Ron E. Knox, Richard D. Cuthbert, Curtis J. Pozniak, Brent D. McCallum, Amidou N’Diaye, Ron M. DePauw, Heather L. Campbell, Catherine Munro, Arti Singh, Colin W. Hiebert, Curt A. McCartney, Andrew G. Sharpe, Asheesh K. Singh, Dean Spaner, D. B. Fowler, Yuefeng Ruan, Samia Berraies, Brad Meyer 2020 Agriculture and Agri-Food Canada

Mapping Quantitative Trait Loci Associated With Leaf Rust Resistance In Five Spring Wheat Populations Using Single Nucleotide Polymorphism Markers, Firdissa E. Bokore, Ron E. Knox, Richard D. Cuthbert, Curtis J. Pozniak, Brent D. Mccallum, Amidou N’Diaye, Ron M. Depauw, Heather L. Campbell, Catherine Munro, Arti Singh, Colin W. Hiebert, Curt A. Mccartney, Andrew G. Sharpe, Asheesh K. Singh, Dean Spaner, D. B. Fowler, Yuefeng Ruan, Samia Berraies, Brad Meyer

Agronomy Publications

Growing resistant wheat (Triticum aestivum L) varieties is an important strategy for the control of leaf rust, caused by Puccinia triticina Eriks. This study sought to identify the chromosomal location and effects of leaf rust resistance loci in five Canadian spring wheat cultivars. The parents and doubled haploid lines of crosses Carberry/AC Cadillac, Carberry/Vesper, Vesper/Lillian, Vesper/Stettler and Stettler/Red Fife were assessed for leaf rust severity and infection response in field nurseries in Canada near Swift Current, SK from 2013 to 2015, Morden, MB from 2015 to 2017 and Brandon, MB in 2016, and in New ...


Fungicide Sensitivity Of Sclerotinia Sclerotiorum Isolates Selected From Five Different States That Use Different Fungicide Treatments, Cristian Wulkop Gil 2020 University of Nebraska - Lincoln

Fungicide Sensitivity Of Sclerotinia Sclerotiorum Isolates Selected From Five Different States That Use Different Fungicide Treatments, Cristian Wulkop Gil

UCARE Research Products

Sclerotinia sclerotiorum is a plant pathogenic fungus that causes a disease called white mold that can infect more than 450 plant species including soybeans, dry beans, green beans, canola, and sunflower. This pathogen is capable of up to $252M in losses every year (U.S. Canola Association, 2014). Fungicides are widely used in developed agricultural systems to control disease. However, resistance to the most effective fungicides has emerged and spread in pathogen populations and there have been multiple reports of S. sclerotiorum isolates becoming resistant to certain fungicides. Since different fields in different states use different fungicide treatments on plants ...


Phenotypic And Genotypic Characterization Of Aroma And Cercospora Janseana Resistance In U.S. Rice, Christopher Keith Addison 2020 Louisiana State University at Baton Rouge

Phenotypic And Genotypic Characterization Of Aroma And Cercospora Janseana Resistance In U.S. Rice, Christopher Keith Addison

LSU Doctoral Dissertations

Rice is a staple food for over one-third of the world’s population. With the increasing population, plant breeders must continue to breed for improved varieties. The utilization of markers to applied breeding program can increase the efficiency of selection for key traits. The targeted traits for this research include grain aroma and resistance to the fungal disease narrow brown leaf spot (Cercospora janseana). Our objective was to characterize SNP diversity across the BADH2 gene in publicly available sequence data of a collection of 2,932 rice varieties was characterized to determine the number of gene haplotypes in O. sativa ...


Low Ribosomal Rna Genes Copy Number Provoke Genomic Instability And Chromosomal Segment Duplication Events That Modify Global Gene Expression And Plant-Pathogen Response, Ariadna Picart-Picolo, Stefan Grob, Nathalie Picault, Michal Franek, Thierry Halter, Tom R. Maier, Christel Llauro, Edouard Jobet, Panpan Zhang, Paramasivan Vijayapalani, Thomas J. Baum, Lionel Navarro, Martina Dvorackova, Marie Mirouze, Frederic Pontvianne 2020 Université de Perpignan

Low Ribosomal Rna Genes Copy Number Provoke Genomic Instability And Chromosomal Segment Duplication Events That Modify Global Gene Expression And Plant-Pathogen Response, Ariadna Picart-Picolo, Stefan Grob, Nathalie Picault, Michal Franek, Thierry Halter, Tom R. Maier, Christel Llauro, Edouard Jobet, Panpan Zhang, Paramasivan Vijayapalani, Thomas J. Baum, Lionel Navarro, Martina Dvorackova, Marie Mirouze, Frederic Pontvianne

Plant Pathology and Microbiology Publications

Among the hundreds of ribosomal RNA (rRNA) gene copies organized as tandem repeats in the nucleolus organizer regions (NORs), only a portion is usually actively expressed in the nucleolus and participate in the ribosome biogenesis process. The role of these extra-copies remains elusive, but previous studies suggested their importance in genome stability and global gene expression. Because the nucleolus is also a platform for nuclear organization, we tested the impact of a decreased amount of rRNA gene copies on the Arabidopsis thaliana 3D genome organization and stability, using an A. thaliana line only containing 20% of rRNA gene copies (20rDNA ...


The Rna Of Maize Chlorotic Mottle Virus - The Essential Virus In Maize Lethal Necrosis Disease - Is Translated Via A Panicum Mosaic Virus-Like Cap-Independent Translation Element, Elizabeth Carino, Kay Scheets, W. Allen Miller 2020 Iowa State University

The Rna Of Maize Chlorotic Mottle Virus - The Essential Virus In Maize Lethal Necrosis Disease - Is Translated Via A Panicum Mosaic Virus-Like Cap-Independent Translation Element, Elizabeth Carino, Kay Scheets, W. Allen Miller

Plant Pathology and Microbiology Publications

Maize chlorotic mottle virus (MCMV) combines with a potyvirus in maize lethal necrosis disease (MLND), an emerging disease worldwide that often causes catastrophic yield loss. To inform resistance strategies, we characterized the translation initiation mechanism of MCMV. We report that, like other tombusvirids, MCMV RNA contains a cap-independent translation element (CITE) in its 3’ untranslated region (UTR). The MCMV 3’ CITE (MTE) was mapped to nucleotides 4164-4333 in the genomic RNA. SHAPE probing revealed that the MTE is a variant of the panicum mosaic virus-like 3’ CITE (PTE). Like the PTE, electrophoretic mobility shift assays (EMSAs) indicated that eukaryotic translation ...


Principles, Applications, And Biosafety Of Plant Genome Editing Using Crispr-Cas9, Kaoutar El-Mounadi, María Luisa Morales-Floriano, Hernan Garcia-Ruiz 2020 Kuztown University of Pennsylvania

Principles, Applications, And Biosafety Of Plant Genome Editing Using Crispr-Cas9, Kaoutar El-Mounadi, María Luisa Morales-Floriano, Hernan Garcia-Ruiz

Papers in Plant Pathology

The terms genome engineering, genome editing, and gene editing, refer to modifications (insertions, deletions, substitutions) in the genome of a living organism. The most widely used approach to genome editing nowadays is based on Clustered Regularly Interspaced Short Palindromic Repeats and associated protein 9 (CRISPR-Cas9). In prokaryotes, CRISPR-Cas9 is an adaptive immune system that naturally protects cells from DNA virus infections. CRISPR-Cas9 has been modified to create a versatile genome editing technology that has a wide diversity of applications in medicine, agriculture, and basic studies of gene functions. CRISPR-Cas9 has been used in a growing number of monocot and dicot ...


A Rapid And Simple Quantitative Method For Specific Detection Of Smaller Co-Terminal Rna By Pcr (Desco-Pcr): Application To The Detection Of Viral Subgenomic Rnas, Pulkit Kanodia, K. Reddisiva Prasanth, Vicky C. Roa-Linares, Shelton S. Bradrick, Mariano A. Garcia-Blanco, W. Allen Miller 2020 Iowa State University

A Rapid And Simple Quantitative Method For Specific Detection Of Smaller Co-Terminal Rna By Pcr (Desco-Pcr): Application To The Detection Of Viral Subgenomic Rnas, Pulkit Kanodia, K. Reddisiva Prasanth, Vicky C. Roa-Linares, Shelton S. Bradrick, Mariano A. Garcia-Blanco, W. Allen Miller

Plant Pathology and Microbiology Publications

RNAs that are 5’-truncated versions of a longer RNA, but share the same 3’ terminus can be generated by alternative promoters in transcription of cellular mRNAs or by replicating RNA viruses. These truncated RNAs cannot be distinguished from the longer RNA by a simple two-primer RT-PCR because primers that anneal to the cDNA from the smaller RNA also anneal to - and amplify - the longer RNA-derived cDNA. Thus, laborious methods, such as northern blot hybridization, are used to distinguish shorter from longer RNAs. For rapid, low-cost and specific detection of these truncated RNAs, we report Detection of Smaller Co-terminal RNA ...


Improving Kentucky's Winter Wheat And Double Crop Soybean Rotation, Katherine Susan Rod 2020 University of Kentucky

Improving Kentucky's Winter Wheat And Double Crop Soybean Rotation, Katherine Susan Rod

Theses and Dissertations--Plant and Soil Sciences

The winter wheat double crop soybean rotation is an economically viable rotation for Kentucky farmers. Recent decreases in commodity prices has warranted the need to evaluate intensive management practices that can increase yields and profitability in this crop rotation. There were three goals of this dissertation: 1.) identify management practices that would decrease deoxynivalenol (DON) in harvested wheat grain and increase wheat heading and anthesis uniformity, 2.) evaluate double crop soybean planting timing and identify intensive management practices to increase seed yield, and 3.) determine the profitability of these management options. These studies were conducted in Princeton KY between 2016 ...


De Novo Transcriptome Of Phakopsora Pachyrhizi Uncovers Putative Effector Repertoire During Infection, Manjula G. Elmore, Sagnik Banerjee, Kerry F. Pedley, Amy Ruck, Steven A. Whitham 2020 Iowa State University

De Novo Transcriptome Of Phakopsora Pachyrhizi Uncovers Putative Effector Repertoire During Infection, Manjula G. Elmore, Sagnik Banerjee, Kerry F. Pedley, Amy Ruck, Steven A. Whitham

Plant Pathology and Microbiology Publications

Phakopsora pachyrhizi, which causes Asian soybean rust (ASR), secretes effector proteins to manipulate host immunity and promote disease. To date, only a small number of effectors have been identified from transcriptome studies. To obtain a more comprehensive understanding of P. pachyrhizi candidate secreted effector proteins (CSEPs), we sequenced the transcriptome using two next-generation sequencing technologies. Short-read Illumina RNA-Seq data was used for reducing base-calling errors for long-read PacBio Iso-Seq. After initial de novo assemblies for RNA-seq and error correction of transcripts for Iso-Seq followed by filtering, we obtained 8,528, 27,647, 26,895, and 17,141 non-plant, non-soybean transcripts ...


Occurrence, Mating Strategy, And Pathogenicity Of Members Of Nectriaceae In Central Appalachia, Cameron Michael Stauder 2020 West Virginia University

Occurrence, Mating Strategy, And Pathogenicity Of Members Of Nectriaceae In Central Appalachia, Cameron Michael Stauder

Graduate Theses, Dissertations, and Problem Reports

Members of the Nectriaceae occupy many ecological niches including dominant canker pathogens, such as Neonectria ditissima and N. faginata. These two pathogens contribute to the decline of American beech (Fagus grandifolia) forests across the Appalachian Mountains due to beech bark disease (BBD). Interestingly, N. ditissima represents a well-known canker pathogen many hardwood species, while N. faginata has not been observed outside of BBD. Additionally, N. faginata occurs at higher incidences than N. ditissima in BBD stands. Nectriaceae in Central Appalachia were surveyed as to further characterize the diversity and possibly identify a non-beech host of N. faginata. This resulted in ...


Biological And Cellular Functions Of The Microdomain-Associated Fwl/Cnr Protein Family In Plants, Sandra Thibivilliers, Andrew Farmer, Marc Libault 2020 University of Nebraska-Lincoln

Biological And Cellular Functions Of The Microdomain-Associated Fwl/Cnr Protein Family In Plants, Sandra Thibivilliers, Andrew Farmer, Marc Libault

Faculty Publications from the Center for Plant Science Innovation

Membrane microdomains/nanodomains are sub-compartments of the plasma membrane enriched in sphingolipids and characterized by their unique protein composition. They play important roles in regulating plant development and plant-microbe interactions including mutualistic symbiotic interactions. Several protein families are associated with the microdomain fraction of biological membranes such as flotillins, prohibitins, and remorins. More recently, GmFWL1, a FWL/CNR protein exclusively expressed in the soybean nodule, was functionally characterized as a new microdomain-associated protein. Interestingly, GmFWL1 is homologous to the tomato FW2-2 protein, a major regulator of tomato fruit development. In this review, we summarize the knowledge gained about the biological ...


Semantic Segmentation Of Sorghum Using Hyperspectral Data Identifies Genetic Associations, Chenyong Miao, Alejandro Pages, Zheng Xu, Eric Rodene, Jinliang Yang, James C. Schnable 2020 University of Nebraska - Lincoln

Semantic Segmentation Of Sorghum Using Hyperspectral Data Identifies Genetic Associations, Chenyong Miao, Alejandro Pages, Zheng Xu, Eric Rodene, Jinliang Yang, James C. Schnable

Faculty Publications from the Center for Plant Science Innovation

This study describes the evaluation of a range of approaches to semantic segmentation of hyperspectral images of sorghum plants, classifying each pixel as either nonplant or belonging to one of the three organ types (leaf, stalk, panicle). While many current methods for segmentation focus on separating plant pixels from background, organ-specific segmentation makes it feasible to measure a wider range of plant properties. Manually scored training data for a set of hyperspectral images collected from a sorghum association population was used to train and evaluate a set of supervised classification models. Many algorithms show acceptable accuracy for this classification task ...


Isoseq Transcriptome Assembly Of C3 Panicoid Grasses Provides Tools To Study Evolutionary Change In The Panicoideae, Daniel S. Carvalho, Aime V. Nishimwe, James C. Schnable 2020 University of Nebraska - Lincoln

Isoseq Transcriptome Assembly Of C3 Panicoid Grasses Provides Tools To Study Evolutionary Change In The Panicoideae, Daniel S. Carvalho, Aime V. Nishimwe, James C. Schnable

Faculty Publications from the Center for Plant Science Innovation

The number of plant species with genomic and transcriptomic data has been increasing rapidly. The grasses—Poaceae—have been well represented among species with published reference genomes. However, as a result the genomes of wild grasses are less frequently targeted by sequencing efforts. Sequence data from wild relatives of crop species in the grasses can aid the study of domestication, gene discovery for breeding and crop improvement, and improve our understanding of the evolution of C4 photosynthesis. Here, we used long-read sequencing technology to characterize the transcriptomes of three C3 panicoid grass species: Dichanthelium oligosanthes, Chasmanthium laxum, and ...


Isoseq Transcriptome Assembly Of C3 Panicoid Grasses Provides Tools To Study Evolutionary Change In The Panicoideae, Daniel S. Carvalho, Aime Nishimwe, James Schnable 2020 University of Nebraska - Lincoln

Isoseq Transcriptome Assembly Of C3 Panicoid Grasses Provides Tools To Study Evolutionary Change In The Panicoideae, Daniel S. Carvalho, Aime Nishimwe, James Schnable

Faculty Publications from the Center for Plant Science Innovation

The number of plant species with genomic and transcriptomic data has been increasing rapidly. The grasses—Poaceae—have been well represented among species with published reference genomes. However, as a result the genomes of wild grasses are less frequently targeted by sequencing efforts. Sequence data from wild relatives of crop species in the grasses can aid the study of domestication, gene discovery for breeding and crop improvement, and improve our understanding of the evolution of C4 photosynthesis. Here, we used long-read sequencing technology to characterize the transcriptomes of three C3 panicoid grass species: Dichanthelium oligosanthes, Chasmanthium laxum, and ...


Campana, (Richard J.) Papers, 1937-1989, Special Collections, Raymond H. Fogler Library, University of Maine 2020 The University of Maine

Campana, (Richard J.) Papers, 1937-1989, Special Collections, Raymond H. Fogler Library, University Of Maine

Finding Aids

Born in Everett, Massachusetts, Richard J. Campana (1918-2005) received a BSF from the University of Idaho in 1943. Campana then served as a surgical technician in the U.S. Army, and earned a Bronze Star award during WWII after being held as a prisoner of war (1943-1946). After the war, Campana earned an MS in Forestry from Yale University in 1974 and a Ph.D. in Forest Pathology in 1952. Soon after, Campana began his professional study and observation of Dutch Elm Disease

In 1958, Campana came to the University of Maine as the head of the Department of Botany ...


Prevalence, Genetic Relationships, And Quantity Of Grapevine Vein Clearing Virus In Aphis Illinoisenesis, Adam Louis Uhls 2020 Missouri State University

Prevalence, Genetic Relationships, And Quantity Of Grapevine Vein Clearing Virus In Aphis Illinoisenesis, Adam Louis Uhls

MSU Graduate Theses

Grapevine vein clearing virus (GVCV) is an emerging pathogen causing severe damage to cultivated grapevines in the Midwest area of the United States. The prevalence of GVCV has been reported in native Vitis spp. and Ampelopsis cordata, a close relative of vitis in the Vitaceae family, which act as a reservoir for the virus. GVCV can be transmitted from wild A. cordata to Vitis spp. by Aphis illinoisensis (grape aphids) under greenhouse conditions, but the prevalence and transmission in native populations remains unknown. Knowing the prevalence and diversity of GVCV variants in natural grape aphid populations would help monitor and ...


The Potential For Dickeya Dianthicola To Be Vectored By Two Common Insect Pests Of Potatoes, Jonas K. Insinga 2019 University of Maine

The Potential For Dickeya Dianthicola To Be Vectored By Two Common Insect Pests Of Potatoes, Jonas K. Insinga

Electronic Theses and Dissertations

Dickeya dianthicola (Samson) causing blackleg and soft rot was first detected in potatoes grown in Maine in 2014. Previous work has suggested that insects, particularly aphids, may be able to vector bacteria in this genus between plants, but no conclusive work has been done to confirm this theory. In order to determine whether insect-mediated transmission is likely to occur in potato fields, two model potato pests common in Maine were used: the Colorado potato beetle (Leptinotarsa decimlineata Say) and the green peach aphids (Myzus persicae Sulzer). Olfactometry and recruitment experiments evaluated if either insect discriminates between infected and uninfected foliage ...


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