Plant Pathology Commons^™

Advances In Plant Phenomics: From Data And Algorithms To Biological Insights, Sunil Kumar Kenchanmane Raju, Addie M. Thompson, James Schnable

Center for Plant Science Innovation: Faculty Publications

The measurement of the characteristics of living organisms is referred to as phenotyping (Singh et al., 2016). While the use of phenotyping in plant biology and genetics can be traced back at least to Gregor Mendel sorting and counting peas by shape and pod color 160 years ago, addressing current questions in plant biology, genetics, and breeding often requires increasingly precise phenotyping of a wide range of traits. Accurate phenotyping has played a role in both novel discoveries about the fundamental biology of plants and the development of improved crop varieties around the world. With the advent of inexpensive genotyping …

Leaf Angle Extractor: A High-Throughput Image Processing Framework For Leaf Angle Measurements In Maize And Sorghum, Sunil Kumar Kenchanmane Raju, Miles Adkins, Alex Enersen, Daniel Santana De Carvalho, Anthony J. Studer, Baskar Ganapathysubramanian, Patrick S. Schnable, James C. Schnable

Center for Plant Science Innovation: Faculty Publications

PREMISE: Maize yields have significantly increased over the past half-century owing to advances in breeding and agronomic practices. Plants have been grown in increasingly higher densities due to changes in plant architecture resulting in plants with more upright leaves, which allows more efficient light interception for photosynthesis. Natural variation for leaf angle has been identified in maize and sorghum using multiple mapping populations. However, conventional phenotyping techniques for leaf angle are low throughput and labor intensive, and therefore hinder a mechanistic understanding of how the leaf angle of individual leaves changes over time in response to the environment.

METHODS …

Methods And Compositions For Obtaining Useful Plant Traits, Sally Mackenzie, Michael Fromm, Kamaldeep Viridi, Yashitola Wamboldt

Center for Plant Science Innovation: Faculty Publications

The present invention provides methods for obtaining plants that exhibit useful traits by perturbation of plastid function in plant rootstocks and grafting the rootstocks to scions. Methods for identifying genetic loci that provide for useful traits in plants and plants produced with those loci are also provided. In addition, plants that exhibit the useful traits, parts of the plants including seeds, and products of the plants are provided as well as methods of using the plants. Recombinant DNA vectors and transgenic plants comprising those vectors that provide for plastid perturbation are also provided.

Interspecific Analysis Of Diurnal Gene Regulation In Panicoid Grasses Identifies Known And Novel Regulatory Motifs, Xianjun Lai, Claire Bendix, Lang Yan, Yang Zhang, James C. Schnable, Frank G. Harmon

Center for Plant Science Innovation: Faculty Publications

Background: The circadian clock drives endogenous 24-h rhythms that allow organisms to adapt and prepare for predictable and repeated changes in their environment throughout the day-night (diurnal) cycle. Many components of the circadian clock in Arabidopsis thaliana have been functionally characterized, but comparatively little is known about circadian clocks in grass species including major crops like maize and sorghum.

Results: Comparative research based on protein homology and diurnal gene expression patterns suggests the function of some predicted clock components in grasses is conserved with their Arabidopsis counterparts, while others have diverged in function. Our analysis of diurnal gene expression in …

Voxel Carving-Based 3d Reconstruction Of Sorghum Identifies Genetic Determinants Of Light Interception Efficiency, Mathieu Gaillard, Chenyong Miao, James C. Schnable, Bedrich Benes

Center for Plant Science Innovation: Faculty Publications

Changes in canopy architecture traits have been shown to contribute to yield in- creases. Optimizing both light interception and light interception efficiency of agri- cultural crop canopies will be essential to meeting the growing food needs. Canopy architecture is inherently three-dimensional (3D), but many approaches to measuring canopy architecture component traits treat the canopy as a two-dimensional (2D) structure to make large scale measurement, selective breeding, and gene identifi- cation logistically feasible. We develop a high throughput voxel carving strategy to reconstruct 3D representations of sorghum from a small number of RGB photos. Our approach builds on the voxel carving …

Compounds For Increasing Lipid Synthesis And Storage, Concetta Dirusso, Nishikant Wase

Center for Plant Science Innovation: Faculty Publications

This invention relates to methods for increasing lipid accumulation and lipid production in cells. Methods of producing biofuel from cells and preparing nutraceuticals comprising lipids produced according to a method provided herein are also provided.

Non-Homology-Based Prediction Of Gene Functions In Maize (Zea Mays Ssp. Mays), Xiuru Dai, Zheng Xu, Zhikai Liang, Xiaoyu Tu, Silin Zhong, James C. Schnable, Pinghua Li

Center for Plant Science Innovation: Faculty Publications

Advances in genome sequencing and annotation have eased the difficulty of identifying new gene sequences. Predicting the functions of these newly identified genes remains challenging. Genes descended from a common ancestral sequence are likely to have common functions. As a result, homology is widely used for gene function pre- diction. This means functional annotation errors also propagate from one species to another. Several approaches based on machine learning classification algorithms were evaluated for their ability to accurately predict gene function from non-homology gene features. Among the eight supervised classification algorithms evaluated, random- forest-based prediction consistently provided the most accurate gene …

A High-Throughput Phenotyping Pipeline For Image Processing And Functional Growth Curve Analysis, Ronghao Wang, Yumuo Qiu, Yuzhen Zhou, Zhikai Liang, James Schnable

Center for Plant Science Innovation: Faculty Publications

High-throughput phenotyping system has become more and more popular in plant science research. The data analysis for such a system typically involves two steps: plant feature extraction through image processing and statistical analysis for the extracted features. The current approach is to perform those two steps on different platforms. We develop the package “implant” in R for both robust feature extraction and functional data analysis. For image processing, the “implant” package provides methods including thresholding, hidden Markov random field model, and morphological operations. For statistical analysis, this package can produce nonparametric curve fitting with its confidence region for plant growth. …

Leaf Angle Extractor: A High-Throughput Image Processing Framework For Leaf Angle Measurements In Maize And Sorghum, Sunil Kumar Kenchanmane Raju, Miles Adkins, Alex Enersen, Daniel Santana De Carvalho, Anthony J. Studer, Baskar Ganapathysubramanian, Patrick Schnable, James C. Schnable

Center for Plant Science Innovation: Faculty Publications

PREMISE: Maize yields have significantly increased over the past half-century owing to advances in breeding and agronomic practices. Plants have been grown in increasingly higher densities due to changes in plant architecture resulting in plants with more upright leaves, which allows more efficient light interception for photosynthesis. Natural variation for leaf angle has been identified in maize and sorghum using multiple mapping populations. However, conventional phenotyping techniques for leaf angle are low throughput and labor intensive, and therefore hinder a mechanistic understanding of how the leaf angle of individual leaves changes over time in response to the environment.

METHODS: High-throughput …

Advances In Plant Phenomics: From Data And Algorithms To Biological Insights, Sunil K. Kenchanmane Raju, Addie M. Thompson, James Schnable

Center for Plant Science Innovation: Faculty Publications

The measurement of the characteristics of living organisms is re- ferred to as phenotyping (Singh et al., 2016). While the use of phe- notyping in plant biology and genetics can be traced back at least to Gregor Mendel sorting and counting peas by shape and pod color 160 years ago, addressing current questions in plant biology, genet- ics, and breeding often requires increasingly precise phenotyping of a wide range of traits. Accurate phenotyping has played a role in both novel discoveries about the fundamental biology of plants and the development of improved crop varieties around the world. With the advent …

Metabolic Profiles Of Six African Cultivars Of Cassava (Manihot Esculenta Crantz) Highlight Bottlenecks Of Root Yield, Toshihiro Obata, Patrick A.W. Klemens, Laise Rosado-Souza, Armin Schlereth, Andreas Gisel, Livia Stavolone, Wolfgang Zierer, Nicolas Morales, Lukas A. Mueller, Samuel C. Zeeman, Frank Ludewig, Mark State, Uwe Sonnewald, H. Ekkehard Neuhaus, Alisdair R. Femie

Center for Plant Science Innovation: Faculty Publications

Cassava is an important staple crop in sub-Saharan Africa, due to its high productivity even on nutrient poor soils. The metabolic characteristics underlying this high productivity are poorly understood including the mode of photosynthesis, reasons for the high rate of photosynthesis, the extent of source/sink limitation, the impact of environment, and the extent of variation between cultivars. Six commercial African cassava cultivars were grown in a greenhouse in Erlangen, Germany, and in the field in Ibadan, Nigeria. Source leaves, sink leaves, stems and storage roots were harvested during storage root bulking and analyzed for sugars, organic acids, amino acids, phosphorylated …

Increased Power And Accuracy Of Causal Locus Identification In Time Series Genome-Wide Association In Sorghum1[Open], Chenyong Miao, Yuhang Xu, Sanzhen Liu, Patrick S. Schnable, James C. Schnable

Center for Plant Science Innovation: Faculty Publications

The phenotypes of plants develop over time and change in response to the environment. New engineering and computer vision technologies track these phenotypic changes. Identifying the genetic loci regulating differences in the pattern of phenotypic change remains challenging. This study used functional principal component analysis (FPCA) to achieve this aim. Time series phenotype data were collected from a sorghum (Sorghum bicolor) diversity panel using a number of technologies including conventional color photography and hyperspectral imaging. This imaging lasted for 37 d and centered on reproductive transition. A new higher density marker set was generated for the same population. Several genes …

Virus-Induced Changes In Nuclear Proteins And Membranes In Nicotiana Benthamiana Cells, Caleb Mathias

Theses and Dissertations--Plant Pathology

Viruses rely on host proteins to complete their life cycles. This results in alterations to normal cell physiology to processes which benefit viral processes such as replication and movement to other cells. This may involve the relocalization of host proteins away from their original subcellular targets to sites which may benefit the virus, a process that is not as well understood as it relates to the nucleus. To identify nuclear proteins that may be involved in such processes, a library of random Nicotiana benthamiana cDNAs were expressed as GFP fusions in a transgenic marker lines expressing a histone 2B:RFP nuclear …

A Comparison Of Media To Determine Optimal Growth In Aquaponics, Rachel L. Fogle, Andrea Nagy, Allison Bernard, Jordan Brown, Samantha Delvalle-Trinh, James Shuler

Harrisburg University Presidential Research Grants

No abstract provided.

A Global Database Of Soil Nematode Abundance And Functional Group Composition, Johan Van Den Hoogen, Stefan Geisen, Thomas W. Crowther, Peter Mullin, Many Co-Authors

Department of Plant Pathology: Faculty Publications

As the most abundant animals on earth, nematodes are a dominant component of the soil community. They play critical roles in regulating biogeochemical cycles and vegetation dynamics within and across landscapes and are an indicator of soil biological activity. Here, we present a comprehensive global dataset of soil nematode abundance and functional group composition. This dataset includes 6,825 georeferenced soil samples from all continents and biomes. For geospatial mapping purposes these samples are aggregated into 1,933 unique 1-km pixels, each of which is linked to 73 global environmental covariate data layers. Altogether, this dataset can help to gain insight into …

Determining The Effects Of Plant Extracts And Saltro Nematicide On Hatching, Mortality And Reproduction Of The Soybean Cyst Nematode (Heterodera Glycines), Bishnu Prasad Dhital

Electronic Theses and Dissertations

Soybean cyst nematode (SCN) is a microscopic worm that infects and feeds from the soybean roots, hence robbing the plant of nutrients, and entry wounds may facilitate other pathogens to infect the roots. Current SCN management practices include cultural, chemical, and biological methods. Cultural practices such as, crop rotation with non-host and different tillage practices are not efficient due to the persistent nature of SCN in the soil. Chemical nematicides, though effective, can be expensive, and some are not environmentally sound. SCN resistant soybean varieties are mainly derived from one source, PI 88788 and SCN population have already evolved to …

Non-Homology-Based Prediction Of Gene Functions In Maize (Zea Mays Ssp. Mays), Xiuru Dai, Zheng Xu, Zhikai Liang, Xiaoyu Tu, Silin Zhong, James Schnable, Pinghua Li

Center for Plant Science Innovation: Faculty Publications

Advances in genome sequencing and annotation have eased the difficulty of identifying new gene sequences. Predicting the functions of these newly identified genes remains challenging. Genes descended from a common ancestral sequence are likely to have common functions.As a result, homology is widely used for gene function prediction. This means functional annotation errors also propagate from one species to another. Several approaches based on machine learning classification algorithms were evaluated for their ability to accurately predict gene function from non-homology gene features. Among the eight supervised classification algorithms evaluated, random forest-based prediction consistently provided the most accurate gene function prediction. …

Characterizing The Roles Of Pipecolic Acid And Reactive Oxygen Species Metabolic Enzymes In Plant Systemic Immunity, Ruiying Liu

Theses and Dissertations--Plant Pathology

Systemic acquired resistance (SAR), initiated by a plant upon recognition of microbial effectors, involves the generation of mobile signals at the primary infection site, which translocate to and activate defense responses in distal tissues. Among the signals contributing to SAR include salicylic acid (SA), nitric oxide (NO), reactive oxygen species (ROS), glycerol-3-phosphate (G3P), and pipecolic acid (Pip). Our previous studies show there are two branches of SAR signaling pathways in Arabidopsis: one regulated by NO/ROS-G3P and the other by SA. Both NO/ROS-G3P and SA-mediated signaling branches function in parallel during SAR. To better understand the role of Pip in SAR …

Pathogenicity, Toxigenic Potential, And Genomics Of Fusarium Graminearum And F. Meridionale Causing Ear And Stalk Rot Of Maize, Franklin Jackson Machado

Theses and Dissertations--Plant Pathology

Gibberella ear (GER) and stalk rot (GSR) diseases of maize in Brazil are caused mainly by Fusarium meridionale, a species belonging to the Fusarium graminearum species complex (FGSC). Another species within this complex, F. graminearum sensu stricto (hereafter F. graminearum), is second in importance on maize, but is the most common species found causing Fusarium Head Blight disease of wheat in Brazil. The latter species is the predominant cause of GER and GSR in North America, where F. meridionale has not been found thus far. In this dissertation I undertook a comparative analysis of pathogenic, saprophytic, toxigenic and …

Diversity And Cross-Infection Potential Of Colletotrichum On Apples And Small Fruits In Kentucky Mixed-Fruit Orchards, Madison Julia Eaton

Theses and Dissertations--Plant Pathology

Fungi in the genus Colletotrichum cause apple, blueberry, and strawberry fruit rots, which result in significant losses for Kentucky growers. Most orchards in Kentucky are agritourism-focused and grow multiple fruits in close proximity. These mixed-fruit orchards may facilitate Colletotrichum cross-infection, which has serious management implications. Small fruit and apple Colletotrichum isolates from Kentucky orchards were characterized by morphotype, phylogenetic species identification, cross-inoculation, genome sequencing, and telomere fingerprinting. The small fruit isolates grouped into seven morphotypes, representing two species complexes: C. acutatum and C. gloeosporioides. All blueberry isolates belonged to the species C. fioriniae, and the majority of strawberry …

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

Department of Plant Pathology: Faculty Publications

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 …

Identification, Aggressiveness And Mycotoxin Production Of Fusarium Graminearum And F. Boothii Isolates Causing Fusarium Head Blight Of Wheat In Nebraska, Esteban Valverde-Bogantes

Department of Food Science and Technology: Dissertations, Theses, and Student Research

Fusarium head blight (FHB) is an economically important disease caused by several Fusarium species affecting wheat. Besides causing significant yield losses, infected grain may be contaminated with mycotoxins, primarily trichothecenes, that are harmful to both humans and animals. In recent years, reports of shifts in FHB pathogen populations in North America have highlighted the need for increased vigilance. This dissertation describes a four-year survey evaluating the species, trichothecene genotype and phenotypic diversity of FHB pathogens infecting Nebraska wheat. Most of the isolates were identified as F. graminearum (n=67). Additional species included F. boothii (n=3), F. poae (n=2) and F. acuminatum …

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 …

Inhibition Of Fusarium Oxysporum F. Sp. Nicotianae Growth By Phenylpropanoid Pathway Intermediates, Timothy E. Shull, Jasmina Kurepa, Robert D. Miller, Natalia Martinez-Ochoa, Jan A. Smalle

Plant and Soil Sciences Faculty Publications

Fusarium wilt in tobacco caused by the fungus Fusarium oxysporum f. sp. nicotianae is a disease‑management challenge worldwide, as there are few effective and environmentally benign chemical agents for its control. This challenge results in substantial losses in both the quality and yield of tobacco products. Based on an in vitro analysis of the effects of different phenylpropanoid intermediates, we found that the early intermediates trans‑cinnamic acid and para‑coumaric acid effectively inhibit the mycelial growth of F. oxysporum f. sp. nicotianae strain FW316F, whereas the downstream intermediates quercetin and caffeic acid exhibit no fungicidal properties. Therefore, our in …

Arthropod Resistant Tomatoes: Screening Tools, Yield And Nutritional Quality Of Interspecific Hybrids, Mohammad Hasan Salman Ali Dawood

Theses and Dissertations--Plant and Soil Sciences

Tomato (Solanum lycopersicum) is one of the most economically important vegetable crops grown around globe but is a host for numerous pests and pathogens. In the future, tomato breeders will have to focus on increasing fruit quantity and on enhancing pest resistance. Many accessions of the wild relative of tomato, S. habrochaites display high levels of resistance towards arthropods such as spider mites. The presence of the sesquiterpene hydrocarbon, 7-epi-zingiberene, found in S. habrochaites type IV trichomes has been associated with arthropod resistance. However, the presence of other compounds in its trichome secretions may also be related …

Mutations In Virus-Derived Small Rnas, Deepti Nigam, Katherine Latourrette, Hernan Garcia Ruiz

Department of Plant Pathology: Faculty Publications

RNA viruses exist as populations of genome variants. Virus-infected plants accumulate 21–24 nucleotide small interfering RnAs (siRnAs) derived from viral RnA (virus-derived siRnAs) through gene silencing. This paper describes the profile of mutations in virus-derived siRNAs for three members of the family Potyviridae: Turnip mosaic virus (tuMV), Papaya ringspot virus (pRSV) and Wheat streak mosaic virus (WSMV). for tuMV in Arabidopsis thaliana, profiles were obtained for mechanically inoculated rosette leaves and systemically infected cauline leaves and inflorescence. Results are consistent withselection pressure on the viral genome imposed by local and systemic movement. By genetically removing gene silencing in the plant …

Variation Profile Of The Orthotospovirus Genome, Deepti Nigam, Hernan Garcia Ruiz

Department of Plant Pathology: Faculty Publications

Orthotospoviruses are plant-infecting members of the family Tospoviridae (order Bunyavirales), have a broad host range and are vectored by polyphagous thrips in a circulative- propagative manner. Because diverse hosts and vectors impose heterogeneous selection constraints on viral genomes, the evolutionary arms races between hosts and their pathogens might be manifested as selection for rapid changes in key genes. These observations suggest that orthotospoviruses contain key genetic components that rapidly mutate to mediate host adaptation and vector transmission. Using complete genome sequences, we profiled genomic variation in orthotospoviruses. Results show that the three genomic segments contain hypervariable areas at homologous locations …

Draft Genome Assembly Of Passalora Sequoiae A Needle Blight Pathogen On Leyland Cypress, Warren E. Copes, Jorge Ibarra Caballero, Ebrahiem Babiker, Jane E. Stewart, Valerie A. Orner, Alan S. Windham, Renee Arias

United States Department of Agriculture-Agricultural Research Service / University of Nebraska-Lincoln: Faculty Publications

Objective: Passalora sequoiae (family Mycosphaerellaceae) causes a twig blight on Leyland cypress that requires numerous fungicide applications annually to minimize economic losses for ornamental plant nursery and Christmas tree producers. The objective was to generate a high-quality draft assembly of the genome of P. sequoiae as a resource for primer development to investigate genotype diversity. Data description: We report here the genome sequence of P. sequoiae 9LC2 that was isolated from Leyland cypress ‘Leighton Green’ in 2017 in southern Mississippi, USA. The draft genome was obtained using Pacific Biosciences (PacBio) SMRT and Illumina HiSeq 2500 sequencing. Illumina reads were mapped …

Metabolite Profiling Of Ganoderma-Infected Oil Palm Tree Grown On Ultisol And Oxisol Soil, Ahmad Muhamad Fadhil

Student Works (2020-2029)

The oil palm industry is a pillar of the Malaysian economy and plays a pivotal role in feeding and fueling a growing global population. In 2018, oil palm contributed 37.9% or RM37.7 billion to the country's' Gross Domestic Products (GDP) of agriculture sector. Despite achieving significant achievements in the industry, Ganoderma sp. infection that cause basal stem rot (BSR) and upper stem rot (USR) disease are considered a threat. The palm oil industry is expected to experience significant losses, thereby affecting yield production and ultimately the dead of trees. Some factors have been reported to affect the occurrence of the …

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

Graduate Theses, Dissertations, and Problem Reports (ETD)

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. …