Molecular Biology Commons^™

Phenotypic And Transcriptomic Characterization Of Rice Snrk1 Mutants Developed By Crispr/Cas9 Mutagenesis, Maria Clara Faria Chaves

Graduate Theses and Dissertations

SnRK1 is a heterotrimeric protein kinase that is composed of a catalytic subunit (α) and two regulatory subunits (β and βγ), and it has a main role in regulating energy homeostasis in the plant by modulating anabolic and catabolic process. SnRK1 phosphorylates and alters the activities of enzymes involved in metabolism and regulates gene expression by altering the activity of chromatin-remodeling enzymes or the transcription factors. Rice contains three functional paralogs of SnRK1α: SnRK1αa (LOC_Os03g17980), SnRK1αb (LOC_Os08g37800), and SnRK1αc (LOC_Os05g45420). This study focused on the function of these SnRK1 paralogs by evaluating the phenotypic and transcriptomic characteristics and the disease …

Resistance Screening And Association Mapping For Resistance To The Downy Mildew Pathogen Of Spinach, Dotun Olaoye

Graduate Theses and Dissertations

Spinach is an important cool leafy vegetable cultivated around the world, with large scale production in California and Arizona in the U.S. Spinach is a highly nutritious vegetable beneficial in the human diet. Spinach is affected by a number of biotic stressors. Downy mildew, caused by the oomycete pathogen Peronospora effusa, is a major threat to spinach as it affects the leaf quality and impacts the economic value of spinach. Several efforts have led to the development of resistant genotypes/cultivars to this pathogen. However, few studies have examined the genetics of resistance to the downy mildew pathogen in detail. This …

Molecular Genetic Analysis Of Drought Resistance And Productivity Traits Of Rice Genotypes, Yheni Dwiningsih

Graduate Theses and Dissertations

Rice (Oryza sativa L.) is the staple food for a majority of the world’s population, and uses 30% of the global fresh water during its life cycle. Drought at the reproductive stage is the most important abiotic stress factor limiting grain yield. The United States is the third largest exporter of rice, and Arkansas is the top rice-producing state. The Arkansas rice-growing region in the Lower Mississippi belt is among the 10 areas with the highest risk of water scarcity. Adapted U.S. rice cultivars were screened for drought resistant (DR) traits to find sources for breeding U.S. rice cultivars for …

Taxonomic And Genetic Diversity, And Pathogenicity Of Diaporthe Species Associated With Soybean, Fakhir Eraheem Hameed Al Shuwaili

Graduate Theses and Dissertations

Diaporthe species (anamorph: Phomopsis) are associated with a wide range of plant hosts as plant pathogens, asymptomatic endophytes, and saprobes. One of these hosts is soybean, which is one of the most important crops in U.S. agriculture. Several Diaporthe species cause important diseases on soybean in the U.S., and specifically in Arkansas. The taxonomy, genetic diversity, and pathogenicity of Diaporthe species associated with asymptomatic infection of soybean are rarely studied with accurate molecular tools. Therefore, this dissertation aimed to assess the diversity and boundaries of Diaporthe associated with soybean in Arkansas. Furthermore, pathogenicity and alternative lifestyles were assessed among Diaporthe …

Dissecting The Cellular Control Of Septin Organization In A Global Cereal Killer, Nawaraj Dulal

Graduate Theses and Dissertations

Rice blast disease, caused by the filamentous fungus Magnaporthe oryzae, destroys sufficient rice each year to feed 60 million people, and is a serious threat to global food security. A wheat-adapted lineage of M. oryzae now poses threat to global wheat production. Rice blast disease is currently controlled using limited fungicides, and the emergence of fungicide resistance within M. oryzae populations is a growing concern. There is a pressing need to identify new classes of fungicides to control the disease, which requires better understanding of the basic biology of the pathogen. To establish disease, M. oryzae forms a specialized dome …

Analyzing Multigene Stacking And Genome Editing Strategies In Rice, Bhuvan Pathak

Graduate Theses and Dissertations

Crop improvement through biotechnology is an integrated effort, incorporating multiple approaches like integration of genes, editing of native genes, and removal of selection marker genes. Before streamlining the protocols, the efficiency and feasibility of the individual approach and their components must be tested. This study evaluated following approaches: 1) stacking an array of genes into a single locus by site-specific integration via Cre-lox recombination in rice, 2) determining the efficiency of I-SceI and the CCR5-ZFN in the targeted excisions of gene fragments in rice and Arabidopsis, and 3) determining the efficiency of CRISPR/Cas9 in generating targeted mutations for genome editing …

Epidemiological Studies Of Soybean Vein Necrosis Virus And Potential Resistance Mechanisms To Its Vector Neohydatothrips Variabilis (Beach), Jing Zhou

Graduate Theses and Dissertations

Soybean (Glycine max (L.) Merrill) is one the most important crops in global agriculture with annual production of over 260 million metric tons. As the dependence of a growing global population to soybean has increased, so does the importance of soybean diseases and pests. Over 200 pathogens attack soybean; among them, viruses pose a major threat to the soybean industries accounting for approximately 10% of the annual yield reduction caused by diseases in the past two decades. Soybean vein necrosis virus (SVNV) is a relatively newly discovered virus causing the homonymous disease. The widespread occurrence of the disease in major …

Gene Expression And Physiological Analysis To Study Differences Between Oryza Sativa Cultivars Susceptible And Resistant To Chalky Grain Formation Subjected To High Nighttime Temperatures., Nicholas Lawson

Graduate Theses and Dissertations

Starch composition and grain quality of rice is greatly influenced by genotype and environmental factors. The detrimental effects of high nighttime temperatures on rice yield and quality has recently become apparent, with some of the warmest average nighttime temperatures being recorded in the past few years. One of the most notable effects of this stress, an increase in grain chalk formation, correlates with a decrease in quality. This effect varies greatly between cultivars as some show less temperature-sensitive quality reduction than others. The goal of this research is to elucidate fundamental changes that occur in developing plants and grains as …

Blackberry Virosome: A Micro And Macro Approach, Archana Khadgi

Graduate Theses and Dissertations

Viruses pose a major concern for blackberry production around the world with more than 40 species known to infect the crop. Virus complexes have been identified recently as the major cause of plant decline with blackberry yellow vein disease (BYVD) being the most important disease of the crop in the Southern United States. The objective of this research was to study the blackberry virosome in both the macro and micro scale. The large scale approach involves identification of the major viruses known to be associated with BYVD in the Southern United States as well as the identification of other viruses …

Understanding The Causal Agent Of Rose Rosette Disease, Patrick Louis Di Bello

Graduate Theses and Dissertations

A number viruses are known to infect roses, ranging from those in the genera Nepovirus, and Ilarvirus, which have been reported since the inception of rose virology, to recently discovered viruses in the genera Carmovirus, Closterovirus, Emaravirus, Luteovirus, Rosadnavirus, and Potyvirus. Of the viral diseases in rose, arguably the most damaging is Rose rosette (RRD), which is associated with the Emaravirus, Rose rosette virus (RRV). The objective of this thesis is to fill in the gaps in knowledge on the epidemiological aspects of RRD and RRV. There has been significant progress in the epidemiology of the RRD agent prior to …

Analysis Of Ac/Ds Activation Tagged Mutants In Tomato (Solanum Lycopersicum), Ipeleng Randome

Graduate Theses and Dissertations

Tomato (Solanum lycopersicum) is a crop of immense economic and nutritional importance worldwide and also a good model organism for genomic studies of other dicot species. The recent completion of the tomato genome sequence is a great milestone towards learning about the tomato genome. Elucidation of the function of the different genes using different functional genomic tools is therefore important in adding to this resource. To this end, we have developed an Ac-Ds transposon ‘activation tagging’ (ATag) system to be able to transpose transposon inserts, bearing a strong 35S-enhancer element, all around the genome. An Ac-Ds ATag construct was used …

Optimizing A Luciferase-Based Tool For Studying The Effects Of Fatty Acid Desaturase 7 On Singlet Oxygen Accumulation In Arabidopsis Thaliana, Abeer Muhammedali Alnasrawi

Graduate Theses and Dissertations

In plants, reactive oxygen species (ROS) are generated as a byproduct of normal metabolism, as well as in response to adverse conditions such as light stress, extreme temperatures, and exposure to pests and pathogens. Singlet oxygen (1O2) is a ROS that is formed during photosynthesis in photosystem II (PSII) of the chloroplasts. Levels of 1O2 and other ROS are tightly controlled in healthy plants, but some studies suggest that levels of fatty acid desaturase (FAD) activity in Arabidopsis thaliana can influence constitutive and/or stress-responsive ROS accumulation. In this study, a luciferase-based reporter gene that is selectively stimulated by 1O2 (AAA-ATPase: …

The Mechanism Of Lhcp Insertion Into Thylakoid Membranes, Larae Brown

Graduate Theses and Dissertations

The light harvesting chlorophyll a/b-binding proteins (LHCPs) are the most abundant membrane proteins. LHCP is a nuclear encoded protein which is targeted to the thylakoid membranes by chloroplast signal recognition particles (cpSRP). Insertion into thylakoid membranes is facilitated by the cpSRP receptor cpFtsY and the Alb3 translocase. Work here focused on understanding the molecular events of LHCP insertion into the thylakoid membranes. Specifically, we sought to develop a tool to detect the insertion of the lumen-localized loop of LHCP into thylakoid membranes, which relies on cleavage of the loop by a thylakoid lumen processing protease. We also sought to understand …

Biology And Control Of Rice False Smut Caused By Ustilaginoidea Virens (Teleomorph Villosiclava Virens), Andrew Clayton Jecmen

Graduate Theses and Dissertations

Rice false smut (FS), a disease caused by Ustilaginoidea virens (Cke.) Takahashi (1896), was first reported in northeastern Arkansas counties in 1997. The first objective of this research was to establish a collection of U. virens isolates from geographically diverse regions of Arkansas. Three U. virens isolates and chlamydospores from `Templeton' and `Clearfield-151' rice cultivars were used to determine the effects of temperature and pH on mycelial growth and germination. A nested-PCR protocol and histological methods were used to determine if U. virens infects and colonizes rice seedlings and spikelets on panicles. The sensitivity of three U. virens isolates was …

Molecular And Biochemical Mechanisms Of Pathogenesis In The Maize Foliar Pathogen Cercospora Zeae-Maydis, Winfred-Peck Dorleku

Graduate Theses and Dissertations

GLS is a serious foliar disease of maize, a major staple crop grown commercially in the USA for both human and animal feed production, and increasingly, for ethanol production. The disease is caused by two Cercospora species, C. zeae-maydis and C. zeina, both of which infect maize in the USA and in other parts of the world, with yield losses potentially greater than 50%, depending on local conditions. In culture, C. zeae-maydis produces a phytotoxic, host non-specific perylenequinone, cercosporin, and abscisic acid (ABA), for which there is no known pathological or physiological function in the fungus. Experimental evidence indicates …

Characterization And Epidemiology Of Soybean Vein Necrosis Associated Virus, Jing Zhou

Graduate Theses and Dissertations

Soybean vein necrosis disease (SVND) is widespread in major soybean-producing areas in the U.S. The typical disease symptoms exhibit as vein clearing along the main vein, which turn into chlorosis or necrosis as season progresses. Double-stranded RNA isolation and shot gun cloning of symptomatic tissues revealed the presence of a new tospovirus, provisionally named as Soybean vein necrosis associated virus (SVNaV). The presence of the virus has been confirmed in 12 states: Arkansas, Illinois, Missouri, Kansas, Tennessee, Kentucky, Mississippi, Maryland, Delaware, Virginia and New York. Symptomatic samples collected from eight states (AR, IL, MO, MS, KS, TN, MD and DE), …

Gene Expression And Physiological Analyses To Study Metabolic Shifts In Medicago Truncatula Subjected To Biotic Stresses, Michelle Ryan Martin

Graduate Theses and Dissertations

Plants are frequently under attack from pests and deploy various defense mechanisms to fight off predators. Many plant defenses are induced following herbivory or pathogen infection. An investment in defense could potentially lead to a diversion of metabolic resources away from primary metabolism, including reduction in plant commitment to photosynthesis. In this thesis, changes in expression levels of representative genes for primary and secondary metabolism were studied using real-time polymerase chain reaction (PCR) in Medicago truncatula Gaertner subjected to beet armyworm (Spodoptera exigua H¨¹bner) damage or Phoma medicaginis Malbr. & Roum. infection. Photosynthetic yield was also measured using chlorophyll fluorescence …

The Role Of Albino3 And The Lipid Environment In Chloroplast Signal Recognition Particle Targeting, Nathan Lewis

Graduate Theses and Dissertations

Signal recognition particles (SRPs) in pro- and eukaryotes function in cotranslational targeting of nascent poplypeptides to an SRP receptor at the target membrane. A unique chloroplast SRP (cpSRP) functions post-translationally to direct light-harvesting chlorophyll-binding proteins (LHCPs) to the receptor cpFtsY at the thylakoid membrane for LHCP insertion in a process involving the integral membrane protein Albino3 (Alb3) and requiring GTP. Work here focuses on understanding cpSRP targeting events at the thylakoid membrane, specifically those involving Alb3 and the lipid environment.

We show an interaction between the novel cpSRP subunit cpSRP43 and the soluble, stromal-exposed C terminus of Albino3 (Alb3-Cterm). We …

Applications Of Site-Specific Recombination Systems In Transgene Expression And Marker Gene Removal, Mehmet Aydin Akbudak

Graduate Theses and Dissertations

Site Specific Recombination systems, such as FLP-FRT and Cre-lox, have been successfully used for site-specific gene integration and marker-gene deletion in plant systems. They are very useful tools in the integration of single-copy full-length transgene cassettes into the genome because the transgene integration via conventional methods often generate multi-copy locus. Such complex locus containing direct and inverted repeats of full-length and truncated copies of the transgene cassette generate aberrant RNA resulting in gene silencing. Therefore, for stable gene expression, a single copy transgene locus is preferred. However, even single copy locus sometimes succumbs to gene silencing. Although the mechanism is …