Genetics and Genomics Commons^™

Role Of Chemotype In Aggressiveness, Toxicity, And Competitive-Ness Of Fusarium Graminearum On Wheat, Simran Goyal

Theses and Dissertations--Plant Pathology

Fusarium Head Blight (FHB) of wheat, caused by the fungus Fusarium graminearum, is a devastating disease that led to epidemics in the U.S. during the 1990s, resulting in economic losses exceeding $2.6 billion. Typical symptoms include bleached spikelets and shriveled grains, often contaminated with trichothecene mycotoxins that make them unsafe for food or feed. FHB severity and mycotoxin production are influenced by a complex interplay between host genotype, environmental factors, and pathogen genotype. Integrated management practices that include the use of more resistant cultivars, crop rotation, and fungicide applications help to reduce disease incidence and severity. Disease forecasting models …

Assessing Genetic Diversity And Population Structure In The Imperiled Aconitum Reclinatum (White Monkshood), An Endemic Wildflower Of Central Appalachia, Diamanda A. Zizis

Master’s Theses

Aconitum reclinatum, white monkshood (Ranunculaceae), is a Pennsylvania critically imperiled plant species found in five states of the Appalachian region of the United States: Pennsylvania, West Virginia, Virginia, North Carolina, and Tennessee. This plant is adapted to cool, moist environments but faces threats from increasing habitat loss, deer browse, logging, and changes in rainfall and temperature associated with climate change. Comprehensive knowledge of A. reclinatum genetic population structure remains limited. To address this, we collaborated with Natural Heritage programs within the range of A. reclinatum to sample populations across the species distribution and generate a genotyping-by-sequencing data set of …

Revolutionizing Grapevine Breeding Programs: A Mobile Genome Editing System For Perennial Crops, Bridget Bolt

Theses and Dissertations--Plant and Soil Sciences

Grapevine (Vitis vinifera) faces unprecedented challenges from climate change, with up to 90% of current growing regions potentially becoming unsuitable for production within decades. Traditional breeding approaches require 25-30 years for variety development, creating a time constraint incompatible with the pace of environmental change. This research establishes the approach for a novel mobile RNA-based gene editing platform that addresses longstanding bottlenecks in grapevine improvement while preserving cultivar identity and reducing breeding timelines.

This research developed a three-component system for transgene-free gene editing in grapevine. First, a mobile CRISPR/Cas9 system was established using Agrobacterium rhizogenes transformation and the cut-and-dip …

Function Over Form: The Benefits Of Aspen As Surrogate Brood-Rearing Habitat For Greater Sage-Grouse, Michel T. Kohl, Charles P. Sandford, Paul C. Rogers, Renee Chi, Terry A. Messmer, David K. Dahlgren

Aspen Bibliography

Species of conservation concern are often habitat specialists, posing significant risk to those species when specific plant communities are threatened. As a result, practitioners habitually focus conservation efforts on these communities while ignoring ecological mechanisms that explain the wildlife–plant relationships. In doing so, practitioners may overlook alternative vegetation communities that could maintain wildlife populations under alternative conditions (e.g., climate change). Here, we term these areas surrogate habitat, defined as vegetation communities or resource sites that provide similar critical resources as conventional sites, and assess their potential for conservation using a case study of greater sage-grouse (Centrocercus urophasianus) on …

Tree Rings Reveal Mixtures Of Aspen And Spruce Exhibit Greater Drought Resilience In A Planted Field Experiment, Jéssica Chaves Cardoso, Linhao Wu, Marcel Schneider, Charles A. Nock

Aspen Bibliography

Boreal forests provide a wealth of ecosystem services, many of which are linked to forest productivity. Climate change is expected to increase the frequency, duration, and severity of drought, and undermine the productivity of western boreal forests. Favouring species mixtures has emerged as a potential strategy to increase forest resilience to drought. To test the hypothesis that mixtures of trembling aspen and white spruce were more productive than pure stands because they were more resistant and resilient to drought, we analyzed community and species responses to drought utilizing measurements of annual growth obtained from stem disc samples from a planted …

Comparing Multivalent Cross-Linked Sodium Alginate/ Montmorillonite Beads Containing Curcumin Or Cayenne Pepper As Drug Carriers And Their Antimicrobial Resistance, Shionainn Traynor, Shubham Sharma

SURE Journal: Science Undergraduate Research Experience Journal

The aim of the following work was to investigate and compare curcumin and cayenne pepper in microbeads composed of sodium alginate (SA) crosslinked with montmorillonite (MMT) to act as drug carriers and their antimicrobial resistance. The microbeads were prepared through ion-exchange in multivalent solutions of CaCl₂, MgCl₂ and AlCl₃. The microbeads were characterized by Scanning Electron Microscopy (SEM), Energy Dispersive X-ray analysis (EDX) and the time required for intercalation of curcumin and cayenne pepper with MMT. Simulated intestinal fluid (pH 7.3) and gastric fluid (pH 1.2) at 37°C were used for comparison in swelling studies. …

Editorial - Sure Journal Vol 6, Anne M. Friel, Eva Campion, Sinead Loughran

SURE Journal: Science Undergraduate Research Experience Journal

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Assessing Spatial Distribution And Quantification Of Native Trees In Saskatchewan's Prairie Landscape Using Remote Sensing Techniques, Elham Shafeian, Bryan J. Mood, Kenneth W. Belcher, Colin P. Laroque

Aspen Bibliography

The importance of trees in non-forest landscapes has been the focus of only a few studies. However, these trees provide many important ecosystem services. In this study, we mapped and quantified these trees using Sentinel-2 (S2) and very high-resolution (VHR) Google satellite imagery without any field campaigns. We performed a Random Forest (RF) classification to map the spatial distribution of native trees in different scenarios. The optimal model showed an overall accuracy and kappa of 0.99 and 0.98, respectively. We mapped 40,500 km² of tree cover, including native tree cover (approximately 29,565 km²≈10.5%), excluding plantations, regional and …

Condition And Management Futures In A Quaking Aspen Recreation Area. Final Report To Snyderville Basin Special Recreation District, Paul C. Rogers, Georgie Corkery, Anna B. Miller

Aspen Bibliography

In partnership with Snyderville Basin Special Recreation District (SBSRD), we undertook a study of ecological conditions and user preferences within a quaking aspen recreational destination forest. The location, in two sections know as Run-A-Muk and Right Turn Sage (RAM/RTS), has experienced some forest die-off in the principally aspen dominated forest dissected by ski, bike, and hiking trails. Graduate student Georgie Corkery led the study and successfully completed a Master's degree, in addition to providing needed information to SBSRD regarding the status, uses, and preferred actions at this facility. Key outcomes regarding aspen conditions include assigning causal factors—ungulate browsing and elevated …

Root Plasticity Of Selected Corn (Zea Mays L.) Varieties Grown For Food And Forage In Response To Fertigroe®-N And Urea, Vanica Apostol, Edna Aguilar, Lilia Fernando, Lourdes Edano Ma., Tonette Laude, Eureka Teresa Ocampo

The Philippine Agricultural Scientist

Root plasticity, the capacity of a corn root system to modify its growth and development in response to varying environmental conditions, is a crucial adaptability trait for optimizing water and nutrient uptake, especially in a challenging environments. Understanding root plasticity provides insights into the pattern basis of crop adaptation, contributing to the development of improved corn varieties and agricultural practices that optimize the production of both ear shoots and forage. This study assessed root traits and other morphological-physiological responses of three corn varieties (NK8840, IPB Var 6, and Pearl Sweet) grown for food (ear shoots) and forage (baby corn fodder) …

An Extensive Exploration Of Generalist Microbotryum Species Through Host Interactions., Emilee Walters

College of Arts & Sciences Senior Theses

The Microbotryum species complex is a group of fungi, commonly known as anther smuts. Anther smuts are plant parasites that must invade a host plant in order to fulfill their life cycle. As the Microbotryum fungus grows, it sterilizes the host plant, such that infected plants produce fungal teliospores instead of pollen on the male reproductive organs and female reproductive structures do not mature. Microbotryum usually exists as a specialist species, however, there is evidence that several species of anther smuts can exist as generalist species. Comparisons of the infection process and the resulting response of both parasite and host …

Multi-Decadal Aspen Dynamics Show Recruitment Bottleneck Across Complex Mountain Community, Michael T. Stoddard, Kyle C. Rodman, Connor D. Crouch, David W. Huffman, Peter Z. Fulé, Kristen M. Waring, Margaret M. Moore

Aspen Bibliography

Changes in forest structure and shifts in tree species composition have occurred globally due to climate change and altered disturbance regimes. With climate trending toward warmer and drier conditions, these altered forest communities may reorganize in diverse and unpredictable ways. This is especially true in mountain environments where a range of vegetation types and abiotic conditions coexist. In this study, we used long-term permanent plot data from a site spanning broad environmental gradients to assess regeneration and mortality patterns in populations of aspen (Populus tremuloides). The study site, located on the San Francisco Peaks, Arizona, USA, is near …

The Role Of Siamese In G2 Checkpoint Regulation In Arabidopsis Thaliana, Martha A. Schwall

LSU Doctoral Dissertations

Cyclin-cyclin dependent kinase (Cyclin-CDK) pairs regulate progression through the checkpoints of the cell cycle. They bind with some specificity and must be bound to for their regulative properties to be active. The presence of cyclin-CDKs is conserved throughout eukaryotes, while differences in specifics exist between yeast, animals, and plants. In Arabidopsis, SIAMESE (SIM) is a CDK inhibitor that restricts progression through mitosis. Overexpression of SIM is required for endoreplication in Arabidopsis trichomes, and overexpression of SIM results in increased endoreplication in leaf epidermal cells. SIM is expressed at high levels in the root elongation zone, where it plays a …

The Primacy Of Density-Mediated Indirect Effects In A Community Of Wolves, Elk, And Aspen, Elaine M. Brice, Eric J. Larsen, Daniel R. Stahler, Daniel R. Macnulty

Aspen Bibliography

The removal or addition of a predator in an ecosystem can trigger a trophic cascade, whereby the predator indirectly influences plants and/or abiotic processes via direct effects on its herbivore prey. A trophic cascade can operate through a density-mediated indirect effect (DMIE), where the predator reduces herbivore density via predation, and/or through a trait-mediated indirect effect (TMIE), where the predator induces an herbivore trait response that modifies the herbivore's effect on plants. Manipulative experiments suggest that TMIEs are an equivalent or more important driver of trophic cascades than are DMIEs. Whether this applies generally in nature is uncertain because few …

Cytotoxic Potential Of Fungi In The Genus Ganoderma, Abril Chao, Omobolanle A. Ayangade, Braham Dhillon, Navi Gill

Mako: NSU Undergraduate Student Journal

Ganoderma lucidum is a mushroom forming fungus that has been used in traditional Chinese medicine for over 2,000 years. G. lucidum, also known as lingzhi or reishi, is consumed in several Asian cultures to promote health and longevity. Bioactive molecules with anticancer properties have been isolated and characterized primarily from the species Ganoderma lucidum, and the cytotoxic potential of other species in the genus Ganoderma remains relatively unclear. Bioactive molecules isolated from mushroom fruiting bodies are demonstrated to have cytotoxicity against different cancer cell lines. Triterpenes and polysaccharides are the two major groups of compounds that exhibit antitumor and anti-inflammatory …

Nursery Cultural Practices Influence Morphological And Physiological Aspen Seedling Traits: Implications For Post-Fire Restoration, Aalap Dixit, Owen Burney

Aspen Bibliography

Aspen forests are threatened by the impacts of a changing climate and are showing large-scale mortality with meager natural regeneration to restore these loses. Therefore, there is an increasing demand for high-quality aspen seedlings to assist with forest restoration efforts. Nursery cultural practices can be used to alter aspen seedling traits to improve adaptability to dry planting conditions. In this study, the effects of container size (SC10 and D30; 158 and 590 mL, respectively) and nursery irrigation treatment (high and low irrigation; 90% and 70% container capacity, respectively) on seedling growth and a suite of morphological and physiological traits were …

Forest Defoliation By And Invasive Outbreak Insect: Catastrophic Consequences For A Charismatic Mega Moth, Richard L. Lindroth, Mark R. Zierden, Clay J. Morrow, Patricia C. Fernandez

Aspen Bibliography

Earth is now experiencing declines in insect abundance and diversity unparalleled in human history. The drivers underlying those declines are many, complex, and incompletely known. Here, using a natural experiment, we report the first test of the hypothesis that forest defoliation by an invasive outbreak insect compromises the fitness of a native insect via damage-induced increases in toxicity of the forest canopy. We demonstrate that defoliation by the invasive spongy moth (Lymantria dispar) elicits an average 8.4-fold increase in foliar defense expression among aspen (Populus tremuloides) genotypes. In turn, elevated defense dramatically reduces survivorship, feeding, and …

Simulating The Long-Term Response Of Forest Succession To Climate Change In The Boreal Forest Of Northern Ontario, Canada, Guy R. Larocque, F. Wayne Bell, Eric B. Searle, Stephen J. Mayor, Thomas Schiks, Parvin Kalantari

Aspen Bibliography

The effect of climate change on forest dynamics is likely to increase in importance in the forthcoming decades. For this reason, it is essential to predict the extent to which changes in temperature, precipitation, and atmospheric CO₂ might affect the development of forest ecosystems and successional pathways. The gap model ZELIG-CFS was used to simulate the potential long-term effects of climate change on species-specific annual change in mean basal area and stand density under two scenarios of representative concentration pathways (RCP), 4.5 and 8.5, for the boreal forest region of Ontario, Canada, where mean temperature, precipitation, and atmospheric CO …

Modelling Climate Effects On Site Productivity And Developing Site Index Conversion Equations For Jack Pine And Trembling Aspen Mixed Stands, Mahadev Sharma

Aspen Bibliography

Forest site productivity estimates are crucial for making informed forest resource management decisions.These estimates are valuable both for the tree species currently growing in the stands and for those being considered for future stands. Current models are generally designed for pure stands and do not account for the influence of climate on tree growth. Consequently, site index (SI) conversion equations were developed specifically for jack pine (Pinus banksiana Lamb.) and trembling aspen (Populus tremuloides Michx.) trees grown in naturally originated mixed stands. This work involved sampling 186 trees (93 of each species) from 31 even-aged mixed stands (3 …

Identifying Genes Linked To Variation In Metabolic And Whole Plant Phenotypes Using Data From Genome Resequencing, Transcriptomics, And Metabolic Profiling Of A Field-Grown Maize Diversity Panel, Ramesh Kanna Mathivanan

Department of Agronomy and Horticulture: Dissertations, Theses, and Student Research

Maize metabolism is highly complex and influenced by genetic variation, yet the specific genes contributing to this variation and their links to non-metabolic traits remain less understood. To address this knowledge gap, we identified genes involved in maize metabolic variation and linked them to non-metabolic traits. We utilized a quadruplicate dataset of whole genome resequencing, transcriptomic, metabolic, and whole plant phenotype data from a single common field experiment of 660 diverse maize inbred lines. Leaf samples were collected shortly before flowering and analyzed using GC-MS for 26 metabolites. A Resampling Model Inclusion Probability Genome-Wide Association Study (RMIPGWAS) of approximately 2.6 …

Using Machine Learning To Combine Genetic And Environmental Data For Maize Grain Yield Predictions Across Multi-Environment Trials, Igor K. Fernandes, Caio C. Vieira, Kaio O.G. Dias, Samuel B. Fernandes

Crop, Soil and Environmental Sciences Faculty Publications and Presentations

Complementing phenotypic traits and molecular markers with high-dimensional data such as climate and soil information is becoming a common practice in breeding programs. This study explored new ways to combine non-genetic information in genomic prediction models using machine learning. Using the multi-environment trial data from the Genomes To Fields initiative, different models to predict maize grain yield were adjusted using various inputs: genetic, environmental, or a combination of both, either in an additive (genetic-and-environmental; G+E) or a multiplicative (genotype-by-environment interaction; GEI) manner. When including environmental data, the mean prediction accuracy of machine learning genomic prediction models increased up to 7% …

Developing A Comprehensive Genome-Scale Metabolic Model For The Arabidopsis Thaliana Root System, Lohani Esterhuizen

Department of Chemical and Biomolecular Engineering: Dissertations, Theses, and Student Research

Arabidopsis thaliana (Arabidopsis) is the most well-established model plant to date. Being the first plant to have its genome mapped, studies on Arabidopsis have provided insurmountable insights into the physiological and biochemical nature of plants. Methods that allow us to computationally study the metabolism of organisms include the use of genome-scale metabolic models (GEMs). Despite its popularity, no GEM currently maps the metabolic activity in the root system of Arabidopsis, which is the first organ to face and respond to stress conditions in the soil. This work aims to develop and implement a comprehensive GEM of the Arabidopsis root system …

Leveraging The Genomic Tools To Explore The Molecular Basis Of Salinity Tolerance In Rice And Soybean, Rajat Pruthi

LSU Doctoral Dissertations

Salinity stress significantly challenges agricultural productivity, particularly affecting major crops like rice and soybean. This research investigates the genetic basis of salt tolerance in both crops through high-resolution genetic mapping, genome-wide association studies (GWAS), and RNA-Seq analysis. In rice, we examined quantitative trait loci (QTLs) associated with salt tolerance at the seedling and flowering stages using a population of advanced backcrossed introgression lines (ILs). A genetic map, constructed with 14,230 polymorphic SNP markers, identified distinct QTLs and candidate genes for salt tolerance at both stages, suggesting differential genetic controls. Notable genes such as OsHAK13 and OsCYP21-4 were upregulated under salt …

New Insights On Hybridization In Potamogeton Floridanus (The Florida Pondweed), Kaitlyn R. Sampson

Graduate Theses and Dissertations (2019 - present)

Freshwater ecosystems are some of the most important and highest threatened habitats in the world, and aquatic plants play an important, but often-overlooked, role in maintaining them. Potamogeton is a diverse and ecologically important aquatic plant genus well known for taxonomic difficulty and rampant hybridization. lbis study aimed to 1) test the hypothesis that Potamogeton jloridanus (Florida pondweed) is a hybrid between P. oakesianus and P. pulcher, and 2) to investigate correlations in ecological conditions for the focal species. This study revealed the discovery of a new population of P. jloridanus in Big Coldwater Creek in Santa Rosa Co., FL, …

Evaluating Past Progress And Assessing Prediction Breeding Strategies For Sustained Genetic Gains In The Louisiana Sugarcane Variety Development Program, Brayden A. Blanchard

LSU Doctoral Dissertations

The aim of this dissertation is to outline important considerations for the Louisiana Sugarcane Variety Development Program (LSVDP) as it pertains to historical progress, impact, goal setting, and new strategies for continued genetic gains. Industry progress was evaluated with robust regression models to quantify rates of productivity gains. Over the last 50 years, statistically significant productivity gains were identified in sucrose content (45%), cane yield (32.2%), and sugar yield (93%) while pairwise comparisons of decades showed that progress was incremental rather than rapid and sustained once achieved. The decade from 1990-1999 was identified as the only decade with a significant …

Evaluation Of Major Physical And Mechanical Properties Of Trembling Aspen Lumber, Dawei Wang, Mengyuan Zhang, Meng Gong, Ying-Hei Chui

Aspen Bibliography

Trembling aspen (Populus tremuloides) is one of the major species within Populus, a predominant genus of hardwoods in North America. However, its utilization has been limited to pulp and paper or wood-based composite boards. This study aimed at evaluating the major physical and mechanical properties of trembling aspen lumber, with an ultimate objective of using this species to produce engineered wood products (EWPs). The testing materials consisted of 2 × 4 (38 mm × 89 mm) trembling aspen lumber pieces in lengths of 8, 10, and 12 feet (2.44, 3.05, and 3.66 m) with two visual grades, …

Isolation Of Gametophytic Selection And Selective Embryo Abortion In Mimulus Guttatus, Desmond C. Willson

University Honors Theses

A lack of genomic studies examining gametophytic selection (GS) and selective embryo abortion (SEA)--which occur during the reproduction of angiosperms--leaves questions regarding the adaptive and evolutionary effects of these processes. Analyzing deviations from Mendelian segregation offers an avenue for identifying loci targeted by GS and SEA, and their contributions to purging of genetic load. However, other selective processes such as meiotic drive and cytonuclear interactions, as well as pollen and ovule abortion, can cause distortion. To distinguish the effects of GS and SEA from other causes of distortion, we will perform reciprocal crosses between highly homozygous and highly heterozygous individuals …

Mixing Trembling Aspen And White Spruce Increases The Understory Vegetation Cover And Improves Soil Properties But Effects Vary With Broadleaf Density, Mostarin Ara, Bradley D. Pinno, Philip G. Comeau

Aspen Bibliography

Despite the importance of species mixtures to ecosystem-based forest management, density effect of broadleaf trees in the mixture on understory vegetation and soil properties are poorly understood. In this study, we examine the effects of trembling aspen [aspen] (Populus tremuloides Michx.) -white spruce [ spruce] (Picea glauca (Moench) Vos) mixtures that vary in the proportion of aspen on understory vegetation cover, soil nutrient supply rates, and soil properties. Data were collected from an established study located in Alberta, Canada at age 20 and included the following treatments: 1. Natural regeneration of pure aspen; 2. Retaining only …

Aspen As Firebreaks At The Development Fringe, Kevin Krasnow, Paul C. Rogers

Aspen Bibliography

Quaking aspen (Populus tremuloides) forests are widely known and prized for their numerous values—biodiversity, habitat, forage, recreation, aesthetics, and others—including as a deterrent to wildfire. This reputation for stopping or slowing flames is explored here, alongside measures that may be taken to facilitate thriving aspen communities near human developments. It is clear that science supporting the premise of aspen as an effective firebreak is far from complete. Yet, how can we benefit from what we do know on this topic to increase the probability of preventing structural fire damage, while also encouraging the valued characteristics of aspen ecosystems?

Climate Considerations For Quaking Aspen Conservation, Douglas Shinneman, Susan Mcilroy, Paul C. Rogers

Aspen Bibliography

Human-caused climate change alters ecosystem processes ranging from local to global scales. As a consequence of climate change we should expect increased rates and intensities of disturbance events. Though we are only beginning to understand what those impacts might be to aspen forests and their diverse plant and animal assemblages, recent science suggests there may be unavoidable effects. In the face of anticipated climate-ecosystem challenges, contemporary managers are searching for guidance on preserving aspen resilience. We suggest crafting strategic yet cautious approaches to minimize effects and facilitate broad resilience. For instance, monitoring conditions in and near aspen forests will help …