Plant Biology Commons^™

Sorghum Association Panel Whole-Genome Sequencing Establishes Cornerstone Resource For Dissecting Genomic Diversity, J. Lucas Boatwright, Sirjan Sapkota, Hongyu Jin, James C. Schnable, Zachary Brenton, Richard Boyles, Stephen Kresovich

Department of Agronomy and Horticulture: Faculty Publications

Association mapping panels represent foundational resources for understanding the genetic basis of phenotypic diversity and serve to advance plant breeding by exploring genetic variation across diverse accessions. We report the whole-genome sequencing (WGS) of 400 sorghum (Sorghum bicolor (L.) Moench) accessions from the Sorghum Association Panel (SAP) at an average coverage of 38× (25–72×), enabling the development of a high-density genomic marker set of 43 983 694 variants including single-nucleotide polymorphisms (approximately 38 million), insertions/deletions (indels) (approximately 5 million), and copy number variants (CNVs) (approximately 170 000). We observe slightly more deletions among indels and a much higher prevalence …

Recombination Hotspots In Soybean [Glycine Max (L.) Merr.], Samantha J. Mcconaughy

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

Recombination allows for the exchange of genetic material between two parents which plant breeders exploit to make new and improved varieties. This recombination is not distributed evenly across the chromosome. In crops, it mostly occurs in the euchromatic regions of the genome and even then, recombination is focused into recombination hotspots flanked by recombination cold spots. Understanding the distribution of these hotspots along with the sequence motifs associated with them may lead to methods that enable breeders to better exploit recombination in breeding.

In chapter 1 background information on recombination, recombination hotspots detection methods, landscape of recombination (describe recombination patterns …

Water Quality, Carrier Volume And Droplet Size Effects On Herbicide Efficacy And Drift Potential, Barbara Houston

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

Herbicide performance is directly related to the amount of active ingredient that has been deposited on the plant. Hence, spray solution characteristics and application parameters are crucial in determining the efficacy of an herbicide application. To maximize the effectiveness of chemical control, methods to deliver full chemical dose must be utilized: allowing the active ingredient to be readily absorbed once added to the carrier and mitigating off-target movement and low herbicide doses. Water is the most frequently used carrier in herbicide applications. Chemical parameters, such as water hardness and pH, can have a critical role in herbicide performance. It is …

Plectus Of The Prairie: A Case Study Of Taxonomic Resolution From A Nematode Biodiversity Survey, Abigail Borgmeier, Kaitlin Gattoni, Timothy Harris, Rebecca Higgins, Peter Mullin, Dorota Porazinska, Kirsten S. Powers, David A. Wedin, Tom Powers

Department of Plant Pathology: Faculty Publications

Taxonomic resolution is a critical component of biodiversity assessments. In this case study, we examined a single taxon within a larger study of nematode diversity to evaluate the taxonomic resolution of different diversity assessment methods. The selected taxon was the microbial-feeding genus Plectus, a group considered to include multiple cosmopolitan species. The methods included a morphological evaluation by light microscopy, Sanger sequencing of PCR amplicons of COI and 18S gene regions, and 18S metabarcoding sequencing. The study sites were 15 remnant tallgrass prairie plots in eastern Nebraska. In the morphological analysis, we observed two basic morphotypes, a short-tailed form …

Association Mapping Across A Multitude Of Traits Collected In Diverse Environments In Maize, Ravi V. Mural, Guangchao Sun, Marcin Grzybowski, Michael C. Tross, Hongyu Jin, Christine Smith, Linsey Newton, Carson M. Andorf, Margaret R. Woodhouse, Addie M. Thompson, Brandi Sigmon, James C. Schnable

Center for Plant Science Innovation: Faculty Publications

Classical genetic studies have identified many cases of pleiotropy where mutations in individual genes alter many different phenotypes. Quantitative genetic studies of natural genetic variants frequently examine one or a few traits, limiting their potential to identify pleiotropic effects of natural genetic variants. Widely adopted community association panels have been employed by plant genetics communities to study the genetic basis of naturally occurring phenotypic variation in a wide range of traits. High-density genetic marker data—18M markers—from 2 partially overlapping maize association panels comprising 1,014 unique genotypes grown in field trials across at least 7 US states and scored for 162 …

Genetically Explicit Model May Explain Multigenerational Control Of Emergent Turing Patterns In Hybrid Mimulus, Emily Simmons

Biology and Medicine Through Mathematics Conference

No abstract provided.

Sodium Mediates Developmentally Plastic Responses In Plants And Herbivores, Luis Santiago-Rosario

LSU Doctoral Dissertations

Sodium plays a crucial role in organismal performance, trophic-level interactions, and eco-evolutionary dynamics. For plants, sodium impacts osmoregulation, growth, and water uptake. For animals, sodium is essential influencing osmoregulatory processes, muscle and neural development, and blood regulation. My dissertation aims to disentangle why sodium mismatch affects resource-consumer interactions and its influence on morphological and behavioral plasticity. First, I identified how sodium impacts plant performance and sodium accumulation strategies. I initially focused my research on understanding how increasing substrate sodium affects plant growth and tissue sodium accumulation strategies in controlled settings using a systematic review approach. I found that saltier plants …

Procedures For Genetic Modification Of Miscanthus X Giganteus, A Biomass Crop, Anjali Arpan

Theses and Dissertations

Development of genetic improvement procedures for the bioenergy crop, Miscanthus × giganteus (M×g; triploid), are desired for trait improvement. Agrobacterium tumefaciens has been used in other Miscanthus spp. for genetic improvement, but not in M×g, nor have more than a few genes been introduced at a given time. Transformation procedures for M×g were developed; studies included use of A.tumefaciens (strain LBA4404) and A. rhizogenes (strain A4) for introduction of seven genes isolated (by other researchers) from Sorghum bicolor involved in sorgoleone biosynthesis (an allelopathic compound), and selectable marker gene neomycin phosphotransferase II. Procedural development included generation of …

Restoration Through Reassembly: Evaluating The Role Of Native Plants In Combatting Chinese Tallow, Olaniyi Ajala

Electronic Theses and Dissertations

Non-native, invasive species disrupt ecological processes and functions, posing a serious threat to natural ecosystems. By examining the growth metrics of the non-native, invasive tree, Chinese tallow (Triadica sebifera [L.] Roxb.), hereafter tallow, across different flooding and light regimes, I investigated how restructuring native communities with valuable native species will prevent the reestablishment of tallow. I studied the changes in morphological and physiological traits of tallow when growing with water tupelo (Nyssa aquatica L.), sugarberry (Celtis occidentalis L.), and green ash (Fraxinus pennsylvanica Marshall). I found that in the non-flooded and high irradiance treatments, tallow's growth …

Isolation Of Arabidopsis Thaliana Plants Homozygous For An Insertional Inactivation Mutation Within Atprp4., Sydney Raitz, Timothy D. Trott

Faculty Works

The AtPRP4 gene in Arabidopsis thaliana has been shown to function in several specific parts of the plant’s cell wall. It is shown to be expressed in the seeds, radicles, roots, leaves, inflorescences, and embryos of Arabidopsis thaliana. These patterns have suggested unique functions for ATPRP4 in determining cell-type-specific wall structure during the development of a plant as well as contributing to defense reactions against physical damage to the plant and pathogen infection within the plant. In this study, a simple DNA prep was performed on the true leaves of Arabidopsis thaliana. Subsequent PCR reactions were performed using …

The Potential Role Of Phenotypic Plasticity In The Ability Of Hydrocotyle Bonariensis To Occupy Two Different Habitats, Harold Ralph Parsons Iii

Honors College Theses

Phenotypic plasticity is the ability of an organism to change morphology and/or physiology in response to changes in the environment. Hydrocotyle bonariensis is a coastal perennial herb found in both coastal sand dunes and inland coastal plain habitats in Georgia. The purpose of this study was to determine if there were differences in leaf morphology for populations of H. bonariensis in coastal sand dune and inland coastal plain habitats. Leaf morphology and microenvironmental variables were compared between H. bonariensis populations at Tybee Island (TI), GA, representing the coastal sand dune habitat, and Georgia Southern University Armstrong Campus (GSU) in Savannah, …

Investigating The Mechanics And Chemistry Of Sickle Polish Development, Justin Jared Dubois

Graduate Theses and Dissertations

This series of experiments is designed to understand the development and chemistry of sickle gloss. Sickles are common in the archaeological record and have long been studied for their eponymous “sickle gloss”. There is debate as to how this gloss is formed. Five experimental sickles containing flint and novaculite blades were used to harvest high and low moisture content rye and common fescue and associated field weeds. The differences in the development of sickle gloss were examined. High moisture content plants create thick, smooth fields of polish with undulating, billowing margins at a higher developmental speed. Low moisture content plants …

Effects Of One-Pass Microwave Drying On Rice’S Utilization In The Brewing Process., Christopher Stuckey

Food Science Undergraduate Honors Theses

Rice is utilized as an adjunct grain by the beer manufacturing industry. Before utilization, the rice has to be dried to a desired moisture content. The drying process employed may have an impact on the rice’s physicochemical properties which influence the rice’s performance in the brewing process. This study focused on investigating the impact of microwave drying on rice’s physicochemical properties and utilization in the brewing process. Rough rice samples at an initial moisture content of 19.7% wet basis were exposed to microwave dryer set to deliver 525 kJ/kg of energy in a single drying pass. The effects of the …

Nitrogen Availability In Dune Systems And Its Effect On Root Fungal Endophyte Communities., Haley E. Sage

College of Arts & Sciences Senior Theses

As global change persists, changes in resource availability can influence plant-microbe interactions. To understand how resource availability can influence these interactions and species diversity, I focused this research on how varying nitrogen (N) levels affect root endophyte communities in the plant species Ammophila breviligulata, an ecosystem engineer in the dune system. I analyzed the relationship between nitrogen addition and microbial community composition across 60 plots treated with three nitrogen addition levels (control, low, and high) in a long-term experimental field site in the Lake Michigan dunes. I identified Ammophila breviligulata's root endophyte community after creating a culture collection and …

Exploration Of Genes Controlling Grain Yield Heterosis In Hybrid Wheat (Triticum Aestivum L.) Utilizing 3ʹ Rna Sequencing, Nichole Lynn Miller

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

The implementation and future success of hybrid wheat (Triticum aestivum L.) is impacted by breeders’ inability to create consistent high yielding, high heterosis hybrids. This research addresses this problem by conducting an exploration of transcriptomes from hybrids and parent lines to determine what genes are active in heterotic or non-heterotic hybrids and how their level of expression can explain the phenotype of grain yield heterosis. Using hybrids that showed positive mid-parent heterosis (MPH), classified as heterotic in our study, and negative or no difference MPH hybrids, classified as non-heterotic, differentially expressed genes (DEGs) potentially related to heterosis and hybrid …

Research Report: High Tunnel Tomato Fruit Cluster Pruning, Caterina Roman, Rebecca G. Sideman

Faculty Publications

Tomatoes are a high value crop grown worldwide. Indeterminate varieties are commonly grown in high tunnel structures throughout New England for the fresh market. Indeterminate tomato plants often suffer from a phenomenon called ‘June drop’ in which the plant’s first four to five cluster of fruit set perfectly but the subsequent two to three clusters have poor set and plant productivity drops suddenly. While cluster thinning (e.g., reducing the number of fruit allowed to mature per cluster) has been successfully shown to increase fruit size, it has generally not increased marketable yield. We hypothesized that reducing the fruit load by …

Potato Processing In The Home: Sustainability And Nutritional Impacts, Aubin Payne

Biological and Agricultural Engineering Undergraduate Honors Theses

Potatoes are the world's fourth most consumed crop. Their versatility and long shelf-life make them a staple food for millions of people worldwide. Still, the increasing consumption of highly processed potato products in developed countries has damaged the public's appreciation of potatoes as a valuable source of essential nutrients. Additionally, as public awareness of environmental sustainability increases, the average consumer is more likely to value processing methods that mitigate environmental damage.

Researchers simulated several home storage and processing conditions to find out how nutrition and environmental impact are affected by the home processing timeline. Then, a nutrient analysis, life cycle …

Chromosome-Level Thlaspi Arvense Genome Provides New Tools For Translational Research And For A Newly Domesticated Cash Cover Crop Of The Cooler Climates, Adam Nunn, Isaac Rodríguez-Arévalo, Zenith Tandukar, Katherine Anna Frels, Adrián Contreras-Garrido, Pablo Carbonell-Bejerano, Panpan Zhang, Daniela Ramos Cruz, Katharina Jandrasits, Christa Lanz, Anthony Brusa, Marie Mirouze, Kevin Dorn, David W. Galbraith, Brice A. Jarvis, John C. Sedbrook, Donald L. Wyse, Christian Otto, David Langenberger, Peter F. Stadler, Detlef Weigel, M. David Marks, James A. Anderson, Claude Becker, Ratan Chopra

Department of Agronomy and Horticulture: Faculty Publications

Thlaspi arvense (field pennycress) is being domesticated as a winter annual oilseed crop capable of improving ecosystems and intensifying agricultural productivity without increasing land use. It is a selfing diploid with a short life cycle and is amenable to genetic manipulations, making it an accessible field-based model species for genetics and epigenetics. The availability of a high-quality reference genome is vital for understanding pennycress physiology and for clarifying its evolutionary history within the Brassicaceae. Here, we present a chromosome-level genome assembly of var. MN106-Ref with improved gene annotation and use it to investigate gene structure differences between two accessions (MN108 …

Floating Treatment Wetlands For Brackish Waters: Plant Selection And Nutrient Uptake Potential., Andrea Landaverde

All Theses

Brackish water bodies in coastal regions provide critical ecosystem services that support human and environmental health. Anthropogenic activities such as agricultural and industrial activities, construction, urban settlements, and tourism contribute to increased inputs of nitrogen (N) and phosphorus (P) in brackish coastal ecosystems. Excess nutrients can lead to impaired water quality and affect marine organisms. Floating treatment wetlands (FTWs) are a vegetated-base technology used to remove contaminants from water column, that has been mainly studied and applied in freshwater systems. Application of FTWs in brackish systems requires further investigation, as high salinity in brackish waters could result in toxicity to …

Investigation Of The Binding Domain Interfaces Of The C-Terminus Of The Albino3 Insertase And The 43kda Chloroplast Signal Recognition Particle Subunit Via Single Molecule Förster Resonance Energy Transfer, Amanda Tomanek

Chemistry & Biochemistry Undergraduate Honors Theses

Fluorescent labeling is a technique used for visualizing functional groups contained in biomolecules by fluorescence imaging. This technique was used in this project to analyze post-translational targeting of light-harvesting chlorophyll-binding proteins (LHCP), which are the core complexes that harvest sunlight to drive photosynthetic electron transfer. This protein is synthesized in the cytosol and post-translationally targeted to the stroma of chloroplasts. CpSRP43 is a signal recognition particle (SRP) subunit unique to chloroplasts, which has been shown to interact with the stroma-soluble C-terminus of the thylakoid-bound Albino3 insertase (Alb3-Cterm). In the chloroplast stroma, targeting to thylakoids is performed via the cpSRP pathway …