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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 …

Scalable Machine Learning Framework For Adaptive Irrigation Management Of Maize And Soybean In The U.S. Midwest, Precious N. Amori, Derek M. Heeren, Yeyin Shi, Eric Wilkening, Ivo Z. Goncalves, Guillermo R. Balboa, Daran R. Rudnick, Abia Katimbo, Randall S. Ritzema

Department of Agricultural and Biological Systems Engineering: Faculty Publications

Conventional soil water balance (SWB) irrigation scheduling tools, such as FAO-56-based Spreadsheets and the Spatial Evapotranspiration Modeling Interface (SETMI), rely heavily on manual inputs and periodic field measurements, leading to delayed recommendations and missed opportunities to prevent crop stress. More critically, these tools lack the computational scalability and adaptability to leverage the high-frequency, high-volume datasets now available through modern sensing technologies. As precision irrigation increasingly depends on integrating spatially and temporally nuanced field information, there is a pressing need for decision-support systems that can process Big Data efficiently and respond in real-time. To overcome these limitations, we developed and validated …

Responses Of Native And Invasive Aquatic Vegetation To Changes In Water Depth In An Ozark Spring-Fed Pond, Daphne Miles

Graduate Theses/Dissertations

Spring-fed aquatic ecosystems in the Ozark Highlands are characterized by stable water depths, clear water, and diverse aquatic vegetation (filamentous algae, submerged, floating, and emergent plants). Sudden changes in water depth can impact aquatic vegetation dynamics but the impacts of prolonged changes are poorly understood. I investigated seasonal and annual changes to aquatic vegetation abundance in a spring impoundment during and after a two-year period of low water depth that was caused by a broken outlet below an artificial dam. Water depth was significantly lower in 2020 and 2021 (low water years), compared to 2022 and 2023 (high water years). …

Identification Of Salt Tolerance And Stress Response In Us Department Of Agriculture Tomato Germplasm At The Seedling Stage, Ibtisam Alatawi, Haizheng Xiong, Kenani Chiwina, Hanan Alkabkabi, Qun Luo, Neelendra K. Joshi, Xiaolun Sun, Xuan Zhuang, Kai-Shi Ling, Ainong Shi

Horticulture Faculty Publications and Presentations

Soil salinity is a significant abiotic factor that impedes sustainable crop production in key agricultural regions worldwide. Saline cultivation adversely affects soil quality, whereas the use of saline water for irrigation disrupts the physiological and biochemical processes of plants. Continuous irrigation with high salt concentrations leads to a gradual buildup of soil salinity, thus hindering optimal plant growth and development. Consequently, there is a growing emphasis on breeding salinity-tolerant cultivars of various crops. In this study, 71 tomato accessions sourced from 20 countries and provided by the US Department of Agriculture were evaluated under controlled greenhouse conditions and subjected to …

Allodus Podophylli: The Infection Cycle Of Mayapple Rust, W. John Hayden

Biology Faculty Publications

This article addresses the parasitic fungus, Allodus podophylli, that causes Mayapple Rust. This disease is extremely common throughout the entire geographic range of Mayap-ple, Podophyllum peltatum, the 2025 VNPS Wildflower of the Year.

Wildflower Of The Year; Mayapple (Podophyllum Peltatum), W. John Hayden

Biology Faculty Publications

Mayapples are perennial herbaceous plants with thick fibrous roots that arise from a creeping rhizome.

Soils From Different Solidago Altissima Clones Mediate Intraspecific Interactions In Schizachyrium Scoparium, Sarah Alharbi

Masters Theses

While previous studies have examined plant intraspecific competition and soil microbial effects separately, fewer studies have investigated how these factors interact, particularly in the context of genotype-specific soil conditioning effects. Plant-soil feedbacks can significantly alter interspecific competitive outcomes, yet few studies have examined how local variation in soil conditioning influences plant responses to density-dependent competition. I investigated how soil inocula derived from four Solidago altissima clones that were previously shown to differ in their soil conditioning effects (Foster et al., 2022) affected the growth and root traits of Schizachyrium scoparium across a gradient of intraspecific competition (1, 2, or 4 …

Optimization Of Transformation And Regeneration In The Sunflower (Helianthus Annuus), Sara M. Kilar

Masters Theses

In addition to their value as prized ornamentals, sunflowers are important crop species due to the nutritional value and high oil content of the seeds. Sunflower oil is a significant contributor to global seed oil production, which can be used as a food additive and cooking agent as well as a raw material for biodiesel production. While traditional breeding efforts have led to the development of many unique cultivars, genetically modified variations have proven more difficult due to the recalcitrance of sunflower plants to genetic transformation. As a result, facile and efficient transformation methods for sunflowers have the potential to …

Improving Reduced Tillage Vegetable Systems For The Northern Great Plains: How Does Early Season Soil Tarping (Solarization And Occultation) Reduce Weeds, Affect Soil Health, And Protect Yield?, Hannah Voye

Electronic Theses and Dissertations

Soil tarping (solarization and occultation) is a no-till weed management practice gaining popularity in the United States for small scale vegetable growers. While many studies have been conducted using variations of this tool in the Northeast United States, minimal research has been done in the windier, sunnier, Midwest climate. Our research explored the effectiveness of early spring solarization and occultation to manage weeds and produce viable onion yield in Eastern South Dakota. Occultation tarps placed in early spring included double sided black and white silage tarps with tarps placed black side up or white side up, each placed 6-, 4-, …

Remote Sensing - Based Mapping And Analysis Of Winter Cover Crop Adoption For Sustainable Agriculture, Minnehaha County, Belinda Buechler

Electronic Theses and Dissertations

Winter cover crops planted by farmers such as cereal rye, crimson clover, radishes, hairy vetch, and winter wheat are used to conserve and protect the soil during winter. These crops offer numerous benefits such as improving soil health, reducing erosion, fixing nitrogen, increasing carbon sequestration, and weed suppression. Over time, winter cover cropping has been recognized as a sustainable agricultural practice and has gained attention from Federal and State conservation programs, farmers, and non-governmental organizations. Due to their vital benefits, agencies such as the United States Department of Agriculture (USDA), Natural Resources Conversation Services (NRCS) have partnered with cost-share programs …

Foliar Corn Diseases In South Dakota: Visual Disease Surveys And The Genetic Studies Of Tar Spot And Bacterial Leaf Streak, Ciera Kotaska

Electronic Theses and Dissertations

Corn (Zea mays L.) is one of the most important crops in South Dakota and the United States. Each year, a variety of diseases impact the production of corn in South Dakota, though very little documentation about these diseases exists in the state. This survey documents the foliar diseases of corn and the distribution of each to create a baseline of knowledge. An additional genetic study was conducted to determine the organisms associated with tar spot of corn and bacterial leaf streak (BLS), two emerging diseases in South Dakota. A variety of studies have been conducted on tar spot, caused …

Evaluation Of Strip-Tillage And Banded Phosphorus And Potassium Fertilizer For Corn Production In Eastern South Dakota, Charles N. Tesch

Electronic Theses and Dissertations

In South Dakota, the adoption of no-till and other conservation tillage practices has grown in recent years. However, conventional tillage is still a common practice in the eastern third of the state, negatively affecting soil health and the environment. Strip-tillage has gained interest in this region as a way to transition to conservation tillage while retaining some benefits of conventional tillage. Strip-tillage also provides the ability to subsurface band nutrients, particularly phosphorus (P) and potassium (K) fertilizers within the tillage strip, potentially improving nutrient accessibility and recovery while reducing environmental risks. This study aimed to investigate (i) the effects of …

Determining The Susceptibility Status Of Red Sunflower Seed Weevil, Smicronyx Fulvus (Coleoptera: Curculionidae) To Pyrethroid Insecticides, Aaron Lee Hargens

Electronic Theses and Dissertations

Although sunflowers are native to North America, the early breeding efforts to improve sunflowers occurred outside of the continent. These hybrids were reintroduced to North America around 1875. In the early 1900’s, efforts to increase oil content were achieved by selective breeding of the reintroduced hybrids. Although this resulted in the development of improved sunflowers, many of the traits that conferred resistance to native insect pests were lost. One insect pest, the red sunflower seed weevil was noted as having caused sunflower production to rapidly decline and eventually end in Illinois and Missouri. Unfortunately, red sunflower seed weevils are still …

Quantification Of Auxin-Cytokinin Response During Lateral Root And Nodule Development In Medicago, Aniket Singh

Electronic Theses and Dissertations

Lateral roots (LRs) and nodules are post-embryonic root organs in legumes formed through the activity of de novo meristem. LRs, which are present in all vascular plants, are developed primarily via intrinsic developmental cues, whereas root nodules, found only in a small group of plants known as legumes, are formed in response to legume–rhizobium symbiosis. LRs arise from the pericycle layer of the root, whereas nodule initiation can begin either in the pericycle (indeterminate nodules with persistent meristem, as in Medicago) or in the cortex (determinate nodules with transient meristem, as in soybean), pointing toward a conserved developmental origin, especially …

Fungal Biotransformation Of Thin Stillage And Soybean Hulls And Bacterial Production Of Lysine In Ethanol Industry Co-Products, Bhawana Khadka

Electronic Theses and Dissertations

Thin stillage (TS) and whole stillage (WS) are major by-products of the corn ethanol industry. These by-products are generated in large quantities and contain nutrients that remain after yeast fermentation. Current industrial utilization of these by-products involves a series of downstream processing steps such as centrifugation and evaporation, which are energy-intensive and often result in nutrient losses. Traditionally, these by-products are dried to produce distillers dried grains with solubles. In this study, microbial fermentation was investigated as an alternative bioprocessing tool to expand the utilization of these by-products. The first objective was to explore the upcycling of TS, both alone …

Ocean Acidification Mitigation: Potential Expansion Of Sav Restoration Strategy In The Chesapeake Bay, Cree N. Taylor

UROP Posters

Zostera marina is a species of marine macrophyte that has been largely prioritized in past submerged aquatic vegetation (SAV) restoration initiatives within the Chesapeake Bay because of its 1) previous abundance, 2) demonstrated carbon burial abilities, and 3) observed ability for meadows of Z. marina to ameliorate low pH conditions. Due to the temperature variability and poor water quality associated with anthropogenic disturbances in the Chesapeake Bay, Z. Marina beds have experienced several die-off events with limited capacity for regrowth. This systematic review explored the possible benefits of focusing future SAV recovery initiatives on ensuring a diverse variety of SAV …

Phytochemical Analysis, Antioxidant, And Antibacterial Properties Of Partition Fractions Of Adansonia Digitata And Annona Muricata Extracts Using Chloroform, Ethyl Acetate, Ethanol, And Aqueous Solvent Systems, Fagbohun Oyenike Bushirat, Hassan Abdusalam Adewuyi, Sakariyau Adio Waheed, Maryam Nana Musa, Timothy God-Giveth Olusegun, Ayomide Babatunde Ishola, Agumage Idoko, Adeola Victor Kolawole, Adesanmi Adefunmilayo Oluwatuyi, Sarah Ngozi Agwasim

Chemistry & Biochemistry Faculty Publications

Adansonia digitata and Annona muricata are traditionally used medicinal plants with reported pharmacological properties. In this study, we aimed to elucidate the phytochemical composition, antioxidant activity, and antibacterial properties of partition fractions of Adansonia digitata and Annona muricata extracts obtained using chloroform, ethyl acetate, ethanol, and aqueous solvent systems. The plant extracts were successively partitioned using chloroform, ethyl acetate, ethanol, and aqueous solvent systems. Phytochemical analysis was performed using standard methods. Antioxidant activity was evaluated using FRAP and DPPH assays. Antibacterial activity was assessed using agar well diffusion and MIC determination. Phytochemical analysis revealed the presence of alkaloids (10.2-15.6%), flavonoids …

Functional Trait Responses Of Invasive Ludwigia Species Tocontrasting Hydrological Conditions, Rebecca E. Drenovsky, Rebecca Reicholf, Caryn Futrell, Blanca Gallego‐Tévar, Brenda J. Grewell

2025 Faculty Bibliography

Premise: Hydrological regime influences wetland plant species distribution andperformance. Global warming and extreme weather events are magnifying floodingpatterns, and understanding how invasive taxa respond across life stages (establish-ment vs. established phase) is important for predicting and managing their coloni-zation and spread. Our objective was to measure flood trait responses at contrastinglife stages in closely related congeners (Ludwigia peploides, diploid; L. hexapetala,decaploid; Onagraceae) differing in their invasiveness in the field.

Methods: In the field, we assessed phenological responses to seasonal hydrological changes,and in mesocosms, we assessed flood stress responses of establishing shoot fragments underdeep‐flooded, shallow‐flooded, and gradual drawdown hydrological …

Understanding Submerged Plant Microbiome And Exploring Plant Microbe Interaction Through Plasma Optimization Studies, Binoop Mohan

All ETDs from UAB

The master's thesis presents research on enhancing plant resilience and growth through the study of the microbiome of submerged aquatic plants and the application of plasma technology in agriculture. We isolated 177 endophytic microbial strains from submerged plants collected from various locations. Screening revealed 50 strains producing ACC deaminase, an enzyme that mitigates plant stress by reducing ethylene levels. Predominant genera included Pseudomonas, Bacillus, and Acinetobacter. Metagenomic analysis characterized the diverse bacterial communities associated with these plants. Different plasma treatments were tested to optimize their effects on plant growth. Atmospheric jet and globe plasma treatments significantly improved root length and …

Evaluating Impacts Of Footpaths On Resiliency Of Restored Dunes At Tybee Island, Georgia, Skyler J. Fox

College of Graduate Studies: Theses & Dissertations

Sand dunes provide critical ecosystem services including storm protection by acting as natural barriers. However, these systems are threatened by human disturbance, particularly pedestrian traffic occurring at footpaths that damages dune vegetation. Vegetation is essential to dune growth and stability, as dune plants trap and bind sand. When trampled, dunes become more vulnerable to erosion and less effective at providing coastal protection. On Tybee Island, Georgia—a popular tourist destination—a vegetated dune was constructed in 2020 to enhance storm protection. This study assessed how footpaths impact dune resiliency and aimed to inform management strategies. I evaluated: (1) how characteristics of vegetation, …

Exploring Biostimulant Efficacy Under Limited Fertilizer And Water In Utah's Watermelon Production, Evan Christensen, Milena Oliveira, Prakriti Nepal, Youping Sun

Plants, Soils and Climate Student Research

The western U.S. has recently experienced some of the driest conditions on record, and Utah has been in a multi-year drought (2019-2023) that affected the agricultural sector, including vegetable producers. While vegetables are not a primary agricultural crop in Utah, they are still an important part of the horticultural economy with 763 farms growing 6,138 acres. As the fourth largest acreage vegetable crop in Utah (almost 10% of the acreage) watermelon and related crops in the gourd family Cucurbitaceae (nearly 36% of total vegetable acreage) are important to vegetable growers. Watermelon is a water-intensive crop and requires an adequate supply …

Analyzing The Population Structure Of The Rhizobia Associated With Astragalus Lentiginosus, Joshua Adam Melnick

Dissertations

Legumes are an incredibly diverse and agriculturally important family of plants. They have a special relationship with symbiotic bacteria known as rhizobia which fix nitrogen into ammonia within nodules on their roots. Astragalus is the largest plant genus on Earth, and the species Astragalus lentiginosus is extraordinarily diverse, consisting of approximately 40 varieties. However, the rhizobia of A. lentiginosus have never been studied. In this study, root nodules were extracted from 17 varieties of A. lentiginosus to obtain rhizobial strains and metagenomes. A. lentiginosus primarily associates with rhizobia from the genera Mesorhizobium and Allomesorhizobium. There was little evidence of horizontal …

Divergent Floral And Vegetative Trait Responses To Abiotic Factors Drive Phenotypic Diversity In Platanthera Dilatata (Orchidaceae) Across Alaska, Marlin L. Bowles, Lisa E. Wallace

Biological Sciences Faculty Publications

Multiple traits make up an integrated phenotype, but traits may be shaped by differing drivers. It is often assumed that selection by biotic agents drives floral variation, but abiotic factors are also known to influence floral traits. Understanding trait covariations and their association with diverse environmental factors is a central question in evolution and ecology. Here, we studied covariation in floral and vegetative traits in relation to climate and topo-edaphic variation in the orchid Platanthera dilatata. In Platanthera, nectar spur length is associated with pollinator tongue length, but much variation exists in other traits too, likely to be …

Efficacy Of Stress Acclimation Techniques In Coastal Wetland Plants (Spartina Alterniflora And S. Patens): Implications For Restoration And Nursery Production, Taylor M. Sloey, Kylie D. Gieser, Kaitlyn Pounders, Sofía E. Báez, Jennifer L. Whytlaw

Biological Sciences Faculty Publications

The implementation of coastal nature-based features, created wetlands, and wetland restoration has increased globally over recent years. Many of these projects have been successful in meeting their goals, however, when projects fail, it is often attributed to mortality of transplanted vegetation. Transplant mortality may be due to inappropriate timing, poor site selection, or abiotic stressors associated with transplant shock. Science-backed guidelines have been well established in many coastal regions regarding site specifications and species selection, but nursery practices for reducing transplant shock remain inconsistent. In this study, we tested a combination of four salinity acclimation treatments and two inundation acclimation …

Mathematical And Computational Modeling For Organic And Insect Frass Fertilizer Production: A Systematic Review, Malontema Katchali, Edward Richard, Henri E.Z. Tonnang, Chrysantus M. Tanga, Dennis Beesigamukama, Kennedy Senagi

All Peer-Reviewed Publications

Organic fertilizers have been identified as a sustainable agricultural practice that can enhance productivity and reduce environmental impact. Recently, the European Union defined and accepted insect frass as an innovative and emerging organic fertilizer. In the wider domain of organic fertilizers, mathematical and computational models have been developed to optimize their production and application conditions. However, with the advancement in policies and regulations, modelling has shifted towards efficiencies in the deployment of these technologies. Therefore, this paper reviews and critically analyzes the recent developments in the mathematical and computation modeling that have promoted various organic fertilizer products including insect frass. …

Earth Observations Reveal Impacts Of Climate Variability On Maize Cropping Systems In Sub-Saharan Africa, Adomas Liepa, Michael Thiel, Hannes Taubenböck, Doris Klein, Ingolf Steffan-Dewenter, Marcell K. Peters, Sarah Schönbrodt-Stitt, Insa Otte, Tobias Landmann, Zeyaur R. Khan, Michael Ochieng Obondo, Frank Chidawanyika, Emily A. Martin, Tobias Ullmann

All Peer-Reviewed Publications

In Kenya, climate variability and change threaten smallholder, rainfed farms, with crop failures, yield reductions, and pest infestations. Efficient agroecological strategies, such as Push-Pull intercropping, offer documented benefits including pest control, improved soil fertility, and water conservation compared to traditional maize monocropping. To date, no studies exist comparing traditional maize monocropping and Push-Pull intercropping using earth observation tools over several growing seasons in East Africa. Our research addresses this by harmonizing Landsat 7, 8, 9 with Sentinel-2 remote sensing time series from 2016 to 2023. Phenological metrics of 15 growing seasons are extracted based on a threshold method using the …

Unpacking The Benefits Of Black Soldier Fly Frass Fertilizer Towards Nematode Suppression And Potato Production, Emmanuel O. Anedo, Dennis Beesigamukama, Benson Mochoge, Nicholas K. Korir, Solveig Haukeland, Xavier Cheseto, Moses Nyongesa, Patrick Pwaipwai, Sevgan Subramanian, Abdou Tenkouano, Betty Kibaara, Chrysantus M. Tanga

All Peer-Reviewed Publications

Potato production is hindered by soil degradation and nematode infestation. Mineral fertilizers and synthetic nematicides are costly and cause negative impacts on humans and the environment, while organic fertilizers are less effective for soil health and nematode management. This study demonstrates the contribution of black soldier fly frass fertilizer (BSFFF) in nematode suppression and potato productivity when compared to commercial mineral fertilizer, organic fertilizer (SAFI), and nematicide. The on-farm experiments consisted of eight treatments: BSFFF, SAFI, BSFFF+5%chitin, NPK+nematicide, 50%BSFFF+50%NPK, 50%SAFI+50%NPK, 50%BSFFF+5% chitin+50%NPK, and control (unfertilized soil). Results revealed that all fertilizer treatments significantly increased potato growth, number of tubers (34 …

Do Rates Matter? Validation Of Insect Frass Fertilizer Rates In A Vegetable Intensified Push-Pull Technology For Optimal Sustainable Production, Priscilla Mwikali Kimuli, Dennis Beesigamukama, Judy Wambua, Bonoukpoe Mawuko Sokame, Chrysantus Mbi Tanga, Frank Chidawanyika, Sevgan Subramanian, Daniel Munyao Mutyambai

All Peer-Reviewed Publications

Push–pull system intensification with vegetables (VIPPT) has contributed significantly in maintaining good control of lepidopteran pests and parasitic weeds with additional food and nutritional security benefits. However, the impact of integration of different rates of black soldier fly frass fertilizer (BSFFF) in the VIPPT to enhance productivity, has not been explored. This study investigated the effects of different BSFFF application rates on growth performance, pest infestation severity, diversity of natural enemies and yield of kale (Brassica oleracea L. var. acephala) grown under VIPPT in two agroecological zones. Plants were grown in soils amended with five different levels of BSFFF (0, …

Can Fungal Endophytes Suppress Trialeurodes Vaporariorum And The Transmission Of Tomato Infectious Chlorosis And Chlorosis Viruses In Field Conditions?, Marial Makur Zechariah Paweer, Everlyne Samita Namikoye, Shem Bonuke Nchore, Komivi Senyo Akutse

All Peer-Reviewed Publications

Field trials were conducted for two seasons in two experimental sites (Mwea in Kirinyaga and Ngoliba in Kiambu counties of Kenya) to assess the efficacy of fungal endophytes Hypocrea lixii F3ST1 and Trichoderma asperellum M2RT4 in the control of Trialeurodes vaporariorum vector of tomato infectious chlorosis virus (TICV) and tomato chlorosis virus (ToCV) through seeds inoculation. TICV and ToCV’s disease incidence, severity and the yield were also evaluated. All the fungal endophytes successfully colonized all the tomato plant parts, but the highest root colonization was observed in H. lixii F3ST1 compared to the T. asperellum M2RT4 in both seasons. The …

Performance Of The Dssat Manihot-Cassava Model For Cassava Cultivation In The Recôncavo Baiano, Diego M. De Melo, Paola De F. Bongiovani, Fabio L.S. Costa, Patricia Moreno-Cadena, Alexandre B. Heinemann, Julian Ramirez-Villegas, Mauricio A. Coelho Filho

All Peer-Reviewed Publications

The aim of the present study was to calibrate the DSSAT MANIHOT-Cassava model with information from cassava varieties grown in the Recôncavo Baiano region, Bahia state, Brazil. The database used to calibrate the model was obtained in the dry sub-humid tropical climate in Cruz das Almas city, from 2019 to 2020. The model was calibrated with experimental data obtained under irrigated and rainfed conditions for the BRS Novo Horizonte and Eucalipto varieties. The calibration was carried out by adjusting parameters related to the characteristics of each variety. Model performance was evaluated with statistical indices that indicate the precision and accuracy …