Plant Biology Commons^™

High Biochar Rate Improves Water Retention In Some Environmentally Sensitive Soils, Samundra Sigdel

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

Improving water retention and other hydraulic properties is key to managing soil water and sustaining crop production under fluctuating and extreme weather events. We assessed how wood biochar (836 g C kg^-1) applied at 0, 6.25, 12.5, 25, and 50 Mg ha^-1 affected: i) soil hydraulic properties after 5 years and ii) corn and soybean yield, and biomass production of cereal rye cover crop (CC) and CC mix (cereal rye, radish, and winter pea) in sandy, sloping, and semi-arid soils in the central U.S. Great Plains over 6 years. Biochar affected field saturated hydraulic conductivity (K_{sat …}

Can Generative Ai Make Farming Decisions? Current Status And Future Pathways: A Case Study In Row Crop Production With Chatgpt, Nipuna Chamara, Yufeng Ge, Joe Luck, Yu Pan, Saleh Taghvaeian, Cory Walters, Christopher Proctor, Daran Rudnick, Daren Redfearn

Department of Agricultural and Biological Systems Engineering: Faculty Publications

The agricultural decision-making process is experience-based, knowledge-dependent, time-sensitive, complex, and driven by historical data. Planting, fertilization, irrigation, and chemigation are key categories in farm decision-making, and currently there is no one-shot decision-support tool that covers all these activities. Generative Artificial Intelligence (AI) models are more advanced than traditional machine learning and deep learning models. These models have been trained on vast amounts of data from the internet, allowing them to accept unstructured data in various forms and generate human-like text, solutions to problems, and scenario predictions. Given this capability, we became interested in exploring the potential of generative AI in …

Evaluating The Impact Of Intercropping Vegetables And Cut Flowers On Yield And Conservation Biological Control, Alliance Igiraneza

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

Specialty crops such as vegetables are some of the most susceptible to yield losses and increased management difficulty over time due to pests. One of the potential solutions to this problem, which aims at ensuring the sustainability of the sector, is using conservation biological control practices such as intercropping to increase diversity, while maintaining the economic feasibility and profitability of the system. This study was conducted to evaluate the impact of this management practice using Bell pepper (Capsicum annuum var. King Arthur) as the main crop, intercropped with flowers including zinnia (Zinnia elegans var. Benary’s Giant), sunflower ( …

Cis-Variant Gene-Expression Association Analysis: A Targeted Approach To Identify Functional Cis-Regulatory Variation, Sofiya Arora

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

Phenotypic diversity in plants is largely driven by changes in gene function arising from mutations in both the coding and regulatory regions. Regulatory variation is particularly pervasive because it can fine-tune gene expression without disrupting protein function and is therefore less likely to be strongly selected against in natural populations. As a result, it has played a central role in evolution and domestication. In our previous genome-wide eQTL mapping study in maize, nearly two-thirds of the expressed genes were found to harbor detectable cis-expression quantitative trait loci (cis-eQTLs) with strong local effects on gene expression. Though these cis-variants are widespread, …

Quantitative Genetics, Genomics, And Phenomics In Maize And Sorghum, Nikee Shrestha

Complex Biosystems Program: Dissertations and Student Research

Generating the best crop varieties and hybrids requires identifying genes associated with the phenotype of interest and screening thousands of varieties across multiple locations. Quantitative genetics, along with comparative genomics, phenomics, and machine learning approaches, can help us identify target genes associated with the phenotype of interest to develop the right genotypes. Satellite platforms offer logistical and technical advantages in scalability and accessibility and could facilitate plot-level predictions, especially with steadily improving spatial resolution, thereby empowering the large-scale screening of thousands of genotypes across diverse locations. In the first chapter, I evaluated over 20,000 plot-level images of over 80 hybrid …

Effects Of Applying Humic Acid In-Furrow At Potato Planting, Jonathan Tyler Price

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

Many products are marketed towards potato farmers that purport to have a positive return on investment for yield and quality. Humic acids, which are comprised of long chained, organic molecules that can be naturally or industrially made, are currently being marketed in this way. The use of these materials is reported to improve nutrient uptake, increase soil health, encourage vigorous growth, and most importantly, increase yields.  From 2023-2025, the in-furrow application of humic acid containing commercial products was evaluated in Pennsylvania on the cultivars ‘Lehigh’ and ‘Waneta’. Black Label Zn, Duo Maxx, Fertiactyl RhiZn, Humi-flex FA, Hydra-Hume, and Monty's Liquid …

Passive Microwave Remote Sensing Of Flash Drought Impacts On Vegetation, Quinton R. Deppert

School of Natural Resources: Dissertations, Theses, and Student Research

In 2002, Dr. Mark Svoboda characterized a new form of drought known as flash drought. Flash drought was defined as a rapid decline in vegetation health caused by severe heat and drought. In recent years, attempts to quantify the impacts of flash drought via precipitation, soil moisture, evapotranspiration, and temperature indicators have proliferated. What has rarely been quantified is what the rapid decline in vegetation health amid flash drought looks like through remote sensing. This is because vegetation health indices like the Normalized Difference Vegetation Index (NDVI) are derived from the visible and infrared regions of the electromagnetic spectrum and …

Spatial Variability Of Nitrates And Nitrogen Mineralization Kinetics And Their Effects In Long-Term Tillage Systems, Bibash Rokaya

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

Nitrogen (N) and water management are essential for water quality protection and crop production. However, soil N and water are spatiotemporally variable. Soil water spatial dependencies are described in the literature with known associations with preferential flows among other factors. In contrast, a knowledge gap exists on the spatial dependence of soil N mineralization kinetics. We hypothesize that soil N mineralization kinetics and soil water have distinct and cross-correlated spatial characteristics among soil management practices and climatic regions. For the field study, we measured soil-N mineralization kinetics, volumetric water content (VWC), and a suite of soil properties along ~70 m …

Evaluation Of Publicly Available Maize Germplasm Adaptation To Environments In Nebraska, Garrett Snodgrass

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

Publicly available maize germplasm represents an important resource for breeding programs seeking to expand genetic diversity and improve hybrid performance. However, effective use requires characterization of per se phenotypic performance of parental lines and evaluation of the parental line’s hybrid progeny adaptation to a given target population of environments. Furthermore, understanding population structure and heterotic grouping is imperative for maximizing efficiency of breeding decisions. The objectives of this study were to (1) evaluate phenotypic performance of parental lines and hybrids across environments in Nebraska, and to (2) refine heterotic group classification of parental lines within the University of Nebraska-Lincoln’s Hybrid …

Hydroponics In The Classroom: Cultivating Plants, Captivating Young People, Stacy A. Adams, Christian Stephenson, Theresa James, Kim Todd

Department of Agronomy and Horticulture: Faculty Publications

Few students take the initiative to pursue coursework beyond that required for progression to graduation. Limited are opportunities that connect educational content to industry application, potentially inspiring young people towards impactful careers. The United States government has emphasized the importance of STEM education to ensure national security and to maintain economic competitiveness globally. STEM education is not a defined discipline but an approach for building knowledge through application and engagement. Developing and managing a hydroponics prototype provides numerous opportunities for embedding STEM content into a fun and interactive project. This poster provides inspiration for constructing a simple deep water culture …

Patch Mow Grazing: Investigating The Effects Of Mowing On Forage Nutritive Value, The Biomass–Nutritive Value Relationship, And Herbivore Selection, Trace R. Stauble

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

Herbivore foraging behavior plays a critical role in shaping grassland structural heterogeneity, with selection often driven by forage biomass and nutritive value. Currently, it is thought that herbivores primarily select areas that are greater in nutritive value, and low in biomass. More specifically, disturbances like fire and grazing have been thoroughly studied showing that recently burned and grazed areas are not only higher in nutritive value but disproportionately selected by herbivores in comparison to undisturbed areas. However, most studies address only narrow ranges of defoliation, comparing intensely defoliated sites (< 10 cm) to those that are either not defoliated or have experienced a much longer time since defoliation, thereby decreasing grazing pressure as biomass increases. However, one of the most widely used methods of defoliation in grasslands, mowing, hasn’t been thoroughly studied for its effects on nutritive value, and how it impacts herbivore selection. Our study aimed to (1) evaluate how mowing treatments—i.e., short (5 cm), medium (18 cm), and tall (>30 cm, unmown)—affect nutritive value and herbivore selection, (2) assess …

Cover Crop Influence On Arthropod Biodiversity And Soil–Water Dynamics In A Semi-Arid Maize–Soybean Sequence Of The Nebraska High Plains, Carlos Eduardo De Oliveira Martins

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

With the expansion of cover crop (CC) use in semi-arid regions, producers in the Nebraska High Plains are increasingly interested in understanding how CCs influence both beneficial arthropods and soil-water within maize-soybean (Zea mays L., Glycine max [L.] Merr.) rotations. Integrating CCs in these systems can enhance soil water availability and beneficial insect activity, but potential trade-offs include higher early-season water use by CCs and the risk of increasing potential pest populations. This thesis addresses these questions through two complementary studies conducted under field conditions near Brule, Nebraska. The first study evaluated the effects of a multi-species CC mixture …

Post-Fire Soil Health Assessment Of The Grasslands And Woodlands In The Semi-Arid Nebraska Sandhills, Stephanie M. Lugo

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

Grasslands in the Nebraska Sandhills are shaped by natural wildfires, which help maintain the structure and function of native grasslands. In recent decades, afforestation with ponderosa pine and eastern redcedar has introduced new woodlands that altered the region’s fire dynamics and raised important questions about the effects of wildfire on different vegetation types. As wildfires become more frequent, understanding their impacts on soil health in grasslands and woodlands becomes increasingly important. This study examines the short-term effects of the 2022 Bovee Fire on physical, chemical, and biological soil properties in native grasslands and ponderosa pine and eastern redcedar afforested woodlands. …

Large Scale Deletion And Rebalancing Within The K1c Kafirin Family In Sorghum, Tyler W. Ferris

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

Sorghum bicolor (L.) Monech (sorghum) is cultivated as food for humans and livestock and is valued for its low input requirements. However, sorghum grain protein is deficient in the essential amino acid lysine and has poor protein digestibility because of the abundance of proline-rich kafirins that constitute >70% of proteins that form low-digestibility protein bodies. To reduce kafirin expression in the endosperm, and elicit wholesale proteome rebalancing to increase non-kafirin proteins, a single-guide RNA (sgRNA) Clustered Regularly Interspaced Short Palindromic Repeats (CRISPR/Cas9) construct was previously used to target members of the highly-repetitive alpha-kafirin family, k1C in RTx430 sorghum. The …

Crop, Soil Nutrient, And Soil Health Responses Within Integrated Crop And Livestock Systems, Alyssa K. Hall

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

We evaluated the influences of grazing livestock on crop production, soil nutrients, and soil health indicators of integrated crop livestock systems using three experiments during a seven-yr. period. Objectives were to (1) determine livestock grazing and cropping system effects on crop yield and soil properties across six yr. in corn-soybean (C-S) and wheat-corn-soybean (W-C-S) systems with and without periodic composted manure application, (2) explore seasonal variation in soil nutrient patterns over two yr., and (3) measure residual responses for corn grain yield plus soil health indicators in yr. seven following a six-yr. study. In experiment 1, neither livestock grazing ( …

Soil Health In Nebraska: Exploring Practitioners' Needs And Insights From A Long-Term Organic Farm, Ingrids Isabel Mata Vigil

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

Soil health is foundational to sustainable agriculture, environmental resilience, and long-term food security. Yet, the adoption of soil health assessments remains limited, often perceived as too technical, costly, or difficult to implement in real-world contexts. To better understand these challenges, the first chapter presents findings from a statewide survey of 41 soil health practitioners in Nebraska, including farmers, extension educators, NRCS staff, and conservation professionals. Respondents highlighted the need for simpler, more accessible, and context-specific tools for soil health assessment that help practitioners make informed decisions aligned with their management goals. Complementing these insights, the second chapter includes an independent, …

Evaluating The Effects Of Row Spacing, Legume Intercropping, Fertilizer Source, And Fertilizer Timing On Intermediate Wheatgrass In Eastern Nebraska, Madeline M. Johnston

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

Kernza^® is the trademarked name of the perennial crop intermediate wheatgrass (Thinopyrum intermedium). In addition to its potential for dual-use as a grain and forage crop, Kernza is marketed to provide needed environmental services by increasing crop biodiversity, sequestering soil carbon, and reducing nitrate leaching. However, more work is needed in cultivar selection and crop management to increase total grain yields and prevent long-term grain yield decline. Furthermore, research in quantifying and understanding Kernza’s ability to affect soil properties and water dynamics is limited.

Two field experiments were conducted at the Eastern Nebraska Research Extension and Education …

Response Of Soybean To Variable Irrigation Levels In Eastern Nebraska Using The Aquacrop Model, Anmol Singh

Department of Agricultural and Biological Systems Engineering: Dissertations, Theses, and Student Research

AquaCrop was calibrated and validated for soybean [Glycine max (L.) Merr.] using 19 irrigation treatments from five years using data from field experiments. The model accurately simulated canopy cover (CC), soil water content (SWC), and grain yield, with overall validation nRMSE values of 12%, 7%, and 7%, respectively. The overall validation nRMSE for SWC in individual 30-cm soil layers was comparatively higher, at 19%. The model was subsequently applied for long-term simulations (2010–2024) to estimate soybean yield and water requirements for two dominant soil types, Yutan silty clay loam and Tomek silt loam under three irrigation levels - rainfed, …

Improving Nitrogen Management And Corn Productivity Through Enhanced Efficiency Fertilizer And Cover Crop Integration In Nebraska Cropping Systems, Madhusudhan Adhikari

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

Effective nitrogen (N) management is vital for sustaining corn yield and reducing environmental impacts in Nebraska cropping systems. Three field studies were conducted to evaluate the impact of 1) fertilizer type (anhydrous ammonia [AA] with nitrification inhibitor: enhanced efficiency fertilizer [EEF] or AA without EEF) and N application timing (pre-plant vs. split with side-dress UAN) on in-season soil N availability, crop response, nitrous oxide (N₂O) emissions, residual soil N and N use efficiencies (NUEs); 2) winter cover crop (CC) species and crop rotation variability on CC biomass production, N uptake, soil N dynamics, and cash crop performance in …

Extending Cover Crop Growing Window To Improve The Health Of Environmentally Sensitive Soils, Noshin Ara Tunazzina

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

Sloping and sandy soils are highly susceptible to degradation. The health of these soils could be improved with cover crops (CCs). However, CC effectiveness in improving soil health mainly depends on CC biomass production, which is often low in temperate regions. The question is: how can we increase CC biomass production? Lengthening the CC growing window can be a potential strategy. This study assessed how 1) interseeded and terminated early (2-3 weeks before crop planting) CC, 2) interseeded and terminated late (at crop planting) CC, 3) drilled (after harvest) and terminated early CC, 4) drilled and terminated late CC, and …

Advancing Mitochondrial Dna Visualization And Dynamics In Plants: Application Of The Mt-Hi-Ness Fluorescent Marker, Madeleine H. Faber

Honors Program: Senior Projects (Public)

Mitochondrial DNA (mtDNA) plays a crucial role in cellular energy production and inheritance, yet its dynamics and exchange remain poorly understood in plant systems due to limitations in visualization techniques. Traditional visualization methods such as exogenous DNA stains and fluorescent protein markers present challenges in specificity and live-cell imaging. To address this challenge, we adapted the MT-HI-NESS fluorescent marker, originally developed for mammalian cells, for use in plant mitochondrial studies. Using Arabidopsis thaliana as a model system, we employed mitochondrial targeting sequences (IVD and AOX) to ensure accurate localization and to confirm mtDNA binding specificity. The validation process included fluorescence-based …

Evaluation Of The Global Durum Panel (Triticum Turgidum Ssp. Durum) For Wheat Streak Mosaic Virus Resistance, Winter Survival, And Seed Characteristics, Megan Engel

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

The majority of durum wheat (Triticum turgidum spp. durum; AABB; 2n=4x=28) is predominantly grown in the northern Great Plains of the United States, and is used in the production of semolina, a coarse flour that makes pasta and couscous. Durum has been widely regarded for being more tolerant to abiotic stress, due to its ability to withstand drought and high temperatures. In this thesis, we conducted greenhouse, field, and lab studies, for the traits wheat streak mosaic virus (WSMV), winter survival, and single kernel characteristics of the Global Durum Panel version 2 (GDPv2 n = 976), a panel …

Genetic And Soil Influences On The Grapevine Rhizosphere Microbiome, Lauren M. Quackenbush

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

In vineyard cropping systems, the rhizosphere microbiome arises through recruitment and filtering of the bulk soil microbiome shaped over time by soil carbon and nitrogen, climate, pH and historical legacies of vineyard management. The recruitment and filtering steps occur under the genetic influences of rootstock and scion that together drive variability in rhizosphere microbiome diversity and composition.

This study compares rhizosphere microbiomes of four Pinot Noir blocks under two rootstocks (101-14 and 420A) and four scions (777, 828, Calera, Mt. Eden). Core microbiomes were consistent across all replicates. The most abundant bacterial phyla were Actinobacteriota, Proteobacteria, and Acidobacteriota …

Geometric Modeling, Reconstruction And Evaluation Of Maize Leaf Morphology In 3d, Zhaocheng Xiang

Dissertations and Doctoral Documents, University of Nebraska-Lincoln, 2023–

Maize is a vital crop for global food security, yet quantitative characterization of its three-dimensional (3D) morphology remains a major challenge due to the geometric complexity of curved leaf structures and occlusions during data collection. This work presents an integrated framework for the digital reconstruction, parametric modeling, and functional analysis of maize leaf morphology and canopy architecture, advancing the precision and interpretability of phenotyping and modeling in smart agriculture.

First, we propose a descriptive and parametric model that represents maize leaves through three fundamental components: midrib, cross-section, and blade contour. Each is described by geometric curves and controlled by biologically …

Greenhouse Management For The Smaller Structure--Educational And Hobby, Stacy A. Adams

Department of Agronomy and Horticulture: Faculty Publications

Greenhouses used for teaching or by hobbyist are smaller than those used for commercial production or found in the retail environment. Structural materials, covering, mechanical equipment, and control systems often are packaged as a kit made available through greenhouse suppliers. Supplier construction services may not be available, in which buyers must use local contractors to complete the installation. Greenhouses are unique structures that differ greatly from sheds or other outbuildings. They have coverings that allow maximum light transmittance, protected from UV degradation, and can handle wide inside to outside temperature extremes. This extension circular provides valuable information on the character, …

Terrarium- An Ecosystem In A Jar, Stacy A. Adams

Department of Agronomy and Horticulture: Faculty Publications

STEM education is supported through hand's-on activities in the classroom. Content understanding and reaffirmation of knowledge is supported through this informative STEM-Quick card that teachers or extension educators can distribute to participants for reference. Terrariums provide an example of a closed ecosystem where water and carbon cycling is demonstrated and plant growth can be observed. This card presents the steps to building and caring for an easy to create terrarium.

Leveraging Within-Field Spatial Variability To Optimize Soybean Yield, Seed Quality, And Profitability, Marina Marly Dalla Betta

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

Optimizing yield and seed quality in soybean production is critical for both profitability and meeting market demands. However, within-field variability in soil properties poses a challenge in determining optimal management strategies to maximize soybean yield, seed quality, and profitability. This work aimed to evaluate the spatial variability of soybean fields to optimize soybean seeding rates, seed quality, and profitability. Two case studies were used to carry over this research. The first study looked at the optimal economical site-specific soybean seeding rates using 11 on-farm precision experiments across Nebraska. The second study looked at the protein and oil variability within 22 …

Nitrogen Limitation In Soybean: Physiology And Diagnosis, Luzviminda Ann Ramos Sazon

Dissertations and Doctoral Documents, University of Nebraska-Lincoln, 2023–

In high-yield soybean environments, the seed yield is limited by nitrogen (N) supply. However, the response of soybean to N fertilizer application is inconsistent. Understanding the seasonal N uptake dynamics in soybean can provide insights on diagnosing N limitation if soybean. To understand soybean N dynamics, we assessed seasonal trends on dry matter and N accumulation in vegetative organs (leaves, stems, and petioles) from 42 field experiments. Each experiment included a ‘zero-N’ treatment, where crops relied on N supply from soil and biological N fixation (BNF), and a ‘full-N’ that received ample N via N fertilizer addition. Vegetative storage proteins …

Broad-Spectrum Resistance To Fungal Foliar Diseases In Wheat: Recent Efforts And Achievements, Amira M.I. Mourad, Asmaa A.M. Ahmed, P. Stephen Baenziger, Andreas Börner, Ahmed Sallam

Department of Agronomy and Horticulture: Faculty Publications

Wheat (Triticum spp.) is one of the most important cereal crops in the world. Several diseases affect wheat production and can cause 20-80% yield loss annually. Out of these diseases, stripe rust, also known as yellow rust (Puccinia striiformis f. sp. tritici), stem rust (Puccinia graminis f. sp. tritici), leaf rust (Puccinia recondita), and powdery mildew (Blumeria graminis f. sp. tritici) are the most important fungal diseases that infect the foliar part of the plant. Many efforts were made to improve wheat resistance to these diseases. Due to the continuous advancement in …

Disentangling Genotype And Environment Specific Latent Features For Improved Trait Prediction Using A Compositional Autoencoder, Anirudha Powadi, Talukder Zaki Jubery, Michael C. Tross, James C. Schnable, Baskar Ganapathysubramanian

Department of Agronomy and Horticulture: Faculty Publications

In plant breeding and genetics, predictive models traditionally rely on compact representations of high-dimensional data, often using methods like Principal Component Analysis (PCA) and, more recently, Autoencoders (AE). However, these methods do not separate genotype-specific and environment-specific features, limiting their ability to accurately predict traits influenced by both genetic and environmental factors. We hypothesize that disentangling these representations into genotype-specific and environment-specific components can enhance predictive models. To test this, we developed a compositional autoencoder (CAE) that decomposes high-dimensional data into distinct genotype-specific and environment-specific latent features. Our CAE framework employed a hierarchical architecture within an autoencoder to effectively separate …