Agronomy and Crop Sciences Commons^™

Transformation And Gene Editing In The Bioenergy Grass Miscanthus, Anthony Trieu, Mohammad B. Belaff, Pradeepa Hirannaiah, Shilpa Manjunatha, Rebekah Wood, Yokshitha Bathula, Rebecca L. Billingsley, Anjali Arpan, Erik J. Sacks, Thomas E. Clemente, Stephen P. Moose, Nancy A. Reichert, Kankshita Swaminathan

Department of Agronomy and Horticulture: Faculty Publications

Background: Miscanthus, a C4 member of Poaceae, is a promising perennial crop for bioenergy, renewable bioproducts, and carbon sequestration. Species of interest include nothospecies M. x giganteus and its parental species M. sacchariforus and M. sinensis. Use of biotechnology-based procedures to genetically improve Miscanthus, to date, have only included plant transformation procedures for introduction of exogenous genes into the host genome at random, non-targeted sites.

Results: We developed gene editing procedures for Miscanthus using CRISPR/Cas9 that enabled the mutation of a specific (targeted) endogenous gene to knock out its function. Classified as paleo-allopolyploids (duplicated ancient …

Yield Prediction Through Integration Of Genetic, Environment, And Management Data Through Deep Learning, Daniel R. Kick, Jason G. Wallace, James C. Schnable, Judith M. Kolkman, Barış Alaca, Timothy M. Beissinger, Jode Edwards, David Ertl, Sherry Flint-Garcia, Joseph L. Gage, Candice N. Hirsch, Joseph E. Knoll, Natalia De Leon, Dayane C. Lima, Danilo E. Moreta, Maninder P. Singh, Addie Thompson, Teclemariam Weldekidan, Jacob D. Washburn

Department of Agronomy and Horticulture: Faculty Publications

Accurate prediction of the phenotypic outcomes produced by different combinations of genotypes, environments, and management interventions remains a key goal in biology with direct applications to agriculture, research, and conservation. The past decades have seen an expansion of new methods applied toward this goal. Here we predict maize yield using deep neural networks, compare the efficacy of 2 model development methods, and contextualize model performance using conventional linear and machine learning models. We examine the usefulness of incorporating interactions between disparate data types. We find deep learning and best linear unbiased predictor (BLUP) models with interactions had the best overall …

Genetic Variation In Common Bunt Resistance In Synthetic Hexaploid Wheat, Amira M. I. Mourad, Alexey Morgounov, P. Stephen Baenziger, Samar M. Esmail

Department of Agronomy and Horticulture: Faculty Publications

Common bunt (caused by Tilletia caries and T. Foetida) is a major wheat disease. It occurs frequently in the USA and Turkey and damages grain yield and quality. Seed treatment with fungicides is an effective method to control this disease. However, using fungicides in organic and low-income fields is forbidden, and planting resistant cultivars are preferred. Due to the highly effective use of fungicides, little effort has been put into breeding resistant genotypes. In addition, the genetic diversity for this trait is low in modern wheat germplasm. Synthetic wheat genotypes were reported as an effective source to increase the …

Is There An Economic Advantage To Planting Diverse Summer Annual Forage Mixtures?, Kelly Mercier, Chris Teutsch, Ray Smith, Kenny Burdine, Edwin Ritchey, Eric Vanzant

The Journal of Extension

This study examined economic implications of planting summer annual mixtures of grasses, legumes, and forbs at varying nitrogen rates. No differences in yield occurred between the three mixtures, indicating that mixtures with lowest seed cost will be most economical. Applying N resulted in yield increases of 12.26 lb DM per lb N applied. Although yield responses to N were positive, sensitivity analyses showed that applying N resulted in positive net returns only when hay prices were high and N prices were low. When utilization rates are accounted for, enterprise budgets determined grazing to be 18% cheaper to implement than haying.

Inheritance Of 2,4‑Dichlorophenoxyacetic Acid (2,4‑D) Resistance In Amaranthus Palmeri, Chandrima Shyam, Dallas E. Peterson, Amit J. Jhala, Mithila Jugulam

Department of Agronomy and Horticulture: Faculty Publications

In this study, the inheritance of 2,4-D resistance in a multiple herbicide-resistant Palmer amaranth (KCTR) was investigated. Direct and reciprocal crosses were performed using 2,4-D-resistant KCTR and susceptible KSS plants to generate F₁ progenies. 2,4-D dose–response assays were conducted to evaluate the response of progenies from each F₁ family along with KCTR and KSS plants in controlled environmental growth chambers. Additionally, 2,4-D-resistant male and female plants from each of the F₁ families were used in pairwise crosses to generate pseudo-F₂ families. Segregation (resistance or susceptibility) of progenies from the F₂ families in response to a …

Comparison Of Maize Hybrids For Production Of Quality Fodder And Silage In Faisalabad, Punjab, Pakistan, Ali Hamed, Muhammad Shahid Ibni Zamir, Asif Tanveer, Muhammad Yaseen

Journal of Bioresource Management

Fodder crops have to compete with those of field crops, and the majority of farmers are smallholders in the circumstances of Pakistan. Therefore, this study was planned to search for the best maize hybrid which would serve dual purposes, i.e. for grain production as well as its later usage as fodder and silage. So, seven maize hybrids most commonly grown in the vicinity were selected and compared for their forage production. Maize hybrids were sown on ridges followed by all cultural operations as carried out by farmers. At harvest, plant morphological parameters were measured before ensiling the whole maize plant. …

Nitrogen Transfer From Cover Crops To The Subsequent Grain Crop And The Influence Of Variability In Winter Conditions, Spencer Heuchan

Electronic Thesis and Dissertation Repository

Cover crops, which are used to provide ground cover after the harvest of the grain crop, can potentially improve the sustainability of agroecosystems by reducing nutrient losses. However, few data are available to document the extent to which cover crops improve both the retention of soil nitrogen (N) and the transfer of this N to the grain crop. The efficiency of this N transfer may be further influenced by variation in winter soil temperature; for example, reduced snow cover can increase the frequency and intensity of soil freezing, which can affect the survival of cover crops and the timing of …

A Stealth Health Approach To Dietary Fibre, P. Stephen Baenziger, Katherine Anna Frels, Steve Greenspan, Julie Jones, Alison Lovegrove, Devin J. Rose, Peter Shewry, Rod Wallace

Department of Agronomy and Horticulture: Faculty Publications

Average dietary fibre intakes have increased little in the past twenty years in many countries, including the USA¹ . Multi-million-dollar campaigns promoting fruits, vegetables, whole grains and other foods high in fibre have delivered only small changes in diets² , and consumers have not changed from traditional staples to whole-grain options³ . UK millers report that consumption of whole-wheat bread has actually declined over the past decade (P. Shewry, personal communication). In the US, white flour, which is lower in fibre than whole-wheat flour, accounts for nearly 40% of the fibre intake⁴ . We believe that …

Aspectos De La Investigación Del Cacao En Municipios De La Zona Del Tequendama, Jenny Paola Moreno Lopez, Laguandio Del Cristo Banda Sánchez, Arlette Ivone Gil Clavijo, Diego Orlando Méndez Pineda, Fabián Giovanny Marquez Niño

Ciencias Agropecuarias

El mejoramiento del manejo fitosanitario en producciones de cacao (Theobrorna cacao L) involucra el uso de alternativas amigables como los productos a base de plantas con actividad antimicrobiana tal es el caso del género Piper. Esta investigación buscó cuantificar las enfermedades presentes en plantaciones de cacao en municipios de la región del Tequendama Cundinamarca-Colombia y evaluar aspectos eco fisiológicos de Piper SP. Se trabajó en seis fincas de la Asociación de Cacaoteros del Bajo Tequendama en Viotá, Anapoima y Tocaima. Se evaluó la incidencia y severidad de las enfermedades y se generaron mapas de calor. Se tomaron muestras vegetales sintomáticas …

Genetic Variations Of Narcissus Tazetta And Selected Narcissus Cultivars Based On The Sequence Analysis Of Nrits And TrnL‑Is‑TrnF Regions, Seo Young Park, Mi Jin Jeon, Young Hee Joung, Keenan L. Amundsen, Gianluca Burchi, Angelo Porcelli, Mark S. Roh

Department of Agronomy and Horticulture: Faculty Publications

Narcissus tazetta var. chinensis (N. taz. var. chi.) accessions collected from the coastal areas of China, Korea, and Japan were compared with accessions of lower ranks of Narcissus tazetta (N. taz.) from Italy to study the genetic variations and with several morphologically similar cultivars available in the trade. Sequences of the internal transcribed spacer (ITS) regions of nuclear ribosomal DNA (nrITS) dendrogram and the chloroplast trnL-IS-trnF intergeneric spacer-gene (cpIS) were analyzed by maximum likelihood (ML) and posterior probability using STRUCTURE program. All single fower form of N. taz. var. chi. collected from China, Korea, and …

Reassessing Nitrogen Management For Maize Production In Mississippi, Camden Dawson Oglesby

Theses and Dissertations

12 N treatments in 2020 and 11 in 2021 were replicated four times over four locations in a randomized complete block design. The first research tested the efficacy of CYG for Mississippi corn (Zea mays L.) production. The optimum N rates were calculated by fitting four models. Differences between the CYG rate and AONR were compared. AONR varied from 134 to 301 kg N ha–1 at different management levels. When we compared the AONR to the CYG rate, the CYG rate over-recommended N in 12 of the 14 possible comparisons. The second study compared different VIs, methods, and sensors at …

Evaluating The Impacts Of Waterlogging Stress On Cowpea (Vigna Unguiculata L.) Growth Traits And Physiological Performance, Omolayo Joshua Olorunwa

Theses and Dissertations

The progressive increase in the global population and the rapidly changing climate have put unprecedented pressure on crop production. Cowpea is one of the world’s most important leguminous crops, contributing to food security and environmental sustainability. However, cowpea productivity is limited due to waterlogging stress. The main objective of this study was to explore physiological and biochemical mechanisms to understand how cowpea genotypes respond to waterlogging stress. Four studies were conducted in controlled and field conditions to achieve these objectives. Study 1 characterized the waterlogging tolerance of 30 cowpea genotypes in a controlled environment using 24 morphophysiological parameters with waterlogging …

Effects Of Soil Management Practices On Water Infiltration And Maize Yield To Improve Mississippi River Valley Alluvial Aquifer Sustainability, Jacob Rix

Theses and Dissertations

Surface sealing and hardpans in loam soils are problematic in the Mid-South U.S. because of intense tillage. Two experiments quantified the effects of soil management practices on infiltration and maize yield in loam soils. The first study measured the impacts of in-row subsoiling frequency × furrow irrigation frequency. In-row subsoiling significantly improved the infiltration of irrigation but not the infiltration of precipitation. In-row subsoiling with low irrigation frequency is optimal to achieve profitable maize yields while encouraging groundwater conservation. In the second study, six soil management treatments were imposed. For single-ring infiltrometer tests, infiltration rates were different between the two …

Evaluation Of Soybean [Glycine Max (L.) Merr.] Cultivar Response To Prophylactic Fungicide Application, Steven B. Stoker

Theses and Dissertations

Soybean growers in the southern United States commonly deal with disease issues that can limit yield potential. As a result, growers have adopted prophylactic fungicide application targeted at specific growth stages as a standard management practice. However, yield responses to prophylactic applications have become sporadic over time. One major change that has occurred is adoption of cultivars with improved disease tolerances. Therefore, the objective of this research was to evaluate yield response of cultivars representing multiple genetic backgrounds to fungicides applied prophylactically at the R4 soybean growth stage. Experiments were conducted in 2020 and 2021 to determine the yield impact …

Evaluation For Using Expended Bioelectrochemical Systems As Soil Amendments For Improved Corn Plant Growth And A Drought Resistant Soil., Jackson Lee Sauers

Theses and Dissertations

A long-held practice is to mix agricultural soil with a soil amendment to improve growing conditions in crops. A common soil amendment is biosolids produced from both municipal and dairy wastewater due to the macro- and micronutrients within it. Both the agricultural and wastewater industries are participating in the Circular Economy concept (CEC). Two experiments explored using expended bioelectrochemical systems (BES) that treated either synthetic dairy wastewater (DWW) or synthetic municipal wastewater (SWW) as soil amendments to improve corn plant growth when treated with three different nutrient treatments: 100%- 50%- and 0% Hoagland Nutrient Solutions. Biochar and used terracotta clay …

An Evaluation On The Effects Of Additions And Deletions Of Specific Nutrient Management Strategies On Corn Yield At Different Plant Densities, James D. Dew

Theses and Dissertations

Improved management strategies are needed to increase yield production and quality. The study aimed to determine suitable cultural practices for improved corn production. Experiments were set up at Verona and Stoneville, Mississippi, from 2020 to 2022. Treatments included row configurations (single and twin-row), plant populations (79,000 and 99,000 seeds ha-1), and six combinations of nutrients with or without fungicide. The nutrients evaluated were two nitrogen rates 235 and 314 kg N ha-1, phosphorus 45 kg P ha-1, potassium 112 kg K ha-1, sulfur 22 kg S ha-1, and zinc 11 kg Zn ha-1, and fungicide at 272 ml ha-1. In …

Biological Remediation Of Fragipan, Corey Hale

Honors College Theses

The fragipan layer in the soil is a naturally occurring subsurface layer that restricts water percolation as well as inhibits root growth. A fragipan layer can be found almost ubiquitously across Southwestern Kentucky. This limits how agriculturalists manage soils in this area. It has been recently discovered by the University of Kentucky that Annual Ryegrass roots produce 3,4 dihydroxyphenylpropionic acid (DHPPA) that reacts with this hardpan to weaken the layer. Certain bacteria, such as Escherichia coli, Lactobacilli, and Bifidobacteria can also synthesize DHPPA through a breakdown process of chlorogenic acid. This reaction typically happens in the human digestive tract. …

Demonstration Farm Provides Educational Opportunity For Ipm, Nick Volesky, Mair Murray

Outcomes and Impact Quarterly

The mission of USU Extension’s Integrated Pest Management (IPM) program is to increase the use of sustainable pest management practices within urban and rural landscapes to provide economic, human, and environmental health in Utah. In the spring of 2022, the IPM program established a vegetable farm to test and demonstrate IPM practices. The farm served as an experiential learning classroom for almost 50 farmers and home gardeners.

Poisson Hurdle Model-Based Method For Clustering Microbiome Features, Zhili Qiao, Elle Barnes, Susannah Tringe, Daniel P. Schachtman, Peng Liu

Department of Agronomy and Horticulture: Faculty Publications

Motivation: High-throughput sequencing technologies have greatly facilitated microbiome research and have generated a large volume of microbiome data with the potential to answer key questions regarding microbiome assembly, structure and function. Cluster analysis aims to group features that behave similarly across treatments, and such grouping helps to highlight the functional relationships among features and may provide biological insights into microbiome networks. However, clustering microbiome data are challenging due to the sparsity and high dimensionality.

Results: We propose a model-based clustering method based on Poisson hurdle models for sparse microbiome count data. We describe an expectation–maximization algorithm and a …

Deciphering The Genetic Architecture Of Key Female Floral Traits For Hybrid Wheat Seed Production, Juan Jimenez

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

Wheat (Triticum aestivum L.) is a staple cereal that provides 20% of the calories and proteins in human intake (Ray et al., 2013). Global population is projected to increase to 9.7 billion by 2050. Food production must increase by 70% to feed this future population. Wheat production is in crisis due to political and environmental challenges and is projected to decline by 0.8% in 2022 (FAO, 2022). To ensure food security yield genetic gain must increase by around 1.4% annually. Taking advantage of heterosis, hybrid wheat has the potential to boost grain yield. However, hybrid wheat seed production systems …

Insights On The Behavior Of Nano-Copper In The Agroecosystem: Mycorrhizal Associations With Spearmint (Mentha Spicata), Suzanne Annette Apodaca

Open Access Theses & Dissertations

Nanotechnology offers significant potential benefits to our society, including the agriculture sector. With the advancement of nano-enabled agrochemicals towards sustainable and efficient agricultural practices, it is essential to address environmental issues associated with the use of nanoscale materials. The same properties that give promise to applications of nanotechnology in modern agriculture could have unintended consequences on ecosystem dynamics. A point of concern for risk management is the impact of engineered nanomaterials (ENMs) to beneficial microbial communities, which support a variety of ecosystem services.

Use of copper (Cu) products in agriculture are based on their abundance, role as a micronutrient, and …

Micronutrient Concentration Effects On Lettuce Growth And Susceptibility To Pythium, Kalyn M. Helms

Graduate Theses and Dissertations

In hydroponic production waterborne pathogens such as Pythium are ubiquitous and continually threaten a wide range of Controlled Environment Agriculture (CEA) crops in hydroponic production, including but not limited to: lettuce, spinach, basil, arugula, cucumber, tomato, sweet pepper, roses, chrysanthemums, and cannabis (Sutton et al., 2006; Gull, 2002; McGehee and Raudales, 2021; Gillespie, 2020). Despite extensive sanitation measures, disease control in hydroponics is fallible and requires constant surveillance and management to minimize outbreaks (Sutton et al., 2006). A potential disease suppression strategy is to increase micronutrient concentrations within hydroponic systems to naturally strengthen plant defenses against pathogens such as Pythium. …

Evaluation Of Biological And Chemical Seed Treatments For Management Of Rice Diseases, Sherif Adam Sharfadine

Graduate Theses and Dissertations

Rice is the primary staple for more than half of the global population and is the second most important cereal worldwide. In the US, rice is primarily grown in the southern states, with Arkansas leading production and responsible for 47% of the total rice production in the country. Diseases cause significant yield losses in rice. Sheath blight, rice blast and bacterial panicle blight are the main diseases in rice and cause significant yield losses. Sheath blight alone could cause up 50% yield loss in heavily damaged fields with highly susceptible cultivars. Additionally, rice seed and seedling diseases primarily caused by …

A Glass Bead Semi-Hydroponic System For Intact Maize Root Exudate Analysis And Phenotyping, Martha G. Lopez-Guerrero, Peng Wang, Felicia Phares, Daniel P. Schachtman, Sophie Alvarez, Karin V. Van Dijk

Department of Agronomy and Horticulture: Faculty Publications

Background: Although there have been numerous studies describing plant growth systems for root exudate collection, a common limitation is that these systems require disruption of the plant root system to facilitate exudate collection. Here, we present a newly designed semi-hydroponic system that uses glass beads as solid support to simulate soil impedance, which combined with drip irrigation, facilitates growth of healthy maize plants, collection and analysis of root exudates, and phenotyping of the roots with minimal growth disturbance or root damage. Results: This system was used to collect root exudates from seven maize genotypes using water or 1 mM CaCl2, …

Comparative Genome Analysis Of Plant Ascomycete Fungal Pathogens With Different Lifestyles Reveals Distinctive Virulence Strategies, Yansu Wang, Jie Wu, Jiacheng Yan, Ming Guo, Lei Xu, Liping Hou, Quan Zou

Department of Agronomy and Horticulture: Faculty Publications

Background: Pathogens have evolved diverse lifestyles and adopted pivotal new roles in both natural ecosystems and human environments. However, the molecular mechanisms underlying their adaptation to new lifestyles are obscure. Comparative genomics was adopted to determine distinct strategies of plant ascomycete fungal pathogens with different lifestyles and to elucidate their distinctive virulence strategies. Results: We found that plant ascomycete biotrophs exhibited lower gene gain and loss events and loss of CAZyme-encoding genes involved in plant cell wall degradation and biosynthesis gene clusters for the production of secondary metabolites in the genome. Comparison with the candidate effectome detected distinctive variations between …

Biobased Sprayable Mulch Films Suppressed Annual Weeds In Vegetable Crops, Eliott Gloeb, Sibel Irmak, Loren Isom, John L. Lindquist, Samuel E. Wortman

Department of Agronomy and Horticulture: Faculty Publications

Biobased sprayable mulch (BSM) films are a potential alternative to herbicides, polyethylene plastic mulch film, and hand weeding for specialty crops. We developed a series of BSM films using locally available biomaterials [including corn (Zea mays) starch, glycerol, keratin hydrolysate, corn gluten meal, corn zein, eggshells, and isolated soy (Glycine max) protein] and tested their effects on weeds and crop yield during a total of seven greenhouse or field trials between 2017 and 2019 in Nebraska, USA. Application rates of BSM films applied in pots (greenhouse), planting holes in plastic film (field), or bed tops (field) …

Comparative Genomics Of Five Valsa Species Gives Insights On Their Pathogenicity Evolution, Guangchao Sun, Shichang Xie, Lin Tang, Chao Zhao, Mian Zhang, Lili Huang

Department of Agronomy and Horticulture: Faculty Publications

Valsa is a genus of ascomycetes within the Valsaceae family. This family includes many wood destructive pathogens such as the well known Valsa mali and Valsa pyri which cause canker diseases in fruit trees and threaten the global fruit production. Lack of genomic information of this family is impeding our understandings about their evolution and genetic basis of their pathogenicity divergence. Here, we report genome assemblies of Valsa malicola, Valsa persoonii, and Valsa sordida which represent close relatives of Valsa mali and Valsa pyri with different host preferences. Comparative genomics analysis revealed that segmental rearrangements, inversions, and translocations …

Nitrogen Use Efficiency Of Pretassel Nitrogen Applications In Corn, Robyn Brittlee Mulloy

Graduate Theses and Dissertations

Corn (Zea mays L.) production continues to be a critical component of row-crop production systems within Arkansas and is seeing a resurgence in recent years. Nitrogen (N) is critical for corn growth and is often one of the single largest input costs associated with corn production. Research objectives for this study were to determine the nitrogen use efficiency (NUE) of late season N applications as influenced by sidedress N rate and timing of pretassel application and to quantify the nutrient uptake and partitioning in modern era corn hybrids within a furrow-irrigated production system. Research was conducted at the Milo J. …

Diagnosing Excess Nitrogen In Rice Using Post-Season Tissue Samples, Kyle Hoegenauer

Graduate Theses and Dissertations

Proper nitrogen (N) management in rice production can be difficult to achieve without the aid of tools such as soil and tissue tests. There are no tests currently available to rice producers that determine whether N has been managed properly throughout the season or that detect instances of over fertilization. Rice stalk samples were collected from N response trials within 3 days of harvest from the primary Arkansas rice growing region in 2016-2018. Stalk samples were analyzed for N concentration through a KCl extraction and spectrofluorometric quantification. Samples analyzed with leaf material intact contained statistically different N concentrations than samples …

Understanding The Potential Utility Of Tamarktm Grain Sorghum, Jacob Alan Fleming

Graduate Theses and Dissertations

Herbicide-resistant crops have been commonly used in corn, cotton, and soybean since the 1990s to control numerous different grass and broadleaf weeds. However, this technology has not been available for grain sorghum producers whom have faced challenges controlling grass weeds. Recently a collaboration between the University of Arkansas and Texas A&M University has resulted in a new bred line of grain sorghum, TamArkTM, which is resistant to ACCase inhibitor herbicides which have been previously used to control grass weeds in broadleaf crops. Multiple studies were conducted to determine the sensitivity of TamArkTM and problematic grass weeds to ACCase inhibitor herbicides, …