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The Role Of A Transcription Factor In Regulating Rice Response To Drought Stress, Diana Ha, Liyuan A. Zhang, Jeffery Shen

Undergraduate Research Opportunities Program (UROP)

The current water shortage is a major concern in regard to our global climate change crisis. A decrease in the availability of water will have direct effects on the development of plants. Some crops, such as Oryza sativa, or commonly known as rice, requires an abundant amount of water for adequate growth. With the water shortage crisis, it will become extremely difficult to harvest such crops to meet the world’s food demand. However, many plants have evolved mechanisms for overcoming and tolerating stresses such as drought. My research focuses on studying the proteins involved with these mechanisms. The WRKY superfamily …

Gata-Family Transcription Factors In Magnaporthe Oryzae, Cristian F. Quispe

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

The filamentous fungus, Magnaporthe oryzae, responsible for blast rice disease, destroys around 10-30% of the rice crop annually. Infection begins when the specialized infection structure, the appressorium, generates enormous internal turgor pressure through the accumulation of glycerol. This turgor acts on a penetration peg emerging at the base of the cell, causing it to breach the leaf surface allowing its infection.

The enzyme trehalose-6- phosphate synthase (Tps1) is a central regulator of the transition from appressorium development to infectious hyphal growth. In the first chapter we show that initiation of rice blast disease requires a regulatory mechanism involving an …

B. R. Wells Rice Research Studies 2010, R. J. Norman, K. A. K. Moldenhauer

Arkansas Agricultural Experiment Station Research Series

The 2010 Rice Research Verification Program ( RRVP) was conducted on twenty-two commercial rice fields across the state. Counties rarticirating in the program included Arkansas, Ashley, Chicot, Clark, Clay, Cross, Desha, Drew, Greene, Jackson, Jefferson, Lafayette, Lawrence, Lonoke, Mississippi, Phillips, Poinsett (2 fields), Prairie, Randolph, St. Francis, and White for a total of 1456 acres. Grain yield in the 2010 RRVP averaged 167 bu/acre ranging from 113 to 215 bu/acre. The 2010 RRVP average yield was 25 bu/acre greater than the estimated Arkansas state average of 142 bu/acre. The highest yielding field was in Clay County with a grain yield …

Herbicide-Resistant Risk Assessment: Response Of Common Nebraska Weeds To Dicamba Dose, Roberto J. Crespo

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

Dicamba-resistant soybeans are being developed to provide an additional herbicide mechanism of action that can be used in soybean, and to provide a tool to help manage or mitigate the evolution of other herbicide-resistant weed populations. The objectives of this thesis were to assess the risk of common Nebraska weeds developing resistance to dicamba, quantify baseline dose-response to dicamba of high-risk weed species, and survey the variability in dicamba dose-response among populations of those species. Twenty-five weed scientists were asked to estimate the risk likelihood of ten weed species evolving resistance to dicamba following the commercialization of dicamba-resistant soybean. Palmer …

Effects Of Xenobiotics And Phytotoxins On Reproduction In Food Animals, Kip E. Panter, Bryan L. Stegelmeier

United States Department of Agriculture-Agricultural Research Service / University of Nebraska-Lincoln: Faculty Publications

The influence of natural toxicants and anthropogenic compounds on reproduction in food animals is significant in its economic impact, and the subject requires more research and further experimental substantiation. Confounding factors such as stress, nutritional status, season of the year, animal species involved, genetic variability, disease conditions, management factors, and so forth exacerbate the difficulty of making an accurate diagnosis and thereby may impede progress to improve reproductive performance on an individual operation. The interaction between the reproductive system and xenobiotics (reproductive toxicology) is a relatively new area of study and a subject of increasing interest, especially in the area …

Sweet Sorghum As An Alternative Cellulosic Biofuel In Eastern Kentucky, Sarah A. Hazenfield

Morehead State Theses and Dissertations

A thesis presented to the faculty of the College of Science and Technology at Morehead State University in partial fulfillment of the requirements for the Degree of Master of Science by Sarah A. Hazenfield in June of 2011.

Generation Of Transgenic Medicago Sativa Overexpressing "Osmotin-Chitinase" Gene Chimera, Jahnavi Reddy Kancharla

Masters Theses & Specialist Projects

Medicago is widely used as a forage crop. It is often susceptible to various pathogenic infections and exhibits low growth in drought and extreme climatic conditions. In the current study, a strategy was developed for over-expressing an “Osmotin-Chitinase” gene chimera in transgenic Medicago that could potentially confer resistance to different biotic and abiotic stresses. Seed germination of several cultivars of Medicago (M. sativa ssp. sativa, M. sativa ssp. falcata, M. sativa ssp. caerulea, M. truncatula, and M. Rugosa) was tested to determine the cultivars with good germination rates. Among these, M. sativa ssp. sativa showed an …

Comparison Of Whole-Genome Amplifications For Microsatellite Genotyping Of Rotylenchulus Reniformis, R. S. Arias, Salliana R. Stetina, Brian E. Scheffler

United States Department of Agriculture-Agricultural Research Service / University of Nebraska-Lincoln: Faculty Publications

Currently, a large number of microsatellites are available for Rotylenchulus reniformis (reniform nematode); however, two barriers exist for genotyping samples from different geographical areas. The limited amount of nucleic acids obtained from single nematodes which would require their multiplication to obtain enough DNA for testing; and the strictly regulated transport of live samples and multiplication in greenhouse for being a plant pathogen. Whole-genome amplification (WGA) of samples consisting of one and five dead gravid females with their associated egg masses was successfully performed on disrupted tissue using three commercial kits. DNA yield after WGA ranged from 0.5 to 8 μg …

First Microsatellites From Spodoptera Frugiperda (Lepidoptera: Noctuidae) And Their Potential Use For Population Genetics, R. S. Arias, Carlos A. Blanco, Maribel Portilla, Gordon L. Snodgrass, Brian E. Scheffler

United States Department of Agriculture-Agricultural Research Service / University of Nebraska-Lincoln: Faculty Publications

This is the first report of sequence-specific microsatellite markers (simple sequence repeats [SSRs]) of fall armyworm, Spodoptera frugiperda (J.E. Smith) (Lepidoptera: Noctuidae), an economically important pest of crops on the Americas.Weisolated 192 microsatellite markers by using pyrosequencing and screened 15 individuals from eight isofamilies collected from three geographical areas: Puerto Rico (PR), Texas (TX), and Mississippi (MS). Isofamilies resistant to Cry toxins from Bacillus thuringiensis (Berliner) (Bacillales: Bacillaceae) also were included. Cluster analysis was performed to determine the potential use of these SSRs in discriminating populations, and colonies were grouped with a reliability of 100% estimated by bootstrap. In this …

Establishing Weed Prevention Areas And Evaluating Their Impact, Stephanie Christensen

All Graduate Theses and Dissertations, Spring 1920 to Summer 2023

The spread of invasive weeds continues to be a serious economic and environmental threat. Weed prevention has the potential to stop weeds before they become well established in an area conserving time, energy, and resources. Unfortunately, weed prevention is often overlooked. Weed Prevention Areas (WPAs) are a relatively new tool developed to help improve the application of weed prevention. They are cooperatively managed areas that focus on implementing prevention and early detection strategies at a community level. The purpose of this research was to establish baseline data that will be used to evaluate the overall effectiveness of the WPA concept, …

Summaries Of Arkansas Cotton Research 2010, Derrick M. Oosterhuis

Arkansas Agricultural Experiment Station Research Series

No abstract provided.

Screening Synteny Blocks In Pairwise Genome Comparisons Through Integer Programming, Haibao Tang, Eric Lyons, Brent S. Pedersen, James C. Schnable, Andrew H. Paterson, Michael Freeling

Department of Agronomy and Horticulture: Faculty Publications

Background:

It is difficult to accurately interpret chromosomal correspondences such as true orthology and paralogy due to significant divergence of genomes from a common ancestor. Analyses are particularly problematic among lineages that have repeatedly experienced whole genome duplication (WGD) events. To compare multiple “subgenomes” derived from genome duplications, we need to relax the traditional requirements of “one-to-one” syntenic matchings of genomic regions in order to reflect “one-to-many” or more generally “many-to-many” matchings. However this relaxation may result in the identification of synteny blocks that are derived from ancient shared WGDs that are not of interest. For many downstream analyses, we …

A First Insight Into Population Structure And Linkage Disequilibrium In The U.S. Peanut Minicore Collection, Vikas Belamkar, Michael Gomez Selvaraj, Jamie L. Ayers, Paxton R. Payton, Naveen Puppala, Mark D. Burow

Department of Agronomy and Horticulture: Faculty Publications

Knowledge of genetic diversity, population structure, and degree of linkage disequilibrium (LD) in target association mapping populations is of great importance and is a prerequisite for LD-based mapping. In the present study, 96 genotypes comprising 92 accessions of the US peanut minicore collection, a component line of the tetraploid variety Florunner, diploid progenitors A. duranensis (AA) and A. ipaënsis (BB), and synthetic amphidiploid accession TxAG-6 were investigated with 392 simple sequence repeat (SSR) marker bands amplified using 32 highly-polymorphic SSR primer pairs. Both distance- and model-based (Bayesian) cluster analysis revealed the presence of structured diversity. In general, the wild-species accessions …

Genes Identified By Visible Mutant Phenotypes Show Increased Bias Toward One Of Two Subgenomes Of Maize, James C. Schnable, Michael Freeling

Department of Agronomy and Horticulture: Faculty Publications

Not all genes are created equal. Despite being supported by sequence conservation and expression data, knockout homozygotes of many genes show no visible effects, at least under laboratory conditions. We have identified a set of maize (Zea mays L.) genes which have been the subject of a disproportionate share of publications recorded at MaizeGDB. We manually anchored these ‘‘classical’’ maize genes to gene models in the B73 reference genome, and identified syntenic orthologs in other grass genomes. In addition to proofing the most recent version 2 maize gene models, we show that a subset of these genes, those that …

Dose–Sensitivity, Conserved Non-Coding Sequences, And Duplicate Gene Retention Through Multiple Tetraploidies In The Grasses, James C. Schnable, Brent S. Pedersen, Sabarinath Subramaniam, Michael Freeling

Department of Agronomy and Horticulture: Faculty Publications

Whole genome duplications, or tetraploidies, are an important source of increased gene content. Following whole genome duplication, duplicate copies of many genes are lost from the genome. This loss of genes is biased both in the classes of genes deleted and the subgenome from which they are lost. Many or all classes are genes preferentially retained as duplicate copies are engaged in dose sensitive protein–protein interactions, such that deletion of any one duplicate upsets the status quo of subunit concentrations, and presumably lowers fitness as a result. Transcription factors are also preferentially retained following every whole genome duplications studied. This …

Proceedings Of The 38th Annual Meeting, Southern Soybean Disease Workers (March 9-10, 2011, Pensacola Beach, Florida), Boyd Padgett, Tom Allen, Jason Bond, Cliff Coker, Stephen R. Koenning

Southern Soybean Disease Workers: Conference Proceedings

Contents

Southern United States Soybean Disease Loss Estimates for 2010. Compiled by SR Koenning

Poster presentation

Soybean Varieties and Breeding Lines Shown With Resistance to Reniform Nematode in Greenhouse Tests, 1998-2010 R. T. Robbins, and L. E. Jackson

Oral presentations

Frogeye Leaf Spot (Cercorosa sojina) symposium (Boyd Padgett, moderator)

Development of Baseline Cercospora sojina Sensitivity Levels to Quinone Outside Inhibitor Fungicides and Monitoring for Resistance. GR Zhang and CA Bradley

Soybean Pathogen Found to be Resistant to Fungicides MA Newman and CA Bradley

Strobilurin-resistant Cercospora sojina in Kentucky: Field History. D Hershman

Graduate student paper competition (Tom Allen, …

Comparison Of Various Configurations Of Cdc-Type Traps For The Collection Of Phlebotomus Papatasi Scopoli In Southern Israel, Daniel L. Kline, Jerome Hogsette, Gunter Muller

United States Department of Agriculture-Agricultural Research Service / University of Nebraska-Lincoln: Faculty Publications

We conducted two experiments to determine the best CDC-trap configuration for catching male and female Phlebotomus papatasi. First, visual features were evaluated. Standard CDC traps were modified to have black or white catch bags, black or white lids, or no lids and these were tried in different combinations. Significantly more male sand flies were caught by darker traps; significantly more females were captured by traps with either all black or a combination of black and white features. Attraction may be due to dark color or contrast in colors. CDC traps with suction and the following features were also evaluated: …

Switchgrass, Kenneth P. Vogel, Gautam Sarath, Aaron J. Saathoff, Robert B. Mitchell

Department of Agronomy and Horticulture: Faculty Publications

17.1 Introduction

Switchgrass (Panicum virgatum L.) is a warm-season perennial grass that is native to North America that is being developed into a biomass energy crop. It has been used in pastures and for conservation purposes in the Great Plains and the Midwest, USA, for over 70 years.1 The research supporting its use as a pasture and conservation species was largely conducted by US Department of Agriculture (USDA) research programs, most notably the Agricultural Research Service (ARS) project located at the University of Nebraska-Lincoln and USDA Plant Materials Centers that are located throughout the United States. In this report, …

Identification Of A Second Asian Soybean Rust Resistance Gene In Hyuuga Soybean, Mandy D. Kendrick, Donna K. Harris, Bo-Keun Ha, D. L. Hyten, P. B. Cregan, Reid D. Frederick, H. Roger Boerma, Kerry F. Pedley

Department of Agronomy and Horticulture: Faculty Publications

Asian soybean rust (ASR) is an economically significant disease caused by the fungus Phakopsora pachyrhizi. The soybean genes Rpp3 and Rpp?(Hyuuga) confer resistance to specific isolates of the pathogen. Both genes map to chromosome 6 (Gm06) (linkage group [LG] C2). We recently identified 12 additional soybean accessions that harbor ASR resistance mapping to Gm06, within 5 centimorgans of Rpp3 and Rpp?(Hyuuga). To further characterize genotypes with resistance on Gm06, we used a set of eight P. pachyrhizi isolates collected from geographically diverse areas to inoculate plants and evaluate them for differential phenotypic responses. …

Mutational Analysis Of The Major Soybean Uref Paralogue Involved In Urease Activation, Joe C. Polacco, D. L. Hyten, Mônica Medeiros-Silva, David A. Sleper, Kristin D. Bilyeu

Department of Agronomy and Horticulture: Faculty Publications

The soybean genome duplicated ~14 and 45 million years ago and has many paralogous genes, including those in urease activation (emplacement of Ni and CO₂ in the active site). Activation requires the UreD and UreF proteins, each encoded by two paralogues. UreG, a third essential activation protein, is encoded by the single-copy Eu3, and eu3 mutants lack activity of both urease isozymes. eu2 has the same urease-negative phenotype, consistent with Eu2 being a single-copy gene, possibly encoding a Ni carrier. Unexpectedly, two eu2 alleles co-segregated with missense mutations in the chromosome 2 UreF paralogue (Ch02UreF), suggesting …

Cytokinin-Mediated Source ⁄Sink Modifications Improve Drought Tolerance And Increase Grain Yield In Rice Under Water-Stress, Zvi Peleg, Maria Reguera, Ellen Tumimbang, Harkamal Walia, Eduardo Blumwald

Department of Agronomy and Horticulture: Faculty Publications

Drought is the major environmental factor limiting crop productivity worldwide. We hypothesized that it is possible to enhance drought tolerance by delaying stress-induced senescence through the stress-induced synthesis of cytokinins in crop-plants. We generated transgenic rice (Oryza sativa) plants expressing an isopentenyltransferase (IPT) gene driven by PSARK, a stress- and maturation-induced promoter. Plants were tested for drought tolerance at two yield-sensitive developmental stages: pre- and post-anthesis. Under both treatments, the transgenic rice plants exhibited delayed response to stress with significantly higher grain yield (GY) when compared to wild-type plants. Gene expression analysis revealed a significant shift in expression of hormone-associated …

The Ability Of Selected Pupal Parasitoids (Hymenoptera: Pteromalidae) To Locate Stable Fly Hosts In A Soiled Equine Bedding Substrate, Jimmy B. Pitzer, Phillip E. Kaufman, Christopher Geden, Jerome A. Hogsette

United States Department of Agriculture-Agricultural Research Service / University of Nebraska-Lincoln: Faculty Publications

The ability of Spalangia cameroni Perkins, Spalangia endius Walker, and Muscidifurax raptorellus Kogan and Legner to locate and attack stable fly hosts was evaluated under laboratory conditions. Postfeeding third-instar stable fly larvae were released and allowed to pupate in two arena types: large 4.8 liter chambers containing a field-collected, soiled equine bedding substrate; or 120-ml plastic cups containing wood chips. At the time of fly pupariation, parasitoids were released and permitted 72 h to locate and attack hosts. On average, parasitism rates of freely accessible stable fly pupae in cups were not significantly different between parasitoid species. However, parasitism rates …

New Records For The Horse Fly Fauna (Diptera: Tabanidae) Of Jordan With Remarks On Ecology And Zoogeography, Günter Müller, Jerome Hogsette, Edita Revay, Vasiliy Kravchenko, Andrey Leshvanov, Yosef Schlein

United States Department of Agriculture-Agricultural Research Service / University of Nebraska-Lincoln: Faculty Publications

The horse fly fauna (Diptera: Tabanidae) of Jordan is, after Israel, the richest in the Levant, with 24 known species. During the 20-year project “The Ecology and Zoogeography of the Lepidoptera of the Near East,” we regularly collected blood-feeding flies, resulting in 11 additional species of Tabanidae for Jordan. The new records are: Atylotus quadrifarius (Loew, 1874), Chrysops caecutiens (Linnaeus, 1758), Dasyrhamphis nigritus (Fabricius, 1794), Haematopota pallens Loew, 1871, Nemorius irritans (Ricardo, 1901), Philipomyia graeca (Fabricius, 1794), Tabanus cordiger Meigen, 1820, Tabanus taeniola Palisot de Beauvois, 1806, Tabanus quatuornotatus Meigen, 1820, Tabanus separatus Effllatoun, 1930, and Tabanus spectabilis Loew, 1858. …

Vector Competence Of The Stable Fly (Diptera: Muscidae) For West Nile Virus, Michael S. Doyle, Bethany N. Swope, Jerome A. Hogsette, Kristen L. Burkhalter, Harry M. Savage, Roger S. Nasci

United States Department of Agriculture-Agricultural Research Service / University of Nebraska-Lincoln: Faculty Publications

In 2006-2007, stable flies, Stomoxys calcitrans (L.) (Diptera: Muscidae), were suspected of being enzootic vectors of West Nile virus (family Flaviviridae, genus Flavivirus, WNV) during a die-off of American white pelicans (Pelecanus erythrorhynchos Gmelin) (Pelecanidae) in Montana, USA. WNV-positive stable flies were observed feeding en masse on incapacitated, WNV-positive pelicans, arousing suspicions that the flies could have been involved in WNV transmission among pelicans, and perhaps to livestock and humans. We assessed biological transmission by infecting stable flies intrathoracically with WNV and testing them at 2-d intervals over 20 d. Infectious WNV was detected in fly bodies …

Dietary Wheat Germ Oil Influences Gene Expression In Larvae And Eggs Of The Oriental Fruit Fly, Thomas A. Coudron, Chiou Ling Chang, Cynthia L. Goodman, David Stanley

United States Department of Agriculture-Agricultural Research Service / University of Nebraska-Lincoln: Faculty Publications

Changes in animal nutrition, particularly essential dietary components, alter global gene expression patterns. Our goal is to identify molecular markers that serve as early indicators of the quality of insect culture media. Markers of deficient culture media will increase the efficiency of developing optimal systems for mass rearing beneficial insects and some pest species because decisions on culture media quality can be made without waiting through one or several life cycles. The objective of our current study is to discover molecular markers of essential dietary lipid deficiency in the oriental fruit fly, Bactrocera dorsalis. We reared groups of fruit …

Outcrossing And Crossbreeding Recovers Deteriorated Traits In Laboratory Cultured Steinernema Carpocapsae Nematodes, John M. Chaston, Adler R. Dillman, David I. Shapiro-Ilan, Anwar L. Bilgrami, Randy Gaugler, Keith R. Hopper, Byron J. Adams

United States Department of Agriculture-Agricultural Research Service / University of Nebraska-Lincoln: Faculty Publications

The nematode Steinernema carpocapsae infects and kills many pest insects in agro-ecosystems and is commonly used in biocontrol of these pests. Growth of the nematodes prior to distribution for biocontrol commonly results in deterioration of traits that are essential for nematode persistence in field applications. To better understand the mechanisms underlying trait deterioration of the efficacy of natural parasitism in entomopathogenic nematodes, we explored the maintenance of fitness related traits including reproductive capacity, heat tolerance, virulence to insects and ‘tail standing’ (formerly called nictation) among laboratory-cultured lines derived from natural, randomly mating populations of S. carpocapsae. Laboratory cultured nematode …

Carbon Dioxide Fluxes In Corn–Soybean Rotation In The Midwestern U.S.: Inter- And Intra-Annual Variations, And Biophysical Controls, Guillermo Hernandez-Ramirez, Jerry L. Hatfield, Timothy B. Parkin, Thomas J. Sauer, John H. Prueger

United States Department of Agriculture-Agricultural Research Service / University of Nebraska-Lincoln: Faculty Publications

Quantifying carbon dioxide (CO₂) fluxes in terrestrial ecosystems is critical for better understanding of global carbon cycling and observed changes in climate. This study examined year-round temporal variations of CO₂ fluxes in two biennial crop rotations during 4 year of corn (Zea mays L.) and soybean [Glycine max (L.) Merr.] production. We monitored CO₂ fluxes using eddy-covariance (EC) and soil chambers in adjacent production fields near Ames, Iowa. Under the non-limiting soil water availability conditions predominant in these fields, diel and seasonal variations of CO₂ fluxes were mostly controlled by ambient temperature and …

Development Of Simple Sequence Repeat Markers For Chionanthus Retusus (Oleaceae) And Effective Discrimination Of Closely Related Taxa, R. S. Arias, Timothy A. Rinehart, Richard T. Olsen, Joseph H. Kirkbride Jr., Brian E. Scheffler

United States Department of Agriculture-Agricultural Research Service / University of Nebraska-Lincoln: Faculty Publications

The genus Chionanthus (Oleaceae Hoffmans. & Link) includes deciduous or evergreen trees and shrubs distributed widely in tropical and sub-tropical areas, including a few temperate species. Although Chionanthus species are planted as ornamental garden plants and commercialized for natural products, genetic information for Chionanthus spp. is lacking. We created micro satellite-enriched libraries of Chionanthus retusus Lindl. & Paxton, assembled 1072 contigs, and detected 1010 repeats. The frequency of the repeats decreased with the increase in repeat length, and the most abundant motifs were: AG, AC, AAG, ACC, AT, and ACTC. We screened 384 markers on 12 accessions of four related …

Identification Of Wild Apple Germplasm (Malus Spp.) Accessions With Resistance To The Postharvest Decay Pathogens Penicillium Expansum And Colletotrichum Acutatum, W. M. Jurick Ii, W. J. Janisiewicz, R. A. Saftner, I. Vico, V. L. Gaskins, E. Park, P. L. Forsline, G. Fazio, W. S. Conway

United States Department of Agriculture-Agricultural Research Service / University of Nebraska-Lincoln: Faculty Publications

Penicillium expansum and Colletotrichum acutatum cause blue mould and bitter rot of apples during storage which results in significant economic losses. Resistance to these pathogens in commercial apple cultivars has not been documented in the literature. An apple germplasm collection, from the centre of origin in Kazakhstan, is maintained in Geneva, New York. This collection represents a more diverse apple gene pool than commercial cultivars and was evaluated for resistance to the pathogens that cause blue mould and bitter rot. Resistance reactions were skewed towards susceptibility for both fungi and comprised the majority of accessions examined. However, resistance to P. …

Spatial Ramifications Of Crop Selection: Water Quality And Biomass Energy, M. P. Russelle, D. W. Kelley, A. S. Birr, D. C. Tiffany

United States Department of Agriculture-Agricultural Research Service / University of Nebraska-Lincoln: Faculty Publications

The use of GIS in concert with simple or complex simulation modeling provides an unparalleled way to generate new data and to help a variety of audiences understand spatial patterns of data. From improved understanding, policy incentives can be crafted to reduce adverse environmental impacts of agricultural production at lower costs than would be necessary otherwise. In this chapter, two case studies demonstrate how GIS and modeling can be used to understand how crop selection and soils interact to effect environmental outcomes across an agricultural landscape. We addressed the needs of two distinctly different audiences: (1) a public drinking water …