Digital Commons Network^™

Triticum Mosaic Virus Exhibits Limited Population Variation Yet Shows Evidence Of Parallel Evolution After Replicated Serial Passage In Wheat, Melissa S. Bartels, Roy French, Robert A. Graybosch, Satyanarayana Tatineni

Department of Plant Pathology: Faculty Publications

An infectious cDNA clone of Triticum mosaic virus (TriMV) (genus Poacevirus; family Potyviridae) was used to establish three independent lineages in wheat to examine intra-host population diversity levels within protein 1 (P1) and coat protein (CP) cistrons over time. Genetic variation was assessed at passages 9, 18 and 24 by single-strand conformation polymorphism, followed by nucleotide sequencing. The founding P1 region genotype was retained at high frequencies in most lineage/passage populations, while the founding CP genotype disappeared after passage 18 in two lineages.We found that rare TriMV genotypes were present only transiently and lineages followed independent evolutionary trajectories, …

Foliar Fungicide Application Timing For Disease Management, Stay Green, And Yield In Nebraska, 2015, J. D. Harbour, T. A. Jackson-Ziems

Department of Plant Pathology: Faculty Publications

The objective of the trial was to compare foliar fungicides applied at different corn growth stages for gray leaf spot (GLS) and southern rust (SR) efficacy. Irrigated corn was grown based on Nebraska Extension irrigation recommendations at the South Central Ag Lab near Clay Center, NE. Soils were a silt loam with 6.7 pH and 1.8 % organic matter, and the previous crop was soybean. Reduced tillage was performed to the field prior to planting. Corn (DKC 65-79 RIB, tolerant to GLS) was planted at approximately 34,000 seed/A on 26 May, which is later than normal, due to wet spring …

Foliar Fungicide Modes Of Action For Southern Rust Management, Push Lodging, And Yield In Nebraska, 2015, J. D. Harbour, T. A. Jackson-Ziems

Department of Plant Pathology: Faculty Publications

The objective of the trial was to compare foliar fungicides with different modes of action for southern rust (SR) efficacy. Irrigated corn was grown based on Nebraska Extension irrigation recommendations at the South Central Ag Lab near Clay Center, NE. Soils were a silt loam with 6.7 pH and 1.8 % organic matter, and the previous crop was soybean. Reduced tillage was performed to the field prior to planting. Corn (DKC 65-79 RIB, tolerant to gray leaf spot (GLS)) was planted at approximately 34,000 seed/A on 26 May. Eight treatments were arranged in a randomized complete block design with six …

Deposition Aid Adjuvants Plus A Fungicide For Southern Rust Management, Stay Green, Push Lodging, And Yield Comparisons In Field Corn In Nebraska, 2015, J. D. Harbour, T. A. Jackson-Ziems

Department of Plant Pathology: Faculty Publications

The objective of the trial was to compare foliar fungicides for southern rust (SR) efficacy. Irrigated corn was grown based on Nebraska Extension irrigation recommendations at the South Central Ag Lab near Clay Center, NE. Soils were a silt loam with 6.7 pH and 1.8 % OM and the previous crop was soybean. Reduced tillage was performed to the field prior to planting. Corn (DKC 65-79 RIB, tolerant to gray leaf spot (GLS)) was planted at approximately 34,000 seed/A on 26 May. Eleven treatments were arranged in a randomized complete block design with six replications. . . . Phytotoxicity was …

Root-Lesion Nematodes, T. A. Jackson-Ziems

Department of Plant Pathology: Faculty Publications

Root-lesion nematodes, Pratylenchus spp., are among the most commonly encountered plant-parasitic nematodes, with one or more species occurring in almost every field. Their small size (0.4-0.7 mm long) relative to most other plant-parasitic nematodes enables them to survive in almost any soil texture. Their wide host range and distribution make them one of the most damaging nematodes worldwide, ranging from cool temperate to tropical environments. At least eight species of root-lesion nematodes have been associated with sunflower.

Root-Knot Nematodes, T. A. Jackson-Ziems

Department of Plant Pathology: Faculty Publications

Root-knot nematodes, Meloidogyne spp., are some of the most damaging plant pathogens. Several of the most common species of root-knot nematodes have been confirmed to reproduce and cause damage on sunflower, including M. arenaria, M. hapla, M. incognita, M. javanica, and M. hispanica.

Meloidogyne spp. occur worldwide but are especially common in temperate, subtropical, and tropical regions. Countries where Meloidogyne spp. have been confirmed to affect sunflower include the United States and the African nations of Egypt, Mozambique, South Africa, and Zambia. Root-knot nematodes tend to cause the most damage to plants grown in sandy …

Northern Corn Leaf Blight, Tamra A. Jackson-Ziems

Department of Plant Pathology: Faculty Publications

Northern corn leaf blight (NCLB) is a disease of corn caused by a fungus, Exserohilum turcicum (sexual stage Setosphaeria turcica). Its development is favored by cool to moderate temperatures and high relative humidity. Historically, NCLB has been more common and severe in states in the eastern Corn Belt, but its incidence has increased in Nebraska and the western Corn Belt in recent years. The disease is distributed throughout most of the corn-growing areas of the United States. The disease also occurs sporadically throughout other humid corn-producing areas of the world. In Nebraska, the disease has been most serious in …

Identification Of Erwinia Rhapontici As The Causal Agent Of Crown And Shoot Rot And Pink Seed Of Pea In Nebraska, Anthony O. Adesemoye, Hsin-Ho Wei, Robert M. Harveson

Department of Plant Pathology: Faculty Publications

Over the last five years, the production of dry yellow peas (Pisum sativum L.) has been increasing in Nebraska and other areas of the Central High Plains, according to a USDA report (Jasa 2013). Dry pea is a short-season crop with a low water requirement, making it a good rotational crop for the high plains. We have noted bacterial pathogens, potentially a disease complex, that may negatively impact the production of pea in this region, and one of the emerging pathogens is Erwinia rhapontici. This pathogen is a gram-negative bacterium that has been reported from soil, seed, and …

Transcriptome Profiling Of Buffalograss Challenged With The Leaf Spot Pathogen Curvularia Inaequalis, Bimal S. Amaradasa, Keenan Amundsen

Department of Plant Pathology: Faculty Publications

Buffalograss (Bouteloua dactyloides) is a low maintenance U. S. native turfgrass species with exceptional drought, heat, and cold tolerance. Leaf spot caused by Curvularia inaequalis negatively impacts buffalograss visual quality. Two leaf spot susceptible and two resistant buffalograss lines were challenged with C. inaequalis. Samples were collected from treated and untreated leaves when susceptible lines showed symptoms. Transcriptome sequencing was done and differentially expressed genes were identified. Approximately 27 million raw sequencing reads were produced per sample. More than 86% of the sequencing reads mapped to an existing buffalograss reference transcriptome. De novo assembly of unmapped reads …

Morphological And Molecular Characterization Of Gracilacus Wuae N. Sp. (Nematoda: Criconematoidea) Associated With Cow Parsnip (Heracleum Maximum) In Ontario, Canada, Qing Yu, Weimin Ye, Thomas O. Powers

Department of Plant Pathology: Faculty Publications

Gracilacus wuae n. sp. from soil associated with cow parsnip in Ontario, Canada is described and illustrated. Morphologically, females have a long stylet ranging from 80 to 93 mmlong, the lip region not offset from the body contour, without lateral lips but with large and flat submedian lobes, the mouth opening slit-like elongated laterally and surrounded by lateral flaps, the excretory pore is anterior to the knobs of the stylet; males without stylet and the pharynx degenerated. The fourth-stage juveniles lack a stylet, the pharynx degenerated, and can be differentiated into preadult females and males based on the position of …

Composting Swine Manure From High Rise Finishing Facilities, Edwin L. Ritchey, Kim Cook

Plant and Soil Sciences Research Report

Swine production has restructured considerably in recent years with increased production on fewer farms (Key et al., 2011). Most swine production facilities manage manure in liquid form either in deep pits underneath production facilities or in lagoons adjacent to the production facilities (Key et al., 2011). This management uses water to rinse manure from the facilities, which dilutes the nutrient concentration and value of the manure. The liquid forms are applied to land through irrigation systems or by liquid manure spreaders. Liquid manure management can have some operational constraints that composting eliminates (Bernal et al., 2009). The most common issue …

Evaluation Of Hazelnuts As A Sustainable Crop In Illinois, Sharon Neva Dubosky

Masters Theses

Production of hazelnuts has historically been limited to regions with mild climates, with almost all hazelnut production in the United States occurring in Oregon. A recent boom in demand, along with an expanded selection of varieties with improved environmental tolerances, has pushed hazelnut production into new regions. Hazelnut production could prove profitable in areas of the Midwest that are less well-suited to the cultivation of maize and soybeans. However, the lack of varieties proven to thrive in the climatological conditions of this region (cold winters, hot summers, frequent drought) presents a barrier to the viability of hazelnut production. A trial …

Prospects Of Genomic Prediction In The Usda Soybean Germplasm Collection: Historical Data Creates Robust Models For Enhancing Selection Of Accessions, Diego Jarquin, James Specht, Aaron Lorenz

Department of Agronomy and Horticulture: Faculty Publications

The identification and mobilization of useful genetic variation from germplasm banks for use in breeding programs is critical for future genetic gain and protection against crop pests. Plummeting costs of next-generation sequencing and genotyping is revolutionizing the way in which researchers and breeders interface with plant germplasm collections. An example of this is the high density genotyping of the entire USDA Soybean Germplasm Collection. We assessed the usefulness of 50K SNP data collected on 18,480 domesticated soybean (G. max) accessions and vast historical phenotypic data for developing genomic prediction models for protein, oil, and yield. Resulting genomic prediction models explained …

Corn (Zea Mays L.) Seeding Rate Optimization In Iowa, Usa, Mark A. Licht, Andrew W. Lenssen, Roger W. Elmore

Department of Agronomy and Horticulture: Faculty Publications

Collecting soil, topography, and yield information has become more feasible and reliable with advancements in precision technologies. Combined with the accessibility of precision technologies and services to farmers, there has been increased interest and ability to make site-specific crop management decisions. The objective of this research was to develop procedures to optimize corn seeding rates and maximize yield using soil and topographic parameters. Experimental treatments included five seeding rates (61 750; 74 100; 86 450; 98 800; and 111 150 seeds ha^-1) in a randomized complete block design in three central Iowa fields from 2012 to 2014 (nine …

Distribution And Characterization Of The Soybean Cyst Nematode, Heterodera Glycines (Hg) Types In South Dakota, Krishna Acharya

Electronic Theses and Dissertations

The soybean cyst nematode (SCN), Heterodera glycines Ichinohe, is an endoparasitic nematode and one of the major pests of soybean (Glycine max L.) in the United State and all over the world where soybean is grown. SCN is ranked first among the biological factors that cause yield loss in soybean. The estimated yield loss by this nematode is $1b annually in the United States alone. SCN is thought to have been first found in China. It was first identified in the United States in 1954 in North Carolina and in South Dakota in 1995. To date, SCN continues to spread …

Comparison Of Pea Seed Germination Due To Manipulation Of Soil Conditions, Ariel M. Kershner

Faculty Curated Undergraduate Works

This experiment was done with the intent to understand optimal soil conditions for pea seed germination. We investigated this using three soil conditions – 100% potting soil, 50% potting soil/50% sand, and 100% sand. Seemingly healthy pea seeds were planted and observed over five weeks. We measured both the total number of sprouts per week and the combined weight of the plants and seeds per condition before planting and after uprooting. We expected to find that the 100% potting soil condition would germinate the best, resulting in the most sprouts and heaviest weight of the condition’s seeds and plants. This …

Quantitative Trait Loci (Qtl) Analysis Of Sulfur Sensitivity In Vitis Aestivalis-Derived 'Norton', Logan Michael Duncan

Graduate Theses/Dissertations

The grape and wine industry relies heavily on sulfur and sulfur containing compounds to control the fungal disease powdery mildew (PM). Sulfur dioxide induces large-scale transcriptomic modification in the Eurasian grape species Vitis vinifera with little to no phytotoxicity. However, genetic factors contributing to sulfur sensitivity, characterized by vegetative necrosis and defoliation, remain undefined in North American grape species and their commercial hybrids. A mapping population, consisting of 147 F1 genotypes, was created by crossing V. aestivalis-derived ‘Norton’ and V. vinifera ‘Cabernet Sauvignon’ to identify the genetic basis for sulfur sensitivity in North American wine grapes. Clonally propagated F1 genotypes …

Response Of Soil And Water Quality To Winter Manure Application From Small Agricultural Watersheds In South Dakota, Shikha Singh

Electronic Theses and Dissertations

The extreme winter conditions prevailing in the state of South Dakota make it difficult for the livestock producers to manage the manure generated at the farm. The South Dakota Department of Environmental and Natural Resources does not recommend manure application in the state during the winter months when the ground is frozen. Thus, producers are left with the options such as storing the manure over a longer period until summer or spreading on snow or frozen ground. Storing manure for longer duration leads to increased risks of concentrated spills into the streams. Thus, it is important to develop management strategies …

Soybean Yield And Plant Response To Phosphorus Fertilization, Rebecca L. Helget

Electronic Theses and Dissertations

Phosphorus (P) is a key limiting nutrient for soybean production in South Dakota. Soil tests have been used as a baseline indicator for plant available P and fertilizer recommendations for over a century. Plant nutrient analysis may be used to complement a soil test as a way to validate fertilizer and management practices. Soybean nutrient sufficiency ranges have only been slightly adjusted since they were published in the 1960’s. The objectives of this study were to update the soil test P and soybean plant P sufficiency level in South Dakota and to recognize implications of improper plant sampling. We also …

Role Of Silencing Rna Fgsir34 In Fusarium Graminearum's Pathogenicity To Wheat, Subha Dahal

Electronic Theses and Dissertations

Fusarium graminearum is an ascomycetous fungal pathogen that causes Fusarium head blight (FHB) disease in wheat and other cereal grains. Mycotoxin produced by the fungus, predominantly deoxynivalenol (DON), is considered as an important virulence factor for the spread of disease. Our previous study of a Dicer-like 2 knockdown mutant has led to our hypothesis that a silencing RNA, fgsiR34, might play a key role in regulating DON biosynthesis and some other virulent factors. To test this hypothesis, we generated an fgsiR34 over-expressing mutant (ΔfgsiR34+) using Inverse Repeat Transgene method and studied the pathogenicity of the mutant in …

Root Rot Pathogens Of Wheat In South Dakota And Their Affect On Seed Germination And Seedling Blight In Spring Wheat Cultivars, Navjot Kaur

Electronic Theses and Dissertations

Crown rot and common root rot are the important root diseases in wheat (Triticum aestivum L.) and other cereals causing significant germination and yield losses in the Northern Great Plains and other parts of the world. Bipolaris sorokiniana (Bs) and Fusarium graminearum (Fg) cause common root rot and crown rot respectively, are the important wheat root pathogens that can affect seed germination, seedling establishment and impact crop productivity. A survey was conducted in the year 2014 and 2015 to study the distribution and the prevalence of root rot pathogens in South Dakota. Out of 31 and eight roots samples …

Senescence Of Native Perennial Warm Season Grasses Senescence Associated Switchgrass Transcriptome, Michaellong Tran

Electronic Theses and Dissertations

Senescence of perennial crops enable continuous harvests after one sowing event. Perennials senesce at adapted rates of their native environments; however, early senescencing crops do not maximize the growing season as nutrient reallocation takes precedence. Chlorophyll degradation and nitrogen reallocation was observed to occur rapidly between mid to late September. Transcriptome analysis on early and late senescencing switchgrass cultivars reveals upregulation of starch metabolism, light reactions, Calvin-Benson Cycle, and anthocyanin synthesis in late senescencing switchgrass. Morphological variations between the two germplasms prolong the growing season of late senescencing switchgrass, maximizing yield. Expression of mRNA as senescence progresses and between the …

Corncob Grit Application As An Alternative To Control Weeds In Two Crop Production Systems, Mauricio Erazo-Barradas

Electronic Theses and Dissertations

Weed management is one of the most challenging production problems in organic cropping systems because of limited weed control methods. Grits, derived from agricultural residues, have been demonstrated to control weed seedlings selectively in corn. This research examined weed efficacy and crop yield of an integrated air-propelled abrasive corncob grit (for in-row weed control) at varying timings and frequencies and flame-weeding or cultivation (for between-row weed control) system in two corn production systems. In the first study efficacy of weed control was assessed with this approach in an organic corn silage production system established in Morris, MN in 2013 and …

Effect Of Endophytes In Physcomitrella Patens On Cellular Respiration During Abiotic Stress, Michael Danh

Undergraduate Honors Thesis Collection

Endophytes are bacteria or fungi that ubiquitously reside in plant tissue and do not cause apparent disease. With the mutually symbiotic relationships between plant and endophyte being scientifically evident, it is supported that endophytes provide an augmentative method to absorb nutrients and additional tolerance under abiotic stress for the plant while benefiting from the host plant’s reduced carbon sources. The moss Physcomitrella patens is expected to share the same type of mutualism with endophytes, being able to treat endophytes as endosymbionts and having a reduced carbon reservoir. However, it is unclear if these endophytic relationships alter under abiotic stress. In …

The Role Of Calcium In Pathogen Defense Responses In The Moss Mnium Cuspidatum, Morgan Blake

Undergraduate Honors Thesis Collection

When exposed to stress, whether that be by pathogen, thermal or weather changes, or other components of the environment, plants employ a variety of defense mechanisms depending on the severity of the stress. When attacked by a pathogen, the moss Mnium cuspidatum utilizes an innate, basal response followed by hypersensitive response (HR) and systemic acquired resistance (SAR). Calcium is known to be involved in signaling cascades that mediate defense responses in other organisms. In the present study, lanthanum nitrate (LaNO3), methoxyerapamil (D600), and ethylene glycol tetraacetic acid (EGTA) were used to inhibit the presence of calcium in M. cuspidatum in …

High And Dry: Post-Fire Tree Seedlingestablishment In Subalpine Forestsdecreases With Post-Fire Drought Andlarge Stand-Replacing Burn Patches, Brian J. Harvey, Daniel C. Donato, Monica G. Turner

Aspen Bibliography

Aim: Climate warming and increased wildfire activity are hypothesized to catalyse biogeographical shifts, reducing the resilience of fire-prone forests world-wide. Two key mechanisms underpinning hypotheses are: (1) reduced seed availability in large stand-replacing burn patches, and (2) reduced seedling establishment/survival after post-fire drought. We tested for regional evidence consistent with these mechanisms in an extensive fire-prone forest biome by assessing post-fire tree seedling establishment, a key indicator of forest resilience.

Location: Subalpine forests, US Rocky Mountains.

Methods: We analysed post-fire tree seedling establishment from 184 field plots where stand-replacing forest fires were followed by varying post-fire climate conditions. Generalized linear …

Aspergillus And Aflatoxin In Groundnut (Arachis Hypogaea L.) And Groundnut Cake In Eastern Ethiopia, Abdi Mohammed, Alemayehu Chala, Mashilla Dejene, Chemeda Fininsa, David A. Hoisington, Victor S. Sobolev, R. S. Arias

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

This study was conducted to assess major Aspergillus species and aflatoxins associated with groundnut seeds and cake in Eastern Ethiopia and evaluate growers’ management practices. A total of 160 groundnut seed samples from farmers’ stores and 50 groundnut cake samples from cafe and restaurants were collected. Fungal isolation was done from groundnut seed samples. Aspergillus flavus was the dominant species followed by Aspergillus parasiticus. Aflatoxin analyses of groundnut seed samples were performed using ultra performance liquid chromatography; 22.5% and 41.3% of samples were positive, with total aflatoxin concentrations of 786 and 3135 ng g⁻¹ from 2013/2014 and 2014/2015 …

The Effect Of Adjuvants On Apple Disease Management, Chelsi Patricia Abbott

Open Access Theses

The management of common apple diseases such as apple scab ( Venturia inaequalis) and bitter rot (Colletotrichum spp.) relies heavily on effective fungicide applications. However, the development of fungicide resistance to newer fungicides has resulted in management failures and significant economic losses. This has led to a greater reliance on captan, an older fungicide, because there is a low risk of pathogens developing resistance. Label restrictions limit growers to 18 kg of captan per season, which may not provide sufficient control of both apple scab and bitter rot in wet years. Consequently, apple growers are faced with two …

Construction Of High Resolution Genetic Linkage Maps To Improve The Soybean Genome Sequence Assembly Glyma1.01, Qijian Song, Jerry Jenkins, Gaofeng Jia, David L. Hyten, Vince Pantalone, Scott A. Jackson, Jeremy Schmutz, Perry B. Cregan

Department of Agronomy and Horticulture: Faculty Publications

Background: A landmark in soybean research, Glyma1.01, the first whole genome sequence of variety Williams 82 (Glycine max L. Merr.) was completed in 2010 and is widely used. However, because the assembly was primarily built based on the linkage maps constructed with a limited number of markers and recombinant inbred lines (RILs), the assembled sequence, especially in some genomic regions with sparse numbers of anchoring markers, needs to be improved. Molecular markers are being used by researchers in the soybean community, however, with the updating of the Glyma1.01 build based on the high-resolution linkage maps resulting from this research, …

Genome-Wide Discriminatory Information Patterns Of Cytosine Dna Methylation, Robersy Sanchez, Sally A. Mackenzie

Department of Agronomy and Horticulture: Faculty Publications

Cytosine DNA methylation (CDM) is a highly abundant, heritable but reversible chemical modification to the genome. Herein, a machine learning approach was applied to analyze the accumulation of epigenetic marks in methylomes of 152 ecotypes and 85 silencing mutants of Arabidopsis thaliana. In an information-thermodynamics framework, two measurements were used: (1) the amount of information gained/lost with the CDM changes I_R and (2) the uncertainty of not observing a SNP LC_R. We hypothesize that epigenetic marks are chromosomal footprints accounting for different ontogenetic and phylogenetic histories of individual populations. A machine learning approach is proposed to …