Agriculture Commons^™

Nucleotide Polymorphism And Copy Number Variant Detection Using Exome Capture And Next-Generation Sequencing In The Polyploid Grass Panicum Virgatum, Joseph Evans, Jeongwoon Kim, Kevin L. Childs, Briaenne Vaillancourt, Emily Crisovan, Aruna Nandety, Daniel J. Gerhardt, Todd A. Richmond, Jeffery A. Jeddeloh, Shawn M. Kaeppler, Michael D. Casler, C Robin Buell

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

Switchgrass (Panicum virgatum) is a polyploid, outcrossing grass species native to North America and has recently been recognized as a potential biofuel feedstock crop. Significant phenotypic variation including ploidy is present across the two primary ecotypes of switchgrass, referred to as upland and lowland switchgrass. The tetraploid switchgrass genome is approximately 1400 Mbp, split between two subgenomes, with significant repetitive sequence content limiting the efficiency of re-sequencing approaches for determining genome diversity. To characterize genetic diversity in upland and lowland switchgrass as a first step in linking genotype to phenotype, we designed an exome capture probe set based on transcript …

Complete Genome Sequence Of Mycobacterium Avium Subsp. Paratuberculosis, Isolated From Human Breast Milk, John Bannantine, Lingling Li, Michael M. Mwangi, Rebecca Cote, Juan Antonio Raygoza Garay, Vivek Kapur

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

Mycobacterium avium subsp. paratuberculosis causes Johne’s disease (JD) in cattle, sheep, goats, and other ruminant animals. JD presents as a chronic granulomatous intestinal infection with a worldwide distribution and imposes a significant economic toll on livestock industries (1). M. avium subsp. paratuberculosis has a complex cell wall structure containing mycolic acids and several lipids similar to those of other members of this genus, yet it is the most slowly growing member. This bacterium often requires 8 to 16 weeks before colonies are visible in culture, which is a major hurdle in diagnostics and therefore in the implementation of optimal JD …

Draft Genome Sequence Of A Mycobacterium Avium Complex Isolate From A Broadbill Bird, John Bannantine, Darrell O. Bayles, Suelee Robbe-Austerman, Angela M. Burrell, Judith R. Stabel

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

Mycobacterium avium complex (MAC) organisms cause opportunistic infections in humans, yet their epidemiology remains poorly understood. They are slowly growing environmental and animal-associated mycobacteria that have little notoriety except for the strains that cause disseminated infections in HIV- infected humans (1). Most MAC organisms are classified taxonomically as a single species, M. avium, which is divided into at least four subspecies, M. avium subsp. avium, M. avium subsp. hominissuis, M. avium subsp. paratuberculosis, and M. avium subsp. silvaticum (2). The only other species in this group is M. intracellulare. Genotyping of this diverse bacterial group has been achieved using intergenic …

Water Demand On Center-Pivot Irrigated Crops In Alabama, Robert Rossell

Summer Community of Scholars Posters (RCEU and HCR Combined Programs)

No abstract provided.

2014 Weed Science Research Report – Tan Section, Ndsu Weed Science, Dept. Of Plant Sciences

Plant Sciences Weed Science Reports

The Weed Science team at North Dakota State University conduct field research in the State of North Dakota. This specific document reports on field research conducted in 2014. It includes work on several adjuvants, spray volume and the management of several weeds in North Dakota.

2014 Weed Science Research Report – Blue Section, Ndsu Weed Science, Dept. Of Plant Sciences

Plant Sciences Weed Science Reports

The Weed Science team at North Dakota State University conduct field research in the State of North Dakota. This specific document reports on field research conducted in 2014. It includes work on corn, soybean and the management of several weeds in North Dakota.

2014 Weed Science Research Report – Gold Section, Ndsu Weed Science, Dept. Of Plant Sciences

Plant Sciences Weed Science Reports

The Weed Science team at North Dakota State University conduct field research in the State of North Dakota. This specific document reports on field research conducted in 2014. It includes work on sugarbeet and the management of several weeds in North Dakota.

2014 Weed Science Research Report – Green Section, Ndsu Weed Science, Dept. Of Plant Sciences

Plant Sciences Weed Science Reports

The Weed Science team at North Dakota State University conduct field research in the State of North Dakota. This specific document reports on field research conducted in 2014. It includes work on small grains and the management of several weeds in North Dakota.

2014 Weed Science Research Report – Yellow Section, Ndsu Weed Science, Dept. Of Plant Sciences

Plant Sciences Weed Science Reports

The Weed Science team at North Dakota State University conduct field research in the State of North Dakota. This specific document reports on field research conducted in 2014. It includes work on several minor crops and the management of several weeds in North Dakota.

2014 Weed Science Research Report – White Section, Ndsu Weed Science, Dept. Of Plant Sciences

Plant Sciences Weed Science Reports

The Weed Science team at North Dakota State University conduct field research in the State of North Dakota. This specific document provides environmental, indexes, abbreviations and collaborators in 2014.

Mapping The Low Palmitate Fap1 Mutation And Validation Of Its Effects In Soybean Oil And Agronomic Traits In Three Soybean Populations, Andrea J. Cardinal, Rebecca Whetten, Sanbao Wang, Jérôme Auclair, D. L. Hyten, P. B. Cregan, Eleni Bachlava, Jason Gillman, Martha Ramirez, Ralph Dewey, Greg Upchurch, Lilian Miranda, Joesph W. Burton

Department of Agronomy and Horticulture: Faculty Publications

Soybean oil with reduced palmitic acid content is desirable to reduce the health risks associated with consumption of this fatty acid. The objectives of this study were: to identify the genomic location of the reduced palmitate fap1 mutation, determine its molecular basis, estimate the amount of phenotypic variation in fatty acid composition explained by this locus, determine if there are epistatic interactions between the fap1 and fap_nc loci and, determine if the fap1 mutation has pleiotropic effects on seed yield, oil and protein content in three soybean populations. This study detected two major QTL for 16:0 content located in …

Estimating The Frequency Of Cry1f Resistance In Field Populations Of The European Corn Borer (Lepidoptera: Crambidae), Blair D. Siegfried, Murugesan Rangasamy, Haichuan Wang, Terence A. Spencer, Chirakkal V. Haridas, Brigitte Tenhumberg, Douglas V. Sumerford, Nicholas P. Storer

School of Biological Sciences: Faculty Publications

Background: Transgenic corn hybrids that express toxins from Bacillus thuringiensis (Bt) have suppressed European corn borer populations and reduced the pest status of this insect throughout much of the US corn belt. A major assumption of the high-dose/refuge strategy proposed for insect resistance management and Bt corn is that the frequency of resistance alleles is low so that resistant pests surviving exposure to Bt corn will be rare. Results: The frequency of resistance to the Cry1F Bt toxin was estimated using two different screening tools and compared with annual susceptibility monitoring based on diagnostic bioassays and LC_{50 …}

Discovery: The Student Journal Of Dale Bumpers College Of Agricultural, Food And Life Sciences - Volume 15 2014, Several Authors

Discovery, The Student Journal of Dale Bumpers College of Agricultural, Food and Life Sciences

No abstract provided.

Soil Microbial Community Distributions And Disease Suppressiveness In The Coastal Plain Of Georgia, Michael J. Sabula

College of Graduate Studies: Theses & Dissertations

This study compared the soil microbial communities of three vegetation types in the coastal plain of Georgia: 1. crop land actively in use for agricultural production, 2. transitional grassland in early stages of secondary succession, and 3. pristine unmanaged forest land. Microbial species diversity and quantities of microbial DNA were determined from each of these vegetation types at three separate locations near Statesboro, Georgia. Length heterogeneity PCR(LH-PCR) methods and subsequent analysis of fungal, bacterial, and metazoan communities by analysis of similarity (ANOSIM) revealed high within-group similarity by vegetation type, indicating land management intensity and vegetation cover is a strong determining …

Evaluation Of Soilless Media Sensors For Managing Winter-Time Greenhouse Strawberry Production Using A Capmat System, George E. Meyer, Ellen T. Paparozzi, Stacy A. Adams, Diego Scacalossi Voltan

Department of Agronomy and Horticulture: Faculty Publications

It is important for a greenhouse strawberry grower to know that their capillary mat (CapMat™) fertigation system is working correctly and that plants are receiving the correct amounts of water and fertilizer. Pots with soilless mix are not expected to hold more than 70% water on a volumetric basis. Pots with less than 40% water content continuously are not supplied enough water and nutrients to the plants. Typically, pots located near the manifold distribution system get a little more water than those at the other locations, but water use will really vary according to the factors listed above as well …

Tall Fescue Ergovaline Concentration Based On Sample Handling And Storage Method, Krista La Moen Lea

Theses and Dissertations--Plant and Soil Sciences

Ergovaline is produced by the endophyte Neotyphodium coenophialum (Morgan-Jones and Gams) in tall fescue (Schedonorus arundinacea (Schreb.) Dumort. = Festuca arundinacea Schreb.) and is blamed for a multitude of costly livestock disorders. Testing of pastures is common in both research and on farm situations. Since ergovaline is known to be unstable and affected by many variables, the objective of this study was to determine the effect of sample handling and storage on the stability of this compound. Homogeneous milled tall fescue sub-samples were analyzed for ergovaline concentration using HPLC after a range of sample handling procedures or storage. Ergovaline …

Fusarium Head Blight Resistance And Agronomic Performance In Soft Red Winter Wheat Populations, Daniela Sarti Dvorjak

Theses and Dissertations--Plant and Soil Sciences

Fusarium head blight (FHB), caused by Fusarium graminearum Schwabe [telomorph: Gibberella zeae Schwein.(Petch)], is recognized as one of the most destructive diseases of wheat (Triticum aestivum L. and T. durum L.) and barley (Hordeum vulgare L.) worldwide. Breeding for FHB resistance must be accompanied by selection for desirable agronomic traits. Donor parents with two FHB resistance quantitative trait loci (QTL) Fhb1 (chromosome 3BS) and QFhs.nau-2DL (chromosome 2DL) were crossed to four adapted SRW wheat lines to generate backcross and forward cross progeny. F₂ individuals were genotyped and assigned to 4 different groups according to presence/ absence of …

Switchgrass Yield And Quality With Multiple Fertilizer Applications And Harvest Dates, Thomas Clarkson Keene

Theses and Dissertations--Plant and Soil Sciences

Switchgrass (Panicum virgatum L.) is an important native warm-season grass for biomass and forage production in the U.S. This research determined the effect of fertilizer type (conventional, manure, and biosolids) and rate on switchgrass biomass yield and forage quality. Fertilizers were added at 0, 33, 67, 100, and 134 kg N ha^-1 on established stands of ‘Kanlow’ switchgrass in three northeastern Kentucky counties. Soils across sites ranged from recently cleared forestland (low pH, P, and K) to productive cropland (high pH, P and K). Stands were sampled for forage nutritive value in June, simulating a hay harvest. Nutritive …

Plant Growth Regulators And Herbicides For Management Of Poa Annua: Impact Of Biotypes And Behavior Of Flurprimidol In Turfgrass Species, Alexandra Perseveranda Williams

Theses and Dissertations--Plant and Soil Sciences

In 2011, Poa annua L. (Poa) biotypes were collected from greens of two golf courses in Lexington, Kentucky: 1.) The Lexington Country Club (LCC) and 2.) The University Club (UC). The samples were collected based on exhibiting one of two appearances while on the same green: 1.) dark green, with few to no flower heads (dark biotype) or 2.) light green, with numerous flower heads (light biotype). Two PGRs, paclobutrazol and flurprimidol, and two herbicides, bispyribac-sodium and amicarbazone, were applied to the plants both in the field and the greenhouse. Quality ratings were recorded weekly in both the …

C And N Cycling Dynamics And Microbial Community Composition In High Tunnel Production Systems, Kavita Lakshmi Mizin

Theses and Dissertations--Plant and Soil Sciences

Across the United States, high tunnels are used as a means of season extension and control over climatic variability in fruit and vegetable production. However, high tunnel systems are an intensive form of agricultural production which may compromise soil and crop quality over time. This study examined the effects of the varying environmental conditions, created in two types of tunnel system, movable and stationary, on the flow of nitrogen from amendment to plant and impact on crop and soil quality parameters. The way nutrients cycled through these systems was different and the nutrient treatments had no consistent effects on soil …

The Influence Of Tall Fescue Cultivar And Endophyte Status On Root Exudate Chemistry And Rhizosphere Processes, Jingqi Guo

Theses and Dissertations--Plant and Soil Sciences

Tall fescue (Lolium arundinaceum (Schreb.) Darbysh.) is a cool-season perennial grass used in pastures throughout the Southeastern United States. The grass can harbor a fungal endophyte (Epichloë coenophiala) thought to provide the plant with enhanced resistance to biotic and abiotic stress. However, the alkaloids produced by the common variety of the endophyte cause severe animal health issues resulting in a considerable amount of research focused on eliminating the toxic class of alkaloids while retaining the positive abiotic and biotic stress tolerance attributes of the other alkaloids. In doing so, very little attention has been paid to the …

Screening Of Mycobacterium Avium Subsp. Paratuberculosis Mutants For Attenuation In A Bovine Monocyte-Derived Macrophage Model, Elise A. Lamont, Adel M. Talaat, Paul M. Coussens, John Bannantine, Yrjo T. Grohn, Robab Katani, Ling-Ling Li, Vivek Kapur, Srinand Sreevatsan

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

Vaccination remains a major tool for prevention and progression of Johne’s disease, a chronic enteritis of ruminants worldwide. Currently there is only one licensed vaccine within the United States and two vaccines licensed internationally against Johne’s disease. All licensed vaccines reduce fecal shedding of Mycobacterium avium subsp. paratuberculosis (MAP) and delay disease progression. However, there are no available vaccines that prevent disease onset. A joint effort by the Johne’s Disease Integrated Program (JDIP), a USDA-funded consortium, and USDA—APHIS/VS sought to identify transposon insertion mutant strains as vaccine candidates in part of a three phase study. The focus of the Phase …

Implementing Green Roofs On Movie Theaters And Shopping Centers: Business Cases In Profitable Sustainability, Ryan J. Miller

Pomona Senior Theses

This thesis presents the business case for installing green roofs on movie theaters and shopping centers. These businesses can then derive increased profits from the environmental benefits of reduced energy use and increased stormwater retention. After presenting the basic design and benefits of a green roof, the thesis develops stand-alone business plans for a movie theater and shopping center. The author finds that green roofs are a profitable sustainability solution for the commercial enterprise.

Growing South Dakota (Winter 2014), College Of Agriculture &. Biological Sciences

Growing South Dakota (Publication of the College of Agriculture, Food and Environmental Sciences)

This issue contains the 2013 SDSU Agricultural Experiment Station Annual Report

[Page] 2 The World’s First: Collaborative Effort Produces Multi-Hybrid Planter To Advance Precision Ag
[Page] 4 70 Years Of Data: Ranchers Benefit From Long-Term Grazing Studies
[Page] 6 Better Beef: Fetal Programming Study Analyzes Effects Of Cow Nutrition On Meat Quality
[Page] 7 Winter College News
[Page] 8 Consumer Sciences, Animal Health, Livestock Marketing: Important Research Continues In These Areas
[Page] 10 Improving Human Health: Role Of Nondigestible Fiber, Antioxidants Studied To Prevent Disease
[Page] 11 Food Safety Focus: Targeting Heat-Resistant Microbes To Improve Dairy Products
[Page] 12 Engineering …

Estimating U.S. Household Seafood Demand Based On Longitudinal And Cross-Sectional Data, Huabo Wang

LSU Doctoral Dissertations

This overall goal of this research is to examine and update U.S. at-home household demand estimates for seafood (including species and generic products) that can be used in policy formulation (by both the private and public sector). As such, this study estimated quantity-based household demand functions for seafood in aggregate, by generic product form (fresh, frozen, and prepared), and primary species. Given that the role of quality has been shown to significantly influence expenditures and seafood demand, this paper also seeks to incorporate the household quality choice into the demand model. In order to help to tailor the market strategy, …

Exchange Rate Volatility Effects On Brics Countries Exports, David Isaias Maradiaga Pineda

LSU Doctoral Dissertations

The leaders of the leading emerging economies Brazil, Russia, India, China, and South Africa (BRICS) claim that increased currency exchange rate volatility (CERV) from USD, EUR, and JPY (G-3) negatively impacts their exports, and expressed their desire for less trade dependence on these currencies. The literature on the impact of CERV on trade is vast. However, no consensus on the impact’s direction and significance has been reached yet. The motivation of this study was: first, to contribute to the existing empirical literature by using an alternative methodology; and second, to provide empirical evidence to the claim’s validity or nullity by …

Quantitative Trait Loci (Qtl) That Underlie Scn Resistance In Soybean [Glycine Max (L.) Merr.] Pi438489b By ‘Hamilton’ Recombinant Inbred Line (Ril) Population, Kassem My Abdelmajid, Laura Ramos, D. L. Hyten, Jason Bond, Abdelhafid Bendahmane, Prakash R. Arelli, Victor N. Njiti, Silvia Cianzio, Stella K. Kantartzi, Khalid Meksem

Department of Agronomy and Horticulture: Faculty Publications

Soybean cyst nematode caused by Heterodera glycines Ichinohe is the most devastating pest in soybean [Glycine max (L.) Merr.]. Resistance to SCN is complex, polygenic, race and cultivar specific, and it is controlled by several quantitative trait loci (QTL). Our objective was to identify and map QTL for SCN resistance to races 3 (HG Type 0) and 5 (HG Type 2.5.7) using a high density SNP-based genetic linkage map based on the PI438489B by ‘Hamilton’ (PIxH, n=50) recombinant inbred line population. The PI438489B by Hamilton map contained 648 SNPs distributed on 31 LGs with coverage of 1,524.7 cM and …

Just Farming: An Environmental Justice Perspective On The Capacity Of Grassroots Organizations To Support The Rights Of Organic Farmers And Laborers, Rebecca Elaine Berkey

Antioch University Dissertations & Theses

This mixed methods study builds upon literature and research in environmental justice, public participation, and community development to examine how justice-related issues impact farmers and workers on organic farms in the Northeastern United States. It also examines how involvement in a grassroots organization helps farmers and workers address these issues. At the core of the study is an exploration of environmental justice and its applications at a broad, systemic level; an examination of the current context of laborers in organic agriculture in the Northeast; and finally an investigation of the effects of grassroots organizing within the Northeast Organic Farming Association …

Effects Of Organic And Conventional Agricultural Practices On Soil Microbial Communities And Molecular Detection Of Soil Borne Disease, Holli K. Milner

College of Graduate Studies: Theses & Dissertations

Agricultural practices affect soil microbial communities and health through the input of pesticides, herbicides, fertilizers, and cycling of crop rotation. By examining the microbial community structure, we analyzed how microbial species respond to the environment that individual farms create. Early detection of soil borne disease is essential for agricultural success. However, monitoring incidence of disease based on plant growth response to pathogenic inoculation may not reveal the amount of pathogenic DNA in soil. A comparative study of tomato production systems was conducted by analysis of soil microbial community structure from four farms in Southeast Georgia for the years 2012 and …

Effect Of Stocking Biomass On Solids, Phytoplankton Communities, Common Off-Flavors, And Production Parameters In A Channel Catfish Biofloc Technology Production System, Bartholomew W. Green, Kevin K. Schrader, Peter W. Perschbacher

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

The effect of initial channel catfish (Ictalurus punctatus, Rafinesque, 1818) fingerling biomass (1.4, 1.8, or 2.3 kg m^-3) on phytoplankton communities, common off-flavours and stocker catfish production parameters was evaluated in biofloc technology production tanks. Stocker catfish size (145.5–172.6 g fish^-1) at harvest did not differ among treatments, but net yield increased linearly as initial biomass increased (R² = 0.633). Mean total feed consumption increased linearly with initial catfish biomass (R² = 0.656) and ranged from 10.7 to 15.8 kg m ^-3. Total suspended solids (TSS) in all treatments increased linearly …