Agronomy and Crop Sciences Commons^™

Image Harvest: An Open-Source Platform For High-Throughput Plant Image Processing And Analysis, Avi C. Knecht, Malachy T. Campbell, Adam Caprez, David R. Swanson, Harkamal Walia

Holland Computing Center: Faculty Publications

High-throughput plant phenotyping is an effective approach to bridge the genotype-to-phenotype gap in crops. Phenomics experiments typically result in large-scale image datasets, which are not amenable for processing on desktop computers, thus creating a bottleneck in the image-analysis pipeline. Here, we present an open-source, flexible image-analysis framework, called Image Harvest (IH), for processing images originating from high-throughput plant phenotyping platforms. Image Harvest is developed to perform parallel processing on computing grids and provides an integrated feature for metadata extraction from large-scale file organization. Moreover, the integration of IH with the Open Science Grid provides academic researchers with the computational resources …

Growing Potato Profitably For Organic Dry Matter Production In Western Nebraska, Alexander Pavlista, Jessica J. Groskopf

Panhandle Research and Extension Center

Growing potato conventionally for dehydration is not economically feasible. The key cost would be seed under organic farming. The objective is to identify seed-piece sizes and spacings producing a profitable return for potato dehydration in western Nebraska. Atlantic potatoes were grown under dryland conditions using organic practices. Rain was 205, 270, and 360 mm in 2013, 2014, and 2015. Seed-pieces were hand-cut into five weights from 42.5 to 85.0 g and planted in five spacings from 15.2 to 45.7 cm. Seeding rates were 1.02 to 6.1 Mg/ha. Yield was highest at the spacing of 15.2 cm (16.1 Mg/ha) and decreased …

Biochar Reduced Nitrous Oxide And Carbon Dioxide Emissions From Soil With Different Water And Temperature Cycles, Jiyul Chang, David E. Clay, Sharon A. Clay, Rajesh Chintala, Janet M. Miller, Thomas Schumacher

Agronomy, Horticulture and Plant Science Faculty Publications

Interactions among biochar, respiration, nitrification, and soils can result in biochar increasing, decreasing, or not impacting greenhouse gas (GHG) emissions. This experiment determined the impact of water-filled porosity (WFP) and corn (Zea mays L.) stover biochar on CO₂ and N₂O emissions in May (spring) and August (summer). The May experiment contained two N rates [0 and 224 kg Ca(NO₃)₂–N ha^–1], whereas the August had three N rates [0, 224 kg Ca(NO₃)₂–N ha^–1, and 224 kg (NH₄)₂SO₄–N ha^{–1 …}

Mapping Qtls And Association Of Differentially Expressed Gene Transcripts For Multiple Agronomic Traits Under Different Nitrogen Levels In Sorghum, Malleswari Gelli, Sharon E. Mitchell, Kan Liu, Thomas E. Clemente, Donald P. Weeks, Chi Zhang, David R. Holding, Ismail M. Dweikat

Department of Agronomy and Horticulture: Faculty Publications

Background: Sorghum is an important C₄ crop which relies on applied Nitrogen fertilizers (N) for optimal yields, of which substantial amounts are lost into the atmosphere. Understanding the genetic variation of sorghum in response to limited nitrogen supply is important for elucidating the underlying genetic mechanisms of nitrogen utilization.

Results: A bi-parental mapping population consisting of 131 recombinant inbred lines (RILs) was used to map quantitative trait loci (QTLs) influencing different agronomic traits evaluated under normal N (100 kg.ha⁻¹ fertilizer) and low N (0 kg.ha⁻¹ fertilizer) conditions. A linkage map spanning 1614 cM was developed …

Proteomic Profiling Of Maize Opaque Endosperm Mutants Reveals Selective Accumulation Of Lysine-Enriched Proteins, Kyla J. Morton, Shangang Jia, Chi Zhang, David R. Holding

Department of Agronomy and Horticulture: Faculty Publications

Reduced prolamin (zein) accumulation and defective endoplasmic reticulum (ER) body formation occurs in maize opaque endosperm mutants opaque2 (o2), floury2 (fl2), defective endosperm*B30 (DeB30), and Mucronate (Mc), whereas other opaque mutants such as opaque1 (o1) and floury1 (fl1) are normal in these regards. This suggests that other factors contribute to kernel texture. A liquid chromatography approach coupled with tandem mass spectrometry (LC-MS/MS) proteomics was used to compare non-zein proteins of nearly isogenic opaque endosperm mutants. In total, 2762 proteins were identified that were enriched for biological processes such …

Simulating Long-Term Impacts Of Cover Crops And Climate Change On Crop Production And Environmental Outcomes In The Midwestern United States, Andrea D. Basche, Sotririos V. Archontoulis, Thomas C. Kaspar, Dan B. Jaynes, Timothy B. Parkin, Fernando E. Miguez

Department of Agronomy and Horticulture: Faculty Publications

It is critical to evaluate conservation practices that protect soil and water resources from climate change in the Midwestern United States, a region that produces one-quarter of the world’s soybeans and one-third of the world’s maize. An over-winter cover crop in a maize–soybean rotation offers multiple potential benefits that can reduce the impacts of higher temperatures and more variable rainfall; some of the anticipated changes for the Midwest. In this experiment we used the Agricultural Production Systems sIMulator (APSIM) to understand how winter rye cover crops impact crop production and environmental outcomes, given future climate change. We first tested APSIM …

Decipher The Molecular Response Of Plant Single Cell Types To Environmental Stresses, Mehrnoush Nourbakhsh-Rey, Marc Libault

Department of Agronomy and Horticulture: Faculty Publications

The analysis of the molecular response of entire plants or organs to environmental stresses suffers from the cellular complexity of the samples used. Specifically, this cellular complexity masks cell-specific responses to environmental stresses and logically leads to the dilution of the molecular changes occurring in each cell type composing the tissue/organ/plant in response to the stress.Therefore, to generate a more accurate picture of these responses, scientists are focusing on plant single cell type approaches. Several cell types are now considered as models such as the pollen, the trichomes, the cotton fiber, various root cell types including the root hair cell, …

Organic Struggle: The Movement For Sustainable Agriculture In The United States [Book Review], Charles A. Francis

Department of Agronomy and Horticulture: Faculty Publications

Organic Struggle chronicles the challenges encountered by innovators in a growing segment of the U.S. food production and marketing system. Practiced for millennia by farmers before the introduction of chemical fertilizers and pesticides, and first developed more formally in Europe, organic farming practices began to gain prominence in the United States only in the 1950s. Far more than a system for producing food, this strategy has become a focus for those supporting healthy and pesticide-free products, for some who embrace the organic system as a food movement, and by many who disagree with the current domination of the country’s food …

Draft Genome Sequence Of Erwinia Tracheiphila, An Economically Important Bacterial Pathogen Of Cucurbits, Lori R. Shapiro, Erin D. Scully, Dana Roberts, Timothy J. Straub, Scott M. Geib, Jihye Park, Andrew G. Stephenson, Erika Salaau Rojas, Quin Liu, Gwyn Beattie, Mark Gleason, Consuelo M. De Moraes, Mark C. Mescher, Shelby G. Fleischer, Roberto Kolter, Naomi Pierce, Olga Zhaxybayeva

Department of Agronomy and Horticulture: Faculty Publications

Erwinia tracheiphila is one of the most economically important pathogens of cucumbers, melons, squashes, pumpkins, and gourds in the northeastern and midwestern United States, yet its molecular pathology remains uninvestigated. Here, we report the first draft genome sequence of an E. tracheiphila strain isolated from an infected wild gourd (Cucurbita pepo subsp. texana) plant. The genome assembly consists of 7 contigs and includes a putative plasmid and at least 20 phage and prophage elements.

Muts Homolog1 Silencing Mediates Orf220 Substoichiometric Shifting And Causes Male Sterility In Brassica Juncea, Na Zhao, Xinyue Xu, Yashitola Wamboldt, Sally Ann Mackenzie, Xiaodong Yang, Zhongyuan Hu, Jinghua Yang, Mingfang Zhang

Department of Agronomy and Horticulture: Faculty Publications

Cytoplasmic male sterility (CMS) has consistently been associated with the expression of mitochondrial open reading frames (ORFs) that arise from genomic rearrangements. Spontaneous fertility reversion in CMS has been observed in several cases, but a clear understanding of fertility reversion controlled by nuclear genetic influences has been lacking. Here, we identified spontaneous fertile revertant lines for Brassica juncea CMS cytoplasm in which the mitochondrial genome has undergone substoichiometric shifting (SSS) to suppress ORF220 copy number. We placed ORF220, with or without a mitochondrial targeting presequence, under the control of the CaMV35S and AP3 promoters in Arabidopsis to confirm that ORF220 …

Correlating Bulk Density (With Dockage) And Test Weight (Without Dockage) For Wheat Samples, Rumela Bhadra, Mark E. Casada, Josephine M. Boac, Aaron P. Turner, Sidney A. Thompson, Michael D. Montross, Ronaldo G. Maghirang, Samuel G. Mcneill

Biosystems and Agricultural Engineering Faculty Publications

In grain bins, the compaction of stored grain is caused by the overbearing pressure of the bulk material in the bin. To predict the amount of grain in the bin, compaction values must be determined based on the average bulk density (BD) of the stored material. However, BD is determined following the Federal Grain Inspection Service (FGIS) guidelines for measuring test weight (TW), which require that dockage be removed prior to measuring wheat TW. Thus, this creates a problem for predicting grain compaction and conducting inventory studies, because the average BD of the grain in a bin for these calculations …

Contents, Discovery Editors

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

No abstract provided.

Discovery: The Student Journal Of Dale Bumpers College Of Agricultural, Food And Life Sciences - Volume 17 2016, Several Authors

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

No abstract provided.

Bumpers College Students In Action, Discovery Editors

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

No abstract provided.

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 …

Effects Of Corn (Zea Mays L.) Stover Removal And Leaching On Soil Test And Whole Plant K Levels In Corn And K Fertilization/High-Input Treatments On Soybean Using Site-Specific Management To Increase Soybean (Glycine Max) Production In South Dakota, Nick J. Schiltz

Electronic Theses and Dissertations

Potassium is important for crop production. Corn stover removal has the potential to reduce exchangeable and soluble soil potassium (K+) needed for optimal plant growth in addition to grain yield. An experiment was conducted in Aurora, SD, USA, to observe the effects of corn stover removal on water soluble and exchangeable soil test K+ (STK) levels and corn grain yields across a five-year period. Abundant K+ reserves were recorded between the initial and final sampling periods. While corn grain yields were affected by removing corn biomass, exchangeable and solution K+ levels were relatively unaffected by stover removal. Potassium fertilizer has …

Restoration Of Eroded Lands With Biochar As Soil Amendment In South Dakota, Saroop S. Sandhu

Electronic Theses and Dissertations

Biochar is produced from incomplete pyrolysis of plant biomass. Due to the unique properties of biochar such as a higher number of micropores, surface area and carbon content, and recalcitrant nature of carbon, biochar is hypothesized to improve physical and hydrological properties of soil. This study assesses the impact of biochar on soil organic carbon, physical and hydrological properties of two landscape positions under a corn (Zea mays L.)-soybean (Glycine max L.) rotation. Three types of biochar including corn stover, ponderosa pine (Pinus ponderosa Lawson and C. Lawson) wood residue, and switchgrass (Panicum virgatum L.) were applied in the field …

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 …

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 …

Expression Of Apoplast-Targeted Plant Defensin Mtdef4.2 Confers Resistance To Leaf Rust Pathogen Puccinia Triticina But Does Not Affect Mycorrhizal Symbiosis In Transgenic Wheat, Jagdeep Kaur, John Fellers, Alok Adholeya, Siva L.S. Velivelli, Kaoutar El-Mounadi, Natalya Nersesian, Thomas Clemente, Dilip Shah

Department of Agronomy and Horticulture: Faculty Publications

Rust fungi of the order Pucciniales are destructive pathogens of wheat worldwide. Leaf rust caused by the obligate, biotrophic basidiomycete fungus Puccinia triticina (Pt) is an economically important disease capable of causing up to 50 % yield losses. Historically, resistant wheat cultivars have been used to control leaf rust, but genetic resistance is ephemeral and breaks down with the emergence of new virulent Pt races. There is a need to develop alternative measures for control of leaf rust in wheat. Development of transgenic wheat expressing an antifungal defensin offers a promising approach to complement the endogenous resistance genes …

Evaluation Of Tillage, Crop Rotation, And Cover Crop Impacts On Corn Nitrogen Requirements In Southeastern South Dakota, Sara Louise Berg

Electronic Theses and Dissertations

Nitrogen (N) is a vital factor of corn (Zea mays) production. Previous work in South Dakota has shown that there is uncertainty as to whether nitrogen requirements are the same for corn raised under no-till (NT) versus conventional till (CT) production systems. The objective of this study was to evaluate whether N requirements continue to be greater under long-term NT versus CT production systems in southeastern South Dakota, while also considering effects from cover crops and crop rotation. This was a two year study conducted at the SDSU Southeast Research Farm near Beresford, SD; it was superimposed on a long-term …

Letter From The Dean, Lona Robertson

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

No abstract provided.

Using Precision Agriculture Field Data To Evaluate Combine Harvesting Efficiency, Justin H. Carroll, Don Johnson, Jeff Miller, Kristofor Brye

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

Soybeans must be harvested during a limited time period using expensive combines and associated equipment. Maximizing combine field efficiency, the ratio of the actual harvesting capacity to theoretical harvesting capacity, is an important objective of machinery managers. Spatial and temporal yield data from a 2012 CaseIH 8120 Axial-Flow combine equipped with a 9 meter MacDon D-65 Draper header and the Case-IH Advanced Farming System (AFS) yield monitoring system were used to examine field efficiency when harvesting soybean in three Arkansas Delta irrigated soybean fields during the 2015 season. Time efficiencies (TE) in the three fields ranged from 72.9% to 85.8% …

Message From The Faculty Editor, Mary Savin

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

No abstract provided.

Instructions For Authors, Discovery Editors

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

No abstract provided.

Molecular Characterization Of Resistance To Soybean Rust (Phakopsora Pachyrhizi Syd. & Syd.) In Soybean Cultivar Dt 2000 (Pi 635999), Tri D. Vuong, David R. Walker, Binh T. Nguyen, Tuyet T. Nguyen, Hoan X. Dinh, David L. Hyten, Perry B. Cregan, David A. Sleper, Jeong D. Lee, James G. Shannon, Henry T. Nguyen

Department of Agronomy and Horticulture: Faculty Publications

Resistance to soybean rust (SBR), caused by Phakopsora pachyrhizi Syd. & Syd., has been identified in many soybean germplasm accessions and is conferred by either dominant or recessive genes that have been mapped to six independent loci (Rpp1 -Rpp6), but No U. S. cultivars are resistant to SBR. The cultivar DT 2000 (PI 635999) has resistance to P. pachyrhizi isolates and field populations from the United States as well as Vietnam. A F_6:7 recombinant inbred line (RIL) population derived from Williams 82 × DT 2000 was used to identify genomic regions associated with resistance to SBR in …

Grain Sorghum Leaf Reflectance And Nitrogen Status, Akwasi A. Abunyewa, Richard B. Ferguson, Charles S. Wortmann, Stephen C. Mason

Department of Agronomy and Horticulture: Faculty Publications

Nitrogen deficiency is a common but readily managed constraint to grain yield. A quick and nondestructive detection of crop N status using remote sensing could be a means to increased N use efficiency. Research was conducted in a greenhouse in 2006 at the University of Nebraska-Lincoln to establish the relationship of spectral reflectance with N status in leaves of grain sorghum, to develop indices for interpretation of the results and to predict chlorophyll content. Nitrogen stress decreased chlorophyll meter reading and leaf N content, but increased leaf and canopy reflectance. The SPAD values were significantly increased by both water and …