Agricultural Science Commons^™

Genetic Characterization Of The Soybean Nested Association Mapping Population, Qijian Song, Long Yan, Charles Quigley, Brandon D. Jordan, Edward Fickus, Steve Schroeder, Bao-Hua Song, Yong-Qiang Charles An, David Hyten, Randall L. Nelson, Katy Rainey, William D. Beavis, Jim Specht, Brian Diers, Perry Cregan

Department of Agronomy and Horticulture: Faculty Publications

A set of nested association mapping (NAM) families was developed by crossing 40 diverse soybean [Glycine max (L.) Merr.] genotypes to the common cultivar. The 41 parents were deeply sequenced for SNP discovery. Based on the polymorphism of the single-nucleotide polymorphisms (SNPs) and other selection criteria, a set of SNPs was selected to be included in the SoyNAM6K BeadChip for genotyping the parents and 5600 RILs from the 40 families. Analysis of the SNP profiles of the RILs showed a low average recombination rate. We constructed genetic linkage maps for each family and a composite linkage map based on …

Editorial: Genomic Approaches For Improvement Of Understudied Grasses, Keenan Amundsen, Gautam Sarath, Teresa Donze-Reiner

Department of Agronomy and Horticulture: Faculty Publications

Grasses are diverse, spanning native prairies to high-yielding grain cropping systems. They are valued for their beauty and useful for soil stabilization, pollution mitigation, biofuel production, nutritional value, and forage quality; grasses encompass the most important grain crops in the world. There are thousands of distinct grass species and many have promiscuous hybridization patterns, blurring species boundaries. Resources for advancing the science and knowledgebase of individual grass species or their unique characteristics varies, often proportional to their perceived value to society. For many grasses, limited genetic information hinders research progress. Presented in this research topic is a brief snapshot of …

Expression Of The Maize Dof1 Transcription Factor In Wheat And Sorghum, Pamela A. Pena, Truyen Quach, Shirley Sato, Zhengxiang Ge, Natalya Nersesian, Taity Changa, Ismail M. Dweikat, Madhavan Soundararajan, Tom E. Clemente

Department of Agronomy and Horticulture: Faculty Publications

Nitrogen is essential for plant growth and development. Improving the ability of plants to acquire and assimilate nitrogen more efficiently is a key agronomic parameter that will augment sustainability in agriculture. A transcription factor approach was pursued to address improvement of nitrogen use efficiency in two major commodity crops. To this end, the Zea mays Dof1 (ZmDof1) transcription factor was expressed in both wheat (Triticum aestivum) and sorghum (Sorghum bicolor) either constitutively, UBI4 promoter from sugarcane, or in a tissue specific fashion via the maize rbcS1 promoter. The primary transcription activation target of ZmDof1 …

High-Throughput Profiling And Analysis Of Plant Responses Over Time To Abiotic Stress, Kira M. Veley, Jeffrey C. Berry, Sarah J. Fentress, Daniel P. Schachtman, Ivan Baxter, Rebecca Bart

Department of Agronomy and Horticulture: Faculty Publications

Sorghum (Sorghum bicolor (L.) Moench) is a rapidly growing, high-biomass crop prized for abiotic stress tolerance. However, measuring genotype-by-environment (G x E) interactions remains a progress bottleneck. We subjected a panel of 30 genetically diverse sorghum genotypes to a spectrum of nitrogen deprivation and measured responses using high-throughput phenotyping technology followed by ionomic profiling. Responses were quantified using shape (16 measurable outputs), color (hue and intensity), and ionome (18 elements). We measured the speed at which specific genotypes respond to environmental conditions, in terms of both biomass and color changes, and identified individual genotypes that perform most favorably. With this …

Influence Of Tillage On Common Ragweed (Ambrosia Artemisiifolia) Emergence Pattern In Nebraska, Ethann R. Barnes, Rodrigo Werle, Lowell Sandell, John L. Lindquist, Stevan Z. Knezevic, Peter H. Sikkema, Amit J. Jhala

Department of Agronomy and Horticulture: Faculty Publications

Spring tillage is a component of an integrated weed management strategy for control of early emerging glyphosate-resistant weeds such as common ragweed; however, the effect of tillage on common ragweed emergence pattern is unknown. The objectives of this study were to evaluate whether spring tillage during emergence would influence the emergence pattern or stimulate additional emergence of common ragweed and to characterize common ragweed emergence in southeast Nebraska. A field experiment was conducted for three years (2014 to 2016) in Gage County, Nebraska in a field naturally infested with glyphosate-resistant common ragweed. Treatments consisted of a no-tillage control and three …

The Effects Of Early Pruning On The Near-Ground Branch Density Of Four Live Fencing Species, Aric Devens

Dissertations, Master's Theses and Master's Reports

Crop losses in home gardens greatly impact the wellbeing of rural West African families. Herbivory by migratory or local livestock represents a significant source of crop loss. Live-fencing gardens with thorny hedges is a low-cost and sustainable strategy for reducing losses due to herbivory. However, guidance on the establishment of thorny hedges is inconsistent, poorly publicized, and often anecdotal. Therefore, this study evaluated the effects of three early pruning treatments on near-ground branch density of four thorny species: Vachellia nilotica, Senegalia laeta, Senegalia mellifera, and Prosopis juliflora. Physical measurements and photographic data indicated that after one growing season, V. …

Can Sub-Saharan Africa Feed Itself?, Martin K. Van Ittersum, Lenny G. J. Van Bussel, Joost Wolf, Patricio Grassini, Justin Van Wart, Nicolas Guilpart, Lieven Claessens, Hugo De Groot, Keith Wiebe, Daniel Mason-D'Croz, Haishun Yang, Hendrik Boogard, Pepijn A. J. Van Oort, Marloes P. Van Loon, Kazuki Saito, Ochieng Adimo, Samuel Adjei-Nsiah, Alhassane Agali, Abdullahi Bala, Regis Chikowo, Kayuki Kaizzi, Mamoutou Kouressy, Joachim H. J. R. Makoi, Korodjouma Ouattara, Kindie Tesfaye, Kenneth G. Cassman

Department of Agronomy and Horticulture: Faculty Publications

Although global food demand is expected to increase 60% by 2050 compared with 2005/2007, the rise will be much greater in sub- Saharan Africa (SSA). Indeed, SSA is the region at greatest food security risk because by 2050 its population will increase 2.5-fold and demand for cereals approximately triple, whereas current levels of cereal consumption already depend on substantial imports. At issue is whether SSA can meet this vast increase in cereal demand without greater reliance on cereal imports or major expansion of agricultural area and associated biodiversity loss and greenhouse gas emissions. Recent studies indicate that the global increase …

Effect Of Smooth Bromegrass Management On Grazing Cattle Dung Decomposition, Co2 Flux, And Soil Nutrient Movement, Bradley D. Schick

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

Rapid nutrient cycling improves forage quality and livestock production in pastures. Interseeding legumes may be a strategy to enhance N cycling, but effects of dung excreted from cattle grazing pastures with legumes on dung decomposition rates and soil N cycling have not been studied. Our objective was to evaluate how dung excreted from cattle grazing legume-interseeded, N-fertilized, and unfertilized smooth bromegrass (Bromus inermis Leyss.) pastures affects dung chemical composition, dry matter decomposition, CO­₂ flux, and N availability in soil. Freshly deposited dung from yearling steers grazing legume-interseeded, N-fertilized, and unfertilized pastures was collected and placed as pats in …

Comparison Of The Production Of Bibb Lettuce Reared In Indoor Aquaponics System Using Large Mouth Bass (Micropterus Salmoides) Vs. Nile Tilapia (Oreochromis Niloticus), George J. Pate

Posters-at-the-Capitol

Aquaponics is a sustainable food production system that combines hydroponic plant growth with fish rearing in a recirculating aquaculture system. Nile tilapia (Oreochromis niloticus) are predominantly raised in aquaponics due to their fast growth rates and ability to tolerate a variety of water conditions. As aquaponics becomes more popular in temperate climate zones, farmers are looking for alternative fish species that are more compatible with cooler temperatures and have a higher market value than tilapia. Authors will determine if plant growth factors as well as, the availability of nutrients in aquaponic systems are affected by the difference in nutrient requirements …

Modeling Long-Term Corn Yield Response To Nitrogen Rate And Crop Rotation, Laila A. Puntel, John E. Sawyer, Daniel W. Barker, Ranae Dietzel, Hanna Poffenbarger, Michael J. Castellano, Kenneth J. Moore, Peter J. Thorburn, Sotirios V. Archontoulis

Department of Agronomy and Horticulture: Faculty Publications

Improved prediction of optimal N fertilizer rates for corn (Zea mays L.) can reduce N losses and increase profits. We tested the ability of the Agricultural Production Systems sIMulator (APSIM) to simulate corn and soybean (Glycine max L.) yields, the economic optimum N rate (EONR) using a 16-year field-experiment dataset from central Iowa, USA that included two crop sequences (continuous corn and soybean-corn) and five N fertilizer rates (0, 67, 134, 201, and 268 kg N ha^-1) applied to corn. Our objectives were to: (a) quantify model prediction accuracy before and after calibration, and report calibration steps; (b) …

Characterization And Development Mechanism Of Apios Americana Tuber Starch, Hanyu Yangchen, Vikas Belamkar, Steven B. Cannon, Jay-Lin Jane

Department of Agronomy and Horticulture: Faculty Publications

Apios americana is a wild legume-bearing plant with edible tubers. Domestication of Apios is in progress because of the superior nutritional value and health benefits of the tuber. Objectives of this study were to: (1) characterize physicochemical properties of the Apios tuber starch; and (2) understand differences in starch structures and properties between the mother (seed) and child (progeny) tubers and the mechanism of starch development. Granules of the Apios tuber starch displayed ellipsoidal, rod, or kidney shape with diameter ranges of 1–30 m. The mother tuber starches displayed greater percentage crystallinity, larger gelatinization enthalpy-changes, longer branch-chain lengths of amylopectin, …

Genomics-Assisted Characterization Of A Breeding Collection Of Apios Americana, An Edible Tuberous Legume, Vikas Belamkar, Andrew Farmer, Nathan T. Weeks, Scott R. Kalberer, William J. Blackmon, Steven B. Cannon

Department of Agronomy and Horticulture: Faculty Publications

For species with potential as new crops, rapid improvement may be facilitated by new genomic methods. Apios (Apios americana Medik.), once a staple food source of Native American Indians, produces protein-rich tubers, tolerates a wide range of soils, and symbiotically fixes nitrogen. We report the first high-quality de novo transcriptome assembly, an expression atlas, and a set of 58,154 SNP and 39,609 gene expression markers (GEMs) for characterization of a breeding collection. Both SNPs and GEMs identify six genotypic clusters in the collection. Transcripts mapped to the Phaseolus vulgaris genome–another phaseoloid legume with the same chromosome number–provide provisional genetic …

Plants Having Increased Bomass And Methods For Making The Same, Aleel K. Grennan, Donald R. Ort, Stephen Patrick Moose, Damla D. Bilgin, Thomas Clemente, Fredy Altpeter, Stephen P. Long

Department of Agronomy and Horticulture: Faculty Publications

The impact of plastid size change in both monocot and dicot plants has been examined. In both, when plastid size is increased there is an increase in biomass relative to the parental lines. Thus, provided herein are methods for increasing the biomass of a plant, comprising decreasing the expression of at least one plastid division protein in a plant. Optionally, the level of chlorophyll in the plant is also reduced.

Cross Species Selection Scans Identify Components Of C4 Photosynthesis In The Grasses, Pu Huang, Anthony J. Studer, James C. Schnable, Elizabeth A. Kellogg, Thomas P. Brutnell

Department of Agronomy and Horticulture: Faculty Publications

C₄ photosynthesis is perhaps one of the best examples of convergent adaptive evolution with over 25 independent origins in the grasses (Poaceae) alone. The availability of high quality grass genome sequences presents new opportunities to explore the mechanisms underlying this complex trait using evolutionary biology-based approaches. In this study, we performed genome-wide cross-species selection scans in C₄ lineages to facilitate discovery of C₄ genes. The study was enabled by the well conserved collinearity of grass genomes and the recently sequenced genome of a C₃ panicoid grass, Dichanthelium oligosanthes. This method, in contrast to previous studies, …

Particular Applications Of Food Irradiation Fresh Produce, Anuradha Prakash

Food Science Faculty Articles and Research

On fresh fruits and vegetables, irradiation at low and medium dose levels can effectively reduce microbial counts which can enhance safety, inhibit sprouting to extend shelf-life, and eliminate or sterilize insect pests which can serve to facilitate trade between countries. At the dose levels used for these purposes, the impact on quality is negligible. Despite the fact that regulations in many countries allow the use of irradiation for fresh produce, the technology remains under-utilized, even in the light of an increase in produce related disease outbreaks and the economic benefits of extended shelflife and reduced food waste. Putative concerns about …

Herbicide Resistantsorghum Mutants, Ismail M. Dweikat

Department of Agronomy and Horticulture: Faculty Publications

This disclosure provides for four different sorghum mutants that exhibit resistance to ALS-inhibiting herbicides. This dis closure also provides for methods of using such Sorghum mutants that exhibit resistance to ALS-inhibiting herbicides in breeding methods to make Sorghum hybrids, varieties, or lines. The Sorghum hybrids, varieties, and lines provided in this disclosure can be used in methods of controlling weeds.

Long-Term Sandhills Prairie Responses To Precipitation, Temperature, And Cattle Stocking Rate, John A. Guretzky, Cheryl Dunn, Heidi L. Hillhouse

Department of Agronomy and Horticulture: Faculty Publications

Understanding of Sandhills prairie, the most expansive sand dune region stabilized by perennial grasses in the Western Hemisphere, is limited by lack of long-term vegetation data. We used a 26-year dataset to evaluate Sandhills prairie responses to yearto- year variation in precipitation, temperature, and cattle stocking rate. Basal cover, a measurement that is constant seasonally and used to detect long-term changes in bunchgrass vegetation, was measured in 38–40 permanent plots positioned along four transects spanning 769 ha from 1979 to 2007. Across this period, total basal cover averaged 2.4 % and was dominated by warm-season grasses (81.1 %). Schizachyrium scoparium …

Managing Drought Stress In California Agricultural Systems, Gregory D. Brittain Jr.

Doctor of Plant Health Program: Dissertations and Student Research

California is currently facing a historic drought, and this has led many farmers in the state to severely cut back on irrigation. Optimal use of water for irrigation requires a comprehensive understanding of how plants respond physiologically to water stress (Chapter 1). By monitoring water requirements in crops and managing irrigation to meet those requirements, growers can significantly reduce water use (Chapter 2). This can be done through improving application efficiency of irrigation technology as well as increasing the water use efficiency of the crops themselves. Deficit irrigation practices can be used to manipulate the physiology of water use in …

Evaluating Pedestrial Compaction Variation & Soil Organic C Content, Gunner B. Decker

Scholars Week

Over time, playing fields are monitored by overall appearance. However, pedestrian compaction is not evenly distributed throughout the entire surface.

Information Thermodynamics Of Cytosine Dna Methylation, Robersy Sanchez Rodriguez, Sally Ann Mackenzie

Department of Agronomy and Horticulture: Faculty Publications

Cytosine DNA methylation (CDM) is a stable epigenetic modification to the genome and a widespread regulatory process in living organisms that involves multicomponent molecular machines. Genome-wide cytosine methylation patterning participates in the epigenetic reprogramming of a cell, suggesting that the biological information contained within methylation positions may be amenable to decoding. Adaptation to a new cellular or organismal environment also implies the potential for genome-wide redistribution of CDM changes that will ensure the stability of DNA molecules. This raises the question of whether or not we would be able to sort out the regulatory methylation signals from the CDM background …

Ws-2 Introgression In A Proportion Of Arabidopsis Thaliana Col-0 Stock Seed Produces Specific Phenotypes And Highlights The Importance Of Routine Genetic Verification, Mon-Ray Shao, Vikas Shedge, Hardik Kundariya, Fredric R. Lehle, Sally Ann Mackenzie

Department of Agronomy and Horticulture: Faculty Publications

Arabidopsis thaliana is an important model organism with a robust network of resources that has been of enormous value to the plant science research community. The use of isogenic material as a reference point or control is critical for many types of experiments in plant molecular biology and genetics. Recently, we noticed that some seed from a common source of the widely used Columbia-0 (Col-0) strain gave rise to plants showing features atypical for this strain. Whole-genome DNA-sequencing and allelespecific PCR assays confirmed that the abnormal individuals contain multiple introgressions from the ecotype Wassilewskija-2 (Ws-2), as described below. This …

Student-Conducted Farmer Video Interviews, Jenn K. Simons, Justin Van Wart, Charles Francis, Kristyn Harms

Department of Agronomy and Horticulture: Faculty Publications

High school agricultural education teachers have expressed concern about the lack of easily accessible educational materials dealing with contemporary topics in sustainable agriculture. There are numerous textbooks and monographs available for farmers and students at the college level, including the highly practical resources available from the Sustainable Agriculture Research and Education (SARE) book series on soil fertility (Magdoff and van Es, 2010), cover crops (Bowman et al., 2007) and building a farm business (DiGiacomo et al., 2003), among others. Although these are full of color photos and easily accessible graphs and tables, they are still in the print media category. …

Comparative Evaluation Of The Effect Of Methyl Bromide Fumigation And Phytosanitary Irradiation On The Quality Of Fresh Strawberries, Tamar Serapian, Anuradha Prakash

Food Science Faculty Articles and Research

Fresh strawberries are highly perishable and have a short shelf-life especially when the cold chain is not maintained. Strawberries exported to Asia are currently fumigated with methyl bromide for phytosanitary purposes, which exposes strawberries to warm temperatures for several hours and air freight without temperature control, resulting in a shelf life of just a few days in the destination country. Irradiation offers an efficacious alternative to fumigation and can be performed on cold fruit. This study was conducted to compare the quality of strawberries subject to methyl bromide fumigation or irradiation followed by simulated commercial air freight shipment of strawberries …

Corn Era Hybrid Response To Nitrogen Fertilization, Krishna P. Woli, Matthew J. Boyer, Roger Wesley Elmore, John E. Sawyer, Lori J. Abendroth, Daniel W. Barker

Department of Agronomy and Horticulture: Faculty Publications

Corn (Zea mays L.) N use is of continued interest due to agronomic performance and environmental issues. This 2-yr study evaluated era hybrid response to fertilizer nitrogen (FN) rate in a factorial arrangement of one popular hybrid per five decades (1960–2000 eras) and five N rates (0–224 kg N ha^–1). An additional hybrid per era was grown at 168 kg N ha^–1. Hybrid productivity and nitrogen use efficiency (NUE) increased across the eras, but not between the 1980 and 1990 eras. Grain yield (GY) increased 65% and total plant biomass 43%, however, total plant nitrogen …

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.