Other Plant Sciences Commons^™

Active-Optical Reflectance Sensing Corn Algorithms Evaluated Over The United States Midwest Corn Belt, G. M. Bean, N. R. Kitchen, J. J. Camberato, R. B. Ferguson, F. G. Fernandez, D. W. Franzen, C. A. M. Laboski, E. D. Nafziger, J. E. Sawyer, P. C. Scharf, J. Schepers, J. S. Shanahan

Department of Agronomy and Horticulture: Faculty Publications

Uncertainty exists with corn (Zea mays L.) N management due to year-to-year variation in crop N need, soil N supply, and N loss from leaching, volatilization, and denitrification. Activeoptical reflectance sensing (AORS) has proven effective in some fields for generating N fertilizer recommendations that improve N use efficiency, but locally derived (e.g., within a US state) AORS algorithms have not been tested simultaneously across a broad region. The objective of this research was to evaluate locally developed AORS algorithms across the US Midwest Corn Belt region for making in-season corn N recommendations. Forty-nine N response trials were conducted across …

Lignocellulosic-Based Bioenergy And Water Quality Parameters: A Review, Bharat Sharma Acharya, Humberto Blanco-Canqui

Department of Agronomy and Horticulture: Faculty Publications

High rates of crop residue removal as biofuel feedstocks could increase losses of nonpoint source pollutants, negatively affecting water quality. An alternative to residue removal can be growing dedicated bioenergy crops such as warm season grasses (WSGs) and short-rotation woody crops (SRWCs). Yet, our understanding of the implications of growing dedicated bioenergy crops on water quality is limited. Thus, we (i) synthesized and compared the impacts of crop residue removal, WSGs, and SRWCs on water quality parameters (i.e., sediment and nutrient runoff, and nutrient leaching) and (ii) identified research gaps for growing dedicated energy crops. Literature indicates that residue removal …

Epigenomic Plasticity Of Arabidopsis Msh1 Mutants Under Prolonged Cold Stress, Sunil Kumar Kenchanmane Raju, Mon-Ray Shao, Yashitola Wamboldt, Sally A. Mackenzie

Department of Agronomy and Horticulture: Faculty Publications

Dynamic transcriptional and epigenetic changes enable rapid adaptive benefit to environmental fluctuations. However, the underlying mechanisms and the extent to which this occurs are not well known. MutS Homolog 1 (MSH1) mutants cause heritable developmental phenotypes accompanied by modulation of defense, phytohormone, stress‐response, and circadian rhythm genes, as well as heritable changes in DNA methylation patterns. Consistent with gene expression changes, msh1 mutants display enhanced tolerance for abiotic stress including drought and salt stress, while showing increased susceptibility to freezing temperatures. Despite changes in defense and biotic stress‐response genes, msh1 mutants showed increasing susceptibility to the bacterial pathogen Pseudomonas syringae. …

Can Bangladesh Produce Enough Cereals To Meet Future Demand?, J. Timsina, J. Wolf, N. Guilpart, L G. J. Van Bussel, P. Grassini, J. Van Wart, A. Hossain, H. Rashid, S. Islam, M. K. Van Ittersum

Department of Agronomy and Horticulture: Faculty Publications

Bangladesh faces huge challenges in achieving food security due to its high population, diet changes, and limited room for expanding cropland and cropping intensity. The objective of this study is to assess the degree to which Bangladesh can be self-sufficient in terms of domestic maize, rice and wheat production by the years 2030 and 2050 by closing the existing gap (Yg) between yield potential (Yp) and actual farm yield (Ya), accounting for possible changes in cropland area. Yield potential and yield gaps were calculated for the three crops using well-validated crop models and site-specific weather,management and soil data, and upscaled …

Parallel Altitudinal Clines Reveal Trends In Adaptive Evolution Of Genome Size In Zea Mays, Paul Bilinski, Patrice S. Albert, Jeremy J. Berg, James A. Birchler, Mark N. Grote, Anne Lorant, Juvenal Quezada, Kelly Swarts, Jinliang Yang, Jeffrey Ross-Ibarra

Department of Agronomy and Horticulture: Faculty Publications

While the vast majority of genome size variation in plants is due to differences in repetitive sequence, we know little about how selection acts on repeat content in natural populations. Here we investigate parallel changes in intraspecific genome size and repeat content of domesticated maize (Zea mays) landraces and their wild relative teosinte across altitudinal gradients in Mesoamerica and South America. We combine genotyping, low coverage whole-genome sequence data, and flow cytometry to test for evidence of selection on genome size and individual repeat abundance. We find that population structure alone cannot explain the observed variation, implying that …

Genomic Prediction Accuracy For Switchgrass Traits Related To Bioenergy Within Differentiated Populations, Jason D. Fiedler, Christina Lanzatella, Serge J. Edme, Nathan A. Palmer, Gautam Sarath, Rob Mitchell, Christian M. Tobias

Department of Agronomy and Horticulture: Faculty Publications

Background: Switchgrass breeders need to improve the rates of genetic gain in many bioenergy-related traits in order to create improved cultivars that are higher yielding and have optimal biomass composition. One way to achieve this is through genomic selection. However, the heritability of traits needs to be determined as well as the accuracy of prediction in order to determine if efficient selection is possible.

Results: Using five distinct switchgrass populations comprised of three lowland, one upland and one hybrid accession, the accuracy of genomic predictions under different cross-validation strategies and prediction methods was investigated. Individual genotypes were collected using GBS …

Method For The Production Of High Saturated, Low Polyunsaturated Soybean Oil, Thomas E. Clemente, Hyunwoo Park, Edgar B. Cahoon, Hanh Nguyen

Department of Agronomy and Horticulture: Faculty Publications

Methods of genetically modifying soybean plants to alter the fatty acid properties of the oil are described.

Cc-Type Glutaredoxins Mediate Plant Response And Signaling Under Nitrate Starvation In Arabidopsis, Ji-Yul Jung, Ji Hoon Ahn, Daniel P. Schachtman

Department of Agronomy and Horticulture: Faculty Publications

Background: Nitrogen is an essential nutrient in plants. Despite the importance of nitrogen for plant growth and agricultural productivity, signal transduction pathways in response to nitrate starvation have not been fully elucidated in plants.

Results: Gene expression analysis and ectopic expression were used to discover that many CC-type glutaredoxins (ROXYs) are differentially expressed in response to nitrate deprivation. A gain-of-function approach showed that ROXYs may play a role in nutrient sensing through the regulation of chlorophyll content, root hair growth, and transcription of nitrate-related genes such as NRT2.1 under low or high nitrate conditions. Reactive oxygen species (ROS) …

Risks And Opportunities Of Gm Crops: Bt Maize Example, Andrea K. Carzoli, Siddique I. Aboobucker, Leah L. Sandall, Thomas T. Lubberstedt, Walter P. Suza

Department of Agronomy and Horticulture: Faculty Publications

The anticipated world population growth emphasizes a need to produce more food on less land. Cutting-edge technologies, including genetic engineering, can help to develop improved crop varieties and protect natural resources. In spite of the potential for genetically-modified (GM) crops to make crop production more efficient, they remain a polarizing issue due to safety concerns. This paper provides an overview of the risk assessment process. The safety of Bacillus thuringiensis (Bt) proteins is used as an example for how risk assessment is applied to GM crops. Risks associated with GM crops have proven to be low to non-existent. Developing countries …

Substantial Contribution Of Genetic Variation In The Expression Of Transcription Factors To Phenotypic Variation Revealed By Erd-Gwas, Hung-Ying Lin, Qiang Liu, Xiao Li, Jinliang Yang, Sanzhen Liu, Yinlian Huang, Michael J. Scanlon, Dan Nettleton, Patrick S. Schnable

Department of Agronomy and Horticulture: Faculty Publications

Background: There are significant limitations in existing methods for the genome-wide identification of genes whose expression patterns affect traits.

Results: The transcriptomes of five tissues from 27 genetically diverse maize inbred lines were deeply sequenced to identify genes exhibiting high and low levels of expression variation across tissues or genotypes. Transcription factors are enriched among genes with the most variation in expression across tissues, as well as among genes with higher-than-median levels of variation in expression across genotypes. In contrast, transcription factors are depleted among genes whose expression is either highly stable or highly variable across genotypes. We developed a …

Estimation Of Irrigation Requirements For Drip-Irrigated Maize In A Sub-Humid Climate, Liu Yang, Hai-Shun Yang, Jiu-Sheng Li, Yan-Feng Li, Hai-Jun Yan

Department of Agronomy and Horticulture: Faculty Publications

Drip-irrigation is increasingly applied in maize (Zea mays L.) production in sub-humid region. It is critical to quantify irrigation requirements during different growth stages under diverse climatic conditions. In this study, the Hybrid-Maize model was calibrated and applied in a sub-humid Heilongjiang Province in Northeast China to estimate irrigation requirements for drip irrigated maize during different crop physiological development stages and under diverse agro-climatic conditions. Using dimensionless scales, the whole growing season of maize was divided into diverse development stages from planting to maturity. Drip-irrigation dates and irrigation amounts in each irrigation event were simulated and summarized in 30-year simulation …

Identifying Ecologically Relevant Scales Of Habitat Selection: Diel Habitat Selection In Elk, Caleb P. Roberts, James W. Cain Iii, Robert D. Cox

Department of Agronomy and Horticulture: Faculty Publications

Although organisms make resource selection decisions at multiple spatiotemporal scales, not all scales are ecologically relevant to any given organism. Ecological patterns and rhythms such as behavioral and climatic patterns may provide a consistent method for identifying ecologically relevant scales of habitat selection. Using elk (Cervus canadensis) as an example species, we sought to test the ability of behavioral patterns to empirically partition diel scales for modeling habitat selection. We used model selection to partition diel scales by shifts in dominant behavior and then used resource selection probability functions to model elk habitat selection hierarchically at diel scales within seasons. …

Effects Of Nitrogen And Phosphorus Fertilizer And Topsoil Amendment On Native Plant Cover In Roadside Revegetation Projects, Heidi L. Hillhouse, Walter H. Schacht, Jonathan M. Soper, Carol E. Wienhold

Department of Agronomy and Horticulture: Faculty Publications

Establishing vegetation on roadsides following construction can be challenging, especially for relatively slow growing native species. Topsoil is generally removed during construction, and the surface soil following construction (“cut-slope soils”) is often compacted and low in nutrients, providing poor growing conditions for vegetation. Nebraska Department of Transportation (NDOT) protocols have historically called for nitrogen (N) and phosphorus (P) fertilization when planting roadside vegetation following construction, but these recommendations were developed for cool-season grass plantings and most current plantings use slower-establishing, native warmseason grasses that may benefit less than expected from current planting protocols. We evaluated the effects of nitrogen and …

Control Of Glyphosate-Resistant Common Ragweed (Ambrosia Artemisiifolia L.) In Glufosinate-Resistant Soybean [Glycine Max (L.) Merr], Ethann R. Barnes, Stevan Z. Knezevic, Peter H. Sikkema, John L. Lindquist, Amit J. Jhala

Department of Agronomy and Horticulture: Faculty Publications

Common ragweed emerges early in the season in Nebraska, USA and is competitive with soybean; therefore, preplant herbicides are important for effective control. Glyphosate has been used as a preplant control option; however, confirmation of glyphosate-resistant (GR) common ragweed in Nebraska necessitates evaluating other herbicide options. The objectives of this study were to (1) evaluate the efficacy of preplant (PP) herbicides followed by (fb) glufosinate alone or in tank-mixture with imazethapyr, acetochlor, or S-metolachlor applied post-emergence (POST) for control of GR common ragweed in glufosinate-resistant soybean; (2) their effect on common ragweed density, biomass, and soybean yield; and (3) the …

Impact Of Seed Protein Alleles From Three Soybean Sources On Seed Composition And Agronomic Traits, Lillian F. Brzostowski, Timothy I. Pruski, James Specht, Brian W. Diers

Department of Agronomy and Horticulture: Faculty Publications

Evaluation of seed protein alleles in soybean populations showed that an increase in protein concentration is generally associated with a decrease in oil concentration and yield.

Soybean [Glycine max (L.) Merrill] meal is one of the most important plant-based protein sources in the world. Developing cultivars high in seed protein concentration and seed yield is a difficult task because the traits have an inverse relationship. Over two decades ago, a protein quantitative trait loci (QTL) was mapped on chromosome (chr) 20, and this QTL has been mapped to the same position in several studies and given the confirmed QTL …

Molecular And Culture-Based Assessment Of Root/Crown Rot Fungal/Oomycete Complex Of Bean In Mozambique, Suzana Vanessa Ismael Fernandes

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

Dry edible beans (Phaseolus vulgaris) play an important role in food security, alleviating hunger and malnutrition and adding value to the economy in Mozambique. Recently, root/crown rot (RCR) has caused yield losses in bean fields in Mozambique. A diverse taxa of fungi and oomycetes have been associated with RCR. However, in Mozambique little information on root rot is available. The purpose of this study is to use Illumina sequencing platform, polymerase chain reaction (PCR) and culture-based methods to identify the primary pathogens associated with RCR in Mozambique. A total of 88 plants showing symptoms of RCR disease were …

Inferring Foliar Water Uptake Using Stable Isotopes Of Water, Gregory R. Goldsmith, Marco M. Lehmann, Lucas A. Cernusak, Matthias Arend, Rolf T.W. Siegwolf

Biology, Chemistry, and Environmental Sciences Faculty Articles and Research

A growing number of studies have described the direct absorption of water into leaves, a phenomenon known as foliar water uptake. The resultant increase in the amount of water in the leaf can be important for plant function. Exposing leaves to isotopically enriched or depleted water sources has become a common method for establishing whether or not a plant is capable of carrying out foliar water uptake. However, a careful inspection of our understanding of the fluxes of water isotopes between leaves and the atmosphere under high humidity conditions shows that there can clearly be isotopic exchange between the two …

Cellular And Molecular Targets Of Menthol Actions, Murat Oz, Eslam El Nebrisi, Keun-Hang Susan Yang, Frank Christopher Howarth, Lina T. Al Kury

Mathematics, Physics, and Computer Science Faculty Articles and Research

Menthol belongs to monoterpene class of a structurally diverse group of phytochemicals found in plant-derived essential oils. Menthol is widely used in pharmaceuticals, confectionary, oral hygiene products, pesticides, cosmetics, and as a flavoring agent. In addition, menthol is known to have antioxidant, anti-inflammatory, and analgesic effects. Recently, there has been renewed awareness in comprehending the biological and pharmacological effects of menthol. TRP channels have been demonstrated to mediate the cooling actions ofmenthol. There has been new evidence demonstrating thatmenthol can significantly influence the functional characteristics of a number of different kinds of ligand and voltage-gated ion channels, indicating that at …

Hydrogenation Of Organic Matter As A Terminal Electron Sink Sustains High Co2:Ch4 Production Ratios During Anaerobic Decomposition, Rachel M. Wilson, Malak M. Tfaily, Virginia I. Rich, Jason K. Keller, Scott D. Bridgham, Cassandra Medvedeff Zalman, Laura Meredith, Paul J. Hanson, Mark Hines, Laurel Pfeifer-Meister, Scott R. Saleska, Patrick Crill, William T. Cooper, Jeff P. Chanton, Joel E. Kostka

Biology, Chemistry, and Environmental Sciences Faculty Articles and Research

Once inorganic electron acceptors are depleted, organic matter in anoxic environments decomposes by hydrolysis, fermentation, and methanogenesis, requiring syntrophic interactions between microorganisms to achieve energetic favorability. In this classic anaerobic food chain, methanogenesis represents the terminal electron accepting (TEA) process, ultimately producing equimolar CO₂ and CH₄ for each molecule of organic matter degraded. However, CO₂:CH₄ production in Sphagnum-derived, mineral-poor, cellulosic peat often substantially exceeds this 1:1 ratio, even in the absence of measureable inorganic TEAs. Since the oxidation state of C in both cellulose-derived organic matter and acetate is 0, and CO₂ has …

Protocol For Enrichment Of The Membrane Proteome Of Mature Tomato Pollen, Puneet Paul, Palak Chaturvedi, Anida Mesihovic, Arindam Ghatak, Wolfram Weckwerth, Enrico Schleiff

Department of Agronomy and Horticulture: Faculty Publications

We established and elaborated on a method to enrich the membrane proteome of mature pollen from economically relevant crop using the example of Solanum lycopersicum (tomato). To isolate the pollen protein fraction enriched in membrane proteins, a high salt concentration (750 mM of sodium chloride) was used. The membrane protein-enriched fraction was then subjected to shotgun proteomics for identification of proteins, followed by in silico analysis to annotate and classify the detected proteins.

Transcriptomic Resources For The Medicinal Legume Mucuna Pruriens: De Novo Transcriptome Assembly, Annotation, Identification And Validation Of Est-Ssr Markers, N. Sathyanarayana, Ranjith Kumar Pittala, Pankaj Kumar Tripathi, Ratan Chopra, Heikham Russiachand Singh, Vikas Belamkar, Pardeep Kumar Bhardwaj, Jeff J. Doyle, Ashley N. Egan

Department of Agronomy and Horticulture: Faculty Publications

Background:

The medicinal legume Mucuna pruriens (L.) DC. has attracted attention worldwide as a source of the anti-Parkinson’s drug L-Dopa. It is also a popular green manure cover crop that offers many agronomic benefits including high protein content, nitrogen fixation and soil nutrients. The plant currently lacks genomic resources and there is limited knowledge on gene expression, metabolic pathways, and genetics of secondary metabolite production. Here, we present transcriptomic resources for M. pruriens, including a de novo transcriptome assembly and annotation, as well as differential transcript expression analyses between root, leaf, and pod tissues. We also develop microsatellite markers …

A Comprehensive Analysis Of Alternative Splicing In Paleopolyploid Maize, Wenbin Mei, Sanzhen Liu, James C. Schnable, Cheng-Ting Yeh, Nathan M. Springer, Patrick S. Schnable, William Brad Barbazuk

Department of Agronomy and Horticulture: Faculty Publications

Identifying and characterizing alternative splicing (AS) enables our understanding of the biological role of transcript isoform diversity. This study describes the use of publicly available RNA-Seq data to identify and characterize the global diversity of AS isoforms in maize using the inbred lines B73 and Mo17, and a related species, sorghum. Identification and characterization of AS within maize tissues revealed that genes expressed in seed exhibit the largest differential AS relative to other tissues examined. Additionally, differences in AS between the two genotypes B73 and Mo17 are greatest within genes expressed in seed. We demonstrate that changes in the level …

Phenotypic Variation And Genetic Purity Of The Original 'Prime-Jim®' X 'Arapaho' Population, Loren M. Luther

Horticulture Undergraduate Honors Theses

In 2013, Castro et al., produced the first linkage map for primocane-fruiting blackberries using the cross ‘Prime-Jim®’ x ‘Arapaho.’ This mapping population has been maintained since the original experiment with the hopes of conducting future studies. Further research was determined to be needed on the population to better characterize additional phenotypic traits, and since nine years had passed since the seedlings were established, there was a need to assess the continued genetic purity of the population using molecular methods. Phenotypic data was collected to analyze the variation of the population including soluble solids content, titratable acidity, average weight, shape, and …

Predicting Trait-Environment Relationships For Venation Networks Elong An Andes-Amazon Elevation Gradient, Benjamin Blonder, Norma Salinas, Lisa Patrick Bentley, Alexander Shenkin, Percy O. Chambi Porroa, Yolvi Valdez Tejeira, Cyrille Violle, Nikolaos M. Fyllas, Gregory R. Goldsmith, Roberta E. Martin, Gregory P. Asner, Sandra Diaz, Brian J. Enquist, Yadvinder Malhi

Biology, Chemistry, and Environmental Sciences Faculty Articles and Research

Understanding functional trait-environment relationships (TERs) may improve predictions of community assembly. However, many empirical TERs have been weak or lacking conceptual foundation. TERs based on leaf venation networks may better link individuals and communities via hydraulic constraints. We report measurements of vein density, vein radius, and leaf thickness for more than 100 dominant species occurring in ten forest communities spanning a 3,300 m Andes-Amazon elevation gradient in Peru. We use these data to measure the strength of TERs at community scale and to determine whether observed TERs are similar to those predicted by physiological theory. We found strong support for …

Ultramafic Geoecology Of South And Southeast Asia, M.L. Galey, A. Van Der Ent, M.C.M. Iqbal, N. Rajakaruna

Biological Sciences

Globally, ultramafic outcrops are renowned for hosting foras with high levels of endemism, including plants with specialised adaptations such as nickel or manganese hyperaccumulation. Soils derived from ultramafic regoliths are generally nutrient-deficient, have major cation imbalances, and have concomitant high concentrations of potentially phytotoxic trace elements, especially nickel. The South and Southeast Asian region has the largest surface occurrences of ultramafic regoliths in the world, but the geoecology of these outcrops is still poorly studied despite severe conservation threats. Due to the paucity of systematic plant collections in many areas and the lack of georeferenced herbarium records and databased information, …

Emergence, Competition, And Management Of Glyphosate-Resistant Common Ragweed (Ambrosia Artemisiifolia L.) In Nebraska Soybean, Ethann R. Barnes

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

Common ragweed (Ambrosia artemisiifolia L.) is a competitive annual broadleaf weed in soybean (Glycine max) production fields throughout North America. The recent confirmation of glyphosate-resistant common ragweed in Nebraska justified the need to assess the emergence pattern and competitive ability of common ragweed in soybean and to evaluate alternative herbicide programs for effective management. The objectives of this research were to: 1) evaluate the effect of tillage and develop a predictive model for the emergence pattern of common ragweed in Nebraska; 2) model the competitive interaction between soybean and common ragweed as influenced by density and irrigation …

Surveying The Distributions Of Melaleuca Quinquenervia, Psidium Cattleianum, And Litsea Glutinosa At Analalava Special Reserve, Hanusia Higgins

Independent Study Project (ISP) Collection

This study surveyed the distributions of three invasive plant species, Melaleuca quinquenervia, Psidium cattleianum, and Litsea glutinosa at the Analalava Special Reserve in Mahavelona, Madagascar. Analalava is a 229-hectare degraded patch of low-elevation humid forest on the northeast coast of Madagascar, and one of the last forest fragments remaining in the region. It is a haven for biodiversity, containing 343 recorded species of plants, 12 of which are locally endemic. Invasive species are considered the second-most significant threat to biodiversity, both worldwide and specifically at Analalava. Based on a systematic transect survey of these three targeted invasive species, their distributions …

Corn Residue Use By Livestock In The United States, Marty R. Schmer, Rachael M. Brown, Virginia L. Jin, Robert B. Mitchell, Daren D. Redfearn

Department of Agronomy and Horticulture: Faculty Publications

Corn (Zea mays L.) residue grazing or harvest provides a simple and economical practice to integrate crops and livestock, but limited information is available on how widespread corn residue utilization is practiced by US producers. In 2010, the USDA Economic Research Service surveyed producers from 19 states on corn grain and residue management practices. Total corn residue grazed or harvested was 4.87 million ha. Approximately 4.06 million ha was grazed by 11.7 million livestock (primarily cattle) in 2010. The majority of grazed corn residue occurred in Nebraska (1.91 million ha), Iowa (385,000 ha), South Dakota (361,000 ha), and Kansas …

A Comprehensive Image-Based Phenomic Analysis Reveals The Complex Genetic Architecture Of Shoot Growth Dynamics In Rice (Oryza Sativa), Malachy T. Campbell, Qian Du, Kan Liu, Chris J. Brien, Bettina Berger, Chi Zhang, Harkamal Walia

Agronomy & Horticulture -- Faculty Publications

Early vigor is an important trait for many rice (Oryza sativa L.)- growing environments. However, genetic characterization and improvement for early vigor is hindered by the temporal nature of the trait and strong genotype × environment effects. We explored the genetic architecture of shoot growth dynamics during the early and active tillering stages by applying a functional modeling and genomewide association (GWAS) mapping approach on a diversity panel of ~360 rice accessions. Multiple loci with small effects on shoot growth trajectory were identified, indicating a complex polygenic architecture. Natural variation for shoot growth dynamics was assessed in a subset …

2001 Lilley Cornett Woods Soil Data, Ryan W. Mcewan, Julia I. Chapman, Robert N. Muller

Data Files: Big Everidge Hollow Permanent Plots

Data collected in 2001 on the soil in the Big Everidge Hollow portion of the Lilley Cornett Woods Appalachian Ecological Research Station in southeastern Kentucky. Data key is provided in a supplemental file.

DOI: http://doi.org/10.26890/lcw.r9anrrko79