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Evolutionary Dynamics Of The Plastid Inverted Repeat: The Effects Of Expansion, Contraction, And Loss On Substitution Rates, Andan Zhu, Wenhu Guo, Weishu Fan, Jeffrey P. Mower

Center for Plant Science Innovation: Faculty Publications

• Rates of nucleotide substitution were previously shown to be several times slower in the plastid inverted repeat (IR) compared with single-copy (SC) regions, suggesting that the IR provides enhanced copy-correction activity.

• To examine the generality of this synonymous rate dependence on the IR, we compared plastomes from 69 pairs of closely related species representing 52 families of angiosperms, gymnosperms, and ferns.

• We explored the breadth of IR boundary shifts in land plants and demonstrate that synonymous substitution rates are, on average, 3.7 times slower in IR genes than in SC genes. In addition, genes moved from the SC into the …

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Insights Into The Molecular Antiviral Mechanism Of Pokeweed Protein From Phytolacca Americana, Valentina R. Aitbakieva, Artem V. Domashevskiy

Publications and Research

Agriculture is an indispensable part of every person’s life, ensuring that nutritious and inexpensive food is readily available. As any other organisms, plants are subject to numerous parasitic infections. Biological evolution has allowed plants to produce a variety of toxic compounds to deal with their pathogens. American pokeweed plant (Phytolacca americana) manufactures pokeweed antiviral protein, a ribosome inactivating protein that disrupts protein synthesis and lowers infectivity of many plant and animal viruses. The intricate mechanism of PAP antiviral activity entails a delicate coordination and interplay of several factors, allowing the plant to battle its invaders. Here, we examine the molecular …

A Floristic Study Of The Oak Leaf Lake Unit Of The Swan Lake Wildlife Management Area In Nicollet County, Minnesota, Heidi Rauenhorst

All Graduate Theses, Dissertations, and Other Capstone Projects

Prairies play an integral ecological role, protecting biodiversity and providing habitat for fauna. The number of prairie acres has significantly declined in Minnesota, making the existing prairies that much more valuable. The Oak Leaf Lake Unit of the Swan Lake Wildlife Management Area in Nicollet County, Minnesota (latitude 44.311050, longitude -94.015577) was purchased by the Minnesota Department of Natural Resources in 1994 and is being managed as tallgrass prairie. Floristic surveys were performed during the 2011 and 2012 growing seasons to gather baseline data. These data were used to assess the quality of the site through calculation of various indices …

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 …

Genome-Wide Association Mapping Of Qualitatively Inherited Traits In A Germplasm Collection, Nonoy B. Bandillo, Aaron J. Lorenz, George L. Graef, Diego Jarquin, David L. Hyten, Randall L. Nelson, James E. Specht

Department of Agronomy and Horticulture: Faculty Publications

Genome-wide association (GWA) has been used as a tool for dissecting the genetic architecture of quantitatively inherited traits. We demonstrate here that GWA can also be highly useful for detecting many major genes governing categorically defined phenotype variants that exist for qualitatively inherited traits in a germplasm collection. Genome-wide association mapping was applied to categorical phenotypic data available for 10 descriptive traits in a collection of ~13,000 soybean [Glycine max (L.) Merr.] accessions that had been genotyped with a 50,000 single nucleotide polymorphism (SNP) chip. A GWA on a panel of accessions of this magnitude can offer substantial statistical …

Dioxygenase-Encoding Atdao1 Gene Controls Iaa Oxidation And Homeostasis In Arabidopsis, Silvana Porco, Aleš Pěnčík, Afaf Rashed, Ute Voβ, Rubén Casanova-Sáez, Anthony Bishop, Agata Golebiowska, Rahul Bhosale, Ranjan Swarup, Kamal Swarup, Pavlína Penáková, Ondrej Novák, Paul E. Staswick, Peter Hedden, Andrew L. Phillips, Kris Vissenberg, Malcolm J. Bennett, Karin Ljung

Department of Agronomy and Horticulture: Faculty Publications

Auxin represents a key signal in plants, regulating almost every aspect of their growth and development. Major breakthroughs have been made dissecting the molecular basis of auxin transport, perception, and response. In contrast, how plants control the metabolism and homeostasis of the major form of auxin in plants, indole-3- acetic acid (IAA), remains unclear. In this paper, we initially describe the function of the Arabidopsis thaliana gene DIOXYGENASE FOR AUXIN OXIDATION 1 (AtDAO1). Transcriptional and translational reporter lines revealed that AtDAO1 encodes a highly root-expressed, cytoplasmically localized IAA oxidase. Stable isotope-labeled IAA feeding studies of loss and …

A Population Of Deletion Mutants And An Integrated Mapping And Exome-Seq Pipeline For Gene Discovery In Maize, Shangang Jia, Aixia Li, Kyla Morton, Penny Avoles-Kianian, Shahryar F. Kianian, Chi Zhang, David Holding

Department of Agronomy and Horticulture: Faculty Publications

To better understand maize endosperm filling and maturation, we used gamma irradiation of the B73 maize reference line to generate mutants with opaque endosperm and reduced kernel fill phenotypes, and created a population of 1788 lines including 47 Mo17 × F2s showing stable, segregating and viable kernel phenotypes. For molecular characterization of the mutants, we developed a novel functional genomics platform that combined Bulked Segregant RNA and Exome sequencing (BSREx-seq) to map causative mutations and identify candidate genes within mapping intervals. To exemplify the utility of the mutants and provide proof-ofconcept for the bioinformatics platform, we present detailed characterization of …

Comprehensive Comparative Genomic And Transcriptomic Analyses Of The Legume Genes Controlling The Nodulation Process, Zhenzhen Qiao, Lise Pingault, Mehrnoush Nourbakhsh-Rey, Marc Libault

Department of Agronomy and Horticulture: Faculty Publications

Nitrogen is one of the most essential plant nutrients and one of the major factors limiting crop productivity. Having the goal to perform a more sustainable agriculture, there is a need to maximize biological nitrogen fixation, a feature of legumes. To enhance our understanding of the molecular mechanisms controlling the interaction between legumes and rhizobia, the symbiotic partner fixing and assimilating the atmospheric nitrogen for the plant, researchers took advantage of genetic and genomic resources developed across different legume models (e.g., Medicago truncatula, Lotus japonicus, Glycine max, and Phaseolus vulgaris) to identify key regulatory protein coding genes of the nodulation …

Comparison Of An Ultra-Low Volume (Ulv) Sprayer Against A Conventional Sprayer, For Foliar Fertiliser And Fungicide Applications In Turfgrass, Jason Connor Ferguson, Roch E. Gaussoin, John A. Eastin, Matthew D. Sousek, Greg R. Kruger

Department of Agronomy and Horticulture: Faculty Publications

Two field studies (I and II) at the University of Nebraska-Lincoln: John Seaton Anderson Turfgrass Research Facility near Mead, NE, USA, were conducted to determine if a new ultra-low volume (ULV) sprayer can apply foliar nutrient, growth regulator, and fungicide treatments, in a manner similar to that of a conventional sprayer. Treatments were applied over creeping bentgrass ‘L-93’ (Agrostis stolonifera L.) managed as a fairway at 561 l · ha⁻¹ and 47 l · ha⁻¹ with the conventional and ULV sprayer, respectfully. Data were collected for chlorophyll content with a chlorophyll meter, and for the normalised difference …

Isoetes Mississippiensis: A New Quillwort From Mississippi, Usa, Peter W. Schafran, Steven W. Leonard, Rebecca D. Bray, W. Carl Taylor, Lytton John Musselman

Biological Sciences Faculty Publications

Isoetes mississippiensis S.W. Leonard, W.C. Taylor, L.J. Musselman and R.D. Bray (Isoetaceae, Lycopodiophyta) is a new species known from two sites along tributaries of the Pearl River in southern Mississippi. This species is distinguished from other species in the southeastern United States by a combination of character states including a basic diploid (2n=22) chromosome count, laevigate megaspores, and a narrow velum covering less than one-third of the adaxial sporangium wall.

Mechanisms, Applications, And Perspectives Of Antiviral Rna Silencing In Plants / Mecanismos, Aplicaciones Y Perspectivas Del Silenciamiento Génico De Virus En Plantas, Hernan Garcia-Ruiz, Mayra Teresa Garcia Ruiz, Sergio Manuel Gabriel Peralta, Cristina Betzabeth Miravel Gabriel, Kaoutar El-Mounadi

Department of Plant Pathology: Faculty Publications

Viral diseases of plants cause important economic losses due to reduction in crop quality and quantity to the point of threatening food security in some countries. Given the reduced availability of natural sources, genetic resistance to viruses has been successfully engineered for some plant-virus combinations. A sound understanding of the basic mechanisms governing plant-virus interactions, including antiviral RNA silencing, is the foundation to design better management strategies and biotechnological approaches to engineer and implement antiviral resistance in plants. In this review, we present current molecular models to explain antiviral RNA silencing and its application in basic plant research, biotechnology and …

Small Unmanned Aerial Vehicles (Micro-Uavs, Drones) In Plant Ecology, Mitchell B. Cruzan, Ben G. Weinstein, Monica R. Grasty, Brendan F. Kohrn, Elizabeth C. Hendrickson, Tina M. Arredondo, Pamela G. Thompson

Biology Faculty Publications and Presentations

Premise of the study: Low-elevation surveys with small aerial drones (micro–unmanned aerial vehicles [UAVs]) may be used for a wide variety of applications in plant ecology, including mapping vegetation over small- to medium-sized regions. We provide an overview of methods and procedures for conducting surveys and illustrate some of these applications.

Methods: Aerial images were obtained by flying a small drone along transects over the area of interest. Images were used to create a composite image (orthomosaic) and a digital surface model (DSM). Vegetation classification was conducted manually and using an automated routine. Coverage of an individual species …

Age-Old Palms On Florida’S Ancient Ridges, Warren G. Abrahamson Ii

Faculty Journal Articles

Genetic fingerprinting, ramet growth rate determinations, and mathematical modeling (Minimum branching trees) were used to estimate clone ages of saw palmettos at Archbold Biological Station in Florida. Growth rates indicate that 500 year old saw palmetto ramets are common. Genetically identified clones (genets) are estimated to be thousands of years old, likely exceeding 5,000 years of age.

Insights Into Triterpene Metabolism In Model Monocotyledonous And Oilseed Plants Genetically Engineered With Genes From Botryococcus Braunii, Chase F. Kempinski

Theses and Dissertations--Plant and Soil Sciences

Isoprenoids are one of the most diverse classes of natural products and are all derived from universal five carbon, prenyl precursors. Squalene and botryococcene are linear, hydrocarbon triterpenes (thirty carbon compounds with six prenyl units) that have industrial and medicinal values. Squalene is produced by all eukaryotes as it is the first committed precursor to sterols, while botryococcene is uniquely produced by the green algae, Botryococcus braunii (race B). Natural sources for these compounds exist, but there is a desire for more renewable production platforms. The model plant Arabidopsis thaliana was engineered to accumulate botryococcene and squalene in its oil …

Investigation Into The Cell Wall And Cellulose Biosynthesis In Model Species And In The C4 Model Plant Setaria Viridis, Mizuki Tateno

Theses and Dissertations--Plant and Soil Sciences

A uniform feature of all plant cells is the presence of a cell wall. The cell wall functions in facilitating directional expansion and is therefore important for cell shape and morphogenesis. All plant cell walls contain cellulose microfibrils embedded in a network of polysaccharides, lignin and protein. Cellulose is evolutionarily conserved and is made by all plants as well as other members of various taxonomic kingdoms. From a human perspective, the field of renewable energy has had an ever increasing interest in using the cell wall for production of renewable platform chemicals and fuels. However, the biosynthesis of these components …

Positive Interactions In Temperate And Tropical Alpine Plant Communities: The Role Of Facilitation In Species-Specific Interactions, Invasion, And Landscape-Scale Distribution, Nicole Hupp

Graduate Student Theses, Dissertations, & Professional Papers

No abstract provided.

The Effects Of Compost And Polyacrylamide Hydrogel On The Re-Vegetation Of Eroded Southern Aspects In The Western Rangeland, Allison R. Klocke, David A. Stein

Undergraduate Theses, Professional Papers, and Capstone Artifacts

MPG Ranch is a conservation-oriented organization in Montana’s Bitterroot valley. Since 2010, MPG has annually planted between 5,000 and 10,000 shrubs and trees with the goal of restoring native plant communities, beautifying the landscape, and providing habitat and forage for wildlife. Plant survival has been lowest on degraded south facing slopes, likely due to a combination of erosion and high solar radiation, which have left the soil with low nutrient content, soil moisture, and high soil temperatures. To resolve these issues, we partnered with MPG to test whether soil amendments can be used to increase plant establishment on degraded hillslopes. …

A Molecular Characterization Of The Fungal Endophytes Within The Needles Of Ponderosa Pine (Pinus Ponderosa), Amy E. Gray

EWU Masters Thesis Collection

"Fungal endophytes (microbial fungi that live in plant tissues without causing disease) are ubiquitous in plants studied to date. Many conifers host endophytes that produce important bioactive secondary metabolites. While the endophytes in Pinus ponderosa roots have been studied, the endophyte communities within the needles are not well characterized by molecular means: thus, the goal of this study was to do so. Needles were sampled at two sites located five kilometers apart along a slight precipitation gradient in Eastern Washington State. Fungal DNA (along with pine DNA) was isolated directly from needles of two ages. Internal transcribed spacer regions of …

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 …

Incidence Of Wheat Streak Mosaic Virus, Triticum Mosaic Virus, And Wheat Mosaic Virus In Wheat Curl Mites Recovered From Maturing Winter Wheat Spikes, E. Byamukama, S. Tatineni, G. Hein, J. Mcmechan, S. N. Wegulo

Department of Plant Pathology: Faculty Publications

Wheat curl mites (WCM; Aceria tosichella) transmit Wheat streak mosaic virus (WSMV), Triticum mosaic virus (TriMV), and Wheat mosaic virus (WMoV) to wheat (Triticum aestivum L.) in the Great Plains region of the United States. These viruses can be detected in single, double, or triple combinations in leaf samples. Information on incidence of viruses inWCM at the end of the growing season is scant. The availability of this information can enhance our knowledge of the epidemiology ofWCM-transmitted viruses. This research was conducted to determine the frequency of occurrence of WSMV, TriMV, and WMoV in WCM populations on fieldcollected maturing …

Developing The Framework For A Risk Map For Mite Vectored Viruses In Wheat Resulting From Pre-Harvest Hail Damage, Anthony L. Nguy-Robertson, Arthur Zygielbaum, Anthony J. Mcmechan, Gary L. Hein, Stephen N. Wegulo, Abby R. Stilwell, Travis M. Smith

Department of Plant Pathology: Faculty Publications

There is a strong economic incentive to reduce mite-vectored virus outbreaks. Most outbreaks in the central High Plains of the United States occur in the presence of volunteer wheat that emerges before harvest as a result of hail storms. This study provides a conceptual framework for developing a risk map for wheat diseases caused by mite-vectored viruses based on pre-harvest hail events. Traditional methods that use NDVI were found to be unsuitable due to low chlorophyll content in wheat at harvest. Site-level hyperspectral reflectance from mechanically hailed wheat showed increased canopy albedo. Therefore, any increase in NIR combined with large …

Cryptic Species: A Leitmotif Of Contemporary Mycology Has Challenges And Benefits For Plant Pathologists, Frank M. Dugan, Sydney Everhart

Department of Plant Pathology: Faculty Publications

Multiple traditional species names for plant pathogenic fungi have been supplemented with new names that delimit formerly cryptic species. In separate instances, isolates within a species are clearly differentiated by both phylogeny and distinctive pathogenic traits and are assigned sub-specific designations. These new species names and the sub-specific designations are both cases of cryptic species that are, in some instances, relevant and/or critical for plant disease management. Here we provide examples of such instances in which newly described taxa differ from the original (“parent”) in phenotypic traits of importance to plant disease management: host range, fungicide sensitivity, environmental niche, metabolite …

Sequence Variation In Two Genes Determines The Efficacy Of Transmission Of Citrus Tristeza Virus By The Brown Citrus Aphid, S. J. Harper, N. Killiny, Satyanarayana Tatineni, S. Gowda, S. J. Cowell, T. Shilts, W. O. Dawson

Department of Plant Pathology: Faculty Publications

Vector transmission is an important part of the viral infection cycle, yet for many viruses little is known about this process, or how viral sequence variation affects transmission efficacy. Here we examined the effect of substituting genes from the highly transmissible FS577 isolate of citrus tristeza virus (CTV) in to the poorly transmissible T36-based infectious clone. We found that introducing p65 or p61 sequences from FS577 significantly increased transmission efficacy. Interestingly, replacement of both genes produced a greater increase than either gene alone, suggesting that CTV transmission requires the concerted action of co-evolved p65 and p61 proteins.

Field Damage Of Sorghum (Sorghum Bicolor) With Reduced Lignin Levels By Naturally Occurring Insect Pests And Pathogens, Patrick F. Dowd, Deanna L. Funnell-Harris, Scott E. Sattler

Department of Plant Pathology: Faculty Publications

Sorghum (Sorghum bicolor (L.) Moench) brown midrib (bmr) mutant lines have reduced levels of lignin, which is a potentially useful trait for bioenergy production, but the effects of this trait on insect and plant pathogen interactions are unknown under field conditions. Field-grown bmr6, bmr12, and wild-type (WT) plants were examined for insect and disease damage. In most cases, observed frequency, population, or leaf area damage caused by insects or pathogens on bmr6 or bmr12 plants were not greater than those observed on WT plants in the field or laboratory assays. European corn borers [Ostrinia nubilalis (Hübner)(Lepidoptera: …

What's New In Plant Pathology, Anthony O. Adesemoye, Loren Giesler, Robert M. Harveson, Tamra A. Jackson-Ziems, Kevin Korus, Stephen N. Wegulo

Department of Plant Pathology: Faculty Publications

Changes to the Disease Management Section of the 2016 Guide for Weed, Disease, and Insect Management in Nebraska

Biological control Products

Trivapro Fungicide

Priaxor D. Fungicide

Table 1. Foliar products for disease control that were updated in the 2016 Guide for Weed, Disease and Insect Management in Nebraska.

Table 2. Seed treatment products for disease control that were updated in the 2016 Guide for Weed, Disease and Insect Management in Nebraska.

Table 3. Seed treatment nematicide product that was updated in the 2016 Guide for Weed, Disease and Insect Management in Nebraska.

Fungicide Application Timing And Disease Control, Tamra A. Jackson-Ziems, Loren J. Giesler, Robert M. Harveson, Stephen N. Wegulo, Kevin Korus, Anthony O. Adesemoye

Department of Plant Pathology: Faculty Publications

Wet weather that persisted during much of the 2015 growing season proved to be very favorable for disease development in several crops across Nebraska. In particular, diseases caused by fungi were favored by repeated rainfall events and high relative humidity, fog, etc., that supported the production of more spores and continuous plant infection. On some susceptible varieties and hybrids, diseases developed early and quickly eventually reaching moderate to severe levels. Foliar fungicides were applied one or more times to some crops in an effort to mitigate losses due to disease. However, low crop prices and narrow profit margins made foliar …

Corn Disease Update, Tamra A. Jackson-Ziems

Department of Plant Pathology: Faculty Publications

The 2015 corn crop was impacted by several corn diseases from the beginning to the end of the season and in all areas of Nebraska. The increased severity and incidence of some diseases was largely due to the extended periods of favorable weather conditions in varying parts of the state that supported the increase in some diseases. In particular, frequent rainfall and high relative humidity were especially favorable for several fungal diseases. Unfortunately, almost all diseases of corn (except rusts) are caused by pathogens that can successfully overwinter in Nebraska. For this reason, making detailed notes on disease development and …

Trivapro A + Trivapro B Application Timing And Disease Efficacy In Field Corn In Nebraska, 2015, J. D. Harbour, T. A. Jackson-Ziems

Department of Plant Pathology: Faculty Publications

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

Foliar Fungicide Comparison For Southern Rust Management, Stay Green, Push Lodging, And Yield In Nebraska, 2015, J. D. Harbour, T. A. Jackson-Ziems

Department of Plant Pathology: Faculty Publications

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