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Genome-Wide Discovery Of Natural Variation In Pre-Mrna Splicing And Prioritising Causal Alternative Splicing To Salt Stress Response In Rice, Huihui Yu, Qian Du, Malachy Campbell, Bin Yu, Harkamal Walia, Chi Zhang

School of Biological Sciences: Faculty Publications

• Pre-mRNA splicing is an essential step for the regulation of gene expression. In order to specifically capture splicing variants in plants for genome-wide association studies (GWAS), we developed a software tool to quantify and visualise Variations of Splicing in Population (VASP).
• VASP can quantify splicing variants from short-read RNA-seq datasets and discover genotype-specific splicing (GSS) events, which can be used to prioritise causal pre-mRNA splicing events in GWAS. We applied our method to an RNA-seq dataset with 328 samples from 82 genotypes from a rice diversity panel exposed to optimal and saline growing conditions.
• In total, 764 significant GSS events …

Complete Genome Sequence Of Geobacter Sp. Strain Feam09, A Moderately Acidophilic Soil Bacterium, Pooja Yadav, Sanjay Antony-Babu, Erin Hayes, Olivia M. Healy, Donald Pan, Wendy H. Yang, Whendee L. Silver, Christopher L. Anderson, Adam Voshall, Samodha C. Fernando, Etsuko N. Moriyama, Joshua R. Herr, Karrie A. Weber

School of Biological Sciences: Faculty Publications

A moderately acidophilic Geobacter sp. strain, FeAm09, was isolated from forest soil. The complete genome sequence is 4,099,068 bp with an average GC content of 61.1%. No plasmids were detected. The genome contains a total of 3,843 genes and 3,608 protein-coding genes, including genes supporting iron and nitrogen biogeochemical cycling.

Gwas Revealed Effect Of Genotype × Environment Interactions For Grain Yield Of Nebraska Winter Wheat, Shamseldeen Eltaher, P Stephen Baenziger, Vikas Belamkar, Hamdy A. Emara, Ahmed A. Nower, Khaled F.M. Salem, Ahmad M. Alqudah, Ahmed Sallam

Department of Agronomy and Horticulture: Faculty Publications

Background: Improving grain yield in cereals especially in wheat is a main objective for plant breeders. One of the main constrains for improving this trait is the G × E interaction (GEI) which affects the performance of wheat genotypes in different environments. Selecting high yielding genotypes that can be used for a target set of environments is needed. Phenotypic selection can be misleading due to the environmental conditions. Incorporating information from phenotypic and genomic analyses can be useful in selecting the higher yielding genotypes for a group of environments. Results: A set of 270 F_3:6 wheat genotypes in the …

An Environmental Assessment Of Cattle Manure And Urea Fertilizer Treatments For Corn Production In The Northern Great Plains, C. Alan Rotz, Senorpe Asem-Hiablie, Erin Cortus, Mindy J. Spiehs, Shafiqur Rahman, Anne Stoner

Roman L. Hruska U.S. Meat Animal Research Center: Reports

Nitrogen (N), phosphorus (P), and carbon (C) emissions from livestock systems have become important regional, national, and international concerns. Our objective was to use process-level simulation to explore differences among manure and inorganic fertilizer treatments in a corn production system used to feed finishing cattle in the Northern Great Plains region of the U.S. Our analysis included model assessment, simulation to compare treatments under recent climate, and comparisons using projected midcentury climate. The Integrated Farm System Model was evaluated in representing the performance and nutrient losses of corn production using cattle manure without bedding, manure with bedding, urea, and no …

Use Of Bedding Materials In Beef Bedded Manure Packs In Hot And Cool Ambient Temperatures: Effects On Ammonia, Hydrogen Sulfide, And Greenhouse Gas Emissions, Jeff P. Jaderborg, Mindy J. Spiehs, Bryan L. Woodbury, Alfredo Dicostanzo, David B. Parker

Roman L. Hruska U.S. Meat Animal Research Center: Reports

Throughout the Upper Midwest, producers have observed increased land and fertilizer prices, resulting in increased popularity of confinement feeding facilities such as mono-slope and hoop barns with bedded packs. Environmental and public pressure has been placed on the agriculture community to reduce ammonia (NH3), hydrogen sulfide (H2S), and greenhouse gas (GHG) emissions from concentrated animal feeding operations (CAFOs). This study was conducted to determine the effects of bedding material (corn stover (CS), bean stover (BS), wheat straw (WS), or pine wood chips (PC)) and ambient temperature (15°C (COOL) or 30°C (HOT)) on NH3, CH4, CO2, N2O, and H2S flux in …

Comparison Of Performance Of F1 Romanov Crossbred Ewes With Wool And Hair Breeds During Spring Lambing Under Intensive And Extensive Production Systems, Brad A. Freking, Thomas W. Murphy

Roman L. Hruska U.S. Meat Animal Research Center: Reports

The objective was to evaluate wool (Dorset and Rambouillet) and hair (Dorper, Katahdin, and White Dorper) breeds for their ability to complement Romanov germplasm in two distinct production systems by estimating direct sire and grandsire effects on lamb growth, survival, and ewe productivity traits. Rams of the five breeds (n = 75) were mated to Romanov ewes (n = 459) over a 3-yr period to produce five types of crossbred lambs (n = 2,739). Sire breed (P > 0.06) did not impact body weight or survival traits of the first-generation crossbred (F1) lambs. The productivity of retained crossbred ewes (n = …

Accuracy Of Gebv Of Sires Based On Pooled Allele Frequency Of Their Progeny, Napoleón Vargas Jurado, Larry A. Kuehn, John W. Keele, Ronald M. Lewis

Roman L. Hruska U.S. Meat Animal Research Center: Reports

Despite decreasing genotyping costs, in some cases individually genotyping animals is not economically feasible (e.g., in small ruminants). An alternative is to pool DNA, using the pooled allele frequency (PAF) to garner information on performance. Still, the use of PAF for prediction (estimation of genomic breeding values; GEBVs) has been limited. Two potential sources of error on accuracy of GEBV of sires, obtained from PAF of their progeny themselves lacking pedigree information, were tested: (i) pool construction error (unequal contribution of DNA from animals in pools), and (ii) technical error (variability when reading the array). Pooling design (random, extremes, K-means), …

Development And Validation Of A Neural Network For The Automated Detection Of Horn Flies On Cattle, Eric T. Psota, E. K. Luc, G. M. Pighetti, L. G. Schneider, R. T. Trout Fryxell, J. W. Keele, L. A. Kuehn

Roman L. Hruska U.S. Meat Animal Research Center: Reports

When the number of horn flies that blood feed on cattle exceeds the economic threshold, they can adversely affect the health and wellbeing of their hosts. Excessive horn fly burdens also lead to reduced weight gain and, consequently, diminished profits for livestock producers. Effective management and treatment require reliable surveillance methods for estimating the degree of horn fly burden (i.e., counting the number of flies on cattle). Traditionally, these estimates are obtained through human visual estimation, either in-person or by counting images on a photo; however, these methods are costly both in terms of time and labor and are prone …

Use Of Bedding Materials In Beef Bedded Manure Packs At Hot And Cold Ambient Temperatures: Effects On Odorous Volatile Organic Compounds And Odor Activity Values, Jeff P. Jaderborg, Mindy J. Spiehs, Bryan L. Woodbury, Alfredo Dicostanzo, David B. Parker

Roman L. Hruska U.S. Meat Animal Research Center: Reports

Beef cattle producers are beginning to raise cattle in confinement facilities such as slatted-floor barns, hoop barns, and mono-slope facilities. Hoop and mono-slope facilities typically use bedding packs as part of their manure management system, with crop residues being the most commonly used bedding material. This study was conducted to determine the effects of bedding material, i.e., corn stover (CS), bean stover (BS), wheat straw (WS), or pine wood chips (PC), and environmental ambient temperature, i.e., cold (15°C) or hot (30°C), on the concentrations of odorous volatile organic compounds (VOCs) in air samples collected in the headspace above lab-scale bedded …

Widespread Mortality Of Trembling Aspen (Populus Tremuloides) Throughout Interior Alaskan Boreal Forests Resulting From A Novel Canker Disease, Roger W. Ruess, Loretta M. Winton, Gerard C. Adams

Department of Plant Pathology: Faculty Publications

Over the past several decades, growth declines and mortality of trembling aspen throughout western Canada and the United States have been linked to drought, often interacting with outbreaks of insects and fungal pathogens, resulting in a “sudden aspen decline” throughout much of aspen’s range. In 2015, we noticed an aggressive fungal canker causing widespread mortality of aspen throughout interior Alaska and initiated a study to quantify potential drivers for the incidence, virulence, and distribution of the disease. Stand-level infection rates among 88 study sites distributed across 6 Alaska ecoregions ranged from <1 to 69%, with the proportion of trees with canker that were dead averaging 70% across all sites. The disease is most prevalent north of the Alaska Range within the Tanana Kuskokwim ecoregion. Modeling canker probability as a function of ecoregion, stand structure, landscape position, and climate revealed that smaller-diameter trees in older stands with greater aspen basal area have the highest canker incidence and mortality, while younger trees in younger stands appear virtually immune to the disease. Sites with higher summer vapor pressure deficits had significantly higher levels of canker infection and mortality. We believe the combined effects of this novel fungal canker pathogen, drought, and the persistent aspen leaf miner outbreak are triggering feedbacks between carbon starvation and hydraulic failure that are ultimately driving widespread mortality. Warmer early-season temperatures and prolonged late summer drought are leading to larger and more severe wildfires throughout interior Alaska that are favoring a shift from black spruce to forests dominated by Alaska paper birch and aspen. Widespread aspen mortality fostered by this rapidly spreading pathogen has significant implications for successional dynamics, ecosystem function, and feedbacks to disturbance regimes, particularly on sites too dry for Alaska paper birch.

Up-Regulation Of Apoptotic- And Cell Survival-Related Gene Pathways Following Exposures Of Western Corn Rootworm To B. Thuringiensis Crystalline Pesticidal Proteins In Transgenic Maize Roots, Brad S. Coates, Emeline Deleury, Aaron J. Gassmann, Bruce E. Hibbard, Lance Meinke, Nicholas J. Miller, Jennifer L. Petzold-Maxwell, B. Wade French, Thomas W. Sappington, Blair D. Siegfried, Thomas Guillemaud

Department of Entomology: Faculty Publications

Background: Resistance of pest insect species to insecticides, including B. thuringiensis (Bt) pesticidal proteins expressed by transgenic plants, is a threat to global food security. Despite the western corn rootworm, Diabrotica virgifera virgifera, being a major pest of maize and having populations showing increasing levels of resistance to hybrids expressing Bt pesticidal proteins, the cell mechanisms leading to mortality are not fully understood.

Results: Twenty unique RNA-seq libraries from the Bt susceptible D. v. virgifera inbred line Ped12, representing all growth stages and a range of different adult and larval exposures, were assembled into a reference transcriptome. Ten-day exposures …

Comment On: “A Review Of The Complementary Principle Of Evaporation: From The Original Linear Relationship To Generalized Nonlinear Functions” By Han And Tian (2020), Richard D. Crago, Jozsef Szilagyi, Russell Qualls

School of Natural Resources: Faculty Publications

The paper by Han and Tian (2020) reviews the history of developments in the complementary relationship (CR) between actual and potential evaporation and introduces the generalized complementary principle (GCP) developed by the authors. This comment assesses whether the GCP: (1) can give reasonable results from a wide range of surfaces worldwide; (2) is supported by experimental data that verify the three stages of evaporation implicit in the GCP, particularly in the wet-surface limit; (3) has been proven to be correct by the authors in a previous paper; and (4) is supported by model studies showing that wet surfaces occur predominantly …

Is Hay For The Birds? Investigating Landowner Willingness To Time Hay Harvests For Grassland Bird Conservation, Matthew P. Gruntorad, Katherine A. Graham, Nico Arcilla, Christopher J. Chizinski

School of Natural Resources: Faculty Publications

Birds in agricultural environments have exhibited steep global population declines in recent decades, and effective conservation strategies targeting their populations are urgently needed. In grasslands used for hay production, breeding birds’ nest success improves substantially if hay harvests are delayed until after mid-July. However, few studies have investigated private hay producers’ willingness to alter their harvesting practices to support bird conservation, a critical factor for bird conservation where most land is privately owned, such as in the North American Great Plains. We surveyed Nebraska hay producers to examine whether livestock production, wildlife knowledge, and hunting activity affects their willingness to …

A Unified Vegetation Index For Quantifying The Terrestrial Biosphere, Gustau Camps-Valls, Manuel Campos-Taberner, Alvaro Moreno-Martinez, Sophia Walther, Gregory Duveiller, Alessandro Cescatti, Miguel D. Mahecha, Jordi Munoz-Mari, Francisco Javier Garcia-Haro, Luis Guanter, Martin Jung, John A. Gamon, Markus Reichstein, Steven W. Running

School of Natural Resources: Faculty Publications

Empirical vegetation indices derived from spectral reflectance data are widely used in remote sensing of the biosphere, as they represent robust proxies for canopy structure, leaf pigment content, and, subsequently, plant photosynthetic potential. Here, we generalize the broad family of commonly used vegetation indices by exploiting all higher-order relations between the spectral channels involved. This results in a higher sensitivity to vegetation biophysical and physiological parameters. The presented nonlinear generalization of the celebrated normalized difference vegetation index (NDVI) consistently improves accuracy in monitoring key parameters, such as leaf area index, gross primary productivity, and sun-induced chlorophyll fluorescence. Results suggest that …

Combining Uav-Rgb High-Throughput Field Phenotyping And Genome-Wide Association Study To Reveal Genetic Variation Of Rice Germplasms In Dynamic Response To Drought Stress, Zhao Jiang, Haifu Tu, Baowei Bai, Chenghai Yang, Biquan Zhao, Ziyue Guo, Qian Liu, Hu Zhao, Wanneng Yang, Lizhong Xiong, Jian Zhang

School of Natural Resources: Faculty Publications

Accurate and high-throughput phenotyping of the dynamic response of a large rice population to drought stress in the field is a bottleneck for genetic dissection and breeding of drought resistance.

Here, high-efficiency and high-frequent image acquisition by an unmanned aerial vehicle (UAV) was utilized to quantify the dynamic drought response of a rice population under field conditions. Deep convolutional neural networks (DCNNs) and canopy height models were applied to extract highly correlated phenotypic traits including UAV-based leaf-rolling score (LRS_uav), plant water content (PWC_uav) and a new composite trait, drought resistance index by UAV (DRI_uav).

The DCNNs achieved high accuracy (correlation …

How Well Do U.S. Western Water Markets Convey Economic Information, R. Rimsaite, K. Fisher-Vanden, S. Olmstead, D. Grogan

School of Natural Resources: Faculty Publications

No abstract provided.

Assessing The Value Extension Adds To Decision Making Among Natural Resource Leaders, R. Rimsaite, M. Kreye

School of Natural Resources: Faculty Publications

No abstract provided.

Guiding Principles For Using Satellite-Derived Maps In Rangeland Management, B.W. Allred, M.K. Creutzburg, J.C. Carlson, C.J. Cole, C.M. Dovichin, M.C. Duniway, O. Jones, J.D. Maestas, D.E. Naugle, T.W. Nauman, G.S. Okin, M.C. Reeves, Matthew C. Rigge, L. Savage, Dirac Twidwell, D.R. Uden, B. Zhou

School of Natural Resources: Faculty Publications

No abstract provided.

Improving Landsat Predictions Of Rangeland Fractional Cover With Multi-Task Learning And Uncertainty, B.W. Allred, B. Bestelmeyer, C.S. Boyd, C. Brown, K.W. Davies, M. Ellsworth, T. Erickson, S.D. Fuhlendorf, T.V. Griffiths, V. Jansen, M.O. Jones, J. Karl, A. Knight, J.D. Maestas, J.J. Maynard, S.E. Mccord, D.E. Naugle, H.D. Starns, D. Twidwell, D.R. Uden

School of Natural Resources: Faculty Publications

No abstract provided.

Tracking Spatial Regimes As An Early Warning For A Species Of Conservation Concern, C.P. Roberts, D.R. Uden, S.M. Cady, B.W. Allred, S.D. Fuhlendorf, M.O. Jones, J.D. Maestas, D.E. Naugle, A.C. Olsen, J. Smith, J. Tack, D. Twidwell

School of Natural Resources: Faculty Publications

No abstract provided.

Iterative Scenarios For Social-Ecological Systems, D. Herrmann, K. Schwarz, C. Allen, D. Angeler, T. Eason, A. Garmestani

School of Natural Resources: Faculty Publications

No abstract provided.

Panarchy And Management Of Lake Ecosystems, D. Angeler, C. Allen, A. Garmestani, L. Gunderson, R. Johnson

School of Natural Resources: Faculty Publications

No abstract provided.

Overcoming An “Irreversible” Threshold: A 15-Year Fire Experiment, Christine H. Bielski, Rheinhardt Scholtz, Victoria Donovan, Craig R. Allen, Dirac Twidwell

School of Natural Resources: Faculty Publications

A key pursuit in contemporary ecology is to differentiate regime shifts that are truly irreversible from those that are hysteretic. Many ecological regime shifts have been labeled as irreversible without exploring the full range of variability in stabilizing feedbacks that have the potential to drive an ecological regime shift back towards a desirable ecological regime. Removing fire from grasslands can drive a regime shift to juniper woodlands that cannot be reversed using typical fire frequency and intensity thresholds, and has thus been considered irreversible. This study uses a unique, long-term experimental fire landscape co-dominated by grassland and closed-canopy juniper woodland …

Joint Effects Of Climate, Tree Size, And Year On Annual Tree Growth Derived From Tree-Ring Records Of Ten Globally Distributed Forests, K.J. Anderson-Teixeira, V. Hermann, C.R. Rollinson, B. Gonzalez, E.B. Gonzalez-Akre, N. Pederson, M.R. Alexander, C.D. Allen, R. Alfaro-Sanchez, T. Awada, J.L. Baltzer, P. J. Baker, J. D. Birch, S. Bunyavejchewin, P. Cherubini, S. J. Davies, C. Dow, R. Helcoski, J. Kaspar, J. A. Lutz, E. Q. Margolis, J. T. Maxwell, S. M. Mcmahon, C. Piponiot, S. E. Russo, P. Samonil, A. E. Sniderhan, A. J. Tepley, I. Vasickova, M Vlam, P. A. Zuidema

School of Natural Resources: Faculty Publications

No abstract provided.

Big Cats In The Big City: Spatial Ecology Of Mountain Lions In Greater Los Angeles, S. P. Riley, J. A. Sikich, J. F. Benson

School of Natural Resources: Faculty Publications

No abstract provided.

A Conceptual Framework For Social, Behavioral, And Environmental Change Through Stakeholder Engagement In Water Resource Management, W. M. Eaton

School of Natural Resources: Faculty Publications

No abstract provided.

Harnessing The Neon Data Revolution To Advance Open Environmental Science With Diverse And Data-Capable Community, R. C. Nagy, J. Corman Et Al.

School of Natural Resources: Faculty Publications

No abstract provided.

Multi-Feature Data Repository Development And Analytics For Image Cosegmentation In High-Throughput Plant Phenotyping, R. Quinones, F. Munoz-Arriola, S. Das Choudhury, A. Samal

School of Natural Resources: Faculty Publications

No abstract provided.

Whooping Crane (Grus Americana) Family Consumes A Diversity Of Aquatic Vertebrates During Fall Migration Stopover At The Platte River, Nebraska, Andrew J. Caven, Keith D. Koupal, David M. Baasch, Emma M. Brinley Buckley, Jenna M. Malzahn, Michael David Forsberg, Mariah Lundgren

School of Natural Resources: Faculty Publications

The Aransas-Wood Buffalo population of Whooping Cranes (Grus americana) migrates approximately 4000 km through the central Great Plains biannually, between their breeding and wintering grounds. Whooping Cranes depend on stopover sites to provide secure resting locations and the caloric resources necessary to complete their migration, such as the USFWS-designated critical habitat area in the Central Platte River Valley (CPRV) of Nebraska. This area includes braided river habitat characterized by low-elevation and submerged sandbars, which provide important roosting and foraging opportunities for migrating Whooping Cranes. We used long-range photography, videography, and behavioral scan sampling to document forage items consumed by Whooping …

Coupling Spectral And Resource-Use Complementarity In Experimental Grassland And Forest Communites, A. K. Schweiger, J. Cavender-Bares, P. Townsend, M. Madritch, J. Grossman, H. Gholizadeh, R. Wang, J. Gamon

School of Natural Resources: Faculty Publications

No abstract provided.