Life Sciences Commons^™

Transformation And Gene Editing In The Bioenergy Grass Miscanthus, Anthony Trieu, Mohammad B. Belaff, Pradeepa Hirannaiah, Shilpa Manjunatha, Rebekah Wood, Yokshitha Bathula, Rebecca L. Billingsley, Anjali Arpan, Erik J. Sacks, Thomas E. Clemente, Stephen P. Moose, Nancy A. Reichert, Kankshita Swaminathan

Department of Agronomy and Horticulture: Faculty Publications

Background: Miscanthus, a C4 member of Poaceae, is a promising perennial crop for bioenergy, renewable bioproducts, and carbon sequestration. Species of interest include nothospecies M. x giganteus and its parental species M. sacchariforus and M. sinensis. Use of biotechnology-based procedures to genetically improve Miscanthus, to date, have only included plant transformation procedures for introduction of exogenous genes into the host genome at random, non-targeted sites.

Results: We developed gene editing procedures for Miscanthus using CRISPR/Cas9 that enabled the mutation of a specific (targeted) endogenous gene to knock out its function. Classified as paleo-allopolyploids (duplicated ancient …

Yield Prediction Through Integration Of Genetic, Environment, And Management Data Through Deep Learning, Daniel R. Kick, Jason G. Wallace, James C. Schnable, Judith M. Kolkman, Barış Alaca, Timothy M. Beissinger, Jode Edwards, David Ertl, Sherry Flint-Garcia, Joseph L. Gage, Candice N. Hirsch, Joseph E. Knoll, Natalia De Leon, Dayane C. Lima, Danilo E. Moreta, Maninder P. Singh, Addie Thompson, Teclemariam Weldekidan, Jacob D. Washburn

Department of Agronomy and Horticulture: Faculty Publications

Accurate prediction of the phenotypic outcomes produced by different combinations of genotypes, environments, and management interventions remains a key goal in biology with direct applications to agriculture, research, and conservation. The past decades have seen an expansion of new methods applied toward this goal. Here we predict maize yield using deep neural networks, compare the efficacy of 2 model development methods, and contextualize model performance using conventional linear and machine learning models. We examine the usefulness of incorporating interactions between disparate data types. We find deep learning and best linear unbiased predictor (BLUP) models with interactions had the best overall …

Genetic Variation In Common Bunt Resistance In Synthetic Hexaploid Wheat, Amira M. I. Mourad, Alexey Morgounov, P. Stephen Baenziger, Samar M. Esmail

Department of Agronomy and Horticulture: Faculty Publications

Common bunt (caused by Tilletia caries and T. Foetida) is a major wheat disease. It occurs frequently in the USA and Turkey and damages grain yield and quality. Seed treatment with fungicides is an effective method to control this disease. However, using fungicides in organic and low-income fields is forbidden, and planting resistant cultivars are preferred. Due to the highly effective use of fungicides, little effort has been put into breeding resistant genotypes. In addition, the genetic diversity for this trait is low in modern wheat germplasm. Synthetic wheat genotypes were reported as an effective source to increase the …

Inheritance Of 2,4‑Dichlorophenoxyacetic Acid (2,4‑D) Resistance In Amaranthus Palmeri, Chandrima Shyam, Dallas E. Peterson, Amit J. Jhala, Mithila Jugulam

Department of Agronomy and Horticulture: Faculty Publications

In this study, the inheritance of 2,4-D resistance in a multiple herbicide-resistant Palmer amaranth (KCTR) was investigated. Direct and reciprocal crosses were performed using 2,4-D-resistant KCTR and susceptible KSS plants to generate F₁ progenies. 2,4-D dose–response assays were conducted to evaluate the response of progenies from each F₁ family along with KCTR and KSS plants in controlled environmental growth chambers. Additionally, 2,4-D-resistant male and female plants from each of the F₁ families were used in pairwise crosses to generate pseudo-F₂ families. Segregation (resistance or susceptibility) of progenies from the F₂ families in response to a …

A Stealth Health Approach To Dietary Fibre, P. Stephen Baenziger, Katherine Anna Frels, Steve Greenspan, Julie Jones, Alison Lovegrove, Devin J. Rose, Peter Shewry, Rod Wallace

Department of Agronomy and Horticulture: Faculty Publications

Average dietary fibre intakes have increased little in the past twenty years in many countries, including the USA¹ . Multi-million-dollar campaigns promoting fruits, vegetables, whole grains and other foods high in fibre have delivered only small changes in diets² , and consumers have not changed from traditional staples to whole-grain options³ . UK millers report that consumption of whole-wheat bread has actually declined over the past decade (P. Shewry, personal communication). In the US, white flour, which is lower in fibre than whole-wheat flour, accounts for nearly 40% of the fibre intake⁴ . We believe that …

Rural Movers Studies ... People Are Moving For Community Attributes And Jobs, Marilyn R. Schlake

Cornhusker Economics

University of Minnesota researchers conducted a Rural Movers Study to determine the motivations of people who moved within one to five years to rural Minnesota communities. Their findings are not unlike earlier research conducted at the University of Nebraska in 2008. The Rural Movers Study showed that 31 % of respondents moved due to a job or job offer. However, this was not one of the primary reasons individuals moved. For those individuals who did not move for employment, 76% wanted to find a good environment for raising their children, 67% moved to be closer to relatives, 64% looked for …

Genetic Variations Of Narcissus Tazetta And Selected Narcissus Cultivars Based On The Sequence Analysis Of Nrits And TrnL‑Is‑TrnF Regions, Seo Young Park, Mi Jin Jeon, Young Hee Joung, Keenan L. Amundsen, Gianluca Burchi, Angelo Porcelli, Mark S. Roh

Department of Agronomy and Horticulture: Faculty Publications

Narcissus tazetta var. chinensis (N. taz. var. chi.) accessions collected from the coastal areas of China, Korea, and Japan were compared with accessions of lower ranks of Narcissus tazetta (N. taz.) from Italy to study the genetic variations and with several morphologically similar cultivars available in the trade. Sequences of the internal transcribed spacer (ITS) regions of nuclear ribosomal DNA (nrITS) dendrogram and the chloroplast trnL-IS-trnF intergeneric spacer-gene (cpIS) were analyzed by maximum likelihood (ML) and posterior probability using STRUCTURE program. All single fower form of N. taz. var. chi. collected from China, Korea, and …

March 1st Filing Deadline, Tina N. Barrett

Cornhusker Economics

One of the many special tax provisions that has applied only to qualified farmers is the relief from estimated tax requirements. A qualified farmer, who is a calendar year taxpayer, can avoid the estimated tax payment penalty by either: 1) Filing an estimated tax payment by January 15th that is either 2/3 of your expected tax for the current year or 100% of last year's tax, whichever is less, or 2) Filing and paying 100% of the tax by March 1'1.

Poisson Hurdle Model-Based Method For Clustering Microbiome Features, Zhili Qiao, Elle Barnes, Susannah Tringe, Daniel P. Schachtman, Peng Liu

Department of Agronomy and Horticulture: Faculty Publications

Motivation: High-throughput sequencing technologies have greatly facilitated microbiome research and have generated a large volume of microbiome data with the potential to answer key questions regarding microbiome assembly, structure and function. Cluster analysis aims to group features that behave similarly across treatments, and such grouping helps to highlight the functional relationships among features and may provide biological insights into microbiome networks. However, clustering microbiome data are challenging due to the sparsity and high dimensionality.

Results: We propose a model-based clustering method based on Poisson hurdle models for sparse microbiome count data. We describe an expectation–maximization algorithm and a …

Deciphering The Genetic Architecture Of Key Female Floral Traits For Hybrid Wheat Seed Production, Juan Jimenez

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

Wheat (Triticum aestivum L.) is a staple cereal that provides 20% of the calories and proteins in human intake (Ray et al., 2013). Global population is projected to increase to 9.7 billion by 2050. Food production must increase by 70% to feed this future population. Wheat production is in crisis due to political and environmental challenges and is projected to decline by 0.8% in 2022 (FAO, 2022). To ensure food security yield genetic gain must increase by around 1.4% annually. Taking advantage of heterosis, hybrid wheat has the potential to boost grain yield. However, hybrid wheat seed production systems …

The Invisible Meat Microcosmos - Investigations Of Processed Meats' Specific Spoilage Organisms, Rebecca Furbeck

Department of Animal Science: Dissertations, Theses, and Student Research

As humankind grows in population, so will our need to compete against bacterial populations which spoil foodstuffs before we are able to consume them. This dissertation aims to identify the bacterial communities responsible for meat spoilage, and the mechanisms that govern the behaviors of these organisms. The literature review summarizes the state of knowledge regarding factors that influence meat microbiome composition, and how analytical methods can influence research outcomes. Study 1 aimed to identify the impact of additional ingredients and processing steps on the microbial ecology of processed turkey products. The main specific spoilage organisms (SSOs) belonged to the orders …

Molecular Mechanisms Underlying Aberrant Circulating Steroid Hormones In Gnrhr-Ii Knockdown Boars And Their Control Littermates, Dorothy Elsken

Department of Animal Science: Dissertations, Theses, and Student Research

Swine are the only livestock species that produce a functional protein for both GnRH-II and its receptor (GnRHR-II). Our laboratory reported that the interaction between GnRH-II and GnRHR-II facilitates testosterone production, independent of LH stimulation. To further examine GnRHR-II function, we developed a swine line with 70% reduced GnRHR-II mRNA levels (GnRHR-II KD) compared to control littermates. Mass spectrometry analysis of serum revealed that circulating levels of gonadal steroids were reduced in mature transgenic vs. control boars. Paradoxically, evaluation of testicular tissue indicated no difference between lines for gonadal steroid hormone levels. To address a potential cause for this discrepancy, …

Variance Component Estimates For Growth Traits In Beef Cattle Using Selected Variants From Imputed Low-Pass Sequence Data, Chad A. Russell

Department of Animal Science: Dissertations, Theses, and Student Research

A beef cattle population (n=2,343) was used to assess the impact of variants identified from imputed low-pass sequence (LPS) on the estimation of variance components and genetic parameters of birth weight (BWT) and post weaning gain (PWG). Variants were selected based on functional impact and were partitioned into four groups (Low, Modifier, Moderate, High) based on predicted functional consequences and re-partitioned based on consequence of mutation, such as missense and untranslated region variants, into six groups (G1-G6). Each subset was used to construct a genomic relationship matrix (GRM) for univariate animal models. Multiple analyses were conducted to compare the proportion …

Environmental Determination Of Gastrointestinal Parasitism In Katahdin Sheep, Brian Arisman

Department of Animal Science: Dissertations, Theses, and Student Research

Gastrointestinal nematodes (GIN) negatively affect the performance and wellbeing of sheep and are difficult to control due to anthelmintic resistance. Producers are therefore choosing breeds naturally resistant to GIN infection, such as the Katahdin. Katahdin are raised in various climates and management systems in the U.S., and those environmental factors can be combined into eco-management clusters. We hypothesized that GIN challenge varies predictably based on the characteristics of these clusters. Katahdin producers from across the U.S. were surveyed for management information. Body weights (BW), fecal egg counts (FEC) and FAMACHA scores (FAM) were collected on 3,527 Katahdin lambs around 90 …

Increased Bundle-Sheath Leakiness Of Co2 During Photosynthetic Induction Shows A Lack Of Coordination Between The C4 And C3 Cycles, Yu Wang, Samantha S. Stutz, Carl J. Bernacchi, Ryan A. Boyd, Donald R. Ort, Stephen P. Long

United States Department of Agriculture-Agricultural Research Service / University of Nebraska-Lincoln: Faculty Publications

Use of a complete dynamic model of NADP-malic enzyme C4 photosynthesis indicated that, during transitions from dark or shade to high light, induction of the C4 pathway was more rapid than that of C3, resulting in a predicted transient increase in bundle-sheath CO2 leakiness (ϕ). Previously, ϕ has been measured at steady state; here we developed a new method, coupling a tunable diode laser absorption spectroscope with a gas-exchange system to track ϕ in sorghum and maize through the nonsteady-state condition of photosynthetic induction. In both species, ϕ showed a transient increase to > 0.35 before declining to a steady state …

2022 Wics Conference. Water And Integrated Cropping Systems: Driving Research, Teaching, And Extension Impact --Slide Presentation

WICS Conferences

What conference attendees had to say:

"The teaching overview and panel discussion provided many insights on how education pathways are evolving and the need to create diverse opportunities to meet dynamic needs."

"The extension component was valuable in seeing how those doing research can collaborate with and assist extension educators to make a greater impact in the state."

"It was good to learn what relevant research is being conducted and also the work being done in teaching in regards to water and cropping systems."

It was a great first WICS Conference. The discussions have only just begun.

A Glass Bead Semi-Hydroponic System For Intact Maize Root Exudate Analysis And Phenotyping, Martha G. Lopez-Guerrero, Peng Wang, Felicia Phares, Daniel P. Schachtman, Sophie Alvarez, Karin V. Van Dijk

Department of Agronomy and Horticulture: Faculty Publications

Background: Although there have been numerous studies describing plant growth systems for root exudate collection, a common limitation is that these systems require disruption of the plant root system to facilitate exudate collection. Here, we present a newly designed semi-hydroponic system that uses glass beads as solid support to simulate soil impedance, which combined with drip irrigation, facilitates growth of healthy maize plants, collection and analysis of root exudates, and phenotyping of the roots with minimal growth disturbance or root damage. Results: This system was used to collect root exudates from seven maize genotypes using water or 1 mM CaCl2, …

Comparative Genome Analysis Of Plant Ascomycete Fungal Pathogens With Different Lifestyles Reveals Distinctive Virulence Strategies, Yansu Wang, Jie Wu, Jiacheng Yan, Ming Guo, Lei Xu, Liping Hou, Quan Zou

Department of Agronomy and Horticulture: Faculty Publications

Background: Pathogens have evolved diverse lifestyles and adopted pivotal new roles in both natural ecosystems and human environments. However, the molecular mechanisms underlying their adaptation to new lifestyles are obscure. Comparative genomics was adopted to determine distinct strategies of plant ascomycete fungal pathogens with different lifestyles and to elucidate their distinctive virulence strategies. Results: We found that plant ascomycete biotrophs exhibited lower gene gain and loss events and loss of CAZyme-encoding genes involved in plant cell wall degradation and biosynthesis gene clusters for the production of secondary metabolites in the genome. Comparison with the candidate effectome detected distinctive variations between …

Biobased Sprayable Mulch Films Suppressed Annual Weeds In Vegetable Crops, Eliott Gloeb, Sibel Irmak, Loren Isom, John L. Lindquist, Samuel E. Wortman

Department of Agronomy and Horticulture: Faculty Publications

Biobased sprayable mulch (BSM) films are a potential alternative to herbicides, polyethylene plastic mulch film, and hand weeding for specialty crops. We developed a series of BSM films using locally available biomaterials [including corn (Zea mays) starch, glycerol, keratin hydrolysate, corn gluten meal, corn zein, eggshells, and isolated soy (Glycine max) protein] and tested their effects on weeds and crop yield during a total of seven greenhouse or field trials between 2017 and 2019 in Nebraska, USA. Application rates of BSM films applied in pots (greenhouse), planting holes in plastic film (field), or bed tops (field) …

Comparative Genomics Of Five Valsa Species Gives Insights On Their Pathogenicity Evolution, Guangchao Sun, Shichang Xie, Lin Tang, Chao Zhao, Mian Zhang, Lili Huang

Department of Agronomy and Horticulture: Faculty Publications

Valsa is a genus of ascomycetes within the Valsaceae family. This family includes many wood destructive pathogens such as the well known Valsa mali and Valsa pyri which cause canker diseases in fruit trees and threaten the global fruit production. Lack of genomic information of this family is impeding our understandings about their evolution and genetic basis of their pathogenicity divergence. Here, we report genome assemblies of Valsa malicola, Valsa persoonii, and Valsa sordida which represent close relatives of Valsa mali and Valsa pyri with different host preferences. Comparative genomics analysis revealed that segmental rearrangements, inversions, and translocations …

Addressing Challenges Of Dryland Production Of Sunflowers And Corn In The Semi-Arid High Plains Of Nebraska, Zhan Orazov

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

Corn and sunflower are value crops for America. Cultivation of corn and sunflower often vary depending on growing environment. Selecting appropriate planting dates, hybrids and plant density frequently concerns farmers. This concern is understandable because the decision made directly impacts final income. The objectives were to evaluate interaction of corn and sunflower planting dates and hybrid maturity and evaluate interaction of corn flex hybrids and plant density under conditions of western Nebraska. Nine corn hybrids with relative maturity ranging from 86 to 105 days were sown between early May and late June in first and between late April and early …

Nitrification Inhibitor, Nitrogen Source, And Herbicide Effects On Soil Nitrogen Transformations And Corn Yield, William Neels

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

Nitrogen fertilizer management continue to be challenging due to potential nitrogen losses under variable weather conditions. The objective of this was to evaluate the performance of nitrification inhibitors, nitrogen sources and herbicides on in-season nitrogen availability and agronomy indicators. A two site-year field experiment was conducted in silty clay loam soil in corn phase of the corn-soybean rotation at Central Nebraska. The treatments included three herbicide (no pre-emergence, Acuron, Resicore) and five nitrogen treatments: 1) control, 2) anhydrous ammonia, 3) anhydrous ammonia without nitrification inhibitor, 4) urea with nitrification inhibitors, and 5) urea without nitrification inhibitors. Results indicated that nitrogen …

Impacts Of Feeding Biochar To Beef Cattle On Greenhouse Gas Emissions And Performance And Characterizing Yearling Steers Grazing Smooth Bromegrass Pasture Using Gps, Holly Heil

Department of Animal Science: Dissertations, Theses, and Student Research

As global warming continues to rise, the pressure and growing demand for sustainable animal production is increasing. Livestock naturally produce greenhouse gas emissions through enteric fermentation. Dietary manipulation strategies have been sought out to decrease emissions in ruminants using feed additives.

Two independent finishing feedlot experiments evaluated two types of biochar and its effects on animal performance, carcass characteristics and greenhouse gas emissions. Experiment 1 utilized pistachio shell biochar and experiment 2 utilized biochar sourced from ponderosa pine wood waste, both types included at 1% of the diet DM. The addition of biochar to the diet did not impact animal …

Evaluation Of Nutritional Factors Affecting Sow Reproductive Longevity, J'Nan E. Wittler

Department of Animal Science: Dissertations, Theses, and Student Research

Sow reproductive longevity is an important trait for swine operations from a production and economic standpoint. Previous research has shown that a sow needs to produce 3 litters before she covers the costs associated with introducing her to the operation. A literature review of research conducted related to sow longevity is discussed in Chapter 1. Chapters 2 and 3 present data from the University of Nebraska – Lincoln’s long-term sow longevity research. The research looks at the effects of energy restriction with soy hulls during gilt development on sow reproductive longevity through 4 parities. Chapter 2 presents data from replications …

Image Analysis And Machine Learning In Agricultural Research, Xinzheng Chen

Doctor of Plant Health Program: Dissertations and Student Research

Agricultural research has been a focus for academia and industry to improve human well-being. Given the challenges in water scarcity, global warming, and increased prices of fertilizer, and fossil fuel, improving the efficiency of agricultural research has become even more critical. Data collection by humans presents several challenges including: 1) the subjectiveness and reproducibility when doing the visual evaluation, 2) safety when dealing with high toxicity chemicals or severe weather events, 3) mistakes cannot be avoided, and 4) low efficiency and speed.

Image analysis and machine learning are more versatile and advantageous in evaluating different plant characteristics, and this could …

Timing Of Implants Use In Backgrounding System, Kylie M. Butterfield

Applied Science Program: Theses

A study was conducted over two years to determine the interactions of winter rate of gain at a high gain (HG) of 0.91 kg and low gain (LG) 0.45 kg, and implant strategy in the backgrounding and subsequent effects in the finishing phases. There were three phases in this study, the winter phase (~148 days), the summer phase (~60 days) and the finishing phase (~120 days). This was a 2 x 3 factorial design. The first factor is a rate of gain at either 0.91 kg (HG) or 0.45 kg (LG). The next factor is the timing of implant where …

Quantifying The Relationship Between Soil Organic Carbon And Soil Color In Nebraska, Aldi J. Airori

Applied Science Program: Theses

Soil color is easily measured in the field and holds potential to be used as an indirect measurement of soil organic carbon (SOC). The main limitation to this approach is knowledge about the specific color-SOC relationship in a region, which often varies in relation to parent material, soil texture, climate, and land use. Furthermore, the Munsell color data is subjective in nature. The objectives of this study are: 1) to develop and evaluate the accuracy of pedotransfer functions (PTFs) for the prediction of SOC based on soil color and texture in the state of Nebraska and 2) to evaluate digital …

Geographic Distribution: Anolis Sagrei (Brown Anole). Usa: Arizona., Addie Leimroth, Louis A. Somma, Dyrana N. Russell, Logan P. Cutts, Mason Ryan, Randall D. Babb, Karen E. Hajek, Andrew T. Holycross

Papers in Herpetology

We discovered the first distributional records for the exotic, Caribbean lizard, Anolis sagrei (Brown Anole), in Arizona.

The Casnr L.I.N.K.S. Newsletter: Learning Innovation Network For K-12 Schools, Edition 11, December 2022, Bailey Feit, Tammy Mittelstet

CASNR L.I.N.K.S. Newsletter

The purpose of this L.I.N.K.S. newsletter is to provide a monthly update of opportunities and resources for K-12 schools to connect with the University of Nebraska's CASNR Food, Energy, Water, and Societal Systems (FEWS²) programs and partners.

This edition includes:

Teachers' corner, K-12 resources

Links to partners' newsletters

Top 5 success stories

FEWSS 2022 highlighted impact

Looking toward 2023

CASNR focus areas

Send your students to campus!

Scholarship opportunities

Seeking Of Agriculture Information Through Mobile Phones By Rice Farmers In Ogoja Agricultural Zone, Cross River State, Nigeria, Friday O. Idiku, Ginini Francis Elemi, Ejeje Igwe Agube, Comfort Aya, Anthonia Egem Okem

Library Philosophy and Practice (e-journal)

Seeking agriculture information is common among rice farmers in many parts of the world. The study was aimed at assessing the Seeking of Agriculture Information through Mobile Phone by Rice Farmers in Ogoja Agricultural Zone of Cross River State Nigeria The specific objectives of the study were to; identify the socio-economic characteristics of the farmers, determine factors influencing the seeking of agriculture information through mobile phones by rice farmers, and to examine the constraints to use of mobile phones by rice farmers in Ogoja Agricultural Zone of Cross River State Nigeria. A multistage sampling technique was adopted to select ninety …