Botany Commons^™

An Integrated Genomics And Phenomics Approach To Study The Evolution Of C4 Photosynthesis, Daniel Santana De Carvalho

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

The C4 photosynthetic pathway was first described over 50 years ago. Today, it is known that C4 evolved independently > 60 in plant lineages, which involves understanding not only the genetic, but also the metabolic features and differences involved in this process. Also, several adaptations are involved in the evolution of this type of photosynthesis, for example: changes in leaf anatomy and the evolution of kranz anatomy, physiology and metabolic pathways. In order to further investigate this pathway, different technologies and methods have been developed to unravel genes involved in C4 photosynthesis. With the advances in molecular biology and bioinformatics tools …

Investigating Parental Effects On End-Use Quality In Hard Winter Wheat (Triticum Aestivum L.) Hybrids, Anthony Delaney

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

To optimize the performance and marketing of hybrid wheat, breeders need to understand the impact parents have on end-use quality. The goal of this study was to investigate the inheritance of end-use quality traits of hard winter wheat reciprocal hybrids produced by Easterly (2017). The 2016 analysis included 71 reciprocal hybrid combinations from 13 parents and the 2017 analysis included 79 reciprocal hybrid combinations from 14 parents. The reciprocals were composed of crosses between the top performing and bottom performing parents with respect to end-use quality as quantified by a Mixograph, a SDS sedimentation assay, and a SDS-SRC hybrid assay. …

Rust And Viral Mosaic Diseases In Biofuel Switchgrass, Anthony A. Muhle

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

Switchgrass (Panicum virgatum L.) is a perennial warm-season monocot that is indigenous to locations in North America east of the Rocky Mountains, and is considered a model grass for biofuel feedstock production. As switchgrass production increases, diseases pose a potential threat to biomass production and ethanol extraction. The two predominant switchgrass diseases in Nebraska are rust caused by Puccinia spp. and a viral mosaic disease caused by Panicum mosaic virus (PMV) and its associated Satellite panicum mosaic virus (SPMV). In this thesis, one study determined how SPMV affects PMV infection and systemic spread in two populations of switchgrass at different …

Hormonal Signaling Induced In Soybean By Lysobacter Enzymogenes Strain C3, Jessica C. Walnut

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

The biological control bacterium Lysobacter enzymogenes strain C3 has been shown to suppress fungal diseases by producing a suite of lytic enzymes and antimicrobial secondary metabolites. Previous studies have found that C3, when applied to grass and cereal plants, also is capable of inducing local and systemic resistance against fungal pathogens. It is unknown, however, whether the bacterium has the ability to induce resistance in dicots and what signaling pathways are involved. This study assessed the ability of C3 to trigger local and systemic induced resistance responses in soybean (Glycine max ‘Williams82’) by analyzing relative expression of salicylic acid …

The Effects Of Clipping On The Biomass Production Of Native Warm Season Grasses On Reclaimed Abandoned Coal Mine Soils, James A K Daniel

Electronic Theses & Dissertations

THE EFFECTS OF CLIPPING ON THE BIOMASS PRODUCTION OF NATIVE

WARM SEASON GRASSES ON RECLAIMED

ABANDONED COAL MINE SOILS

James A K Daniel

Strip mining leaves behind highly disrupted plant and soil communities. Mined land reclamation returns the land back to a natural or economically usable state, however, reclamation cannot completely restore the soils to their original state. Subsequently, normal frequencies of management practices may not be as effective as in undisturbed soils. Understanding how the severity of soil disturbance affects plant production is important for habitat rehabilitation and determining effective management techniques to be implemented following reclamation. This project …

How Do Ecological Resilience Metrics Relate To Community Stability And Collapse?, Caleb P. Roberts, Dirac L. Twidwell Jr, David G. Angeler, Craig R. Allen

Department of Agronomy and Horticulture: Faculty Publications

The concept of ecological resilience (the amount of disturbance a system can absorb before collapsing and reorganizing) holds potential for predicting community change and collapse—increasingly common issues in the Anthropocene. Yet neither the predictions nor metrics of resilience have received rigorous testing. The crossscale resilience model, a leading operationalization of resilience, proposes resilience can be quantified by the combination of diversity and redundancy of functions performed by species operating at different scales. Here, we use 48 years of sub-continental avian community data aggregated at multiple spatial scales to calculate resilience metrics derived from the cross-scale resilience model (i.e., cross-scale diversity, …

Estimating Live Fuel Moisture Using Smap L-Band Radiometer Soil Moisture For Southern California, Usa, Shenyue Jia, Seung Hee Kim, Son V. Nghiem, Menas Kafatos

Mathematics, Physics, and Computer Science Faculty Articles and Research

Live fuel moisture (LFM) is a field-measured indicator of vegetation water content and a crucial observation of vegetation flammability. This study presents a new multi-variant regression model to estimate LFM in the Mediterranean ecosystem of Southern California, USA, using the Soil Moisture Active Passive (SMAP) L-band radiometer soil moisture (SMAP SM) from April 2015 to December 2018 over 12 chamise (Adenostoma fasciculatum) LFM sites. The two-month lag between SMAP SM and LFM was utilized either as steps to synchronize the SMAP SM to the LFM series or as the leading time window to calculate the accumulative SMAP SM. …

Identification Of Loci Controlling Adaptation In Chinese Soya Bean Landraces Via A Combination Of Conventional And Bioclimatic Gwas, Ying-Hui Li, Delin Li, Yong-Qing Jiao, James C. Schnable, Yan-Fei Li, Hui-Hui Li, Huai-Zhu Chen, Hui-Long Hong, Ting Zhang, Bin Liu, Zhang-Xiong Lui, Qing-Bo You, Yu Tian, Yong Guo, Rong-Xia Guan, Li-Juan Zhang, Ru-Zhen Chang, Zhiwu Zhang, Jochen Reif, Xin-An Zhou, Patrick S. Schnable, Li-Juan Qiu

Department of Agronomy and Horticulture: Faculty Publications

Landraces often contain genetic diversity that has been lost in modern cultivars, including alleles that confer enhanced local adaptation. To comprehensively identify loci associated with adaptive traits in soya bean landraces, for example flowering time, a population of 1938 diverse landraces and 97 accessions of the wild progenitor of cultivated soya bean, Glycine soja was genotyped using tGBS. Based on 99 085 high-quality SNPs, landraces were classified into three subpopulations which exhibit geographical genetic differentiation. Clustering was inferred from STRUCTURE, principal component analyses and neighbour-joining tree analyses. Using phenotypic data collected at two locations separated by 10 degrees of latitude, …

Warm Stratification Increases Germination Of Dendromecon Rigida And Ehrendorferia Chrysantha, Cesar Garcia

Electronic Theses, Projects, and Dissertations

We explored the seasonal factors that might play a role in triggering germination of Dendromecon rigidaand Ehrendorferia chrysantha.D. rigida and E. chrysantha have been found difficult to germinate using common greenhouse techniques, Keeley and Fotheringham successfully germinated both species after storing their seeds in the field over a year and treating them with smoke. Identifying the specific seasonally changing factors that stimulated germination could have implications for understanding germination requirements for these and other hard-to-germinate chaparral species.

Dendromecon rigidaand Ehrendorferia chrysanthaare part of the Papaveraceae family and both are found in the chaparral environment in …

Introduction To Sorghum Paper Production, Zachary Christman

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

Sorghum is a tall grass used for many commercial products such as fodder and syrup. The 10 to 15 feet stalk of the plant has lower lignin than wood and provides a fiber length of 2.31 mm in the outer covering and 1.38 mm for the leaf. Sorghum fiber makes a high quality, strong paper suitable for printing, packaging and paperboard.

Use Of Annual Forage Mixtures In Crop/Livestock Production Systems In Nebraska, Nathan Paul Pflueger

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

Success of integrating annual forages into crop and livestock systems throughout Nebraska may be variable depending on field location, field/forage crop management, and precipitation. There are many different warm- and cool-season annual forage species available for integrating crop and livestock systems at different times of the year. Mixtures of cereal species, such as oats (Avena sativa)) and spring peas (Pisum sativum)), are often used to optimize forage quantity and forage quality. Our two-year, three location study across Nebraska’s precipitation gradient suggested that forage quantity and quality may vary by location due to different precipitation amounts received …

Dna Barcoding Of Pratylenchus From Agroecosystems In The Northern Great Plains Of North America, Mehmet Ozbayrak

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

Pratylenchus species are among the most common plant parasitic nematodes in the Great Plains Region. The objectives of this study were to barcode Pratylenchus specimens for species identification in the Great Plains region using mitochondrial CO1 DNA barcode. In order to (1) determine species boundaries, (2) assess the host associations of barcoded Pratylenchus, (3) to determine the distribution patterns across the Great Plains Region and, (4) to evaluate the species status of P. scribneri and P. hexincisus by a multivariate morphological analysis of haplotype groups identified by DNA barcoding. Soil samples, primarily associated with eight major crops, were collected …

Establishment Of Perennial Legumes With An Annual Warm-Season Grass As A Companion Crop, Martina N. La Vallie

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

The yields of perennial forage legumes are often hindered during the establishment year due to slow germination rates and weed competition. This study was conducted to determine if sorghum-sudangrass (Sorghum bicolor x S. bicolor var. sudanese) is a compatible annual companion crop for increased forage production, weed suppression, and legume establishment. In 2016, sorghum-sudangrass was paired with alfalfa (Medicago sativa L. ‘Ranger’), birdsfoot trefoil (Lotus corniculatus L.), Illinois bundleflower [Desmanthus illinoensis (Michx.) MacMill. ex B.L. Rob. & Fernald], purple prairie clover (Dalea purpurea Vent.), red clover (Trifolium pratense L.), and roundhead lespedeza (Lespedeza capitata Michx.). We studied effects of a …

Genome-Wide Association Studies In Maize And Sorghum, Preston Hurst

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

Genome-wide association studies are used to identify genetic variants associated with a particular phenotype. GWAS has been used in a variety of taxa, from humans, to fish to plants . The present analysis is focused on two species important to the human species: maize and sorghum. A GWAS in maize was carried out on the modification of the Ga1-s allele. The Ga1 locus has long been studied as being involved in a unilateral crossing barrier . However, it has long been suspected that the locus is modified by background genetic factors . GWAS was used to observe candidates for this …

Nutrient Management Suggestions For Corn, Charles A. Shapiro, Richard Ferguson, Charles S. Wortmann, Bijesh Maharjan, Brian T. Krienke

Department of Agronomy and Horticulture: Faculty Publications

Fertilizer nutrient requirements for corn are based on expected yield and soil nutrient availability. The preplant nitrogen (N) recommendation equation, with adjustment for fertilizer cost and time of application, is retained from the previous edition of this publication. Suggestions for in-season nitrogen decisions are briefly outlined. The major change is providing a phosphorus (P) recommendation based on yield history with an implied intent to build and maintain soil test P above the critical level, which has not changed.

Development Of A Nitrogen Recommendation Tool For Corn Considering Static And Dynamic Variables, Laila A. Puntel, Agustin Pagani, Sotirios V. Archontoulis

Department of Agronomy and Horticulture: Faculty Publications

Many soil and weather variables can affect the economical optimum nitrogen (N) rate (EONR) for maize. We classified 54 potential factors as dynamic (change rapidly over time, e.g. soil water) and static (change slowly over time, e.g. soil organic matter) and explored their relative importance on EONR and yield prediction by analyzing a dataset with 51 N trials from Central-West region of Argentina. Across trials, the average EONR was 113 ± 83 kg N ha⁻¹ and the average optimum yield was 12.3 ± 2.2 Mg ha⁻¹, which is roughly 50% higher than the current N rates used …

Purification And Characterization Of A Nonspecific Lipid Transfer Protein 1 (Nsltp1) From Ajwain (Trachyspermum Ammi) Seeds, Meshal Nazeer, Humera Waheed, Maria Saeed, Saman Yousuf Ali, M. Iqbal Choudhary, Zaheer Ul-Haq, Aftab Ahmed

Pharmacy Faculty Articles and Research

Ajwain (Trachyspermum ammi) belongs to the family Umbelliferae, is commonly used in traditional, and folk medicine due to its carminative, stimulant, antiseptic, diuretic, antihypertensive, and hepatoprotective activities. Non-specific lipid transfer proteins (nsLTPs) reported from various plants are known to be involved in transferring lipids between membranes and in plants defense response. Here, we describe the complete primary structure of a monomeric non-specific lipid transfer protein 1 (nsLTP1), with molecular weight of 9.66 kDa, from ajwain seeds. The nsLTP1 has been purified by combination of chromatographic techniques, and further characterized by mass spectrometry, and Edman degradation. The ajwain nsLTP1 …

Seasonal Origins Of Soil Water Used By Trees, Scott T. Allen, James W. Kirchner, Sabine Braun, Rolf T. W. Siegwolf, Gregory R. Goldsmith

Biology, Chemistry, and Environmental Sciences Faculty Articles and Research

Rain recharges soil water storages and either percolates downward into aquifers and streams or is returned to the atmosphere through evapotranspiration. Although it is commonly assumed that summer rainfall recharges plant-available water during the growing season, the seasonal origins of water used by plants have not been systematically explored. We characterize the seasonal origins of waters in soils and trees by comparing their midsummer isotopic signatures (δ2H) to seasonal isotopic cycles in precipitation, using a new seasonal origin index. Across 182 Swiss forest sites, xylem water isotopic signatures show that summer rain was not the predominant water source …

Response Surface Analysis Of Genomic Prediction Accuracy Values Using Quality Control Covariates In Soybean, Diego Jarquin, Reka Howard, George L. Graef, Aaron Lorenz

Department of Agronomy and Horticulture: Faculty Publications

An important and broadly used tool for selection purposes and to increase yield and genetic gain in plant breeding programs is genomic prediction (GP). Genomic prediction is a technique where molecular marker information and phenotypic data are used to predict the phenotype (eg, yield) of individuals for which only marker data are available. Higher prediction accuracy can be achieved not only by using efficient models but also by using quality molecular marker and phenotypic data. The steps of a typical quality control (QC) of marker data include the elimination of markers with certain level of minor allele frequency (MAF) and …

Closing Yield Gaps For Rice Self-Sufficiency In China, Nanyan Deng, Patricio Grassini, Haishun Yang, Jianliang Huang, Kenneth G. Cassman, Shaobing Peng

Department of Agronomy and Horticulture: Faculty Publications

China produces 28% of global rice supply and is currently self-sufficient despite a massive rural-to-urban demographic transition that drives intense competition for land and water resources. At issue is whether it will remain self-sufficient, which depends on the potential to raise yields on existing rice land. Here we report a detailed spatial analysis of rice production potential in China and evaluate scenarios to 2030. We find that China is likely to remain self-sufficient in rice assuming current yield and consumption trajectories and no reduction in production area. A focus on increasing yields of double-rice systems on general, and in three …

Assessing Variation In Us Soybean Seed Composition (Protein And Oil), Yared Assefa, Larry C. Purcell, Montse Salmeron, Seth Naeve, Shaun N. Casteel, Peter Kovacs, Sotirios Archontoulis, Mark Licht, Fred Below, Herman Kandel, Laura E. Lindsey, John Gaska, Shawn Conley, Charles Shapiro, John M. Orlowski, Bobby R. Golden, Gurpreet Kaur, Maninderpal Singh, Kurt Thelen, Randall Laurenz, Dan Davidson, Igancio A. Ciampitti

Department of Agronomy and Horticulture: Faculty Publications

Soybean [Glycine max (L.) Merr.] seed composition and yield are a function of genetics (G), environment (E), and management (M) practices, but contribution of each factor to seed composition and yield are not well understood. The goal of this synthesis-analysis was to identify the main effects of G, E, and M factors on seed composition (protein and oil concentration) and yield. The entire dataset (13,574 data points) consisted of 21 studies conducted across the United States (US) between 2002 and 2017 with varying treatments and all reporting seed yield and composition. Environment (E), defined as site-year, was the dominant …

Assessing The Value Of Grazed Corn Residue For Crop And Cattle Producers, Daren Redfearn, Jay Parsons, Mary Drewnoski, Marty Schmer, Rob Mitchell, James Macdonald, Jaymelynn Farney, Alexander Smart

Department of Agronomy and Horticulture: Faculty Publications

Integrated crop–livestock systems have included grazing perennial grasses during the spring and summer and corn (Zea mays L.) residues during the winter. Our objectives were to identify opportunities for expanded corn residue use through grazing and provide an economic assessment for value-added grazing. We estimated the economic value to the crop sector through grazing leased corn residue at over $95 million for Nebraska, South Dakota, Kansas, and North Dakota under current management. Additionally, gross economic value to the livestock sector in these states was estimated at greater than $191 million. Advantages for increased grazing use of corn residue include …

Climate-Smart Practices For Improvement Of Crop Yields In Mid-Hills Of Nepal, Roshan Subedi, Laxmi Dutt Bhatta, Erica Udas, Nand Kishor Agrawal, Keshab Datta Joshi, Dinesh Panday

Department of Agronomy and Horticulture: Faculty Publications

Farming in Nepal mostly represents the hill farming system with the dominance of small-holder farmers. In recent days, farmers in the country are impacted by climate change. Events of surface runoff, landslides, and soil erosions, along with changes in rainfall pattern and intensity have elevated a decline in crop productivity and soil fertility. Considering the situation, a pilot project on Resilient Mountain Village was implemented in Kavrepalanchowk district of Nepal from 2014–2016 with a participatory approach to demonstrate climate-smart practices. These practices include the application of locally prepared bio-fertilizer (named as “jholmal”), green manuring in rice (Oryza sativa L.) …

Drought Stress Tolerance In Wheat And Barley: Advances In Physiology, Breeding And Genetics Research, Ahmed Sallam, Ahmad M. Alqudah, Mona F. A. Dawood, P. Stephen Baenziger, Andreas Borner

Department of Agronomy and Horticulture: Faculty Publications

Climate change is a major threat to most of the agricultural crops grown in tropical and sub-tropical areas globally. Drought stress is one of the consequences of climate change that has a negative impact on crop growth and yield. In the past, many simulation models were proposed to predict climate change and drought occurrences, and it is extremely important to improve essential crops to meet the challenges of drought stress which limits crop productivity and production. Wheat and barley are among the most common and widely used crops due to their economic and social values. Many parts of the world …

Generating High Density, Low Cost Genotype Data In Soybean [Glycine Max (L.) Merr.], Mary M. Happ, Haichuan Wang, George L. Graef, David L. Hyten

Department of Agronomy and Horticulture: Faculty Publications

Obtaining genome-wide genotype information for millions of SNPs in soybean [Glycine max (L.) Merr.] often involves completely resequencing a line at 5X or greater coverage. Currently, hundreds of soybean lines have been resequenced at high depth levels with their data deposited in the NCBI Short Read Archive. This publicly available dataset may be leveraged as an imputation reference panel in combination with skim (low coverage) sequencing of new soybean genotypes to economically obtain high-density SNP information. Ninety-nine soybean lines resequenced at an average of 17.1X were used to generate a reference panel, with over 10 million SNPs called using …

Assessing Precipitation, Evapotranspiration, And Ndvi As Controls Of U.S. Great Plains Plant Production, Maosi Chen, William J. Parton, Melannie D. Hartman, Stephen J. Del Grosso, William K. Smith, Alan K. Knapp, Susan Lutz, Justin D. Derner, Compton J. Tucker, Dennis S. Ojma, Jerry D. Volesky, Mitchell B. Stephenson, Walter H. Schacht, Wei Gao

Department of Agronomy and Horticulture: Faculty Publications

Productivity throughout the North American Great Plains grasslands is generally considered to be water limited, with the strength of this limitation increasing as precipitation decreases. We hypothesize that cumulative actual evapotranspiration water loss (AET) from April to July is the precipitation-related variable most correlated to aboveground net primary production (ANPP) in the U.S. Great Plains (GP). We tested this by evaluating the relationship of ANPP to AET, precipitation, and plant transpiration (Tr). We used multi-year ANPP data from five sites ranging from semiarid grasslands in Colorado and Wyoming to mesic grasslands in Nebraska and Kansas, mean annual NRCS ANPP, and …

Estimating Percentages Of Fusarium-Damaged Kernels In Hard Wheat By Near-Infrared Hyperspectral Imaging, Stephen R. Delwiche, I. Torres Rodriguez, S. R. Rausch, R. A. Graybosch

Department of Agronomy and Horticulture: Faculty Publications

Fusarium head blight (FHB) is among the most common fungal diseases affecting wheat, resulting in decreased yield, low-density kernels, and production of the mycotoxin deoxynivalenol, a compound toxic to humans and livestock. Human visual analysis of representative wheat samples has been the traditional method for FHB assessment in both official inspection and plant breeding operations. While not requiring specialized equipment, visual analysis is dependent on a trained and consistent workforce, such that in the absence of these aspects, biases may arise among inspectors and evaluation dates. This research was intended to avoid such pitfalls by using longer wavelength radiation than …

Can Ratoon Cropping Improve Resource Use Efficiencies And Profitability Of Rice In Central China?, Shen Yuan, Kenneth G. Cassman, Jianliang Huang, Shaobing Peng, Patricio Grassini

Department of Agronomy and Horticulture: Faculty Publications

Identifying cropping systems with small global warming potential (GWP) per unit of productivity is important to ensure food security while minimizing environmental footprint. During recent decades, double-season rice (DR) systems in central China have progressively shifted into single-crop, middle-season rice (MR) due to high costs and labor requirements of double-season rice. Ratoon rice (RR) has been proposed as an alternative system that reconciliates both high annual productivity and relatively low costs and labor requirements. Here we used onfarm data collected from 240 farmer fields planted with rice in 2016 to evaluate annual energy balance, environmental impact, and net profit of …

Unraveling The Influence Of Female Flowering Characteristics And Chemical Hybridizing Agent Formulations On Hybrid Wheat (Triticum Aestivum L.) Seed Production, Hannah K. Stoll

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

The success of hybrid wheat (Triticum aestivum L.) is largely limited by inefficiencies in seed production. This research aims to address these inefficiencies by examining various Chemical Hybridizing Agent (CHA) formulations using the chemical Croisor®100 on sterility, CHA damage, and female flowering characteristics. In addition, an efficient method of phenotyping female flowering characteristics (contributing factors in hybrid production seed yield) were identified using Stepwise Regression, ANCOVA, and Pearson R-Correlations, and duration of stigma receptivity in the cytoplasmic male sterile (CMS; Triticum timopheevii Zhuk.) background was determined. At an optimally timed spray application, including a moderate rate of CHA with …

Beyond Bird Feed: Proso Millet For Human Health And Environment, Saurav Das, Rituraj Khound, Meenakshi Santra, Dipak K. Santra

Department of Agronomy and Horticulture: Faculty Publications

Domesticated in 8000–10,000 BP in northern China, proso millet (Panicum miliaceum L.) is the best adaptive rotational crop for semiarid central High Plains of the USA, where average annual precipitation is 356–407 mm. Proso millet has multiple benefits when consumed as human food. Proso millet is rich in minerals, dietary fiber, polyphenols, vitamins and proteins. It is gluten-free and therefore, ideal for the gluten intolerant people. Proso millet contains high lecithin which supports the neural health system. It is rich in vitamins (niacin, B-complex vitamins, folic acid), minerals (P, Ca, Zn, Fe) and essential amino acids (methionine and cysteine). …