Botany Commons^™

Evaluating The Evolutionary And Genetic Relationships Of The Andean Orchids Of Northwestern Ecuador, Kylie Bucalo

Theses and Dissertations

DNA barcoding is a molecular based technique used to separate and identify individual species. Here we establish a DNA Barcode library for the orchid flora of an Andean cloud forest in Northwestern Ecuador. The library contains 135 matK and 136 rbcL DNA Barcodes representing over 33 Orchidaceae genera. Sequence analysis shows percent species resolution was higher for matK (98.8%) than rbcL (70.24%), with a large portion of the unresolved species for the rbcL loci coming from taxonomically complex genera in the subtribe Pleurothallidinae. Neighbor Joining (NJ) trees revealed that the orchid flora of Siempre Verde is divided taxonomically into …

Successional Changes In Leaf Nutrient Concentrations Of Woody And Herbaceous Species, Daniel Walter Kuchta

Masters Theses

Leaf nutrient concentrations are an example of a functional trait, a trait that can be used to understand community dynamics by observing how plants interact with their environment. I explored how leaf nutrient concentrations were affected over successional time by environmental changes. The majority of prior research on functional traits focuses on either woody or herbaceous species, but not both life forms simultaneously. To address this, I also explored the successional changes to leaf nutrient concentrations, separating the plant community into woody and herbaceous species.

Healthy, mature leaves were taken from 122 taxa of woody and herbaceous species in a …

Plant Functionality Across An Environmental Gradient, Taylor L. Price, Julie Zinnert

UROP Posters

Community assemblages provide insight into ecosystem processes, both spatially and temporally. They interact with biotic and abiotic factors that vary with habitat structure, influencing community composition. Ecological theory demonstrates that species have the potential for a wide fundamental niche, but habitat range may be restricted by factors exposed to species in their realized niche. In barrier island ecosystems, edaphic and environmental characteristics (e.g. elevation and distance to shoreline) are major drivers determining where and how plant communities establish. Physical stressors, such as salt stress and drought influence community grouping and can alter plant function within the environment. With projected increases …

Mechanisms Of Native Shrub Encroachment On A Virginia Barrier Island, Joseph Thompson

Theses and Dissertations

Species composition, temperature, soil nutrients, and leaf area index (LAI) were recorded across three encroaching Morella cerifera thicket edges and three free- standing shrubs on Hog Island, Virginia to characterize the effect of shrub thickets on the plant community and microclimate. Electron transport rate (ETR) was taken on shrub leaves to determine if microclimate benefits M. cerifera physiology. Species richness was lowest inside shrub thickets. Soil water content and LAI were higher in shrub thickets compared to grassland. Soil organic matter, N, and C were higher inside shrub thickets. Summer and fall maximum temperatures were more moderate in shrub thickets …

What Would The Babel Fish Say?, Monica Gagliano

Animal Sentience

Starting with its title, Key’s (2016) target article advocates the view that fish do not feel pain. The author describes the neuroanatomical, physiological and behavioural conditions involved in the experience of pain in humans and rodents and confidently applies analogical arguments as though they were established facts in support of the negative conclusion about the inability of fish to feel pain. The logical reasoning, unfortunately, becomes somewhat incoherent, with the arbitrary application of the designated human criteria for an analogical argument to one animal species (e.g., rodents) but not another (fish). Research findings are reported selectively, and questionable interpretations are …

Land Use And Land Cover Classification And Change Detection Using Naip Imagery From 2009 To 2014: Table Rock Lake Region, Missouri, Dexuan Sha Sha

Graduate Theses/Dissertations

Land use and land cover (LULC) of Table Rock Lake (TRL) region has changed over the last half century after the construction of Table Rock Dam in 1959. This study uses one meter spatial resolution imagery to classify and detect the change of LULC of three typical waterside TRL regions. The main objectives are to provide an efficient and reliable classification workflow for regional level NAIP aerial imagery and identify the dynamic patterns for study areas. Seven class types are extracted by optimal classification results from year 2009, 2010, 2012 and 2014 of Table Rock Village, Kimberling City and Indian …

Fidelity And Survival Of Breeding Mallards In The Nebraska Sandhills, Zachary J. Cunningham, Larkin Powell, Mark P. Vrtiska

The Prairie Naturalist

Assessment of demographic parameters of a population allows managers to better understand factors affecting populations and increase efficiency of conservation efforts. Few data on demographics exist for mallards (Anas platyrhynchos) breeding in the Nebraska Sandhills. Thus, we used banding data to estimate probabilities of fidelity, survival, band recovery, and recapture of mallards banded in the eastern Sandhills, 2005–2008. Our recapture probability estimate for mallards was 0.074 (95% CI: 0.033–0.158), and the recovery probability estimate was 0.300 (95% CI: 0.156–0.497). Mallard annual survival was 0.795 (95% CI: 0.609–0.906) with a fidelity probability of 0.618 (95% CI: 0.283–0.868). High annual …

Genomic Prediction Of Single Crosses In The Early Stages Of A Maize Hybrid Breeding Pipeline, Dnyaneshwar C. Kadam, Sarah M. Potts, Martin O. Bohn, Alexander E. Lipka, Aaron J. Lorenz

Department of Agronomy and Horticulture: Faculty Publications

Prediction of single-cross performance has been a major goal of plant breeders since the beginning of hybrid breeding. Recently, genomic prediction has shown to be a promising approach, but only limited studies have examined the accuracy of predicting single-cross performance. Moreover, no studies have examined the potential of predicting single crosses among random inbreds derived from a series of biparental families, which resembles the structure of germplasm comprising the initial stages of a hybrid maize breeding pipeline. The main objectives of this study were to evaluate the potential of genomic prediction for identifying superior single crosses early in the hybrid …

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 …

The Draft Genome Of The C3 Panicoid Grass Species Dichanthelium Oligosanthes, Anthony J. Studer, James C. Schnable, Sarit Weissmann, Allison R. Kolbe, Michael R. Mckain, Ying Shao, Asaph B. Cousins, Elizabeth A. Kellogg, Thomas P. Brutnell

Department of Agronomy and Horticulture: Faculty Publications

Background: Comparisons between C₃ and C₄ grasses often utilize C₃ species from the subfamilies Ehrhartoideae or Pooideae and C₄ species from the subfamily Panicoideae, two clades that diverged over 50 million years ago. The divergence of the C₃ panicoid grass Dichanthelium oligosanthes from the independent C₄ lineages represented by Setaria viridis and Sorghum bicolor occurred approximately 15 million years ago, which is significantly more recent than members of the Bambusoideae, Ehrhartoideae, and Pooideae subfamilies. D. oligosanthes is ideally placed within the panicoid clade for comparative studies of C₃ and C₄ grasses.

Results: …

Yield Gap Analysis Of Us Rice Production Systems Shows Opportunities For Improvement, Matthew B. Espe, Kenneth Cassman, Haishun Yang, Nicolas Guilpart, Patricio Grassini, Justin Van Wart, Merle Anders, Donn Beighley, Dustin Harrell, Steve Linscombe, Kent Mckenzie, Randall Mutters, Lloyd T. Wilson, Bruce A. Linquist

Department of Agronomy and Horticulture: Faculty Publications

Many assessments of crop yield gaps based on comparisons to actual yields suggest grain yields in highly intensified agricultural systems are at or near the maximum yield attainable. However, these estimates can be biased in situations where yields are below full yield potential. Rice yields in the US continue to increase annually, suggesting that rice yields are not near the potential. In the interest of directing future efforts towards areas where improvement is most easily achieved, we estimated yield potential and yield gaps in US rice production systems, which are amongst the highest yielding rice systems globally. Zones around fourteen …

Smokey Comes Of Age: Unmanned Aerial Systems For Fire Management, Dirac L. Twidwell Jr., Craig R. Allen, Carrick Detweiler, James Higgins, Christian Laney, Sebastian Elbaum

Department of Agronomy and Horticulture: Faculty Publications

During the past century, fire management has focused on techniques both to protect human communities from catastrophic wildfire and to maintain fire-dependent ecological systems. However, despite a large and increasing allocation of resources and personnel to achieve these goals, fire management objectives at regional to global scales are not being met. Current fire management techniques are clearly inadequate for the challenges faced by fire managers, and technological innovations are needed. Advances in unmanned aerial systems (UAS) technology provide opportunities for innovation in fire management and science. In many countries, fire management organizations are beginning to explore the potential of UAS …

Soil Water Improvements With The Long-Term Use Of A Winter Rye Covercrop, Andrea D. Basche, Thomas C. Kaspar, Sotirios V. Archontoulis, Dan B. Jaynes, Thomas J. Sauer, Timothy B. Parkin, Fernando E. Miguez

Department of Agronomy and Horticulture: Faculty Publications

The Midwestern United States, a region that produces one-third of maize and one-quarter of soybean grain globally, is projected to experience increasing rainfall variability. One approach to mitigate climate impacts is to utilize crop and soil management practices that enhance soil water storage and reduce the risks of flooding as well as drought-induced crop water stress. While some research indicates that a winter cover crop in maize-soybean rotations increases soil water availability, producers continue to be concerned that water use by cover crops will reduce water for a following cash crop. We analyzed continuous in-field soil water measurements from 2008 …

Shrubland Resilience Varies Across Soil Types: Implications For Operationalizing Resilience In Ecological Restoration, Carissa L. Wonkka, Dirac L. Twidwell, Jacob B. West, William E. Rogers

Department of Agronomy and Horticulture: Faculty Publications

In ecosystems with alternative stable states, restoration success can be thought of as overcoming the resilience of an undesirable state to promote an alternative state that yields greater ecosystem services. Since greater resilience of undesirable states translates into reduced restoration potential, quantifying differences in resilience can enhance restoration planning. In the context of shrub- encroached rangeland restoration, shrubland resilience is the capacity of a woody vegetated state to absorb management interventions designed to produce a more desirable grass- dominated state, and remain within its current regime. Therefore, differences in the resilience of a state can be quantifi ed in a …

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 …

Letter To The Editor Ws-2 Introgression In A Proportion Of Arabidopsis Thaliana Col-0 Stock Seed Produces Specific Phenotypes And Highlights The Importance Of Routine Genetic Verification, Mon-Ray Shao, Vikas Shedge, Hardik Kundariya, Fredric R. Lehle, Sally Ann Mackenzie

Department of Agronomy and Horticulture: Faculty Publications

Arabidopsis thaliana is an important model organism with a robust network of resources that has been of enormous value to the plant science research community. The use of isogenic material as a reference point or control is critical for many types of experiments in plant molecular biology and genetics. Recently, we noticed that some seed from a common source of the widely-used Columbia-0 (Col-0) strain gave rise to plants showing features atypical for this strain. Whole genome DNA-sequencing and allele-specific PCR assays confirmed that the abnormal individuals contain multiple introgressions from the ecotype Wassilewskija-2 (Ws-2), as described below. This emphasizes …

Construction Of High Resolution Genetic Linkage Maps To Improve The Soybean Genome Sequence Assembly Glyma1.01, Qijian Song, Jerry Jenkins, Gaofeng Jia, David L. Hyten, Vince Pantalone, Scott A. Jackson, Jeremy Schmutz, Perry B. Cregan

Department of Agronomy and Horticulture: Faculty Publications

Background: A landmark in soybean research, Glyma1.01, the first whole genome sequence of variety Williams 82 (Glycine max L. Merr.) was completed in 2010 and is widely used. However, because the assembly was primarily built based on the linkage maps constructed with a limited number of markers and recombinant inbred lines (RILs), the assembled sequence, especially in some genomic regions with sparse numbers of anchoring markers, needs to be improved. Molecular markers are being used by researchers in the soybean community, however, with the updating of the Glyma1.01 build based on the high-resolution linkage maps resulting from this research, …

Muts Homolog1 Silencing Mediates Orf220 Substoichiometric Shifting And Causes Male Sterility In Brassica Juncea, Na Zhao, Xinyue Xu, Yashitola Wamboldt, Sally Ann Mackenzie, Xiaodong Yang, Zhongyuan Hu, Jinghua Yang, Mingfang Zhang

Department of Agronomy and Horticulture: Faculty Publications

Cytoplasmic male sterility (CMS) has consistently been associated with the expression of mitochondrial open reading frames (ORFs) that arise from genomic rearrangements. Spontaneous fertility reversion in CMS has been observed in several cases, but a clear understanding of fertility reversion controlled by nuclear genetic influences has been lacking. Here, we identified spontaneous fertile revertant lines for Brassica juncea CMS cytoplasm in which the mitochondrial genome has undergone substoichiometric shifting (SSS) to suppress ORF220 copy number. We placed ORF220, with or without a mitochondrial targeting presequence, under the control of the CaMV35S and AP3 promoters in Arabidopsis to confirm that ORF220 …

Growing Sensitivity Of Maize To Water Scarcity Under Climate Change, Qingfeng Meng, Xinping Chen, David B. Lobell, Zhenling Cui, Yi Zhang, Haishun Yang, Fusuo Zhang

Department of Agronomy and Horticulture: Faculty Publications

Climate change can reduce crop yields and thereby threaten food security. The current measures used to adapt to climate change involve avoiding crops yield decrease, however, the limitations of such measures due to water and other resources scarcity have not been well understood. Here, we quantify how the sensitivity of maize to water availability has increased because of the shift toward longer-maturing varieties during last three decades in the Chinese Maize Belt (CMB). We report that modern, longer-maturing varieties have extended the growing period by an average of 8 days and have significantly offset the negative impacts of climate change …

Information Thermodynamics Of Cytosine Dna Methylation, Robersy Sanchez Rodriguez, Sally Ann Mackenzie

Department of Agronomy and Horticulture: Faculty Publications

Cytosine DNA methylation (CDM) is a stable epigenetic modification to the genome and a widespread regulatory process in living organisms that involves multicomponent molecular machines. Genome-wide cytosine methylation patterning participates in the epigenetic reprogramming of a cell, suggesting that the biological information contained within methylation positions may be amenable to decoding. Adaptation to a new cellular or organismal environment also implies the potential for genome-wide redistribution of CDM changes that will ensure the stability of DNA molecules. This raises the question of whether or not we would be able to sort out the regulatory methylation signals from the CDM background …