Life Sciences Commons^™

Characterization Of Lignin Structural Variability And The Associated Application In Genome Wide Association Studies, Nathan D. Bryant

Doctoral Dissertations

Poplar (Populus sp.) is a promising biofuel feedstock due to advantageous features such as fast growth, the ability to grow on marginal land, and relatively low lignin content. However, there is tremendous variability associated with the composition of biomass. Understanding this variability, especially in lignin, is crucial to developing and implementing financially viable, integrated biorefineries. Although lignin is typically described as being comprised of three primary monolignols (syringyl, guaiacyl, p-hydroxyphenyl), it is a highly irregular biopolymer that can incorporate non-canonical monolignols. It is also connected by a variety of interunit linkages, adding to its complexity. Secondary cell wall …

Understanding Host-Microbe Interactions In Maize Kernel And Sweetpotato Leaf Metagenomic Profiles., Alison K. Adams

Doctoral Dissertations

Functional and quantitative metagenomic profiling remains challenging and limits our understanding of host-microbe interactions. This body of work aims to mediate these challenges by using a novel quantitative reduced representation sequencing strategy (OmeSeq-qRRS), development of a fully automated software for quantitative metagenomic/microbiome profiling (Qmatey: quantitative metagenomic alignment and taxonomic identification using exact-matching) and implementing these tools for understanding plant-microbe-pathogen interactions in maize and sweetpotato. The next generation sequencing-based OmeSeq-qRRS leverages the strengths of shotgun whole genome sequencing and costs lower that the more affordable amplicon sequencing method. The novel FASTQ data compression/indexing and enhanced-multithreading of the MegaBLAST in Qmatey allows …

Functional Analysis Of Soybean Proteinase Inhibitor Genes And Cyst Nematode-Inducible Synthetic Promoters For Insects And Nematode-Resistance In Plants, Mst Shamira Sultana

Doctoral Dissertations

Proteinase inhibitors (PIs) from legumes have the potential for use as protectants in response to pests and pathogens. Soybean (Glycine max) contains two trypsin inhibitors (TIs): Kunitz trypsin inhibitor (KTI) and Bowman-Birk inhibitor (BBI). In this study, the possible role of soybean TIs in plant defense against insects and nematodes was investigated. In addition to the three known TIs (KTI1, KTI2 and KTI3), novel inhibitors KTI5, KTI7, and BBI5 were identified in soybean. Their functional role was further examined by overexpression in soybean and Arabidopsis. In vitro enzyme inhibitory assays showed significant increase in trypsin and chymotrypsin inhibitory …

Better Understanding Genomic Architecture With The Use Of Applied Statistics And Explainable Artificial Intelligence, Jonathon C. Romero

Doctoral Dissertations

With the continuous improvements in biological data collection, new techniques are needed to better understand the complex relationships in genomic and other biological data sets. Explainable Artificial Intelligence (X-AI) techniques like Iterative Random Forest (iRF) excel at finding interactions within data, such as genomic epistasis. Here, the introduction of new methods to mine for these complex interactions is shown in a variety of scenarios. The application of iRF as a method for Genomic Wide Epistasis Studies shows that the method is robust in finding interacting sets of features in synthetic data, without requiring the exponentially increasing computation time of many …

Genome Evolution In The Salicaceae: Genetic Novelty, Horizontal Gene Transfer, And Comparative Genomics, Timothy Yates

Doctoral Dissertations

Genome evolution is a powerful force which shapes genomes over time through processes like mutation, horizontal transfer, and sexual reproduction. Although questions which aim to explore genome evolution are broad, they are all understood through the discovery and comparison of genetic variation. For example, genetic diversity may explain differences in phenotypes, etiology of disease, and is essential for phylogenomic analysis. Recently, the democratization of next generation and third generation DNA sequencing technologies have allowed for genomics to produce large amounts of sequence data. This has facilitated the capture of genetic variation at species and population scales.

Populus and Salix are …

Erecta Family Genes Regulate The Shoot Apical Meristem And Organ Formation, Daniel A. Degennaro

Doctoral Dissertations

Plants are sessile and must adjust their organ growth to their environments. A reservoir of stem cells in the shoot apical meristem (SAM) supplies cells for differentiation into organs. The SAM must balance organ production with stem cell maintenance. The ERECTA family (ERfs) encodes the leucine-rich repeat receptor-like kinases ERECTA (ER), ERECTA-LIKE 1 (ERL1), and ERL2. ERf signaling regulates organ initiation and stem cell maintenance. Results presented in this work include the following:

1) WUSCHEL (WUS) and CLAVATA3 (CLV3) make up a negative feedback loop to maintain SAM size. WUS and CLV3 expression localization is critical for …

Genetic And Epigenetic Control Of Soybean Agronomic Traits, Daniel Niyikiza

Doctoral Dissertations

Greater soybean productivity depends on the genetic improvement of yield components, epigenetic effects and the interactions with surrounding environment. We explored the possibility of soybean improvement by conventional biparental crossing of soybean lines, differing by seed quality, yield, and resistance to a range of pathogens, including soybean cyst nematode (SCN). We investigated the role of Resistance to Heterodera glycines (Rhg) 1 and 4 loci in soybean resistance to SCN, race 2 and 3. Further, we evaluated the adaptability of temperate-origin soybean lines in tropical environments of Rwanda. Lastly, we examined gene expression, RNA splicing, DNA methylation and their interactions in …

Evaluation Of Off-Type Grasses In Interspecific Hybrid Bermudagrass [Cynodon Dactylon (L.) Pers. X C. Transvaalensis Burtt-Davy] Putting Greens, Eric Hall Reasor

Doctoral Dissertations

The economic impact of the golf industry in the United States (U.S.) in 2011 was estimated to be $176.8 billion. Interspecific hybrid bermudagrasses [Cynodon dactylon (L.) Pers. x C. transvaalensis Burtt-Davy] are some of the most widely utilized grasses on golf courses throughout tropical, subtropical, and temperate climates. In 2007, bermudagrass was grown on 80% of putting green acreage in the southern U.S. ‘Tifgreen’ and ‘Tifdwarf’ were two of the first widely established cultivars on putting greens, but their genetic instability led to the occurrence of phenotypically different off-type (OT) grasses. Several OT grasses were selected and released as …

Nanocomposite Adhesive Of English Ivy (Hedera Helix): Bioproduction, Nanoparticle Isolation, And Molecular Analysis, Jason Neil Burris

Doctoral Dissertations

English ivy naturally produces organic nanoparticles from its adventitious root hairs, and possesses characteristics that may allow them to replace metal-based nanoparticles in common applications, such as sunscreen. At the onset of the research, it was hypothesized that a physical mechanism of attachment, similar to the gecko footpad, was used to generate the adhesive force for attachment; however, through the results obtained from recent work, it is clear that a biochemical mechanism is involved in the generation of the strength of adhesion. Therefore, the goal of this research was to provide a better understanding of the genetic basis of nanoparticle …

Molecular Breeding Strategies For Improvement Of Complex Traits In Soybean, Christopher Joseph Smallwood

Doctoral Dissertations

Soybean [Glycine max (L.) Merrill] is the leading oilseed crop grown in the world. Yield, fatty acids, protein, and oil are commercially important soybean traits; thus evaluation of breeding strategies for improvement of these traits is merited. To accomplish this, a comparison of molecular and phenotypic breeding strategies from progeny row selections was performed. From this it was determined that molecular strategies consistently outperformed phenotypic selections (PS) in the progeny row stage for soybean yield, fatty acids, protein, and oil. For yield, Epistacy was the preferred selection method. For fatty acids, protein, and oil, the genomic selection (GS) strategies were …

Assessing The Genetic Diversity Of The Genus Viburnum Using Simple Sequence Repeats, Deborah Dean

Doctoral Dissertations

The genus Viburnum was established in 1753 by Linnaeus and is the largest genus in the Adoxaceae and consists of approximately 160 species. Viburnum species are small trees which grow throughout the temperate regions of the Northern Hemisphere (Hoch, 1995). While this genus shares little variety in fruit and flower morphology, it is diverse in many other traits. As molecular studies advance, this large genus continues to undergo reclassification. Here three SSR libraries were constructed to discern additional molecular insight into this vast genus.

Microsatellite markers were developed to characterize Viburnum on several different levels. V. dilatatum is an introduced …

Evaluation Of Traits Associated With Breeding For Improved Biomass And Ethanol Yield In Switchgrass, Virginia Roseanna Sykes

Doctoral Dissertations

Switchgrass (Panicum virgatum L.) is a perennial, warm season grass that can be used as a biofuel. A greater understanding of the relationship of biomass yield and ethanol yield with disease susceptibility and morphological traits, estimation of the underlying genetic parameters of these traits, and the efficacy of selection at different maturity and under different production conditions could help breeders more effectively develop improved biofuel switchgrass cultivars. To examine these issues, three studies were performed. The first examined switchgrass leaves exhibiting low, medium, and high severity of rust symptoms, caused by infection with Puccinia emaculata. Results indicate P. …

Effects Of Leaflet Orientation And Root Morphology On Physiological Traits And Yield In Soybeans., Richard Dewayne Johnson

Doctoral Dissertations

Drought is the most important abiotic stress adversely affecting soybean (Glycine max (L.) Merr.) yield. Leaflet orientation has been shown to reduce leaflet temperatures and transpiration while root morphology has been related to slower wilting phenotypes. The objective of this study was to investigate effects of leaflet orientation and rooting morphology on whole plant transpiration, yield, water use efficiency, and other physiological traits in soybeans using grafting techniques, population lines, near-isogenic lines, and restrained leaf canopy experiments. Experiments were conducted in Knoxville, TN with additional yield trial plots at Springfield, Spring Hill, and Milan, TN. Data were collected on …

Detection Of Soybean Amino Acid Qtls And Seed Yield Qtls Using Selective Genotyping, Benjamin David Fallen

Doctoral Dissertations

The U.S. Census Bureau projects the world’s population will top more than nine billion by 2050. Today, soybeans account for 56 % of the world oilseed production and 68 % of the world protein meal consumption, with U.S. soybean production accounting for 33 % of the world soybean production. So, to meet the demand of the world’s growing population and of the livestock industry improvements in both the composition and the yield of soybean is essential.

The primary objective of this project was to use molecular markers to identify genomic regions associated with amino acid composition and yield in soybean. …

Assessing The Efficiency Of Phenotypic And Molecular Genotype Selection Methods For Complex Traits In Soybean, Catherine Nyaguthii Nyinyi

Doctoral Dissertations

Soybean [Glycine max (L.) Merrill] is an important source of protein and oil for both nutritional and industrial applications. Increasing seed yield and protein concentration is the main goal of many soybean breeders to meet market demands. Soybean breeders have occasionally succeeded in producing high yielding cultivars with increased protein content using conventional means despite the negative correlation that exists between these two traits. The efficiency of breeding for seed yield and protein concentration improvement in soybean could be increased using marker assisted selection (MAS) breeding strategies to select genotypes containing favorable alleles for faster cultivar development. The objective …

Steps Toward Butternut (Juglans Cinerea L.) Restoration, Sunshine L. Brosi

Doctoral Dissertations

Butternut (Juglans cinerea L.), a lesser-known relative of black walnut (Juglans nigra L.), is a native tree species beneficial for wildlife, valuable for timber, and part of the great diversity of species in the eastern forests of North America. Populations of butternut are being devastated by butternut canker disease, caused by the fungus Sirococcus clavigignenti-juglandacearum (V.M.G. Nair, Kostichka, & Kuntz), which is thought to be introduced to North America. The disease causes multiple branch and stem cankers that eventually girdle trees. Small population sizes, lack of sprouting, and shade intolerance exacerbates the disease and results in permanent losses of butternut …

Molecular Evolution Of Mads-Box Genes In Cotton (Gossypium L.), Wusheng Liu

Doctoral Dissertations

The purpose of this study was to examine the molecular evolution of floral developmental MADS-box genes in diploid and allotetraploid cotton (Gossypium, Malvaceae). We isolated and characterized both cDNA and genomic DNA sequences of four MADS-box genes, B-sister, APETALA3 (AP3), PISTILLATA (PI, two copies) and AGAMOUS (AG), in seven Gossypium species (2 A-genome species, 2 D-genome species, 1 C-genome species and 2 AD-genome species) as well as an outgroup species, Gossypioides kirkii. We then studied the expression patterns of each gene by reverse-transcriptase PCR (RT-PCR) in each flower part for different flower stages of G. …