Genetics and Genomics Commons^™

Haplotype Diversity And Population Genetic Structure Of Antistrophus Gall Wasps Associated With Two Silphium Species And Implication For Host Mediated Speciation, Jiaxin Deng

Masters Theses

Gall making insects form a special feeding guild of phytophagous animals, and by manipulating host plant tissue differentiation, are able to avoid plant chemical defenses and thus have no need for counter defense mechanisms. Host plant selection is crucial to the evolution of these insects because successful gall formation is largely dependent on host plant ability to respond to stimuli. In Illinois and neighboring states, Antistrophus gall wasps associated with the rosin weed (S. integrifolium) and the cup plant (S. perfoliatum) are morphologically indistinguishable and thus have been treated as belonging to single species. However, the wasps from the host …

Development Of Computational Techniques For Identification Of Regulatory Dna Motif, Cankun Wang

Electronic Theses and Dissertations

Identifying precise transcription factor binding sites (TFBS) or regulatory DNA motif (motif) plays a fundamental role in researching transcriptional regulatory mechanism in cells and helping construct regulatory networks for biological investigation. Chromatin immunoprecipitation combined with sequencing (ChIP-seq) and lambda exonuclease digestion followed by high-throughput sequencing (ChIP-exo) enables researchers to identify TFBS on a genome-scale with improved resolution. Several algorithms have been developed to perform motif identification, employing widely different methods and often giving divergent results. In addition, these existing methods still suffer from prediction accuracy. Thesis focuses on the development of improved regulatory DNA motif identification techniques. We designed an …

Application Of Short Tandem Target Mimic (Sttm) Technique For Functional Analysis Of Micro-Rna396 In Transgenic Poplar Trees, Surattana Boonsai

Dissertations, Master's Theses and Master's Reports

Short Tandem Target Mimic (STTM) is a commonly technique used for functional studies of a number of genes in several plant model systems. However, very little is known about application of STTM technique in tree species. In this study, STTM was applied to knock down microRNA396 (miR396) in transgenic poplar trees for the first time. STTM396 expression resulted in dramatic decrease in miR396 expression levels leading to taller plants with larger leaves and larger leaf cell size. Additionally, an expression analysis of growth regulating factor genes (GRFs) that are members of miR396 target gene family showed up-regulation of GRF07 gene …

Intraspecific Variation In Dehydration Tolerance: Insights From The Tropical Plant Marchantia Inflexa, Rose A. Marks

Theses and Dissertations--Biology

Plants are threatened by global change, increasing variability in weather patterns, and associated abiotic stress. Consequently, there is an urgent need to enhance our ability to predict plant community dynamics, shifts in species distributions, and physiological responses to environmental challenges. By building a fundamental understanding of plant stress tolerance, it may be possibly to protect the ecological services, economic industries, and communities that depend on plants. Dehydration tolerance (DhT) is an important mechanism of water stress tolerance with promising translational applications. Here, I take advantage natural variation in DhT to gain a deeper insight into this complex trait. In addition, …

A Pipeline For Exogenous Gene Expression And Biomass Analysis In Plants, Bijay Bisunke

Masters Theses

Biological pretreatment of biomass is typically required for the production of liquid biofuels, which are viable alternatives to traditional fossil fuels. While traditional thermomechanical pretreatments are effective at helping to deconstruct lignocellulose, they are often expensive and tend to generate environmentally dangerous waste materials. An alternative to traditional pretreatment strategies is biological pretreatment, which has focused on lignocellulose-degrading organisms, such as white-rot fungi. While direct pretreatment of biomass with white-rot fungi has shown great promise, directly expressing functional white-rot fungi genes in plants (i.e. in planta expression) has the potential to be even more efficient because the biomass itself …

Genetic Regulation Of The Elicitation Of Glyceollin Biosynthesis In Soybean, Md. Asraful Jahan

Graduate Theses, Dissertations, and Problem Reports (ETD)

Glyceollin phytoalexins are the pathogen-elicited defense metabolites that belong to the isoflavonoid family of molecules of soybean (Glycine max L. Merr). Phytophthora root and stem rot of soybean caused by Phytophthora sojae is a destructive disease throughout the soybean-growing regions worldwide causing devastating economic damages (globally $1-2 billion and over $250 million in the USA) every year. Engineering soybean plants that produce higher levels of glyceollins could confer resistance against this pathogen. Glyceollins also show anticancer and neuroprotective activities in mammals, therefore they are important for agriculture and medical research. Firstly, we were interested in understanding how biotic and …

Enhancing Water Stress Tolerance In Floriculture Crops, Suejin Park

Graduate Theses, Dissertations, and Problem Reports (ETD)

Water deficit is one of the major constraints on plant growth and development, causing reduction of crop productivity. To minimize water loss, among many adaptation strategies, plants close their stomata to reduce transpiration. The stomatal closure is regulated by light, internal CO2 concentration, and plant hormones, mainly abscisic acid. Plants’ response mechanisms to water deficit are complex processes involving numerous genes and various signaling pathways. Floriculture crops are often exposed to water deficit during shipping and retailing, and these periods often result in damaged crops and profit loss. Understanding of plant responses to water deficit stress will provide us an …

The New Natural Distribution Area Of Aspen (Populus Tremula L.) Marginal Populations In Pasinler In The Erzurum Province, Turkey, And Its Stand Characteristics, Halil Bariş Özel, Sezgin Ayan, Serdar Erpay, Bojan Simovski

Aspen Bibliography

Background and Purpose: Genetic diversity is the basis for adaptation and survival of tree species under changing environmental conditions, representing the key issue of stability and productivity of forest ecosystems. This paper studies the marginal population characteristics and stand dynamics of aspen tree (Populus tremula L.) in natural, pure and mixed forest stands with Scots pine (Pinus sylvestris L.). These populations were observed on founding sites between Timarli Valley and Timan Plateau located in Pasinler in the Erzurum Province in Turkey.
Materials and Methods: Three replicated sample sites were established according to a randomised block design …

Dependence Of Aspen Stands On A Subsurface Water Subsidy: Implications For Climate Change Impacts, D. M. Love, M. D. Venturas, J. S. Sperry, P. D. Brooks, J. L. Pettit, Y. Wang, W. R. L. Anderegg, X. Tai, D. S. Mackay

Aspen Bibliography

The reliance of 10 Utah (USA) aspen forests on direct infiltration of growing season rain versus an additional subsurface water subsidy was determined from a trait- and process-based model of stomatal control. The model simulated the relationship between water supply to the root zone versus canopy transpiration and assimilation over a growing season. Canopy flux thresholds were identified that distinguished nonstressed, stressed, and dying stands. We found growing season rain and local soil moisture were insufficient for the survival of 5 of 10 stands. Six stands required a substantial subsidy (31–80% of potential seasonal transpiration) to avoid water stress and …

Gene Network Analysis Of Poplar Root Transcriptome In Response To Drought Stress Identifies A Ptajaz3ptarap2.6-Centered Hierarchical Network, Madhumita Dash, Yordan S. Yordanov, Tatyana Georgieva, Hairong Wei, Victor Busov

College of Forest Resources and Environmental Science Publications

Using time-series transcriptomic data from poplar roots undergoing polyethylene glycol (PEG)-induced drought stress, we built a genetic network model of the involved putative molecular responses. We found that the network resembled a hierarchical structure. The highest hierarchical level in this structure is occupied by 9 genes, which we called superhubs because they were primarily connected to 18 hub genes, which are then connected to 2,934 terminal genes. We were only able to regenerate transgenic plants overexpressing two of the superhubs, suggesting that the majority of the superhubs might interfere with the regeneration process and did not allow recovery of transgenic …

Phylogeographic Analyses Of A Widely Distributed Populus Davidiana: Further Evidence For The Existence Of Glacial Refugia Of Cool‐Temperate Deciduous Trees In Northern East Asia, Zhe Hou, Zhaoshan Wang, Zhanyang Ye, Shuhui Du, Shuya Liu, Jianguo Zhang

Aspen Bibliography

Despite several phylogeographic studies had provided evidence to support the existence of glacial refugia of cool‐temperate deciduous trees in northeast China, the species used in these studies were limited by the species ranges, which could not exclude the possibility that northern populations were the colonists from southern refugial populations during the last glacial maximum (LGM). Here, we estimated the nucleotide variation in Populus davidiana, a widespread species distributed in Eurasia. Three groups in northeast, central, and southwest China were constructed according to the simulation results from SAMOVA, composition of chloroplast haplotypes and structure results. We revealed that the northeast …

Generation And Evaluation Of Modified Opaque-2 (O2) Popcorn Suggests A Route To Quality Protein Popcorn (Qpp), Ying Ren

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

I have been working on a Quality Protein Popcorn breeding project where QPM conversion is carried out simultaneously for several elite popcorn germplasms. During my study in the graduate program, I led the following aspects of the Quality Protein Popcorn Breeding Project:

1. Identified suitable QPMs as opaque-2 allele donors.

2.Examined the feasibility of quick introgression of the opaque-2 allele into popcorn lines via marker-assisted selection.

3. Monitored modification by SDS-PAGE zein profiling and light box phenotypic selection to make sure multiple modifier loci for opaque-2 were incorporated each time generation advancement was carried out.

4. Carried out high throughput …

Breeding For Resilience To Increasing Temperatures: A Field Trial Assessing Genetic Variation In Soft Red Winter Wheat, Kathleen Russell, David Van Sanford

Plant and Soil Sciences Faculty Publications

Breeding for resilience to climate change is a daunting prospect. Crop and climate models tell us that global wheat yields are likely to decline as the climate warms, causing a significant risk to global food security. High temperatures are known to affect crop development yet breeding for tolerance to heat stress is difficult to achieve in field environments. We conducted an active warming study over two years to quantify the effects of heat stress on genetic variation of soft red winter (SRW) wheat (Triticum aestivum L.). Forty SRW cultivars and breeding lines were chosen based on marker genotypes at …

Sip-428, A Sir2 Deacetylase Enzyme And Its Role In Biotic Stress Signaling Pathway, Bal Krishna Chand Thakuri

Electronic Theses and Dissertations

SABP2 (Salicylic Acid Binding Protein 2) plays a vital role in the salicylic acid signaling pathway of plants both regarding basal resistance and systemic acquired resistance against pathogen infection. SIP-428 (SABP2 Interacting Protein-428) is a Silent information regulator 2 (SIR2) like deacetylase enzyme that physically interacts with SABP2 in a yeast two-hybrid interaction and confirmed independently by a GST pull-down assay. We demonstrated that SIP- 428 is an NAD+ dependent SIR2 deacetylase enzyme. Transgenic tobacco plants silenced in SIP- 428 expression via RNAi showed enhanced basal resistance to microbial pathogens. Moreover, these SIP-428-silenced lines also exhibited a robust induction of …

A Common Genetic Mechanism Underlies Morphological Diversity In Fruits And Other Plant Organs, Shan Wu, Biyao Zhang, Neda Keyhaninejad, Gustavo R. Rodríguez, Hyun Jung Kim, Manohar Chakrabarti, Eudald Illa-Berenguer, Nathan K. Taitano, M. J. Gonzalo, Aurora Díaz, Yupeng Pan, Courtney P. Leisner, Dennis Halterman, C. Robin Buell, Yiqun Weng, Shelley H. Jansky, Herman Van Eck, Johan Willemsen, Antonio J Monforte, Tea Meulia, Esther Van Der Knaap

Plant and Soil Sciences Faculty Publications

Shapes of edible plant organs vary dramatically among and within crop plants. To explain and ultimately employ this variation towards crop improvement, we determined the genetic, molecular and cellular bases of fruit shape diversity in tomato. Through positional cloning, protein interaction studies, and genome editing, we report that OVATE Family Proteins and TONNEAU1 Recruiting Motif proteins regulate cell division patterns in ovary development to alter final fruit shape. The physical interactions between the members of these two families are necessary for dynamic relocalization of the protein complexes to different cellular compartments when expressed in tobacco leaf cells. Together with data …

Repeat Elements Organise 3d Genome Structure And Mediate Transcription In The Filamentous Fungus Epichloë Festucae, David J. Winter, Austen R. D. Ganley, Carolyn A. Young, Ivan Liachko, Christopher L. Schardl, Pierre-Yves Dupont, Daniel Berry, Arvina Ram, Barry Scott, Murray P. Cox

Plant Pathology Faculty Publications

Structural features of genomes, including the three-dimensional arrangement of DNA in the nucleus, are increasingly seen as key contributors to the regulation of gene expression. However, studies on how genome structure and nuclear organisation influence transcription have so far been limited to a handful of model species. This narrow focus limits our ability to draw general conclusions about the ways in which three-dimensional structures are encoded, and to integrate information from three-dimensional data to address a broader gamut of biological questions. Here, we generate a complete and gapless genome sequence for the filamentous fungus, Epichloë festucae. We use Hi-C …

Genome Wide Association Studies For Identification Of Markers Linked To Sucrose Traits In Sugarcane, Nathanael Darrell Fickett

LSU Doctoral Dissertations

Sugarcane, being a complex aneu-polyploid, poses unique challenges to fine mapping of quantitative trait loci (QTL) controlling agronomic traits of interest. Genome-wide association studies (GWAS) could be a better alternative to identify molecular markers associated with specific traits due to high linkage disequilibrium in sugarcane. In the first study, marker-trait associations (MTAs) were evaluated for three sucrose traits, Brix, total recoverable sugar (TRS), and percent sucrose on 48 elite and historic Louisiana breeding clones using 1,062 alleles. These sucrose traits were highly correlated (P-value < 0.0001) at >0.96. TASSEL 5.1 and JMP Genomics 8.0 were compared with eight models run in each program. …

Iac Gene Expression In The Indole-3-Acetic Acid-Degrading Soil Bacterium Enterobacter Soli Lf7, Isaac V. Greenhut, Beryl L. Slezak, Johan H. J. Leveau

Plant and Soil Sciences Faculty Publications

We show for soil bacterium Enterobacter soli LF7 that the possession of an indole-3-acetic acid catabolic (iac) gene cluster is causatively linked to the ability to utilize the plant hormone indole-3-acetic acid (IAA) as a carbon and energy source. Genome-wide transcriptional profiling by mRNA sequencing revealed that these iac genes, chromosomally arranged as iacHABICDEFG and coding for the transformation of IAA to catechol, were the most highly induced (>29-fold) among the relatively few (iac cluster were genes for a major facilitator superfamily protein (mfs) and enzymes of the β-ketoadipate pathway (pcaIJD-catBCA), which channels …

Developmental Variation In Fruit Polyphenol Content And Related Gene Expression Of A Red-Fruited Versus A White-Fruited Fragraria Vesca Genotype, Sutapa Roy, Sanjay Singh, Douglas D. Archbold

Horticulture Faculty Publications

Two cultivars of F. vesca, red-fruited Baron Solemacher (BS) and white-fruited Pineapple Crush (PC), were studied to compare and contrast the quantitative accumulation of major polyphenols and related biosynthetic pathway gene expression patterns during fruit development and ripening. Developing PC fruit showed higher levels of hydroxycinnamic acids in green stages and a greater accumulation of ellagitannins in ripe fruit in comparison to BS. In addition to anthocyanin, red BS fruit had greater levels of flavan-3-ols when ripe than PC. Expression patterns of key structural genes and transcription factors of the phenylpropanoid/flavonoid biosynthetic pathway, an abscisic acid (ABA) biosynthetic gene, …

Aspen Recruitment In The Yellowstone Region Linked To Reduced Herbivory After Large Carnivore Restoration, Luke E. Painter, Robert L. Beschta, Eric J. Larsen, William J. Ripple

Aspen Bibliography

Quaking aspen (Populus tremuloides) recruitment during the 1980s–90s was suppressed by Rocky Mountain elk (Cervus canadensis) herbivory on winter ranges in the Yellowstone region, and saplings (young aspen taller than 2 m) were rare. Following the 1995–96 reintroduction of gray wolves (Canis lupus), browsing decreased and sapling recruitment increased in Yellowstone National Park. We compared aspen data from inside the park to data collected in three winter ranges outside the park. For most areas, the percentage of young aspen browsed annually was 80–100% in 1997–98, decreasing to 30–60% in 2011–15. Sapling recruitment was inversely …

Effects Of Stand Structure, Browsing, And Biophysical Conditions On Regeneration Following Mountain Pine Beetle In Mixed Lodgepole Pine And Aspen Forests Of The Southern Rockies, Kristen A. Pelz, Frederick W. Smith

Aspen Bibliography

Aspen (Populus tremuloides) and lodgepole pine (Pinus contorta var. latifolia) co-occur in the southern Rocky Mountains (USA), where mountain pine beetle (MPB, Dendroctonus ponderosae) has caused extensive lodgepole pine mortality since the late 1990s. Both species excel in post-disturbance high-light environments, but lodgepole pine has generally been thought to establish poorly on undisturbed seedbeds, and aspen suckering may be inhibited by intact aspen overstory. We ask whether lodgepole pine and aspen will regenerate in sufficient quantities to revegetate these forests. We visited a random sample of aspen and lodgepole pine stands across the affected landscape …

Characterization Of Mrna Polyadenylation In The Apicomplexa, Ashley T. Stevens, Daniel K. Howe, Arthur G. Hunt

Plant and Soil Sciences Faculty Publications

Messenger RNA polyadenylation is a universal aspect of gene expression in eukaryotes. In well-established model organisms, this process is mediated by a conserved complex of 15–20 subunits. To better understand this process in apicomplexans, a group of unicellular parasites that causes serious disease in humans and livestock, a computational and high throughput sequencing study of the polyadenylation complex and poly(A) sites in several species was conducted. BLAST-based searches for orthologs of the human polyadenylation complex yielded clear matches to only two—poly(A) polymerase and CPSF73—of the 19 proteins used as queries in this analysis. As the human subunits that recognize the …

Mobile Elements Shape Plastome Evolution In Ferns, Tanner A. Robison, Amanda L. Grusz, Paul G. Wolf, Jeffrey P. Mower, Blake D. Fauskee, Karla Sosa, Eric Schuettpelz

Biology Faculty Publications

Plastid genomes display remarkable organizational stability over evolutionary time. From green algae to angiosperms, most plastid genomes are largely collinear, with only a few cases of inversion, gene loss, or, in extremely rare cases, gene addition. These plastome insertions are mostly clade-specific and are typically of nuclear or mitochondrial origin. Here, we expand on these findings and present the first family-level survey of plastome evolution in ferns, revealing a novel suite of dynamic mobile elements. Comparative plastome analyses of the Pteridaceae expose several mobile open reading frames that vary in sequence length, insertion site, and configuration among sampled taxa. Even …

Double-Stranded Rna Binding Protein, Staufen, Is Required For The Initiation Of Rnai In Coleopteran Insects, June-Sun Yoon, Kanakachari Mogilicherla, Dhandapani Gurusamy, Xien Chen, Shankar C. R. R. Chereddy, Subba R. Palli

Entomology Faculty Publications

RNA interference (RNAi) is being used to develop methods to control pests and disease vectors. RNAi is robust and systemic in coleopteran insects but is quite variable in other insects. The determinants of efficient RNAi in coleopterans, as well as its potential mechanisms of resistance, are not known. RNAi screen identified a double-stranded RNA binding protein (StaufenC) as a major player in RNAi. StaufenC homologs have been identified in only coleopteran insects. Experiments in two coleopteran insects, Leptinotarsa decemlineata and Tribolium castaneum, showed the requirement of StaufenC for RNAi, especially for processing of double-stranded RNA (dsRNA) to small interfering …

Grapevine Vein Clearing Virus: Epidemiological Patterns And Construction Of A Clone, Cory Von Keith

Graduate Theses/Dissertations

Grapevine vein clearing virus (GVCV) is a recently discovered virus belonging to the Badnavirus genus. Characteristic to its name, the virus is associated with a disease where symptoms manifest as pronounced vein-clearing, resulting in severe berry deformation and vine decline in susceptible grape varieties. Sustainable production of wine is dependent on healthy plants. The associated disease is mainly found in Midwest vineyards. Attempts were made in this thesis to provide evidence of causality of the virus to the associated disease and to infer the historical path and migration pattern of GVCV. Conclusions and discussions will provide grape producers with the …

Genome-Wide Atlas Of Alternative Polyadenylation In The Forage Legume Red Clover, Manohar Chakrabarti, Randy D. Dinkins, Arthur G. Hunt

Plant and Soil Sciences Faculty Publications

Studies on prevalence and significance of alternative polyadenylation (APA) in plants have been so far limited mostly to the model plants. Here, a genome-wide analysis of APA was carried out in different tissue types in the non-model forage legume red clover (Trifolium pratense L). A profile of poly(A) sites in different tissue types was generated using so-called ‘poly(A)-tag sequencing’ (PATseq) approach. Our analysis revealed tissue-wise dynamics of usage of poly(A) sites located at different genomic locations. We also identified poly(A) sites and underlying genes displaying APA in different tissues. Functional categories enriched in groups of genes manifesting APA between …

Fitness Consequences Of Interspecific Nesting Associations Among Cavity-Nesting Birds, James C. Mouton, Thomas E. Martin

Aspen Bibliography

Interspecific aggregations of prey may provide benefits by mitigating predation risk, but they can also create costs if they increase competition for resources or are more easily detectable by predators. Variation in predation risk and resource availability may influence the occurrence and fitness effects of aggregating in nature. Yet tests of such possibilities are lacking. Cavity-nesting birds provide an interesting test case. They compete aggressively for resources and experience low nest predation rates, which might predict dispersion, but across 19 years of study we found that they commonly aggregate by sharing nest trees. Tree sharing was more common when aspen …

Removal Of Invasive Plants From Pando Exclosure 2018, Marc Coles-Ritchie

Aspen Bibliography

On July 10-11, 2018 volunteers and staff from Great Old Broads for Wilderness and Grand Canyon Trust removed invasive plants from the Pando exclosure, a fenced portion of the Pando Clone aspen forest adjacent to Fish Lake, in Central Utah. This area has been fenced to restore a portion of the Pando Clone that has been lacking recruitment for decades, by protecting young aspen from browsing by deer and cattle. We have been removing invasive species for five years from this exclosure.

The 2018 trip included 10 women and one staffer of Great Old Broads for Wilderness, from the states …

Phytochemical Screening Of Quaking Aspen (Populus Tremuloides) Extracts By Uplc-Qtof-Ms And Evaluation Of Their Antimicrobial Activity, Annabelle St-Pierre, Dorian Blondeau, André Lajeunesse, Julien Bley, Nathalie Bourdeau, Isabel Desgagné-Penix

Aspen Bibliography

The continual emergence of pathogen resistance is a recurring challenge and pushes for the development of antimicrobial compounds. Here, we investigated compounds from quaking aspen trees (Populus tremuloides) as potential antimicrobial agents. Several extractions using different solvents were realized, and corresponding antimicrobial activity was tested against eight microorganisms. Results revealed that polar extraction solvents including water, ethanol and methanol gave the best extraction yields (>15.07%). Minimal inhibition concentration (MIC) and minimal bactericidal/fungicidal concentration (MBC/MFC) demonstrated that water extracts had the best antimicrobial activity by a weak to moderate inhibition of growth of all eight tested microorganisms in addition to …

How Does Climate Change Affect Endophytic Fungi?, Amber Toussaint, Natalie Christian, Katy Heath

PRECS student projects

Plant-associated microorganisms can have major effects on plant health, but climate change can affect plant microbiomes. While it is unknown how climate change will affect aboveground plant-associated microorganisms, such as foliar endophytic fungi, we hypothesize that increased CO₂ concentrations will increase species richness and diversity in endophytic fungal communities, because increased plant photosynthesis under elevated CO₂ will increase the resources available to the fungi.