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No description available.

In the modern era, maize has become the most successful crop grown in the United States. According to the USDA over 90 million acres of land are planted to corn and 96.2% of the U.S feed grain production is made up of the cereal. Part of the success of maize is due to its floral architecture, and its pollination technique in which the flower opens, exposing stamens containing pollen into the air. A unique organ called the lodicule functions as a release mechanism, forcing the flower to open. Lodicules from grasses and eudicot petals are homologous, yet there is little known of how lodicules are specified during development. Other examples of maize mutants with defects in the lodicule have been discovered including silky1, bearded ear, and sterile tassel silky ear1, but there has been no definitive pathway found that specifies the developmental characteristics of the lodicule. My work has focused on a maize mutant, tasselsheath3 (tsh3), which displays a floral phenotype in the lodicule whorl to better understand this organ. Analysis of tsh3 was separated into two sections: a quantitative phenotypic analysis of the tsh3 floral mutant phenotype, compared to a previously unstudied floral phenotype of tasselsheath1 (tsh1), as well as a tsh1; tsh3 double mutant. I found that lodicule morphology and lodicule number was affected in tsh1, tsh3, and the tsh1; tsh3 mutants. Section two was to identify the single gene that was disrupted in tsh3 mutants. Through both fine mapping and next generation sequencing I was able to localize tsh3 to a region between 148.1mbp and 152.8mbp on chromosome 6. This 4.7mbp region of interest contains 64 protein coding genes. As evidenced by the phenotyping data, tsh3 plays a role specifying lodicule identity during development and has been localized to this region of chromosome 6 on the maize genome.

Iron is among the essential micronutrients for all living organisms and is a cofactor for many cellular redox reactions. Although iron is a highly abundant metal element found in the earth’s crust, it is also a limiting factor in plant development when it is present as insoluble ferric oxides. Plants have evolved two strategies to acquire soluble iron referred to as Strategy I and Strategy II. Our lab has focused on the Arabidopsis thaliana double mutant ysl1ysl3. The mutants display a chlorotic phenotype and are unable to correctly respond to iron deficiency. Grafting is a common method for joining different plant tissues and has been used for studies of long distance signaling. Past studies of iron signaling in Arabidopsis have not been able to provide a mechanism for how plants are able to signal the iron status of the shoot, where iron demand is high, to roots, where iron uptake occurs. The iron signaling experiments included in this thesis follow a seedling-graft approach to understand if grafts are capable of properly sensing iron. A longstanding question of iron homeostasis in plants is the identity of the iron sensors in plants. It was hypothesized that YSL1 and YSL3 have both a transporter function and a receptor function, and therefore function as transceptors. In our predicted model it was proposed that YSL1 and/or YSL3 are directly involved in iron status signaling either in perception and/or transmission of the signal. As evidenced through seedling grafting experiments here, YSLs play a critical part of long distance signaling that plant shoots use to signal their iron status to the roots. In this thesis, YSL1 and YSL3 are shown to be required in the shoots in order for signaling to occur correctly in the roots. To facilitate the analysis of gene expression in the grafts, a FRO3promoter:GUS construct was used in the Col-O WT background. The FRO3 promoter was selected because it is expressed in both leaves and roots under iron deficiency. Experiments showed that the genotype of the shoot used in the grafts is critical for Fe-deficiency induced gene expression in the roots. Thus, grafting has revealed that root iron deficiency responses require YSL1 and YSL3 in leaves for signal transmission. This directly links them to long-distance signaling, and supports the idea that these proteins could be acting as transceptors.

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<p>Like other eukaryotic cells, plant cells contain an endomembrane system composed of compartmentalized organelles with specialized functions. Vesicle trafficking mediates the transport of materials between different organelles and between cells and the environment. The vesicle trafficking process is highly dynamic and plays essential roles in maintaining cellular homeostasis and environmental adaptation. Because of the essential roles of vesicle trafficking in plant growth and development, genes that are involved in vesicle trafficking often have redundant function when they exist as a large family or cause embryonic lethality when they exist as a signal gene or small gene family. Chemical genetics uses small molecule inhibitors to affect protein function without interfering with plant’s genome. Bioactive small molecules can generate a temporary perturbation of a biological system in a reversible and dose-dependent fashion, which allow us to observe dynamic cellular processes and discover new components in trafficking machineries. We recently discovered two small molecules named Endosidin2 (ES2) and Endosidin20 (ES20) that disrupt vesicle trafficking in plants. ES2 inhibits exocytosis by targeting the EXO70A1 subunit of the exocyst complex in plant cells. ES20 targets cellulose synthase (CESA) at the catalytic site and inhibits the delivery of Cellulose Synthase Complex (CSC) to the plasma membrane. This research thesis aims to characterize the specificity of ES2 on EXO70 homologs and identify new genes that mediate CSC trafficking. Drug Affinity Responsive Target Stability (DARTS) assay was used to test the specificity of ES2 in targeting different EXO70s in Arabidopsis. Chemical genetic screen for mutants that have increased sensitivity was conducted to identify novel genes related to CSC trafficking. This project provides new insights in the specificity of ES2 in targeting different EXO70s in plants and the regulatory mechanisms of CSC trafficking that control plant cellulose synthesis.</p><p><br></p>

Master of Science / Department of Biology / Carolyn J. Ferguson / The genus Phlox L. presents intriguing opportunities for systematics research, and P. nana is of particular interest. Phlox nana occurs chiefly in mountains of the Chihuahuan desert to northern New Mexico, and it exhibits much morphological variation across its range. Historically, this taxon has been recognized as a single species (sometimes with infraspecific taxa), or as several species. Perhaps most interesting, variation in ploidy level (cytotypic variation) has been evidenced for P. nana. This research employed flow cytometry methods in conjunction with chromosome counts to document patterns of cytotypic variation. Intensive fieldwork in Arizona, New Mexico and Texas enabled excellent sampling, and evaluation of ploidy level for 76 populations was achieved. Diploid and tetraploid chromosome counts were made (four diploid counts; five tetraploid counts), and flow cytometry was conducted on all populations, providing evidence for diploid, tetraploid and hexaploid populations. Polyploids were found to occur in many geographical areas, and in some regions, diploids and polyploids occur in close geographical proximity (e.g., within both the Davis Mountains and the Chisos Mountains of west Texas). Genome size data are presented (with discussion of unusual populations), and geographic patterns of cytotypic variation are presented and discussed. Patterns are also briefly considered with respect to morphology and taxonomy: cytotypic variation does not readily align with historical recognition of taxonomic variation, and this work sets the stage for ongoing, detailed morphometric study. Research on particular species of Phlox benefits from an understanding of a broad phylogenetic context, and low copy nuclear DNA regions are an important resource for phylogeny development. This research further evaluated part of the NADP-dependent isocitrate dehydrogenase gene (idhB) for its usefulness in inferring relationships in Phlox. Samples were PCR amplified for idhB and cloned, and resulting sequences were added to a larger set of idhB sequence data previously developed in the lab. A total of 163 samples were included, and Bayesian Inference and Maximum Parsimony analyses were conducted for complete data sets. Phylogenetic findings are discussed in light of previous work based on chloroplast and high copy nuclear DNA regions, and challenges and utility of using idhB are discussed.

Master of Science / Department of Biology / David C. Hartnett / The effects of bison activities on forb diversity and cover have been well-established, but less is known about how forb life history is altered by bison-mediated habitat changes. This study had three main objectives: 1) to evaluate the hypothesis that release from aboveground competition with grasses may contribute to the increased cover and diversity of forbs in prairie grazed by bison relative to ungrazed prairie, 2) to determine whether differences in forb reproductive effort between grazed and ungrazed habitats were size-dependent, and 3) to look for evidence of a trade-off between allocation to vegetative and sexual reproduction. The growth, biomass allocation, and sexual reproduction of six common unpalatable perennial species were measured and compared between bison-grazed and ungrazed tallgrass prairie burned at 2-year intervals: Ambrosia psilostachya, Artemisia ludoviciana, Baptisia australis, Psoralidium tenuiflorum, Solidago canadensis, and Vernonia baldwinii. Vegetative reproduction was also measured for B. australis¸ S. canadensis, and V. baldwinii. Light availability, canopy density and height, and percent cover of neighboring plants were measured in each studied individual’s immediate neighborhood and compared between habitats to establish the possibility of differing aboveground competition. Aboveground competition may be lower in bison-grazed habitats, as evidenced by differences in habitat characteristics and plant performance found in this study. In bison-present habitats, sexual reproduction was elevated for all six species and average plant size was greater for all species except A. psilostachya. Vegetative reproduction was not clearly different between habitats for all three species examined. Sexual reproduction increased with size for all species, and the relationship differed significantly between habitats for all species except A. psilostachya. Allocation to vegetative reproduction was not generally related to aboveground biomass, nor was there a clear trade-off between allocation to vegetative and sexual reproduction. The results of this study provide evidence that release from aboveground competition with grasses promotes the growth and sexual reproduction of the studied species of forb, and that differences in sexual reproduction are not entirely size-dependent. Patterns in allocation to vegetative reproduction were less clear and were not clearly tied to sexual reproductive allocation.

<p>Plants use an array of photoreceptors to measure the quality, quantity, and direction of light in order to respond to ever-changing light environments. Photoreceptors not only determine how and when individual plants complete their life cycles, but they also have a profound and long-term macroevolutionary influence on species diversification. Despite their significances, very little is known about photoreceptors across plants as whole, and we lack a comprehensive view of photoreceptor evolution. </p><p> In my dissertation, I investigate the origin and evolution of three of the most prominent photoreceptor gene families in plants: phytochromes, phototropins and neochromes. Using newly available transcriptomic and genomic data, I completed the first in-depth survey of these photoreceptor families across land plants, green algae, red algae, glaucophytes, cryptophytes, haptophytes, and stramenopiles. </p><p> Phytochromes are red/far-red photoreceptors that play essential roles in seed germination, seedling photomorphogenesis, shade-avoidance, dormancy, circadian rhythm, phototropism, and flowering. Here, I show that the canonical plant phytochromes originated in a common ancestor of streptophytes (charophyte green algae plus land plants), and I identify the most likely sequence whereby the plant phytochrome structure evolved from its ancestral phytochrome. Phytochromes in charophyte algae are structurally diverse, including canonical and non-canonical forms, whereas in land plants, phytochrome structure is highly conserved. Liverworts, hornworts, and Selaginella apparently possess a single phytochrome gene copy, whereas independent gene duplications occurred within mosses, lycopods, ferns, and seed plants, leading to diverse phytochrome families in these clades. My detailed phylogeny encompasses all of green plants and enables me to not only uncover new phytochrome lineages, but also to make links to our current understanding of phytochrome function in Arabidopsis and Physcomitrella (the major model organism outside of flowering plants). Based on this robust evolutionary framework, I propose new hypotheses and discuss future directions to study phytochrome mechanisms.</p><p> Phototropins are blue-light photoreceptors that regulate key adaptive physiological responses, including shoot-positive phototropism, root-negative phototropism, chloroplast accumulation/avoidance, stomatal opening, circadian rhythm, leaf expansion, and seedling elongation I show that phototropins originated in the common ancestor of Viridiplantae (all green algae [charophytes, chlorophytes, prasinophytes] plus land plants). Phototropins repeatedly underwent independent duplications in all major plant lineages (mosses, lycopods, ferns and seed plants), except for liverworts and hornworts, where phototropin is a single-copy gene. Following each major duplication event, phototropins subsequently differentiated in parallel, resulting in two specialized (yet partially overlapping) functional forms that primarily mediate either low- or high-light responses. My gene phylogeny further suggests that phototropins have co-evolved with phytochromes, as is evident from their molecular interactions and strikingly similar gene duplication patterns. I hypothesize that the co-evolution of phototropins with phytochromes, together with their subsequent convergent functional divergences in phototropic responses, contributed to the success of plants in adapting to diverse and heterogeneous habitats.</p><p> Neochromes are chimeric photoreceptors that, by fusing phytochrome and phototropin modules into a single protein, are able to use both red/far-red and blue light to modulate phototropic responses. Neochromes were first discovered in ferns, and the evolution of neochromes was implicated as a key innovation that facilitated fern diversification under the low-light angiosperm canopies. Despite its significance from an evolutionary standpoint, the origin of neochromes has remained a mystery. Here I present the first evidence for neochrome in hornworts (a bryophyte lineage) and demonstrate that ferns acquired neochrome from hornworts via horizontal gene transfer (HGT). Fern neochromes are nested within hornwort neochromes in my large-scale phylogenetic reconstructions of phototropin and phytochrome gene families. Divergence date estimates further support the HGT hypothesis, with fern and hornwort neochromes diverging 179 MYA, long after the split between the two plant lineages (at least 400 MYA). By analyzing the draft genome of the Anthoceros punctatus hornwort, I also discovered a novel phototropin gene that likely represents the ancestral lineage of the neochrome phototropin module. Thus, a neochrome originating in hornworts was horizontally transferred to ferns, where it may have played a significant role in the diversification of modern ferns. </p><p> In summary, my studies identified the molecular origins of phytochromes, phototropins and neochromes, and reconstructed their respective evolutionary histories. This new framework for photoreceptor evolution will stimulate new research linking ecology, evolution, and photochemistry to understand how plants adapt to variable light environments.</p> / Dissertation