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.

Doctor of Philosophy / Department of Biology / David C. Hartnett / Grazing and drought are instrumental in the development and maintenance of perennial grasslands. In this research I tested the belowground bud bank contribution to tallgrass prairie resistance and resilience when perturbed by grazing and drought. First, I tested the bud bank role in vegetation response to and recovery from severe drought (Chapter 2). I compared above- and belowground responses of experimentally droughted plots to ambient controls and irrigated plots during two years of severe drought and two years of recovery. I found that although aboveground net primary productivity declined 30-60% during drought, bud bank density and demography were insensitive to drought. These results suggest that grassland resistance and resilience when perturbed by drought may be mediated by stability of belowground bud banks. Second, I investigated vegetation and soil nutrient legacies following release from long-term grazing (Chapter 3). I documented a relatively rapid shift in aboveground vegetation within four years of grazer exclusion, with productivity, stem density, and diversity becoming relatively more similar to ungrazed than grazed prairie. The density and composition of the belowground bud bank and soil seed bank shifted more slowly, remaining more similar to grazed than ungrazed prairie. Responses of soil nutrients to removal of grazers varied, and in some cases was affected by recent fire history. These results demonstrate the contribution of belowground propagules to the maintenance of a diverse plant community both during grazing and after grazers are removed. Finally, I examined short-term vegetation responses to both drought and grazing (Chapter 4). Despite extreme drought and simulated grazing that reduced productivity and increased mortality of individual stems, the dominant C4 grasses maintained a stable bud bank. Aboveground net primary productivity and bud bank density of sedges and forbs, however, were reduced by both drought and grazing. This differential response of species to extreme drought and grazing led to shifts in community composition and species diversity over one growing season. Across drought and grazing treatments, live rhizome biomass was highly correlated with bud bank density and may be a useful, more easily measured index of bud bank density.

Master of Science / Department of Agronomy / William T. Schapaugh Jr / Crops research moving forward faces many challenges to improve crop performance. In breeding programs, phenotyping has time and economic constraints requiring new phenotyping techniques to be developed to improve selection efficiency and increase germplasm entering the pipeline. The objectives of these studies were to examine the changes in spectral reflectance with soybean breeding from 1923 to 2010, evaluate band regions most significantly contributing to yield estimation, evaluate spectral reflectance data for yield estimation modeling across environments and growth stages and to evaluate the usefulness of spectral data as an optimized phenotyping technique in breeding programs. Twenty maturity group III (MGIII) and twenty maturity group IV (MGIV) soybeans, arranged in a randomized complete block design, were grown in Manhattan, KS in 2011 and 2012. Spectral reflectance data were collected over the growing season in a total of six irrigated and water- stressed environments. Partial least squares and multiple linear regression were used for spectral variable selection and yield estimation model building. Significant differences were found between genotypes for yield and spectral reflectance data, with the visible (VI) having greater differences between genotypes than the near-infrared (NIR). This study found significant correlations with year of release (YOR) in the VI and NIR portions of the spectra, with newer released cultivars tending to have lower reflectance in the VI and high reflectance in the NIR. Spectral reflectance data accounted for a large portion of variability for seed yield between genotypes using the red edge and NIR portions of the spectra. Irrigated environments tended to explain a larger portion of seed yield variability than water-stressed environments. Growth stages most useful for yield estimation was highly dependent upon the environment as well as maturity group. This study found that spectral reflectance data is a good candidate for exploration into optimized phenotyping techniques and with further research and validation datasets, may be a suitable indirect selection technique for breeding programs.

Doctor of Philosophy / Department of Biology / David C. Hartnett / Perennial grass populations propagate vegetatively via the belowground bud bank. Climate, photosynthetic pathway, and growth form impact bud production, longevity, and dormancy; leading to alterations in bud bank and tiller dynamics. Previous research in mesic C₄-dominated tallgrass prairie revealed that a C₄ grass had greater bud longevity and differing bud bank dynamics than a C₃ species. This study examined the bud bank dynamics of rhizomatous and caespitose grasses in a more arid C₃ dominated prairie to gain insights into how bud banks differ among grass species, growth forms, and environments, and the relationship between bud bank characteristics and grass architecture and growth patterns. The bud bank and tiller dynamics of four perennial grasses in the C₃-dominated northern mixed grass prairie were examined over 15 months. The C₃ caespitose and rhizomatous grasses produced similar numbers of buds per tiller and their bud longevity was [greater than or equal to] 2 years. Tiller longevity drove the turnover within the bud bank of the dominant C₃ caespitose grasses Hesperostipa comata and Nassella viridula. Their polycyclic tillers (tillers that lived for more than one year) created multi-aged bud banks. The rhizomatous C₃ grass Pascopyrum smithii also had a multi-aged bud bank because buds were able to live longer than its annual tillers. Differences between caespitose and rhizomatous C₃ grass bud banks were driven by differences in tiller and rhizome production and spatial distribution. Responses to water availability fluctuations are likely buffered by the maintenance of polycyclic tillers in the caespitose grasses and flexible timing of annual tiller recruitment in the rhizomatous grass. The C₄ rhizomatous grass Andropogon gerardii had similar phenology to populations in its tallgrass prairie range center. Despite declines in bud production per tiller and lowered flowering probability in mixed-grass prairie, A. gerardii maintained a multi-aged bud bank and a positive population growth rate via vegetative reproduction at both the center and edge of its range. Bud bank dynamics of different growth forms and photosynthetic pathways, as they offer insight into the control of grass population dynamics and production, will enhance understanding of the mechanisms by which management practices and environmental change can alter perennial grasslands.

Doctor of Philosophy / Department of Biology / Ruth Welti / The molecular mechanisms by which plants respond to environmental stresses to sustain growth and yield have great importance to agriculture. Lipid metabolites are a major element of plant stress responses. The model plant Arabidopsis thaliana is well-suited to study stress-driven compositional dynamics, metabolism, and functions of lipid metabolites. When Arabidopsis plants were subjected to wounding, infection by Pseudomonas syringae pv tomato DC3000 expressing AvrRpt2 (PstAvr), infection by Pseudomonas syringae pv. maculicola (Psm), and low temperature, and 86 oxidized and acylated lipids were analyzed using mass spectrometry, different sets of lipids were found to change in level in response to the various stresses. Analysis of plant species (wheat versus Arabidopsis), ecotypes (Arabidopsis Columbia 0 versus Arabidopsis C24), and stresses (wounding, bacterial infection, and freezing) showed that acylated monogalactosyldiacylglycerol was a major and diverse lipid class that differed in acyl composition among plant species when plants were subjected to different stresses. Mass spectrometry analysis provided evidence that oxophytodienoic acid, an oxidized fatty acid, is significantly more concentrated on the galactosyl ring of monogalactosyldiacylglycerol than on the glycerol backbone. A mass spectrometry method, measuring 272 lipid analytes with high precision in a relatively short time, was developed. Application of the method to plants subjected to wounding and freezing stress in large-scale experiments showed the method produces data suitable for lipid co-occurrence analysis, which identifies groups of lipid analytes produced by identical or inter-twined enzymatic pathways. The mass spectrometry method and lipid co-occurrence analysis were utilized to study the nature of lipid modifications and the roles of lipoxygenases and patatin-like acyl hydrolases in Arabidopsis during cold acclimation, freezing, and thawing.

Master of Science / Department of Horticulture, Forestry, and Recreation Resources / Chad T. Miller / Kimberly A. Williams / Intumescences are a physiological disorder characterized by hypertrophy and possibly hyperplasia of plant cells. Many plant species are susceptible to intumescence development, but the specific causative factors remain uncertain. Ultimately, this disorder results in the death of the affected cells. Previous observations and research suggest that the quality and quantity of light to which plants are exposed may be a factor in development of the disorder. The purpose of the first study was to assess the preventive effect of UVB radiation on intumescence development in ornamental sweet potato (Ipomoea batatas). Two sweet potato cultivars, ‘Sidekick Black’ and ‘Ace of Spades,’ were grown under four light treatments of 1) Normal; 2) UVB; 3) UVB-Blocked; 4) Full-Spectrum. The ‘Ace of Spades’ cultivar was highly susceptible to intumescence development, while ‘Sidekick Black’ was much less susceptible to the disorder. For ‘Ace of Spades,’ the addition of UVB radiation significantly reduced the number of leaves affected with intumescences when compared to plants grown under the other light treatments. This study indicates a cultivar-specific effect of UVB light in minimizing intumescence development on ornamental sweet potato, therefore suggesting a potential genetic component in intumescence susceptibility. Many plant species are prone to similar physiological disorders in which lesions develop on the leaf tissue. Nomenclature for such lesions has varied significantly in the literature. Interchangeably using these terms causes confusion as to whether these names refer to the same or different disorders. The objective of the second study was to characterize the development of lesions on ornamental sweet potato (Ipomoea batatas ‘Blackie’), tomato (Solanum lycopersicum ‘Maxifort’) and interspecific geranium (Pelargonium בCaliente Coral’). Light microscopy, field emission scanning electron microscopy (FESEM), and digital photography were used to observe lesion development on each species. Lesions on ornamental sweet potato predominately involved the hypertrophy of the palisade parenchyma through the upper epidermis, while geranium lesions involved the hypertrophy of spongy parenchyma cells restricted by the lower epidermis. Tomato lesions involved both the hypertrophy and hyperplasia of the lower epidermis and spongy parenchyma. Thus, different species possess varied cellular responses when developing lesions due to physiological causes.

Doctor of Philosophy / Department of Agronomy / P.V. Vara Prasad / The pathway for the movement of water through plants, from the soil matrix to the atmosphere, constitutes the hydraulic architecture of a plant. The linkage between the hydraulic architecture of woody plants and drought tolerance has received considerable attention, but much less work has been done on grasses. I investigated the linkage between the hydraulic architecture of grasses to physiological patterns of water use across a range of species and conditions. The rate of stomatal conductance (g[subscript]s) and photosynthesis (A) increased acropetally along the leaves of 5 grass species, which is a unique feature of this growth form. The internal structure of leaves also changed acropetally in order to minimize the pressure gradient across the mesophyll that would otherwise occur as a result of increasing g[subscript]s. The resistance to water movement through the mesophyll represented 80-90% of leaf resistance in six genotypes of Sorghum bicolor L. (Moench). This resistance was most important in controlling g[subscript]s and A when water was readily available, but as soil-moisture decreased it was the efficient transport of water through the xylem that was most important in maintaining plant function. I also investigated the relationship between hydraulic architecture and stomatal responses of grasses to increasing Vapor Pressure Deficit (D). Grasses with a larger proportion of their hydraulic resistance within the xylem were less sensitive to increasing D and plants with high root conductance maintained higher rates of gas exchange D increased. Finally, I investigated the tolerance of grasses to extreme drought events to test if there was a trade-off between drought tolerance and growth in grasses. Plants with drought tolerant leaf traits typically sacrificed the ability to move water efficiently through their leaves. Having drought tolerant leaves did not limit the plants ability to have high rates of gas exchange, and, in fact, the most drought tolerant plants had the high rates of g[subscript]s when expressed on a mass basis. Leaf-level drought tolerance did contribute to species’ occurrence, as the drought intolerant species I studied are not commonly found in low precipitation systems. The results presented here highlight the importance of studying the hydraulic architecture of plants to provide a better understanding of what controls plant function across a range of environmental conditions.

Doctor of Philosophy / Agronomy / Kevin Price / Stephen M. Welch / Plant phenotyping has been studied for decades for understanding the relationship between plant genotype, phenotype, and the surrounding environment. Improved accuracy and efficiency in plant phenotyping is a critical factor in expediting plant breeding and the selection process. In the past, plant phenotypic traits were extracted using invasive and destructive sampling methods and manual measurements, which were time-consuming, labor-intensive, and cost-inefficient. More importantly, the accuracy and consistency of manual methods can be highly variable. In recent years, however, photogrammetry and 3D modeling techniques have been introduced to extract plant phenotypic traits, but no cost-efficient methods using these two techniques have yet been developed for large-scale plant phenotyping studies. High-throughput 3D modeling techniques in plant biology and agriculture are still in the developmental stages, but it is believed that the temporal and spatial resolutions of these systems are well matched to many plant phenotyping needs. Such technology can be used to help rapid phenotypic trait extraction aid crop genotype selection, leading to improvements in crop yield. In this study, we introduce an automated high-throughput phenotyping pipeline using affordable imaging systems, image processing, and 3D reconstruction algorithms to build 2D mosaicked orthophotos and 3D plant models. Chamber-based and ground-level field implementations can be used to measure phenotypic traits such as leaf length, rosette area in 2D and 3D, plant nastic movement, and diurnal cycles. Our automated pipeline has cross-platform capabilities and a degree of instrument independence, making it suitable for various situations.