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.

Master of Science / Department of Biology / David C. Hartnett / Perennial grasses on tallgrass prairie primarily reproduce vegetatively via the belowground bud bank, yet the production, dynamics, and morphology of belowground buds is largely unexplored. Since the two main photosynthetic pathway guilds (C3 and C4) on tallgrass prairie vary in their aboveground phenology, their belowground phenology would also be expected to vary. Differences in bud production, development, and spatial arrangement result in different growth forms. Therefore, an extensive biweekly examination of a dominant tallgrass prairie C4 rhizomatous grass Andropogon gerardii and C3 caespitose grass Dichanthelium oligosanthes was conducted over an entire year. Andropogon gerardii and D. oligosanthes have multiple distinctive bud developmental stages. Andropogon gerardii was synchronous in its bud development and its bud bank was composed of multiple annual cohorts. The bud bank of D. oligosanthes was developmentally asynchronous and was comprised of a single bud cohort since its bud bank underwent a complete turnover in early summer. The different roles of buds in the life history of each species reflected their differences in bud longevity, quality, and dormancy. In D. oligosanthes, belowground buds enabled plant survival over the C3 summer dormant period whereas juvenile tillers overwintered during the longer winter dormant period. In contrast, A. gerardii survived its single, winter dormant period as dormant buds. The higher-order bud production observed in D. oligosanthes multiplied its tiller production potential and, along with its shortened internodes, contributed to its caespitose growth form. The rhizomatous growth form of A. gerardii resulted from its lack of higher-order bud production and its elongated internodes. Differences in production of buds per vegetative and flowering tiller were quantified in A. gerardii. Flowering tillers of A. gerardii produced larger numbers of buds per tiller and transitioned a larger proportion of their buds to tillers than did vegetative tillers. Therefore, no tradeoff between sexual and vegetative reproduction was evident. Developmental constraints likely prevented such a tradeoff. Bud bank dynamics offer insight into the control of grass population dynamics, production, and ultimately aboveground net primary production (ANPP) and will be useful in understanding the underlying mechanisms by which management practices and environmental change can alter perennial grasslands.

Eurybia et ses proches parents Oreostemma, Herrickia et Triniteurybia sont appelés le grade des eurybioïdes. Comprenant 31 espèces vivaces, ce grade appartient au clade Nord-américain de la tribu des Astereae. Les analyses moléculaires antérieures ont montré que ce groupe est à la fois paraphylétique aux Machaerantherinae et un groupe frère aux Symphyotrichinae. Les relations infragénériques partiellement résolues et faiblement supportées empêchent d’approfondir l'histoire évolutive des groupes et ce, particulièrement dans le genre principal Eurybia. Le but de cette étude est de reconstruire les relations phylogénétiques au sein des eurybioïdes autant par l'inclusion de toutes les espèces du grade que par l’utilisation de différents types de régions et de méthodes d'inférence phylogénétique. Cette étude présente des phylogénies basées sur l'ADN ribosomal nucléaire (ITS, ETS), de l'ADN chloroplastique (trnL-F, trnS-G, trnC-ycf6) et d’un locus du génome nucléaire à faible nombre de copie (CNGC4). Les données sont analysées séparément et combinées à l’aide des approches de parcimonie, bayesienne et de maximum de vraisemblance. Les données ADNnr n’ont pas permis de résoudre les relations entre les espèces polyploïdes des Eurybia. Les analyses combinées avec des loci d’ADNnr et d’ADNnr+cp ont donc été limitées à des diploïdes. Les analyses combinées ont montré une meilleure résolution et un meilleur support que les analyses séparées. La topologie de l’ADNnr+cp était la mieux résolue et supportée. La relation phylogénétique de genres appartenant au grade des eurybioïdes est comme suit : Oreostemma (Herrickia s.str. (Herrickia kingii (Eurybia (Triniteurybia - Machaerantherinae)))). Basé sur la topologie combinée de l’ADNnr+cp, nous avons effectué des analyses de biogéographie à l’aide des logiciels DIVA et LaGrange. Ces analyses ont révélé une première radiation des eurybioïdes dans l’Ouest de l’Amérique du Nord, suivi de deux migrations indépendantes dans l’Est de l’Amérique du Nord chez les Eurybia. Due au relatif manque de variabilité de l’ADNnr, l’ADNcp et CNGC4, où le triage de lignés incomplet était dominant, l'origine du grade est interprétée comme récente, possiblement du Pliocène. La diversification du groupe a été probablement favorisée par les glaciations Pléistocènes. / Eurybia and it relatives, Oreostemma, Herrickia, and Triniteurybia, are collectively called the eurybioid grade. Comprising 31 perennial species, this grade belongs to the North American clade of the tribe Astereae. Early molecular analyses had inferred that this group is paraphyletic to the Machaerantherinae and sister to the Symphyotrichinae. The partially resolved and poorly supported relationships at the infrageneric level within the group, particularly within the core genus Eurybia, is preventing further insights into the evolutionary history of the group. The aim of this study is to reconstruct the phylogenetic relationships among the eurybioids by including all species of the grade and by using both different types of regions and multiple phylogenetic inference methods. The present study provides phylogenies based on nuclear ribosomal DNA (ITS, ETS), chloroplastic DNA (trnL-F, trnS-G, trnC-ycf6), and a low-copy nuclear locus (CNGC4), in separate and combined datasets analyzed using maximum parsimony, Bayesian and maximum likelihood approaches. In a separate analysis of the nrDNA dataset, the relationships of polyploids in Eurybia proved to be impossible to resolve. The nrDNA and nr+cpDNA combined analyses therefore were restricted to diploids. The combined analyses provided greater resolution and support than separate analyses. The nr+cpDNA phylogeny was the best resolved and supported. The phylogenetic relationship of genera belonging to the eurybioid grade is as follows: Oreostemma (Herrickia s.str. (Herrickia kingii (Eurybia (Triniteurybia – Machaerantherinae)))). Based on the nr+ cpDNA combined topology, we performed biogeographical analyses using DIVA and LaGrange. These analyses revealed an initial radiation of the eurybioids in western North America, with two independent migrations to eastern North America within Eurybia. Based on the relative lack of variation in nrDNA, cpDNA and CNGC4, where incomplete lineage sorting was dominant, the origin of the grade is interpreted as recent, probably from the Pliocene. Diversification of the group was probably favored by the Pleistocene glaciations.

La culture de saules (Salix sp.) est une pratique courante en Europe et en Amérique du Nord pour produire de la biomasse végétale. Cependant, le développement d’outils moléculaires est très récent. De plus, la phylogénie des saules est incomplète. Il y a un manque d’information pour les programmes de sélection d'espèces indigènes et pour la compréhension de l’évolution du genre. Le genre Salix inclut 500 espèces réparties principalement dans les régions tempérées et boréo-arctique de l’hémisphère nord. Nous avons obtenu l’ensemble des espèces retrouvées naturellement en Amérique (121 indigènes et introduites). Dans un premier temps, nous avons développé de nouveaux outils moléculaires et méthodes : extraction d’ADN, marqueurs microsatellites et gènes nucléaires. Puis, nous avons séquencé deux gènes chloroplastiques (matK et rbcL) et la région ITS. Les analyses phylogénétiques ont été réalisées selon trois approches : parcimonie, maximum de vraisemblance et Bayésienne. L’arbre d’espèces obtenu a un fort support et divise le genre Salix en deux sous-genres, Salix et Vetrix. Seize espèces ont une position ambiguë. La diversité génétique du sous-genre Vetrix est plus faible. Une phylogénie moléculaire complète a été établie pour les espèces américaines. D’autres analyses et marqueurs sont nécessaires pour déterminer les relations phylogénétiques entre certaines espèces. Nous affirmons que le genre Salix est divisé en deux clades. / Fast growing willows (Salix sp.) are increasingly used in Europe and North America for biomass production and other environmental applications. However, the development of molecular tools is recent. The phylogeny of willows is incomplete, which slows down the selection of suitable native species and the development of improvement programs. The genus Salix includes approximately 500 species worldwide, and these are mainly located in temperate and cold regions of the Northern Hemisphere. We gathered leaf material from all 121 willows of North America (species native and introduced). We developed three molecular tools-methods: DNA extraction, SSR markers, and nuclear genes. We sequenced two chloroplast genes matK and rbcL and the ITS region. Phylogenetic analyses were carried out using parsimony, maximum likelihood and Bayesian approaches. The species tree provides strong support for a division of the genus into two subgenera, Salix and Vetrix. Sixteen species have ambiguous positions. A complete molecular phylogeny of American willows has been established. It needs to be confirmed and further resolved using other molecular data. Nonetheless, the genus clearly has two clades.

Bauhinia s.l. est le plus vaste genre de la tribu des Cercideae (Ceasalpinioideae, Leguminoseae), avec plus de 300 espèces. Il présente une distribution pantropicale et une grande variabilité morphologique. Ces deux caractéristiques ont limité les études taxonomiques sur le genre complet, résultant en plusieurs études taxonomiques de certains groupes seulement. En 1987, Wunderlin et al. proposent une vaste révision taxonomique de la tribu des Cercideae, basée sur des données morphologiques, et divisent le genre Bauhinia en quatre sous-genres. En 2005, Lewis et Forest publient une nouvelle classification préliminaire basée sur des données moléculaires, mais sur un échantillonnage taxonomique restreint. Leurs conclusions remettent en question le monophylétisme du genre Bauhinia et suggèrent plutôt la reconnaissance de huit genres au sein du grade Bauhinia s.l. Afin de vérifier les hypothèses de Lewis et Forest, et obtenir une vision plus claire de l’histroire de Bauhinia s.l., nous avons séquencé deux régions chloroplastiques (trnL-trnF et matK-trnK) et deux régions nucléaires (Leafy et Legcyc) pour un vaste échantillonnage représentatif des Cercideae. Une première phylogénie de la tribu a tout d’abord été réalisée à partir des séquences de trnL-trnF seulement et a confirmé le non-monoplylétisme de Bauhinia s.l., avec l’inclusion du genre Brenierea, traditionnellement reconnu comme genre frère de Bauhinia s.l. Afin de ne pas limiter notre vision de l’histoire évolutive des Cercideae à un seul type de données moléculaires et à une seule région, une nouvelle série d’analyse a été effectuée, incluant toutes les séquences chloroplastiques et nucléaires. Une phylogénie individuelle a été reconstruite pour chacune des régions du génome, et un arbre d’espèce ainsi qu’un arbre de supermatrice ont été reconstruits. Bien que certaines contradictions apparaissent entre les phylogénies, les grandes lignes de l’histoire des Cercideae ont été résolues. Bauhinia s.l. est divisée en deux lignées : les groupes Phanera et Bauhinia. Le groupe Bauhinia est constitué des genres Bauhinia s.s., Piliostigma et Brenierea. Le groupe Phanera est constitué des genres Gigasiphon, Tylosema, Lysiphyllum, Barklya, Phanera et Schnella. Les genres Cercis, Adenolobus et Griffonia sont les groupes-frères du clade Bauhinia s.l. Au minimum un événement de duplication de Legcyc a été mis en évidence pour la totalité de la tribu des Cercideae, excepté Cercis, mais plusieurs évènements sont suggérés à la fois par Legcyc et Leafy. Finalement, la datation et la reconstruction des aires ancestrales de la tribu ont été effectuées. La tribu est datée de 49,7 Ma et est originaire des régions tempérées de l’hémisphère nord, probablement autour de la mer de Thétys. La tribu s’est ensuite dispersée vers les régions tropicales sèches de l’Afrique, où la séparation des groupes Bauhinia et Phanera a eu lieu. Ces deux groupes se sont ensuite dispersés en parallèle vers l’Asie du sud-est au début du Miocène. À la même période, une dispersion depuis l’Afrique de Bauhinia s.s. a permis la diversification des espèces américaines de ce genre, alors que le genre Schnella (seul genre américain du groupe Phanera) est passé par l’Australie afin de rejoindre le continent américain. Cette dispersion vers l’Australie sera également à l’origine des genres Lysiphyllum et Barklya / Bauhinia s.l. is the largest genus of the tribe Cercideae (Ceasalpinioideae, Leguminoseae), with over 300 species. It has a pantropical distribution and high morphological variability. These two features have resulted in few studies that focus on the entire genus, resulting in several regional studies or studies of certain subgroups only. In 1987, Wunderlin et al. presented a broad taxonomic revision of the tribe Cercideae, based on morphological data, and divided the genus Bauhinia into four subgenera. In 2005, Lewis and Forest published a new preliminary classification based on molecular data, but for a limited taxonomic sampling. Their findings question the monophyly of the genus Bauhinia and suggest instead the recognition of eight genera in the Bauhinia s.l. grade. To test the hypotheses of Lewis and Forest, and to obtain a clearer view of the history of Bauhinia s.l., we sequenced two chloroplast regions (trnL-trnF and matK-trnK) and two nuclear regions (Leafy and Legcyc) for a large representative sampling of the Cercideae. A primary phylogeny of the tribe was first generated based on trnL-trnF sequences only and confirmed the non-monophyly of Bauhinia s.l., with the inclusion of the genus Brenierea, traditionally recognized as sister group of Bauhinia s.l. In order to obtain a deaper view of the evolutionary history of the Cercideae, a new series of analysis was performed, including all nuclear and chloroplast sequences. Individual phylogenies were reconstructed for each region of the genome, and both a species and a supermatrix trees were reconstructed. Although certain conflicting relationships appear between phylogenies, the outline of the history of the Cercideae has been resolved. Bauhinia s.l. is divided into two lineages: Phanera and Bauhinia groups. The Bauhinia group includes Bauhinia s.s., Piliostigma and Brenierea. The Phanera group is composed of Gigasiphon, Tylosema, Lysiphyllum, Barklya, Phanera and Schnella. Cercis, Griffonia and Adenolobus are sister groups of Bauhinia s.l. At least one duplication event of Legcyc has been highlighted for the entire tribe Cercideae, excluding Cercis. Several other duplication events are also suggested by both Legcyc and Leafy . Finally, a divergence time analysis and a reconstruction of ancestral areas were conducted. The root of the tribe is evaluated to be 49.7 Mya old, and to originate from temperate regions in the northern hemisphere, mostly around the Tethys Sea. The tribe then dispersed into drier biomes in Africa, where the separation of the Bauhinia and the Phanera groups occurred. These two lineages then dispersed following parallel routes to Southeast Asia in the early Miocene. At the same time, a dispersal of the African Bauhinia s.s. to South America permitted the diversification of the American species of this genus, and Schnella (the only American genus within the Phanera group) dispersed to the American continent from Australia. This dispersal to Australia is also at the origin of Lysiphyllum and Barklya.

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.

ABA insensitive mutants (abi1 - abi5) have been isolated in germination screens that use high concentrations of exogenous ABA, and this method is believed to be saturated. To overcome this problem, a sensitized screen that used much lower concentration of exogenous ABA was performed to isolate new ABA insensitive mutants. Some of the isolated mutants had defects in light or retrograde signalling. One particular mutant (18-11) developed long hypocotyls under normal light condition. Based on its response to blue, red and far-red light conditions, this mutant is likely a novel hy mutant. Genetic analysis revealed that while ABA insensitivity in this mutant is recessive, the long hypocotyl phenotype is dominant. Positional cloning is currently being carried out to identify the gene. Findings from this study supports that ABA signalling interacts with light signalling networks.