Dissertations / Theses on the topic 'Plant adaptation'

Understanding how local adaptation arises within species is essential when making predictions about how populations may respond to environmental change. Serpentine soils present an ideal system to study the processes leading to local adaptation in plant populations. Theses soils have a scattered distribution, are deficient in several nutrient minerals, have high heavy metal content, and a poor water holding capacity; all factors contributing to a strong selective pressure against plant growth. This thesis investigates local adaptation to serpentine soil in populations of Arabidopsis lyrata ssp. petraea, a perennial of low competition habitats and which within Scotland occurs both on and off serpentine soil. Trait measures were made of plants from twelve populations across the species’ Scottish range to explore if there are trait patterns which are particular to the serpentine sites, finding that climatic and soil factors both contributed to observed trait patterns. In a controlled growth room experiment the response of five of the populations to growth on serpentine and non-serpentine soil treatments was assessed to determine if trait differences were the result of local adaptation. Plants from serpentine populations survived and performed well on all treatments, while non-serpentine plants showed reduced survival and poor growth on serpentine soil. Combined with patterns of differentiation in microsatellite markers indicating that there is not a single serpentine genetic strain of Scottish A. l. petraea it appears that serpentine populations have adapted to serpentine soil, and separately more than once. Finally, an individual based computer model was developed to explore the evolutionary consequences of local adaptation in a changing environment, finding that the strength of local adaptation, gene flow, and population size are all important determinants of population survival. These results have implications for conservation management practices used to protect small populations in changing environments; especially where local adaption is likely.

Plant morphology and function are sensitive to rising atmospheric carbon dioxide (CO2) concentrations, but evidence that CO2 concentration can act as a selective pressure driving evolution is sparse. Plants originating from naturally high CO2 springs are subjected to elevated CO2 concentration over multiple generations, providing an opportunity to predict how adaptation to future atmospheres may occur, with important implications for future plant conservation and crop breeding strategies. Using Plantago lanceolata L. from such a site (the ‘spring’ site) and from an adjacent ambient CO2 site (‘control’ site), and growing the populations in ambient and elevated CO2 at 700 μmol mol-1, I have characterised, for the first time, the functional and population genomics, alongside morphology and physiology, of plant adaptation to elevated CO2 concentrations. Growing plants in elevated CO2 caused relatively modest changes in gene expression, with fewer changes evident in the spring than control plants (33 vs 131 genes differentially expressed [DE], in spring and control plants respectively). In contrast, when comparisons were made between control and spring plants grown in either ambient or elevated CO2, there were a much larger number of loci showing DE (689 in the ambient and 853 in the elevated CO2 environment). Population genomic analysis revealed that genetic differentiation between the spring and control plants was close to zero with no fixed differences, suggesting that plants are adapted to their native CO2 environment at the level of gene expression. Growth at elevated CO2 led to an unusual phenotype, with an increase in stomatal density and index in the spring, but not in control plants. Focussing on previously characterised stomatal patterning genes revealed significant DE (FDR < 0.05) between spring and control plants for three loci (YODA, CDKB1;1, and SCRM2) and between ambient and elevated CO2 for four (ER, YODA, MYB88, and BCA1). We propose that the up-regulation in spring plants of two positive regulators of stomatal numbers (SCRM2 and CDKB1;1) act here as key controllers of stomatal adaptation to elevated CO2 on an evolutionary timescale. Significant transcriptome reprogramming of the photosynthetic pathway was identified, with an overall decrease in expression across the pathway in control plants, and an increase in spring plants, in response to elevated CO2. This was followed up by physiological measurements, where a significant increase (P < 0.05) in photosynthetic capacity and regeneration rate was exhibited in spring plants, compared to control plants, at both elevated and ambient CO2 concentrations. Through this comprehensive analysis, we have identified the basis of plant adaptation to elevated CO2 likely to occur in the future.

This study lends strong support to the idea that members of Bromeliaceae have undergone a recent adaptive radiation, and therefore show that, at least in part, diversity in the tropics is due to a fast speciation rate and that the tropics can be a "cradle" for new diversification and exploitation of varying ecological niches through the diversification of ecophysiological traits within a lineage.

The obligately outbreeding root hemiparasite Striga hermonthica (Orobanchaceae)is a serious threat to subsistence agriculture in sub-Saharan Africa. Resistance to this parasite in its crop hosts, such as rice, sorghum and maize, is not common, and the evolution of host adaptations that are able to overcome new sources of resistance is an ever-present risk. Research into host adaptation in S. hermonthica has generally sought to correlate the genetic relationship between Striga individuals with host identity; however, such approaches must be supported by lab-based evidence of host adaptation, otherwise ad hoc field sampling may result in the confounding of host identity with isolation-by-distance. Additionally, genetic variation used to reconstruct relationships is unlikely to provide an insight into relationships at functional loci underlying host adaptation. In this thesis, I use a range of new approaches to investigate several different aspects of parasite adaptation in the S. hermonthica-Sorghum bicolor pathosystem. Host adaptations, or pre-adaptations, are commonly revealed using tests for differential virulence between Striga populations and host genotypes; that is, by demonstrating population-level genotype-by-genotype interactions. Evidence for such interactions was found between three West African populations of S. hermonthica and five sorghum cultivars. These interactions were shown to be strongest at the parasite post-attachment life stage, and to depend on the parasite virulence metric used. Environmental influences on host-parasite interactions were strong and variable between years and sites. Candidate genetic loci for virulence, responding to selection in a micro-evolutionary fashion, were identified by Fst differentiation-based approaches ('outlier analyses') that aim to uncover associations between particular loci and environmental drivers, such as host identity. An AFLP outlier analysis was used on Striga plants parasitising nine sorghum cultivars in a field trial in Burkina Faso. Significant locus-specific differentiation was detected at 14 out of 1275 loci. However, predicted allele frequencies at these loci did not correlate with a field measure of Striga virulence across host-selected sub-populations. Simulation results suggested that the estimated levels of Fst at outlying loci could mean that alleles underlying host adaptation exist at intermediate frequencies in populations. A three-generation pedigree, created from a cross between S. hermonthica individuals from an East African and a West African population, enabled further insights into the genetics of adaptation. Individuals from a pseudo-backcrossed F1 (BCF1) generation, grown on two different sorghum hosts and in axenic culture, indicated significant host-related segregation distortion. Analyses of virulence in the BCF1 also provided strong evidence for epistasis, and for an effect of maternal identity. A second outlier analysis of host adaptation, investigating the East African population used in the pedigree, indicated some correspondence between outlier loci and loci found to be differentially segregating between different hosts in the BCF1 generation, and demonstrated the differing genomic extents of these phenomena. The results accumulated across these experiments provide evidence for a complex, polygenic basis to virulence in S. hermonthica.

Multi environment trials conducted over mapping population are often used to test genotypes in a set of environments that represent the target environmental range. The first part of this work is the evaluation of the ‘Nure’ x ‘Tremois’ double-­‐haploid mapping population, together with an association panel comprising 185 barley varieties representative of the barley germplasm cultivated in the Mediterranean basin. Plant material was tested across eighteen site by year field trials combination, in six countries across the Mediterranean basin. Trials were growth at sites contrasting for natural rainfall (high vs low on the base of past meteorological data) or at the same site with one being rainfed and the other with supplementary irrigation. Trials conducted for two years in each one of the sites and this allowed tocollect a huge data series comprising agronomical traits defining grain yield and yield components, phenological and environmental data, subsequently used to identify genomic regions involved in barley adaptation. The 118 doubled haploid lines of the mapping population were genotyped with Diversity Array Technology® (DaRT) marker assay and subsequently a total of 15 CAPS and SSCP marker for candidate genes involved in phenology regulation and abiotic stress response were added to the linkage map based on DaRT markers. Data collected were firstly used to perform QTLs analysis with composite interval mapping for any environment/ trait combination, results showed eight QTLs for grain yield, days to heading and grain yield components. . The two mostly frequents QTLs for grain yield and days to heading were located on barley chromosome 1H (3 trials), 2H (8 trials) and 5H (5 trials) overlapping respectively HvFT3 gene, the earliness per se locus (eam6/Eps-­‐2) and the vernalization gene Vrn_H1. A further QTL multi-­‐environment analysis was performed and revealed that across the 18 field trials QTL for eam6/Eps-­‐2 (2H) and Vrn-­‐H1 (5H) were commons for days to heading and grain yield. We use all the environmental information collected to check QTLs sensitivities to co-­‐environmental co-­‐variables. Most of significant associations collected were related to temperature and temperature-­‐based variables troughtout the growing cycle. Eam6/Eps-­‐2 showed non-­‐crossover QTL.E interaction, while for Vrn-­‐H1 crossover interactions were revealed. The 185 barley accession were genotyped with 1536 SNPs and data collected for this population for cold resistance in two field trials in Spain an Italy, the first trial was characterized by an exceptional winter, while the second was previously know has frost-­‐prone environment. Results from genome wide association analysis showed 13 positive associations with specific genomic regions. Interestingly several of these QTL were coincident with the position of previously mapped loci for cold tolerance, on chromosomes 2HL, 4HL and 5HL.
Els assajos en localitats múltiplas de poblacions de mapeo s'utilitzen freqüentment per a testar genotips en un conjunt d'ambients representatius de la condicions climàtiques on es volen introduir aquests genotips. La primera part d'això treball ha estat l'avaluació de la població de mapeo ‘Nure x Tremois’ constituïda de 118 de doble haploides d'ordi, juntament amb panell d'associació que comprèn 185 varietats d'ordi representatives del germoplasma conreat en la conca Mediterrània. El material vegetal ha estat assajat en una combinació de divuit camps per any desllorigats en sis països de la conca mediterrània. Els assajos s'han portat a terme en camps amb diferent disponibilitat d'aigua, classificats sobre la base de les dades relatives a les freqüència i quantitat de les precipitacions o en el mateix lloc amb un camp en secà i altre regat. Els assajos es van portar a terme per dos anys en cada localitat i això va permetre la recollida d'un gran volum de dades que comprenen caràcters agronómicos relacionats amb rendiment i components del rendiment, dades fenológicos i ambientals. Aquestes dades es van utilitzar després per a la identificació de regions genomicas involucrades en l'adaptació de l'ordi a l'ambient. Els 118 dobles haploides de la població ‘Nure x Tremois’ es genotiparon amb marcadors DaRT (Diversity Array Technology), després un set de 15 marcadors CAPS I SCCP per a gens candidats involucrats en la regulació de les fases fenológicas van ser afegits al mapa de lligament construït amb els marcadors DaRT. Les dades van ser utilitzats per a fer una anàlisi de QTL amb procediment ‘Composite Interval Mapping’ para cada combinació ambienti/ caràcter. Es van trobar diversos QTLs per rendiment i data d'espigolat i components del rendiment. Els QTL mes freqüents trobats per rendiment i data de floració i components del rendiment estan localitzats en els cromosomes 1H (3 camps), 2H (8 camps) i 5H (5 camps) coincidents respectivament amb HvFT3 locus, eam6/Eps-­‐2 (earliness per se) locus i amb el locus de vernalización Vrn-­‐H1. Una ulterior anàlisi de QTL feta amb el mètode “Multi Environment Trial” ha revelat que els QTL localitzats en el locus eam6/Eps-­‐2 (cromosoma 2H) i Vrn-­‐H1 (cromosoma 5H) són comunes per rendiment i data de floració en els 18 camps d'assaig. Per això utilitzem tots el dades ambientals col·leccionades durant tot el cicle del cultiu per a investigar la sensibilitat de dites QTL a les co-­‐variables ambientals. La majoria de les associacions oposades estan relacionades amb temperatures i variables relacionades amb aquestes. Eam6/Eps-­‐2 mostra una interacció de tipus quantitatiu amb aquestes variables mentre Vrn-­‐H1 mostra una interacció de tipus qualitatiu amb aquestes variables. Les 185 varietats assajades van ser genotipadas amb 185 SNPs i fenotipadas per resistència a fred en dos assajos uneixo a Espanya i altre a Itàlia. El primer assaig va ser caracteritzat per un hivern excepcionalment fred, mentre el d'Itàlia ha estat utilitzat en passat per testar resistència a fred a causa de els hiverns rígids que solen registrar-­‐se en aquesta localitat. Les dades van ser utilitzats per a portar a terme la analisis GWAS “Genome Wide Association Analysis” . Els resultats van permetre identificar 13 regions genomicas involucrades en la resistència a frio. Entre elles tres regions coincideixen amb loci ja mapeados i coneguts per ser involucrats en la resposta a frio en los cromosomes 2HL, 4HL i 5HL.
Los ensayos en localidades múltiplas de poblaciones de mapeo se utilizan frecuentemente para testar genotipos en un conjunto de ambientes representativos de la condiciones climáticas donde se quieren introducir dichos genotipos. La primera parte de esto trabajo ha sido la evaluación de la población de mapeo ‘Nure x Tremois’ constituida de 118 de doble haploides de cebada, junto con panel de asociación que comprende 185 variedades de cebada representativas del germoplasma cultivado en la cuenca Mediterránea. El material vegetal ha sido ensayado en una combinación de dieciocho campos por año dislocados en seis países de la cuenca mediterránea. Los ensayos se han llevado a cabo en campos con diferente disponibilidad de agua, clasificados en base a los datos relativos a las frecuencia y cantidad de las precipitaciones o en el mismo sitio con un campo en secano y otro regado. Los ensayos se llevaron a cabo por dos años en cada localidad y esto permitió la recogida de un gran volumen de datos que comprenden caracteres agronómicos relacionados con rendimiento y componentes del rendimiento, datos fenológicos y ambientales. Dichos datos se utilizaron después para la identificación de regiones genomicas involucradas en la adaptación de la cebada al ambiente. Los 118 dobles haploides de la población ‘Nure x Tremois’ se genotiparon con marcadores DaRT (Diversity Array Technology), después un set de 15 marcadores CAPS Y SCCP para genes candidatos involucrados en la regulación de las fases fenológicas fueron añadidos al mapa de ligamento construido con los marcadores DaRT. Los datos fueron utilizados para hacer una análisis de QTL con procedimiento ‘Composite Interval Mapping’ para cada combinación ambiente/ carácter. Se encontraron varios QTLs por rendimiento y fecha de espigado y componentes del rendimiento. Los QTL mas frecuentes encontrados por rendimiento y fecha de floración y componentes del rendimiento están localizados en los cromosomas 1H (3 campos), 2H (8 campos) y 5H(5 campos) coincidentes respectivamente con HvFT3 locus, eam6/Eps-­‐2 (earliness per se) locus y con el locus de vernalización Vrn-­‐H1. Una ulterior análisis de QTL hecha con el método “Multi Environment Trial” ha revelado que los QTL localizados en el locus eam6/Eps-­‐2 (cromosoma 2H) y Vrn-­‐H1 (cromosoma 5H) son comunes por rendimiento y fecha de floración en los 18 campos de ensayo. Por esto utilizamos todos lo datos ambientales coleccionadas durante todo el ciclo del cultivo para investigar la sensibilidad de dichos QTL a las co-­‐variables ambientales. La mayoría de las asociaciones encontradas están relacionadas con temperaturas y variables relacionadas con estas. Eam6/Eps-­‐2 muestra una interacción de tipo cuantitativo con dichas variables mientras Vrn-­‐H1 muestra una interacción de tipo cualitativo con dichas variables. Las 185 variedades ensayadas fueron genotipadas con 185 SNPs y fenotipadas por resistencia a frío en dos ensayos uno en España y otro en Italia. El primer ensayo fue caracterizado por un invierno excepcionalmente frío, mientras el de Italia ha sido utilizado en pasado por testar resistencia a frío debido a los inviernos rígidos que suelen registrarse en dicha localidad. Los datos fueron utilizados para llevar a cabo la analisis GWAS “Genome Wide Association Analysis”. Los resultados permitieron identificar 13 regiones genomicas involucradas en la resistencia a frio. Entre ellas tres regiones coinciden con loci ya mapeados y conocidos por ser involucrados en la respuesta a frio en los cromosomas 2HL, 4HL y 5HL.

Species extinction rates are causing alarm. Anthropogenic distortion of the climate system is rapidly altering the natural environment. Arabidopsis thaliana is a model species in molecular biology with widespread wild populations showing functional diversity however its ecology and evolution is poorly understood. Faced with a changing natural world, what is the adaptive potential of the model plant species Arabidopsis thaliana? This thesis focuses on the interactions of genotypes, phenotypes and environments to assess the current state of adaptation in this vagile species and to identify mechanisms for rapid adaptation to future stress, focusing on plant pathogens. Here I show that A. thaliana populations in England exhibit evidence of local adaptation and genetic structure. A large common garden experiment using genotypes gathered in natural habitats revealed functional fitness differences in genotype-by-environment interactions. Wild populations showed differential representation of RPM1 alleles suggesting non-random processes are responsible for the exhibited patterns. A further common garden experiment demonstrated ‘home site advantage’ through a correlation between fitness and home site climate, which suggests that local adaptation had occurred. Phenotypic plasticity and mechanisms for rapid adaptation could be essential for plant survival under predicted climate change. Using Xanthomonas spp. as xenopathogens, I show differing levels of pre-adaptation for pathogen response exists in wild UK populations of A. thaliana. By using a multi-generation study, I found some evidence that epigenetic modification enabled rapid adaptation to pathogen stress. Finally, I compared the metabolic expressions of phenotype among genotypes in two artificial environments. Environmental effects detected by this method are far greater than genetic ones, suggesting that metabolic plasticity can underpin environmental adaptation. Taken together, my results suggest that wild populations of A. thaliana contain a range of mechanisms for rapid adaptation to environmental change. If these capacities are general, my work offers a note of optimism about the fate of some wild plant species in the face of global climate change. Additionally, as A. thaliana is a model species in genomics, my findings may facilitate future exploitation of these traits by crop geneticists.

As the demand for energy rises, Populus species are increasingly grown as bioenergy crops. Meanwhile, due to global change, predictions indicate that summer droughts will increase in frequency and intensity over Europe. This study was carried out to evaluate the adaptation to drought in Populus, at different levels: genetic, genomics and physiology. Forests trees such as poplar are very important ecologically and economically but the Populus genus is known to be drought sensitive. Consequently, it is essential to understand drought response and tolerance for those trees. Two populations of poplar were used for this study, a mapping population (Family 331) and a natural population of Populus nigra. The F2 mapping population obtained from a cross of Populus deltoides and Populus trichocarpa, showed differences in stomatal conductance and carbon isotope composition in both clones and the F2 progeny. It was also used to discover QTL related to water use efficiency highlighting interesting areas of the genome. Combining QTL discovery and microarray analysis of the two clones in response to drought, a list of candidate genes was defined for water use efficiency. The natural population of Populus nigra consisting of 500 genotypes of wild black poplar showed variation in numerous physiological measurements such as leaf development and carbon isotope discrimination in well-watered conditions depending on their latitude of origin. The drier genotypes (from Spain and South France) had the smallest leaf area which could be linked to an adaptation to drought. Physiological measurements of extreme genotypes in leaf size of this population revealed differences in response to water depending on their latitude of origin. Stomatal conductance rapidly decreased and water use efficiency improved for Spanish genotypes after a slow and moderate drought stress. Direct comparisons between the transcriptome of extreme genotypes from Spain and North Italy in well watered and drought conditions provided an insight into the genomic pathways induced during water deficit. Six candidate genes were selecting for further analysis using real-time PCR: two stomatal development genes (ERECTA and SPEECHLESS), two ABA related genes (ATHVA22A and CCD1), a second messenger (IP3) and a NAC transcription factor (RD26)

L'informatique ubiquitaire et la variété croissante des plates-formes et dispositifs changent les attentes des utilisateurs en termes d'interfaces utilisateur. Les systèmes devraient être en mesure de s'adapter à leur contexte d'utilisation, à savoir, la plate-forme (par exemple un PC ou une tablette), les utilisateurs qui interagissent avec le système (par exemple, les administrateurs ou les utilisateurs réguliers), et l'environnement dans lequel le système s'exécute (par exemple une pièce sombre ou en extérieur). La capacité d'une interface utilisateur à s'adapter aux variations de son contexte d'utilisation tout en préservant son utilisabilité est appelée plasticité.La plasticité fournit aux utilisateurs différentes versions d'une interface utilisateur. Bien qu'elle enrichisse les interfaces utilisateur, la plasticité complexifie leur développement: la cohérence entre plusieurs versions d'une interface donnée (une pour chaque contexte d'utilisation) devrait être assurée. Étant donné le grand nombre de versions possibles d'une interface utilisateur, il est coûteux de vérifier ces exigences à la main. Des automatisations doivent être alors fournies afin de vérifier la plasticité.Cette complexité est accentuée quand il s'agit de systèmes critiques. Les systèmes critiques sont des systèmes dans lesquels une défaillance a des conséquences graves (par exemple, décès ou blessures de personnes, dommages à l'environnement, perte ou endommagement de l'équipement, etc.). La complexité de ces systèmes se reflète dans les interfaces utilisateur, qui doivent maintenant non seulement fournir des moyens corrects, intuitifs, non ambiguës et adaptables pour les utilisateurs pour atteindre un but, mais qui doivent aussi faire face aux exigences de sécurité visant à assurer que les systèmes sont raisonnablement sûrs avant d'être mis sur le marché.Plusieurs techniques existent afin d'assurer la qualité des systèmes en général, qui peuvent être également appliquées pour les systèmes critiques. La vérification formelle fournit un moyen d'effectuer une vérification rigoureuse, qui est adaptée pour les systèmes critiques. Notre contribution est une approche de vérification des systèmes interactifs critiques et plastiques à l'aide de méthodes formelles. Avec l'utilisation d'un outil performant, notre approche permet :- La vérification d'ensembles de propriétés sur un modèle du système. Reposant sur la technique de "model checking", notre approche permet la vérification de propriétés sur la spécification formelle du système. Les propriétés d'utilisabilité permettent de vérifier si le système suit de bonnes propriétés ergonomiques. Les propriétés de validité permettent de vérifier si le système suit les exigences qui spécifient son comportement attendu.- La comparaison des différentes versions du système. Reposant sur la technique "d'équivalence checking", notre approche vérifie dans quelle mesure deux interfaces utilisateur offrent les mêmes capacités d'interaction et la même apparence. Nous pouvons ainsi montrer si deux modèles d'une interface utilisateur sont équivalents ou non. Dans le cas où ils ne sont pas équivalents, les divergences de l'interface utilisateur sont listées, offrant ainsi la possibilité de les sortir de l'analyse. De plus, l'approche permet également de montrer qu'une interface utilisateur peut contenir au moins toutes les capacités d'interaction d'une autre interface utilisateur.Nous présentons également dans cette thèse trois études de cas industriels dans le domaine des centrales nucléaires dans lesquelles l'approche a été appliquée. Ces études de cas montrent ainsi de nouvelles applications des méthodes formelles dans un contexte industriel
The advent of ubiquitous computing and the increasing variety of platforms and devices change user expectations in terms of user interfaces. Systems should be able to adapt themselves to their context of use, i.e., the platform (e.g. a PC or a tablet), the users who interact with the system (e.g. administrators or regular users), and the environment in which the system executes (e.g. a dark room or outdoor). The capacity of a UI to withstand variations in its context of use while preserving usability is called plasticity.Plasticity provides users with different versions of a UI. Although it enhances UI capabilities, plasticity adds complexity to the development of user interfaces: the consistency between multiple versions of a given UI should be ensured. Given the large number of possible versions of a UI, it is time-consuming and error prone to check these requirements by hand. Some automation must be provided to verify plasticity.This complexity is further increased when it comes to UIs of safety-critical systems. Safety-critical systems are systems in which a failure has severe consequences. The complexity of such systems is reflected in the UIs, which are now expected not only to provide correct, intuitive, non-ambiguous and adaptable means for users to accomplish a goal, but also to cope with safety requirements aiming to make sure that systems are reasonably safe before they enter the market.Several techniques to ensure quality of systems in general exist, which can also be used to safety-critical systems. Formal verification provides a rigorous way to perform verification, which is suitable for safety-critical systems. Our contribution is an approach to verify safety-critical interactive systems provided with plastic UIs using formal methods. Using a powerful tool-support, our approach permits:-The verification of sets of properties over a model of the system. Using model checking, our approach permits the verification of properties over the system formal specification. Usability properties verify whether the system follows ergonomic properties to ensure a good usability. Validity properties verify whether the system follows the requirements that specify its expected behavior.-The comparison of different versions of UIs. Using equivalence checking, our approach verifies to which extent UIs present the same interaction capabilities and appearance. We can show whether two UI models are equivalent or not. When they are not equivalent, the UI divergences are listed, thus providing the possibility of leaving them out of the analysis. Furthermore, the approach shows that one UI can contain at least all interaction capabilities of another.We also present in this thesis three industrial case studies in the nuclear power plant domain which the approach was applied to, providing additional examples of successful use of formal methods in industrial systems

Thesis (Ph. D.)--University of Oregon, 2006.
Typescript. Includes vita and abstract. Includes bibliographical references (leaves 96-103). Also available for download via the World Wide Web; free to University of Oregon users.

The working hypothesis for this dissertation was that the contrasting plant architecture, and the distinct native environments of Hesperaloe funifera and H. nocturna should be reflected in differences in their eco-physiological responses, and that these, in turn, would determine these species' adaptability limits and productivity under cultivation. The objective of this dissertation project was to evaluate plant morphological characteristics and their effect on physiological processes, and how environmental factors interact with these processes in H. funifera and H. nocturna. Common to both Hesperaloe funifera and H. nocturna is the possession of constitutive crassulacean acid metabolism (CAM). The major implication of CAM is a prominent water use efficiency (WUE). Although instantaneous net CO₂ uptake rates of both Hesperaloe funifera and H. nocturna are low when compared with C₃ plants, integrated 24-hr net CO₂ uptake rates are within the lower range of C₃ species. Because there is a relatively large range of conditions in which photosynthesis occurs (i.e., both Hesperaloe species have a long growing season), net CO₂ uptake in Hesperaloe integrated throughout the year may reach or surpass that of C₃ crops. Daily integrated CO₂ uptake during late fall, winter and early spring were similar in Hesperaloe funifera and H. nocturna. A major peak in CO₂ uptake was found during the fall for H. funifera but not for H. nocturna. Also, no reduction in integrated CO₂ uptake was found in H. nocturna during the summer months, while H. funifera showed a considerable reduction in CO₂ uptake during this season. The increase in photosynthetic activity in H. nocturna coincided with the emergence of the inflorescence. Contrastingly, flowering did not appear to increase net CO₂ uptake in H. funifera. In this species a flush of new leaf production (increased sink demand) coincides with the observed increase in photosynthesis during the fall. The late fall peak of CO₂ uptake found in H. funifera could also be caused by a photoperiodic stimulation of CO₂ uptake. Significant differences in WUE between the two Hesperaloe species were found. These differences were, at least, partially explained by contrasting plant architecture and differences in leaf morphology.

Les facteurs environnementaux, au premier rang desquels la température, ont un impact sur la biologie des micro-organismes foliaires. Ils peuvent aussi modifier significativement leurs dynamiques populationnelles, voire leurs trajectoires évolutives. Classiquement, les modèles épidémiologiques, utilisés pour mieux gérer les maladies des plantes, intègrent l’influence des conditions météorologiques. Ils s’intéressent surtout à des réponses et des effets moyennés, ne tenant compte ni des variations des réponses individuelles, ni de l’hétérogénéité des changements environnementaux aux échelles réellement perçues par les agents pathogènes. Ces deux niveaux de simplification sont acceptables lorsque les états individuels et les variables continues qui leur sont associées, peu diversifiés, sont représentatifs de ceux de l'ensemble de la population. Il en va différemment lorsque les populations présentent des niveaux substantiels de variation individuelle susceptibles d’influencer leur capacité à s’adapter à leur environnement, et, par voie de conséquence, la dynamique des épidémies sous un climat fluctuant ou changeant. Pour mettre en évidence les conséquences de ces hypothèses réductrices, j’ai étudié comment la variation individuelle et l'hétérogénéité environnementale affectent simultanément la fitness, la composition phénotypique et la résilience des populations d'un agent pathogène foliaire (Zymoseptoria tritici) dans des couverts de blé. Trois étapes clés ont structuré l’exploration de ce cas d’étude. Tout d’abord, un protocole in vitro de phénotypage haut débit a été spécifiquement développé, validé et utilisé pour caractériser la diversité des réponses à la température de populations de Z. tritici échantillonnées à des échelles climatiques contrastées (variation spatiale et saisonnière) ainsi que leurs patrons d’adaptation. Les variations environnementales spatio-temporelles rencontrées dans les couverts de blé, considérées comme exerçant des pressions sélectives différentielles sur ces sensibilités thermiques individuelles, ont ensuite été examinées. Enfin, la façon dont la sélection de « thermotypes » (groupes fonctionnels rassemblant des individus présentant une même sensibilité thermique) détermine la dynamique adaptative des populations en réponse à l'hétérogénéité environnementale a été étudiée. Pour cela, des approches expérimentales (in vitro, in planta et in natura) et de modélisation (in silico) ont été couplées. Elles ont notamment porté sur plusieurs générations de populations placées dans des environnements sélectifs de plus en plus complexes. Ces travaux ont montré que le fait de négliger l'amplitude réelle de la variation phénotypique inter-individuelle d'une population microbienne et l'hétérogénéité des pressions de sélection, s’exerçant des échelles phyllo- à mésoclimatiques, conduit à sous-estimer la résilience de cette population, et donc son potentiel adaptatif. Les résultats de cette thèse, à l’interface entre épidémiologie, micrométéorologie et écologie, améliorent notre compréhension d’une part, de l'importance de la variation individuelle dans la dynamique adaptative des populations et, d’autre part, de la manière dont l'hétérogénéité environnementale permet de maintenir des populations globalement très diverses. Elle permet finalement d’expliquer l’existence de patrons d’adaptation, à la fois à des échelles locales et à des échelles très larges, par des dynamiques adaptatives «à deux vitesses»
Environmental drivers, most notably temperature, affect the biology of phyllosphere microorganisms but also induce changes in their population dynamics, even in their evolutionary trajectories. The impact of climate on foliar plant disease epidemics is usually considered in forecasting models to inform management strategies. Such models focus on averages of environmental drivers but disregard both individual variation within populations and the scale and extent of biologically relevant environmental changes. These simplifications are glossing over substantial levels of individual variation that may have important consequences on the capacity of a population to adapt to environmental changes, and thus on the dynamics of epidemics in a fluctuating or changing climate. To examine the range of validity and consequences of these simplifying assumptions, I investigated how individual variation and environmental heterogeneity jointly affect fitness, phenotypic composition and resilience of populations of a foliar pathogen (Zymoseptoria tritici) inhabiting wheat canopies. Three complementary ways of exploration were adopted in this case study. First, an in vitro high-throughput phenotyping framework was developed, validated, and used to characterise the diversity in patterns of thermal responses existing across Z. tritici populations that were sampled over contrasted scales (spatial and seasonal variation of temperature). Second, the spatio-temporal thermal variations encountered in a wheat canopy, considered as a habitat exerting fluctuating selective pressures on these differential thermal sensitivities of individuals, were investigated in depth. Third, the way selection of “thermotypes” (functional groups of individuals displaying a similar thermal sensitivity) occurs and drives dynamics of Z. tritici populations was examined. To this end, both empirical (in vitro, in planta and in natura) and theoretical (in silico) competition experiments were conducted under increasingly complex selective environments. This research work demonstrates that glossing over the natural extent of individual phenotypic diversity in a phyllosphere microbial population and over the heterogeneity of selective pressures – from phyllo- to mesoclimate – leads to underestimate the resilience of this population, and thus its adaptive potential to environmental variations. In doing so, the results of this thesis, at the interface between epidemiology, micrometeorology, and ecology, improve our understanding of how important is individual variation to population dynamics and how environmental heterogeneity allows to maintain population diversity. Finally, this thesis provides insight into how large-scale patterns and local population processes are interlinked and display a “two-tier” adaptive dynamics

Amaranthus tuberculatus (Common Waterhemp) is a prevalent, problematic weed in Midwestern USA, where genetically-modified crops are widely grown, resulting in multiple annual applications of glyphosate. Such practices provide the selection pressure for the evolution of glyphosate resistance. Evolutionary theory predicts that adaptation to novel stresses, such as herbicide application, will incur a cost in the original (herbicide-free) environment. This project aims to identify whether glyphosate resistance in a population of Amaranthus tuberculatus was associated with a fitness cost in the absence of glyphosate. Initial dose response experiments on the study population determined a resistance index of 3.2 compared to a standard sensitive population. To generate appropriate material for comparisons between phenotypes, individual plants were cloned and their resistance status determined by glyphosate application. Parent plants were designated as resistant or susceptible and appropriate crosses were performed to generate seed lines. The incomplete segregation of resistant and susceptible seed lines indicated that resistance was controlled by a quantitative trait. EPSPS gene amplification was elucidated as the primary mechanism of glyphosate resistance. There was a strong positive relationship between half-sibling seed family LD50 and relative EPSPS gene copy number indicating that resistance was primarily caused by target-site gene amplification. Subsequent fitness experiments used seed families to determine that no fitness trade-off was associated with resistance (or gene copy number) when plants are grown without competition, in glasshouse and polytunnel growth environments. However, a small growth penalty was associated with elevated gene copy number in plants grown in a polytunnel, without competition (10% biomass reduction at +20 EPSPS copies), this led to competition experiments. A fitness cost was associated with resistance under intra-phenotypic competition; however, the cost was mitigated under inter-specific competition with maize. A cost was associated with glyphosate resistance and this cost was influenced by interactions with biotic and abiotic factors.

Le genre Nepenthes regroupe environ 160 espèces de lianes carnivores, principalement situées en Asie du Sud-Est, sur des sols pauvres en nutriments assimilables. L’apex de leurs feuilles est modifié en une vrille portant une urne qui leur permet de capturer des proies et d’acquérir des nutriments, principalement de l’azote. Réputées toutes insectivores, avec des urnes équipées de cire glissante sur la paroi interne et un liquide enzymatique à rôle digestif, ces plantes ont en fait un régime alimentaire plus diversifié. Des espèces sont coprophages, détritivores ou encore spécialisées sur une guilde particulière d’insectes. Elles poussent dans des milieux variés, plus ou moins ouverts, sur sols sableux ou tourbeux. Les traits fonctionnels des pièges de Nepenthes varient selon les espèces, avec présence ou non d’une collerette attractive, d’une zone cireuse glissante, et un liquide, viscoélastique ou non, hébergeant une faune spécifique (inquilines). Ces traits peuvent représenter autant d’adaptations attestant d’une diversité de stratégies de séquestration de l’azote. Beaucoup d’études se sont intéressées au rôle des parois glissantes dans la capture des insectes, peu aux propriétés du fluide digestif. La quantité d’azote disponible du milieu et la forme sous laquelle il se présente influencent-elles la concentration en azote des feuilles de la plante, l’origine de ses ressources azotées et son degré de carnivorie ? Quel est le rôle du fluide dans la capture et la digestion des proies, dans la stratégie de séquestration de l’azote de la plante ? Quid des différences d’acidité, de viscoélasticité ou de pool enzymatique entre espèces ? Des différences d’abondance et de composition de la faune inquiline ? Quelles sont les conséquences de toutes ces différences en termes de recyclage d’azote pour la plante ?Cette thèse explore la contribution du fluide digestif, de ses propriétés physico-chimiques et biotiques à la capture et la digestion des proies de 7 espèces de Nepenthes du Brunei (Bornéo).Dans un premier volet, nous montrons que les espèces sont adaptées à des milieux de richesse variée en azote édaphique et biotique grâce à différentes stratégies d’acquisition de l’azote. Le contenu des urnes montre une variation du degré d’insectivorie. La diversité de leurs traits fonctionnels expliquerait les différences dans la nature des proies et l’efficacité de capture. Nectar extrafloral, fluide digestif acide et cire épicuticulaire glissante sont associés à la capture de fourmis, trichomes glandulaires, fourmi symbiotique et urnes cylindriques à la capture de termites et enfin, fluide acide et viscoélastique, mais surtout urne en entonnoir, à grande ouverture et production d’odeur florale expliquent l’abondance d’insectes volants. Les espèces varient aussi fortement dans leurs sécrétions enzymatiques et dans leurs cortèges d’inquilines. Dans un second volet, nous montrons in situ que les propriétés physicochimiques et biotiques du fluide expliquent en partie les différences de stratégies d’acquisition de l’azote chez les Nepenthes. Le pH et la viscoélasticité du fluide influencent la quantité et la nature des proies capturées. Ses propriétés physicochimiques conditionnent également la richesse de l’écosystème aquatique associé au fluide, avec une macrofaune aquatique plus abondante et diverse dans les urnes au liquide peu acide et au diamètre d’ouverture large. Cette macrofaune inquiline joue un rôle important dans la dégradation des proies, et la présence d’un top-prédateur s’avère essentielle dans le recyclage de l’azote. Nous discutons enfin du rôle majeur du fluide dans le régime alimentaire de la plante et dans la probable radiation adaptative du genre Nepenthes et concluons par une réflexion sur les différentes formes de carnivorie observées chez ces plantes et leurs systèmes de digestion, allant d’une stratégie agressive autonome à une stratégie mutualiste, redéfinissant par-là le concept de carnivorie dans le monde végétal
The Nepenthes carnivorous plants genus encompasses about 160 species growing mostly in Southeast Asia in habitats characterised by their scarcity in absorbable nutrients. The leaf apex is modified into a tendril bearing a pitcher trap which allows the plant catching its prey and taking up the nutrients indispensable for its growth, mainly nitrogen. Reputed to be insectivorous, bearing traps equipped with a slippery wax covering the inner pitcher wall and with an enzymatic liquid involved in the digestion, Nepenthes species actually have a more diverse diet. Coprophagous, detritivorous, and insect-guild specialised species have been reported. These plants grow in more or less open environments, on sandy or peaty soils. Nepenthes traps show an inter-specific diversity of functional traits, bearing or not an attractive collar, a slippery waxy zone, and a viscoelastic liquid, which shelters a species-specific living infauna. Such different traits may reflect as many adaptations attesting to a diversity of nitrogen-sequestration. Many studies have focused on the role of slippery walls in insect capture but few of them have investigated the importance of the digestive fluid in both capture and digestion. Do the quantity of nitrogen available in the environment and the form of its availability influence the nitrogen foliar concentration of these plants, the source of their nitrogen supply and their carnivorous habit? How does the fluid influence prey capture and digestion? Can it contribute to the nitrogen-sequestration strategy of the plant? Do the fluids differ in their acidity, viscoelasticity, enzymatic pool, and in the abundance and species diversity of their infauna? What are the consequences of all these differences in terms of nitrogen recycling for the host plant?This PhD thesis explores the contribution of the digestive fluid and its physico-chemical and biotic properties on prey capture and digestion in 7 Nepenthes species in Brunei (Borneo).The first part shows that Nepenthes species have adapted to habitat differing in edaphic and biotic nitrogen available through distinct strategies of nitrogen acquisition. Pitcher contents’ analyses show that plants vary for their degree of insectivory. The variety of functional traits could explain the differences in their capture efficiency and prey diversity. While extrafloral nectar, slippery epicuticular wax and acidic fluid pH are associated with ants’ capture, cylinder-shaped traps, glandular trichomes and ant-association increase termites’ capture. Yellow colour, acidic pH and fluid viscoelasticity but above all, pitcher conicity, wide aperture diameter and magnitude of floral odour account for the abundance of flying insects. These Nepenthes species also strongly vary in their enzymatic secretions and inquilines spectra.In a second part, we show in situ how such differences in physico-chemical and biotic properties of the fluid partly account for the differences in nitrogen-sequestration strategy in these plants. Fluid pH and viscoelasticity influence the quantity and the nature of prey. Those physico-chemical properties also condition the richness of the aquatic ecosystem associated to the fluid, with an aquatic macrofauna more abundant and diverse in pitchers with lowly-acidic liquids and wide pitcher-openings. This inquiline macrofauna plays an essential role in prey degradation, and the presence of a top-predator is crucial for the nitrogen recycling to the plant.We finally discuss the major contribution of the fluid in the plant’s diet and its role in the probable adaptive radiation of the Nepenthes genus and conclude by a survey of the various forms of carnivory in these plants and their digestive systems, which range from an autonomous aggressive strategy to a mutualistic strategy, thus redefining the concept of carnivory in the plant’s world

Global climate change is a real-time problem that presents threats to many species. Climate change can alter ecosystems and may lead to species extinction. Species can respond to climate change by moving to a better environment or adapting. Therefore, it is necessary to rely on several approaches and perspectives to anticipate ecological impacts of climate change. A common strategy uses models to understand how populations respond to different climate scenarios. Ecological models have helped usunderstand population persistence, but they often ignore how populations adapt to environmental stress. Adaptive evolution has been ignored because it was assumed that evolution was too slow to have any effect on ecology. Current research has shown that some populations are able to rapidly adapt to novel environments and this is essential for population persistence. We used a population genomics approach to understand how different precipitation regimes affect the perennial bunchgrass, Pseudoroegneria spicata, in the eastern Idaho sagebrush steppe. Our objective was to determine how genetic diversity changes under manipulated precipitation regimes and whether these changes were consistent with patterns of genetic diversity under natural precipitation regimes. The manipulated precipitation regimes consist of three precipitation treatments: control, drought with 50% ambient precipitation, and irrigation with 150% ambient precipitation. The natural precipitation regimes consist of two treatments: low elevation (drier than the experimental site) and high elevation (wetter). We collected plant tissue to isolate plant DNA and then used sequenced DNA for analyses. We used a hierarchical Bayesian model to estimate genotypes and allele frequencies across all loci. We found that there were low levels of genetic variation across all experimental precipitation treatments. When examining genetic differentiation, we found there was stronger differentiation in the natural precipitation regimes. Our study focuses on the short-term responses to climate to understand how environmental stress influences genetic diversity.

Les plantes produisent une remarquable diversité de métabolites pour faire face aux contraintes d’un environnement en constante fluctuation. Cependant la manière dont les plantes ont atteint un tel degré de complexité métabolique et les forces responsables de cette diversité chimique reste largement incomprise. On considère généralement que le mécanisme de duplication des gènes contribue pour une grande part à l’évolution naturelle. En absence de transfert horizontal, les gènes d’évolution récente se cantonnent généralement chez quelques espèces et sont soumis à une évolution rapide, alors que les gènes conservés et plus anciens ont une distribution beaucoup plus large et sont porteurs de fonctions essentielles. Il est donc intéressant d’étudier l’adaptation des plantes en analysant parallèlement les gènes qui présentent soit une large distribution taxonomique, soit une distribution plus restreinte, de type lignée-spécifique. Les cytochromes P450 (CYP) constituent l’une des plus vastes familles de protéines chez les plantes, présentant des phylogénies très conservées ou très branchées qui illustrent la plasticité métabolique et la diversité chimique. Pour illustrer l’évolution des fonctions des cytochromes P450 dans le métabolisme végétal, nous avons sélectionné trois gènes, l’un très conservé au cours de l’évolution, CYP715A1 et les deux autres, CYP98A8 et CYP98A9, très récemment spécialisés de manière lignée spécifique chez les Brassicaceae. Les gènes appartenant à la famille CYP715 ont évolué avant la divergence entre gymnospermes et angiospermes, et sont le plus souvent présent en copie unique dans les génomes végétaux. Ceci suggère que leur fonction est essentielle et très conservée chez les plantes à graines (spermaphytes). Sur la base d’une analyse transcriptionnelle et de l’expression du gène GUS sous le contrôle du promoteur de CYP715A1, il est apparu que ce gène est spécifiquement exprimé au cours du développement floral, dans les cellules tapétales des jeunes boutons floraux ainsi que dans les filaments lors de l’anthèse. CYP715A1 est également fortement induit dans les cellules du péricycle de la zone d’élongation racinaire en réponse au stress salin. L’induction par le sel nécessite une région promotrice située entre 2 et 3 kb en amont de la région codante (i.e ; codon START), ce qui suggère la présence d’un facteur cis à cet endroit. Afin de déterminer la fonction de CYP715A1 chez Arabidopsis thaliana, j’ai identifié deux mutants d’insertion de T-DNA par génotypage et complémenté ces mutants avec le gène natif. La perte de fonction de CYP715A1 n’a pas d’impact sur la croissance et la fertilité de la plante en conditions de laboratoire. Cependant, une analyse par microscopie électronique en transmission montre un phénotype d’intine ondulée. La perte de fonction du gène CYP715A1 a également entraîné une réduction de la taille des pétales et un défaut d’anthèse. [...]
Plants produce a remarkable diversity of secondary metabolites to face continually challenging and fluctuating environmental constraints. However, how plants have reached such a high degree of metabolic complexity and what are the evolutionary forces responsible for this chemodiversity still remain largely unclarified. Gene evolution based on gene birth and extinction has been reported to nicely reflect the natural evolution. Without horizontal gene transfer, young genes are often restricted to a few species and have undergone rapid evolution, whereas old genes can be broadly distributed and are always indicative of essential housekeeping functions. It is thus of interest to study plant adaptation with parallel focus on both taxonomically widespread and lineage-specific genes. P450s are one of the largest protein families in plants, featuring both conserved and branched phylogenies. Examples of P450 properties reflecting metabolic versatility, chemodiversity and thus plant adaptation have been reported. To illustrate evolution of P450 functions in plant metabolism, we selected two P450 genes, one evolutionary conserved CYP715A1 and the second a recently specialized lineage-specific gene CYP98A9 in Arabidopsis thaliana.CYP715s evolved before the divergence between gymnosperms and angiosperms and are present in single copy in most sequenced plant genomes, suggesting an essential housekeeping function highly conserved across seed plants. Based on transcriptome analysis and promoter-driven GUS expression, CYP715A1 is selectively expressed in tapetal cells of young buds and filaments of open flowers during flower development. In addition, CYP715A1 is highly induced in the pericycle cells of the root elongation zone upon salt stress. The salt induction relies on the 2-3kb region of CYP715A1 promoter, suggesting some salt-response elements may exist in this area. To characterize the function of CYP715A1 in Arabidopsis, I identified two T-DNA insertion mutants by genotyping and confirmed by complementation with native CYP715A1 gene. Loss of function of CYP715A1 has no impact on plant growth and fertility in laboratory conditions. However, transmission electron microscopy (TEM) analysis has shown constant undulated intine phenotype in two knockout mutants and also the petal growth is significantly inhibited. These two phenotypes nicely match the native expression pattern of CYP715A1. Gene co-expression analysis suggests involvement of CYP715A1 in gibberellin (GA) metabolism under salt treatment. GAs profiling on mutant flowers also indicates reduced accumulation specific GAs. Unfortunately, no significant phenotype either related to root growth or root architecture under salt treatment can be observed. Recombinant expression of the CYP715A1 enzyme in yeast so far does not allow confirming GAmetabolism. However, metabolic profiling of inflorescences in mutants and over-expression lines, together with transcriptome analysis of the loss of function cyp715a1 mutants strongly support a CYP715A1 role in signaling, hormone homeostasis and volatile emission in agreement with the purifying selection leading to gene conservation observed in spermatophytes.[...]

Understanding the dynamical bases of the interaction between the plant mineral nutrition and the circadian clock could contribute to improve crop yield and resistance to adverse conditions, such as mineral element deficiencies. Magnesium is an essential element that catalyzes more than six hundred enzymatic reactions and occupies the center of the chlorophyll structure in plants. Physiological targets of magnesium deficiency are generally better described in aerial than in belowground organs. In this thesis, we first characterized the root morphology of the model species Arabidopsis thaliana (Columbia-0) in response to magnesium supply during in vitro culture. The length of primary root and the number and length of lateral roots decreased during magnesium depletion. A local magnesium-rich source does not enhance the root foraging capacity, unlike some other major nutrients. Auxin and abscisic acid emerged as two hormones shaping root morphology in response to magnesium deficiency. Second, we investigated the natural variation of the root morphology response to magnesium supply in Arabidopsis. Thirty-six accessions were screened in vitro. Compared to the reference Columbia-0, some accessions had higher number and length of lateral roots at low magnesium supply. Root or shoot magnesium concentrations did not implicitly correlate with the root morphological traits. However, shoot calcium and root phosphorus concentrations correlated positively with the lateral root number and length, while root iron negatively with the length of primary root. Third, we focused on the interaction between the plant magnesium nutrition and the circadian clock circuit. We tested for a possible involvement of PHYTOCHROME INTERACTING FACTOR 3-LIKE 1 (PIL1) - a clock-associated gene that is down-regulated during magnesium depletion - in morphological and physiological responses, and for a circadian connection of PIL1 in the context of magnesium deficiency. The phenotypes of loss-of-function and overexpression lines did not reveal a major role of PIL1 in the magnesium deficiency symptom manifestation but rather in the plant mineral profile. The expression of PIL1 was apparently not under any circadian control. However, PIL1 seemed to regulate the expressions of some core clock genes (CCA1, LHY and PRR9), which were also targets during magnesium deficiency. In conclusion, PIL1 has a link with the circadian rhythm machinery but it does not emerge as a pivotal regulator of magnesium stress responses.
Doctorat en Sciences
info:eu-repo/semantics/nonPublished

Bibliography: leaves 123-134.
This thesis deals with host relationships in an enigmatic and seemingly primitive group of weevils belonging to the genus Antliarhinus (Coleoptera: Brentidae). These beetles occur only on species of the cycad genus Encephalartos and appear to retain an ancient association with cycads, a group of plants that were widespread in the Mesozoic era (ca. 200 MYA) before the rise of the angiosperms and which are now represented by 11 genera with relict distributions in the tropics and sub-tropics. The primary aim of this research was to determine the possible causes of narrow host specialization in Antliarhinus zamiae (Thunberg) and A. signatus Gyllenhal, two species which develop exclusively on the ovules of their cycad hosts.

Kyoto University (京都大学)
0048
新制・課程博士
博士(農学)
甲第15420号
農博第1805号
新制||農||978(附属図書館)
学位論文||H22||N4519(農学部図書室)
27898
京都大学大学院農学研究科地域環境科学専攻
(主査)教授 二井 一禎, 教授 舟川 晋也, 教授 渡邊 隆司
学位規則第4条第1項該当

Thesis (Ph. D.) -- University of Maryland, College Park, 2008.
Thesis research directed by: Dept. of Entomology. Title from t.p. of PDF. Includes bibliographical references. Published by UMI Dissertation Services, Ann Arbor, Mich. Also available in paper.

The objectives of this work were to investigate the effects of unconventional oils rich in phenolic compounds and rumen adaption on methane (CH4) gas production and rumen fermentation characteristics under in vitro rumen conditions. For this purpose, two sets of trials were conducted. In the first trial, the effects of blackberry, blueberry, raspberry, pomegranate, black seed and hemp oils on CH4 production and fermentation were examined in three 24 h batch culture experiments. Treatments in each experiment consisted of control (no oil supplement), control plus corn oil, or control plus two of the unconventional oils. Oils were added to rumen cultures at 500 mg/L (equivalent to 3.3 g oil/kg of diet dry matter (DM)). After 24 h of incubation, CH4 production was not different between the control and the corn oil treatments. Of the six unconventional oils tested, only hemp and blueberry oils reduced (P<0.05) CH4 production by 9-16% relative to the control and corn oil treatments. No significant differences were observed between treatments in dry matter digestibility (DMD) or total volatile fatty acids (tVFA). Except for a reduction (P<0.05) in acetate concentration with the raspberry oil, and an increase (P<0.05) in valerate concentration with the pomegranate oil, all other treatments had similar VFA concentrations. In the second trial, the effects of adding oregano essential oil (OEO) to adapted and unadapted rumen cultures on CH4 production and rumen fermentation were evaluated under in vitro condition. Rumen cultures were obtained from continues culture fermenters fed a control diet or control diet plus OEO at 250 mg/day for 10 days. The addition of OEO decreased (P<0.05) ii CH4 production only in adapted cultures. Total VFA and acetate concentrations were greater (P<0.05) in the unadapted than adapted cultures and their concentrations decreased (P<0.05) with the addition of OEO particularly when added to the adapted cultures. Propionate concentrations were also greater (P<0.05) in the unadapted than the adapted cultures and concentrations decreased (P<0.05) with the addition of OEO. Dry matter degradability and total gas production decreased (P<0.03) with the addition of OEO in both cultures and total gas production tended (P<0.13) to be lower when added to the adapted cultures. In conclusion, our results showed that hemp and blueberry oils were moderately effective in reducing rumen CH4 formation without compromising rumen fermentation and digestibility. Oregano Essential oil addition negatively affected rumen fermentation in both adapted and unadapted cultures and the effect was greater in the adapted cultures. The greater effects of OEO on CH4 production in the adapted cultures most likely due to the lower fermentation efficiency in these cultures.

Increasing temperatures resulting from climate change have within recent years been shown to advance phenological events in a large number of species worldwide. Species can differ in their response to increasing temperatures, and understanding the mechanisms that determine the response is therefore of great importance in order to understand and predict how a warming climate can influence both individual species, but also their interactions with each other and the environment. Understanding the mechanisms behind responses to increasing temperatures are however largely unexplored. The selected study system consisting of host plant species of the Brassicaceae family and their herbivore Anthocharis cardamines, is assumed to be especially vulnerable to climatic variations. Through the use of this study system, the aim of this thesis is to study differences in the effect of temperature on development to start of flowering within host plant species from different latitudinal regions (study I), and among host plant species (study II). We also investigate whether different developmental phases leading up to flowering differ in sensitivity to temperature (study II), and if small-scale climatic variation in spring temperature influence flowering phenology and interactions with A. cardamines (study III). Finally, we investigate if differences in the timing of A. cardamines relative to its host plants influence host species use and the selection of host individuals differing in phenology within populations (study IV). Our results showed that thermal reaction norms differ among regions along a latitudinal gradient, with the host plant species showing a mixture of co-, counter- and mixed gradient patterns (study I). We also showed that observed differences in the host plant species order of flowering among regions and years might be caused by both differences in the distribution of warm days during development and differences in the sensitivity to temperature in different phases of development (study II). In addition, we showed that small-scale variations in temperature led to variation in flowering phenology among and within populations of C. pratensis, impacting the interactions with the butterfly herbivore A. cardamines. Another result was that the less the mean plant development stage of a given plant species in the field deviated from the stage preferred by the butterfly for oviposition, the more used was the species as a host by the butterfly (study IV). Finally, we showed that the later seasonal appearance of the butterflies relative to their host plants, the higher butterfly preference for host plant individuals with a later phenology, corresponding to a preference for host plants in earlier development stages (study IV). For our study system, this thesis suggest that climate change will lead to changes in the interactions between host plants and herbivore, but that differences in phenology among host plants combined with changes in host species use of the herbivore might buffer the herbivore against negative effects of climate change. Our work highlights the need to understand the mechanisms behind differences in the responses of developmental rates to temperature between interacting species, as well as the need to account for differences in temperature response for interacting organisms from different latitudinal origins and during different developmental phases in order to understand and predict the consequences of climate change.

At the time of the doctoral defense, the following papers were unpublished and had a status as follows: Paper 2: Manuscript. Paper 3: Manuscript. Paper 4: Manuscript.

Thesis (PhD)--Macquarie University, Division of Environmental and Life Sciences, Dept. of Biological Sciences, 2005.
Bibliography: p. 178-203.
Introduction -- Study sites -- Leaf characteristics and resource availability -- Insect herbivory and resource availability -- Insect communities and resource availability -- Influence of resource availability on recovery from herbivory -- Conclusions.
This project used the resource availability hypothesis (Coley et al., 1985) as a framework for investigating the relationship between resource availability (as defined by soil nutrients), leaf traits, insect herbivore damage and insect community structure. According to the hypothesis, plants from low resource environments should be better-defended, have longer leaf lifespans and slower growth rates than plants from higher resource environments. Higher resource plant species are expected to suffer higher levels of herbivory and recover faster from herbivory than low resource plant species (Coley et al. 1985). A corollary to this hypothesis is that plants from higher resource sites should support greater densities of insect herbivores than low resource species. Comparisons between high and low resource sites were made in terms of: (i) leaf traits of mature and immature leaves; (ii) phenology of leaf maturation; (iii) herbivore damage in the field and laboratory; (iv) diversity and abundance of herbivorous insect fauna; and (v) ability to recover from herbivory.
Mode of access: World Wide Web.
243 p. ill., maps

The accumulation of salts in soil is an important agricultural problem that limits crop productivity. Salts containing sodium (Na⁺) are particularly problematic, as cytosolic Na⁺ can interfere with cellular metabolism and lead to cell death. Maintaining low levels of cytosolic Na⁺, therefore, is critical for plant survival during growth in salt. Mechanisms to regulate Na⁺ accumulation in plant cells include extrusion of Na⁺ from the cell and sequestration of Na⁺ into intracellular compartments. Both of these processes are controlled in part through the action of Na⁺/H⁺ exchangers belonging to the Cation/Proton Antiporter-1 (CPA1) gene family. Genes belonging to this family have been identified in both salt-sensitive and salt-tolerant species, suggesting that salt-tolerant species may have evolved salt tolerance through modification of these existing pathways. The research presented here has focused on understanding how salt tolerance has evolved in Brassicaceae species, and particularly on the role that CPA1 genes have played in the adaptation to salinity of Eutrema salsugineum. Specific projects have sought to understand 1) how copy number variation and changes in coding sequences of CPA1 genes contribute to salt tolerance in E. salsugineum and its salt-tolerant relative Schrenkiella parvula, 2) whether functional or regulatory changes in Salt Overly Sensitive 1 (SOS1) from E. salsugineum (EsSOS1) contribute to its enhanced salt tolerance, and 3) whether accessions of Arabidopsis thaliana differ significantly in their response to salt stress.The results indicate that EsSOS1 and SOS1 from S. parvula (SpSOS1) both confer greater salt tolerance in yeast than SOS1 from A. thaliana (AtSOS1) when activated by the complex of the SOS2 kinase and SOS3 calcium-binding protein, whereas only EsSOS1 confers enhanced salt tolerance in the absence of activation. When expressed in A. thaliana, EsSOS1 also confers greater salt tolerance than AtSOS1 through regulatory changes that likely involve differences in expression pattern. Together, the results presented here suggest that mechanisms regulating cellular Na⁺ accumulation that exist in salt-sensitive crop species could be altered to enhance growth in salty soils. In addition, the 19 A. thaliana accessions used to create the MAGIC population were shown to differ significantly in their response to salt stress.

All species on Earth occupy limited geographic space. More than a century of observational, experimental, and theoretical work investigating the factors that drive species distributions have demonstrated the importance of the interactions between abiotic, biotic, and demographic factors in determining why species are found where they are. However, it is still unclear when and where these factors interact to set species range limits. Filling the existing knowledge gaps is imperative for the accurate predictions of how species will respond to global change, and particularly for invasive species, many of which are expected to benefit from global change. Here, I sought to investigate the mechanisms that enable, as well as limit, the range expansion of the globally invasive plant Sorghum halepense (L.) Pers. (Johnsongrass). I performed a series of field and laboratory experiments to study population and range dynamics throughout Johnsongrass's North American distribution, and test for the effects of climate, local habitat, and competition on multiple functional traits. I found Johnsongrass consistently demonstrated impressive performance across varying environments, often growing more than 3 m tall, producing hundreds of flowering culms within a single growing season, and maintaining positive population growth rates, even under intense competition with resident weeds. I also found evidence that seed germination has adapted to varying climates encountered during Johnsongrass's range expansion resulting in a shift in the germination temperature niche from warmer to cooler as Johnsongrass spread from warmer climates in the south to more temperate climates in higher latitudes. This shift in the germination temperature niche may have been an important contributing factor in the range expansion of Johnsongrass by enabling the optimization of seed germination in varying climates. On the other hand, results from a field study suggested a possible trade-off between flowering time and growth in populations originating from the range periphery (i.e., range boundary) which may be limiting, or slowing, continued range expansion of Johnsongrass. Together, the outcomes of this work contribute to our understanding of the factors involved in the distribution of species, which is a fundamental goal of Ecology, and essential to accurately predict how invasive species will respond to global change.
Doctor of Philosophy
Invasive species threaten our natural ecosystems, our agricultural systems, and even our infrastructure, and we spend billions of dollars each year attempting to control them and reduce their negative impacts. Climate change, habitat destruction, and other forms of global change, will benefit many of these species, magnifying their impacts and promoting their invasion into new territories. Because of the damaging effects of invasive species, and the costs to control them, it is imperative that we are able to predict how they will respond to global change so that we can improve plans to reduce their impact and spread. First, we need to understand the processes that promote their invasion across large swaths of land. Just as importantly, we must study the processes that prevent their invasion of certain areas. Here, I investigated some of the processes that have facilitated, as well as hampered, the spread of the invasive plant Johnsongrass. For this work, I used Johnsongrass plants originating from different habitats, including regions where Johnsongrass is highly invasive and those where Johnsongrass is very rare. I found Johnsongrass originating from regions where it is highly invasive were able to grow very large and produce thousands of seeds that were able to germinate under a range of conditions. These traits may have contributed to the invasion success of this species. However, I found a different pattern for plants that originated from regions where Johnsongrass is rare. These plants reached reproductive age earlier and grew smaller across all environmental conditions, potentially due to the less hospitable climates of these range edges. These findings allow us to project into future climate change scenarios, because it is likely that, as temperatures warm, invasive species will be able to invade new regions, where they will impact the work of conservationists, natural resource professionals, agricultural produces, and other land managers.

Le Rice yellow mottle virus (RYMV) est un virus émergeant qui constitue actuellement une contrainte majeure à la riziculture sur le continent africain. Quelques rares variétés de riz, issues des espèces cultivées de riz africain et asiatique (respectivement Oryza glaberrima et O. sativa), ont récemment été identifiées comme hautement résistantes au RYMV. Ce phénotype de résistance est dû à un gène récessif RYMV1 codant le facteur d'initiation de la traduction eIF(iso)4G1 du riz.Les objectifs de cette thèse sont (i) d'étudier la durabilité de la résistance élevée du riz contre le RYMV avant son déploiement à large échelle, (ii) de caractériser les mécanismes d'émergence de génotypes contournants et (iii) d'identifier des signatures moléculaires influençant ces processus d'adaptation. Ainsi, le contournement de deux allèles de résistance, identifiés chez les deux espèces de riz cultivés, a été relié à l'émergence de mutations dans la protéine virale VPg qui permettent de rétablir l'interaction avec le facteur eIF(iso)4G1 de l'hôte résistant. Un site sous sélection diversificatrice de la VPg influence directement la capacité de contournement de la résistance élevée en fonction de l'espèce hôte. Ce site, proche des mutations de contournement, est impliqué dans l'adaptation du virus à l'espèce O. glaberrima au cours de son histoire évolutive. La démarche employée au cours de ce travail combine des études d'évolution expérimentale à des analyses fonctionnelles. Les résultats obtenus par cette approche intégrative participeront à la mise en place de stratégies de lutte intégrée à la fois efficaces et durables face à la maladie de la panachure jaune du riz en Afrique
The Rice yellow mottle virus (RYMV) is an emerging virus currently considered as the major constraint to rice production in Africa. Some varieties of African and Asian cultivated rice (Oryza glaberrima and O. sativa, respectively), have recently been identified as highly resistant to RYMV. This resistance phenotype is caused by a recessive gene RYMV1 encoding the translation initiation factor eIF(iso)4G1 of rice.The objectives of this thesis are (i) to investigate the durability of the high resistance of rice against RYMV before broadly deployment in fields, (ii) to characterize the mechanisms of emergence of resistance-breaking (RB) genotypes and (iii) to identify molecular signatures that influence these processes of adaptation. The resistance-breaking of two resistance alleles, identified in both cultivated rice species, is mainly associated with the emergence of mutations in the viral protein VPg that restore in resistant hosts the interaction with the factor eIF(iso)4G1. A site of VPg under diversifying selection directly affects the ability to overcome the high resistance depending on the host species. This site, near the RB mutations, is involved in the adaptation of the RYMV to O. glaberrima species during its evolutionary history. The approach used during this work combines experimental evolution and functional analyses. The results of this integrative study will participate in the development of effective and sustainable control strategies toward the Rice yellow mottle virus in Africa

Patterns of woody-plant mortality have been linked to global-scale environmental changes, such as extreme drought, heat stress, more frequent and intense fires, and episodic outbreaks of insects and pathogens. Although many studies have focussed on survival and mortality in response to specific physiological stresses, little attention has been paid to the role of genetic heritability of traits and local adaptation in influencing patterns of plant mortality, especially in non-native species. Tamarix spp. is a dominant, non-native riparian tree in western North America that is experiencing dieback in some areas of its range due to episodic herbivory by the recently introduced northern tamarisk leaf beetle (Diorhabda carinulata). We propose that genotype x environment interactions largely underpin current and future patterns of Tamarix mortality. We anticipate that (i) despite its recent introduction, and the potential for significant gene flow, Tamarix in western North America is generally adapted to local environmental conditions across its current range in part due to hybridization of two species; (ii) local adaptation to specific climate, soil and resource availability will yield predictable responses to episodic herbivory; and (iii) the ability to cope with a combination of episodic herbivory and increased aridity associated with climate change will be largely based on functional tradeoffs in resource allocation. This review focusses on the potential heritability of plant carbon allocation patterns in Tamarix, focussing on the relative contribution of acquired carbon to non-structural carbohydrate (NSC) pools versus other sinks as the basis for surviving episodic disturbance. Where high aridity and/or poor edaphic position lead to chronic stress, NSC pools may fall below a minimum threshold because of an imbalance between the supply of carbon and its demand by various sinks. Identifying patterns of local adaptation of traits related to resource allocation will improve forecasting of Tamarix population susceptibility to episodic herbivory.

Mycorrhizal fungi are soil-borne organisms that form symbiotic associations with the majority of land plants. These fungi gather and exchange mineral nutrients with plants for photosynthetically derived carbohydrates. Mycorrhizal fungi can also confer other benefits onto plants, e.g. defense against pathogens, improved water relations, tolerance to heavy metal toxicity and herbivory. The influence of mycorrhizal fungi on plant mineral nutrition and response to stress suggests that these organisms may have a role to play sustainable agriculture as well as in bioremediation and ecosystem restoration. In contributing to this important research, I investigated host-specific interactions between mycorrhizal fungi and the sex morphs of the gynodioecious perennial herb Polemonium foliosissimum (Polemoniaceae) and their mycorrhizal associates in the field. I hypothesized that the genders of this species differed in their associations with mycorrhizal fungi in benefits received. I performed a full factorial simulated herbivory experiment and evaluated the extent of mycorrhizal colonization in the roots as well as the concentrations of nutrients in leaf tissue. Mycorrhizal colonization and leaf nutrient concentrations did not differ between the genders nor were influenced by the experimental treatments. This suggests that the genders of Polemonium foliosissimum do not interact differently with mycorrhizal fungi, and thus do not represent different "hosts". Also, I investigated local adaptation of mycorrhizal associations by exploring the effect of large herbivore grazing on plant-mycorrhizal associations. I hypothesized that grazing by large herbivores results in locally adapted symbioses that enhance plant response to herbivory. I grew the perennial bunchgrass Themeda triandra (Poaceae) in inoculum prepared from soils collected from three field exclosures with differing histories of large herbivore exclusion in the Kenya Long Term Exclosure Experiment. I conducted a full factorial simulated herbivory experiment in which plants were subject to two clipping events over the course of 5-months, and evaluated plant regrowth as well as mycorrhizal colonization for plants in the experiment. Plants grown in inoculum from exclosures in which large herbivores have had access produced more root mass when mycorrhizal fungi were present. Further, I found equivalent biomass production of clipped and non-clipped plants in inoculum prepared from the exclosure with only native large herbivore access while equivalent biomass production was not found in the substrate prepared from areas with a history of large herbivore exclusion. This suggests that mycorrhizal fungi mediate plant growth and response to herbivory in this system.

Les plantes vivent en association avec une grande diversité de microorganismes qui forment son microbiota. Ce microbiote fournit des fonctions clés qui influencent tous les aspects de la vie d'une plante, de l'établissement à la croissance jusqu'à la production. Cette thèse a pour intention de déterminer les règlent d'assemblage du microbiote et ses conséquences pour le phénotypel l'adaptation et l'évolution des plantes. Pour atteindre cet objectif nous avont utilisé différentes approches expérimentales comprenant des plantes clonales comme organismes modèles ainsi que des mésocosmes prairiaux pour analyses à l'échelle des communautés. Nos résultats ont démontré i) que les Champignons Mycohiziens à Arbuscules induisent d'important es variations phénotypiques pour les traits des plantes clonales impliqués dans l'exploration de l'espace et l'exploitation des ressources. Ces changements dépendent de l'identité des symbiontes et altèrent les capacités des plantes à développer des réponses plastiques à l'hétérogénéité environnementale. ii) Les plantes ont évolué un méchanisme permettant la transmission d'une partie de leur microbiote a leur descendance, assurant la qualité de leur habitat. iii) Le contexte spécifique des communautés de plantes est un facteur majeur structurant l'assemblage du microbiota des plantes à échelle locale. L'abondance de certaines espèces de plante dans le voisinage d'une plante cible augmente ou diminue la diversité de son microbiote, déterminant in fine ses performances. De manière générale, cette thèse démontre l'importance des organismes symbiotiques dans la compréhension de l'adaptation et de l'évolution des plantes
Plants live in association with a wide diversity of microorganisms forming the microbiota. The plant microbiota provides a variety of key functions that influence many aspects of plant's life comprising establishment, growth and reproduction. The present thesis aims at determining the assembly rules of the plant microbiota and its consequences for plant phenotype, adaptation and evolution. To fulfill this objective, we used different experimental approaches using either clonal plants as model organisms or grassland mesocosms for community-wide analyses. Our results demonstrated i) that Arbuscular Mycorrhizal Fungi induce important phenotypic variations in clonal plants traits involved in space exploration and resources exploitation. These changes depended on the identity of the symbionts and altered the plants ability to produce plastic responses to environmental heterogeneity. ii) Plants have evolved a mechanism allowing the transmission of a part of their microbiota to their progeny, ensuring thus their habitat quality. iii) The plant community context is a major factor structuring local plant microbiota assembly. Particular plant species identity in the neighborhood increase or decrease the microbiota diversity and ultimately determine the focal plant performance. This thesis overall demonstrates the importance of symbiotic microorganisms in the understanding of the plant adaptation and evolution. From the knowledges acquired we developed a novel understanding of symbiotic interactions in clonal plants by extending the holobiont theory to the meta-holobiont theory

The conservation of historic cultural landscapes in Queensland is in its infancy. Effective conservation practice, however is based on sound historical information, and no previous study has investigated the historical development of local parks, gardens and other landscapes. The objectives of this research were to examine the factors which influenced landscape design in Queensland, to identify the forms and expressions of design derived from these influences, and to identify any distinctive aspects related to local landscape character. The timeframe chosen for this investigation was from the beginning of the separate colony of Queensland (1859) to the outbreak of World War 2 (1939). Using historical method, the research began with an exploration of published primary sources (particularly garden literature from the 1860s to 1930s) related to Queensland and other 'tropical' areas. A series of hypotheses was proposed to explain the findings, and these were tested by further analysis and data gathering. There followed a triple-layered central proposition, suggesting that: (i) in Queensland, the traditional delineation of styles to describe landscape design is of limited application because of the lack of elite professional designers and wealthy clients; (ii) there developed a discernible 'tropical landscape design character' in suitable climatic areas, which included two distinct visual aspects expressed in the landscape (the 'exotic' and the 'prosaic'); and, (iii) these design outcomes were the result of a design process of 'acclimatisation' experienced by early settlers (gardeners and designers) working in unfamiliar lands and climates, and includes the stages of experimentation, adaptation and innovation.

Phosphoenolpyruvate carboxylase (PEPC) was examined during cold acclimation of seedlings of the freezing-tolerant cultivar (Medicago sativa ssp falcata cv Anik) and the relatively freezing-sensitive cultivar (Medicago sativa cv Trek) of alfalfa. With four days of cold acclimation, PEPC activity increased to 3.5-fold and 2-fold the control levels in Anik and Trek, respectively. This was associated with an increase in the level of a 110 kD PEPC protein and a decrease in the amount of a 120 kD PEPC polypeptide in both cultivars. The role of reversible phosphorylation in regulating PEPC activity was demonstrated by in vitro phosphorylation and dephosphorylation, which caused partial activation and deactivation of PEPC, respectively. In vivo phosphorylation experiments revealed that the 110 kD PEPC subunit is phosphorylated on serine residue(s) during cold acclimation in Anik but not in Trek. Increased PEPC activity could account for the 70% increase in the non-autotrophic or dark fixation of carbon observed in cold acclimated Anik seedlings. A possible role for dark carbon fixation in the cold-induced development of freezing tolerance is through the production of NADPH. Such a source of reducing power may be required for the repair of cold-induced damage and restoration of normal cellular functions.

Biological invasions have been observed throughout the world for centuries, often with major consequences to biodiversity and food security. Tying invasion to species identity and associated traits has led to numerous hypotheses on why, and where, some species are invasive. In recent decades, attention to intraspecific variation among invaders has produced questions about their adaptation to climate, land use, and environmental change. I examined the intraspecific variation of invasive Johnsongrass's (Sorghum halepense (L.) Pers.) seedling stress response, propagule cold tolerance, and large-scale niche dynamics for correlation with populations' climatic and ecotypic (i.e., agricultural vs. non-agricultural) origin. Overall, I found a greater number of home climate effects than ecotypic effects on various traits. Non-agricultural seed from cold climates and agricultural seed from warm climates germinated more and faster, while non-agricultural seedlings showed uniform chlorophyll production regardless of home soil carbon origin, unlike their agricultural counterparts. Neither seedling stress response nor propagule cold tolerance interacted with ecotype identity; however, drought stress varied with population origins' aridity and soil fertility, and seed from warm/humid and cold/dry climates was most germinable. Comparison of seed and rhizome cold tolerance also suggested that the latter is a conserved trait that may be limiting S. halepense poleward range expansion. This physiological limit, an unchanged cold temperature niche boundary between continents and ecotypes, and a narrowed niche following transition to non-agricultural lands all imply low likelihood of spread based on climatic niche shift. Instead, evidence points to range expansion driven primarily by climate change and highlights agriculture's role in facilitating invasibility. This tandem approach to climate and land use as drivers of intraspecific variation is transferable to other taxa and can help refine our conception of and response to invasion in the Anthropocene.
Doctor of Philosophy
Exotic invasive species are a global problem, threatening biodiversity and biosecurity now and in the future. In the last several decades, ecologists have studied many individual invaders and their traits to understand what drives their spread. More recently, abundant differences in traits between populations within an invasive species have raised questions about humans' role in facilitating invasion through climate change, land use, and other disturbances. I studied the invasive Johnsongrass's (Sorghum halepense (L.) Pers.) response to drought, nutrient limitation, and freezing to detect differences between populations based on their climate and ecotype (agricultural vs. non-agricultural) origin. I also tracked differences in the climates the species occupied across the globe and North America and projected its future distribution under climate change. Overall, I found a greater number of home climate effects than ecotypic effects on various traits. Non-agricultural seed from cold climates and agricultural seed from warm climates germinated the most, while non-agricultural seedlings performed consistently regardless of soil carbon origin, unlike their agricultural counterparts. In addition, drought stress varied with population origins' rainfall and soil fertility, and seed germination favored warm/humid and cold/dry origin. Rhizome (underground stem) cold tolerance appears to be a trait that limits S. halepense poleward range expansion. Along with no change in the coldest climates occupied worldwide and no spread to new climates with transition to non-agricultural lands, this implies that Johnsongrass is unlikely to expand its range without external forces. Instead future range expansion will likely be driven by climate change. This coupled approach to climate and land use affecting invasion is transferable to other species and can help refine both our concepts and response strategies.

Pflanzenwurzeln reagieren auf Phosphat- oder Eisenmangel mit einer vermehrten Wurzelhaarbildung, was eine Vergrößerung der absorptiven Oberfläche bewirkt. Die erhöhte Anzahl an Wurzelhaaren wird dabei auf verschiedene Weise gebildet. Phosphat-defiziente Arabidopsis-Pflanzen erhöhen die Anzahl an Wurzelhaarzellen, während sich unter Eisenmangel verzweigte Wurzelhaare entwickeln. Die Fe- und P-Homöostase wird durch systemische und lokale Signalwege reguliert. Der Einfluss dieser Signale auf die Fe- bzw. Psensitive Wurzelhaarentwicklung wurde mithilfe von split-root-Experimenten untersucht, die mit einem systemischen Mangel- oder Suffizienzsignal kombiniert wurden. Die Verzweigung der Wurzelhaare Fe-defizienter Pflanzen wurde durch ein dominantes Suffizienzsignal reprimiert, unabhängig von seiner lokalen oder systemischen Herkunft. Die Erhöhung der Wurzelhaarzahl bei P-Mangelpflanzen wurde durch ein dominantes Defizienzsignal induziert. Um herauszufinden, welches Entwicklungsstadium von dem jeweiligen Nährstoff beeinflusst wird, wurden Mutanten mit Defekten in frühen und späten Wurzelhaarentwicklungsstadien untersucht. Mutanten mit beeiträchtigter Wurzelhaar-Spezifikation wichen in ihrer Wurzelhaarzahl und –lokalisation vom Wildtyp ab, zeigten aber eine Fe- oder P-sensitive Veränderung. Die Gene aus frühen Entwicklungsstadien sind demnach essentiell für die Reaktion, sind aber nicht das direkte Ziel der Mangelsignale. Frühe Zelleigenschaften in der meristematischen Region waren durch die Eisen- oder Phosphatverfügbarkeit nicht verändert, was darauf hindeutet, dass die Wurzelhaarbildung erst in einem späteren Entwicklungsstadium durch die Nährstoffe beeinflusst wird. Mutanten mit Defekten in späteren Entwicklungsstadien zeigten kurze oder verformte Wurzelhaare unabhängig von der Nährstoffversorgung. Das Fe- oder P-Signal mündet also vor der Wirkung dieser Komponenten in die Wurzelhaarbildung ein. Das heisst, nachdem die korrekte Wurzelhaar-Position und -Anzahl in Anpassung an das Fe- oder P-Angebot festgelegt wurde, werden die Wurzelhaare unter allen Wachstumsbedingungen von einer gemeinsamen Maschinerie elongiert. Zur Identifikation potentiell neuer Gene, die die Wurzelhaarbildung in Anpassung an P-Mangel regulieren, wurden sechs Mutanten isoliert, die keine Wurzelhaare bei P-Mangel bilden, aber nach dem Transfer auf P-suffizientes Medium nicht beeinträchtigt waren. Eine dieser Mutanten, per2, wurde phänotypisch und genetisch charakterisiert. Neben der veränderten Wurzelhaarbildung zeigte per2 auch eine konstitutiv erhöhte Lateralwurzelbildung und eine erhöhte Anthozyan-Akkumulation bei P-Mangel. Laut epistatischen Analysen gehört die per2 Mutante zu einem Signalweg, der unabhängig von frühen Zellspezifikationsgenen wirkt. Der per2-Locus wurde innerhalb eines 87,5 kpb großen Abschnittes auf dem oberen Arm von Chromosom 3 kartiert. Mutanten die einen per2-ähnlichen Phänotyp zeigen, wurden bisher nicht beschrieben. Daher handelt es sich bei PER2 möglicherweise um ein neues Gen, das die Wurzelhaarbildung bei Phosphatmangel reguliert und weitere P-Mangelreaktionen beeinflusst.
Limitation of immobile nutrients, such as iron (Fe) and phosphate (P), induces the development of additional root hairs that lead to an increase of the absorptive surface of the root. The increased root hair frequency of Fe- and P-deficient Arabidopsis was realized by different strategies. Phosphate-deficient plants increased the number of root hairs while in Festarved plants root hairs were branched. The Fe and P starvation responses in plants are thought to be regulated by a systemic signaling mechanism that communicates the nutrient status of the shoot to the root and by a local signaling mechanism that perceives the Fe or P availability in the soil. The influence of local and systemic signals on the respective root hair phenotype was investigated in split-root experiments. This treatment was combined with either a nutrient-sufficient or -deficient shoot. The root hair branching typical of Fe-deficient plants only occured in the presence of both a local and a systemic Fe-deficiency signal. As a consequence, an Fe sufficiency signal acted dominantly to any deficiency signal, independent of its origin. The increased number of root hairs in P-deficient plants, conversely, was activated through either a local or a systemic P deficiency signal. Thus, the P deficiency signal acted dominantly to any sufficiency signal. To determine, which stage of root hair development was influenced by iron and phosphate, mutants with defects in different stages of root hair development were investigated for their root hair phenotype. Mutants affected in the early stages of root hair development, such as specification, displayed marked changes in the number and localization of root hairs. However, the nutritional signal was perceived and translated in this group of mutants. This indicates that the specification genes are involved in the nutrient-sensitive root hair formation, but may not be the direct targets. Early cell characteristics of root hairs in the late meristematic region of the root, like the expression of marker genes, were unaltered in plants adapted to Fe or P deficiency. This suggested the nutritional signal modulates root hair development after these characteristics have been established. Mutants with defects in the later stages of root hair development, such as root hair elongation, showed short or deformed root hairs in the proper position and frequency and were, thus, impaired independent of the Fe or P supply. Thus, the nutritional signal may enter the root hair developmental pathway around the stage of root hair initiation and bulge formation. Finally, six mutants were screened that did not form root hairs under P deficiency but developed normal, when the plants were transferred to P-sufficient medium. One of these mutants, per2 (phosphate deficiency root hair defective2), was characterized phenotypically and genetically. In addition to the impaired root hair growth, the per2 mutant displayed a constitutively high lateral root number and accumulated an increased amount of anthocyanins under P starvation. Epistatic analysis revealed that per2 action is independent of early cell specification genes. The per2 mutation was mapped to a 87.6 kbp region on the upper arm of chromosome 3 containing 19 genes. The per2 phenotype has not been described before. Thus, PER2 is a potential new gene involved in root hair development under phosphate deficiency.

Homologous recombination represents a DNA repair pathway. Its role in a plant cell is not limited to double strand break repair. It also extends to genome evolution via rearranging of DNA sequences, and has an important application in foreign DNA integration in the plant genome. Our study demonstrated that effects exerted by stress on homologous recombination and genome stability are not restricted to the exposed generation. The progeny of plants exposed to stress exhibited elevated spontaneous homologous recombination, changes in DNA methylation and higher tolerance to stress. These heritable changes are mediated by an unknown stress-inducible epigenetic signal. Furthermore, we demonstrated that using factors that enhance homologous recombination can improve the efficiency of genetic transformation by Agrobacterium. We have developed and patented a plant growth medium enhancing homologous recombination and significantly increasing the transformation frequency. The role of several other chemicals for the improvement of transformation was also evaluated.
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L'acide ascorbique (AsA, vitamine C) est l'un des composés parmi les plus importants chez les eucaryotes. En raison de son potentiel antioxydant élevé, l'AsA représente un trait important de la qualité nutritionnelle des végétaux. Au-delà de sa valeur bénéfique pour la santé, une augmentation de la teneur en AsA des fruits bénéficierait probablement à la qualité post-récolte et à la résistance aux pathogènes. Pour mieux comprendre ces régulations chez les plantes et leurs impacts sur la qualité des fruits, une collection de tomates EMS hautement mutée (cv. Micro-Tom) a été criblée pour identifier des mutants dont les fruits sont enrichis en AsA. Cette stratégie de génétique directe associant le criblage à une approche de cartographie par séquençage devait permettre d’identifier de nouveaux gènes liés au caractère AsA+. L'un des mutants, noté P21H6, présentait un enrichissement en AsA de 2 à 4 fois supérieur à celui du WT, et fut le premier à être génétiquement caractérisé. Cette étude a permis de mettre en évidence une nouvelle classe de photorécepteurs impliqués dans la détection de la lumière bleue, appelée SlPLP, en tant que régulateur négatif de l'accumulation d'AsA dans la tomate. Le rôle de PLP dans le phénotype AsA+ du fruit a été confirmé par une stratégie de mutagenèse dirigée, avant d’entreprendre sa caractérisation fonctionnelle. Nous avons démontré que SlPLP interagit avec SlGGP (GDP-L-galactose phosphorylase), une enzyme clé de la voie du L-Galactose, sous contrôle de la lumière bleue et que cette interaction a lieu dans le cytoplasme et le noyau. Nos résultats renforcent le rôle central du GGP dans la biosynthèse de l'AsA et suggèrent un nouveau mécanisme de régulation par la lumière bleue de la fonction du GGP, en plus de son activité métabolique. Parallèlement, nous avons entrepris la caractérisation d’un autre mutant, le P17C5-3, qui présentait le plus fort taux d'AsA (jusqu'à 10 fois le WT). Outre le phénotype AsA+, le mutant P17C5 présentait de fortes altérations morphologiques, notamment l’absence de graines, rendant la mise en place de la stratégie de cartographie difficile. Grâce à un croisement avec la variété commerciale M82, la mutation causale pu être identifiée dans un ORF cis-régulateur en amont de GGP. Ce résultat confirme le rôle clé de GGP dans la voie L-Galactose. Des études préliminaires liées au phénotype parthénocarpique suggèrent un problème de stérilité mâle associé aux processus de développement du pollen. Enfin, dans l’étude de la qualité des fruits après la récolte, des expériences de stress froid effectuées avec les fruits P21H6 semblent démontrer que l’augmentation de la teneur en AsA améliore la durée de conservation et la capacité de maturation des fruits. Dans l'ensemble, nos résultats confirment la position clé de la protéine GGP dans la voie de biosynthèse de l'AsA, et fournissent des outils et du matériel végétal précieux pour décortiquer la régulation de l'AsA et son rôle physiologique dans la qualité des fruits et les caractères post-récolte
Ascorbic acid (AsA, vitamin C) is one of the most important biochemical in living organisms. Due to its high antioxidant potential, AsA represents an important trait of nutritional quality in fruits and vegetables. In addition to its beneficial health value in fruit consumption, increasing fruit AsA content would likely affect postharvest quality and resistance to pathogens. Thus, understanding the regulation of AsA accumulation in order to improve crop species of agronomical interest is an important issue in plant breeding for many fleshy fruit species. To get a better understanding of the regulation of AsA level in plants and its impact on fruit quality, a highly mutagenized EMS tomato collection (cv. Micro-Tom) was screened for AsA+ fruit mutants. This forward genetic strategy combined with a mapping-by-sequencing approach, had allowed identifying new genes related to the AsA+ trait. One of the mutant line named P21H6, displayed an AsA-enrichment 2 to 4 fold that of the WT, and was the first to be genetically characterized. It allowed highlighting a new class of photoreceptor involved in blue light sensing named SlPLP as a negative regulator of AsA accumulation in tomato. We confirmed the role of the PLP in the fruit AsA+ phenotype using a directed mutagenesis strategy, undertaking its functional characterization. We demonstrate that PLP interacts with GGP (GDP-L-galactose phosphorylase), a key enzyme of the L-Galactose pathway, under blue light control and that this interaction takes place in the cytoplasm and the nucleus. Our results strengthen the central role of GGP in the AsA biosynthesis and suggest a new regulation mechanism by blue light of the GGP function in addition to its metabolic activity. Besides we started the characterization another mutant, the P17C5-3, which displayed the highest level of AsA (up to 10 times the WT). Beyond its AsA+ content, the P17C5 mutant showed strong morphological alterations including a seedless phenotype making the mapping difficult at first. Thanks to the crossing with the commercial M82 tomato cultivar, the causal mutation was identified in a cis-acting ORF, upstream of the GGP gene. This result confirmed the key role of GGP in the L-Galactose pathway. Preliminary studies related to the parthenocarpic phenotype suggest a problem of male sterility associated with pollen development processes. Finally, in the study of the post-harvest fruit quality, chilling stress experiments carried out with the P21H6 fruits seem to demonstrate that increasing AsA content improve the fruit shelf life and its maturation capacity. Taken as a whole, our results confirmed the key position of the GGP protein in the AsA biosynthesis pathway and they provided precious tools and plant material for deciphering the regulation of AsA and its physiological role in fruit quality and post-harvest traits