Dissertations / Theses on the topic 'Plant traits'

In this thesis we tested the predictions from the CSR theory for the community membership. Predictions are that, in the absence of competition, species from all strategies (Competitors, Ruderals and Stress-tolerants) will persist in low-stress habitats, whereas in high-stress habitats, only species with Stress-tolerant traits will survive. CSR recognizes that species evolved similar traits to one universal stress. For this reason, we were interested in testing which strategies will survive in different sources of stress. Our results from field and greenhouse experiments suggest that CSR theory does not predict community membership from the initial stages of a plant life-cycle. Instead, we found that the habitat stress plays a major role in determining the species that are incorporated into a community. In this thesis we also used a trait-based approach to evaluate: 1) the relationship between key traits using annuals species, and 2) the links between genome size and phenotypic variation within species. Firstly, we studied the triangular relationship reported for seed mass and leaf area in woody species. These traits are involved in the plant reproduction strategy and plant water and energy-use. We found a triangular relationship in annuals species, suggesting that is conserved across groups (woody and annuals). We also found that the driver of this relationship is related to soil fertility. Finally, for the relationship between genome size and phenotypic variation within species, we found that larger genome species display higher variation in traits than small genome species. This can be a potential advantage in heterogeneous environments where the amount of phenotypic variation would allow the species to adapt to them.

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

Abstract Most plants grow in association with arbuscular mycorrhizal (AM) fungi in their roots forming the so-called AM symbiosis. AM symbiosis is usually beneficial to the host as it improves plant survival and performance. However, AM symbiosis also entails a cost to the plant in terms of the carbon allocated to the fungus. In sexually dimorphic plants, more than one type of individual can be recognised with regard to their sexual expression or gender. The cost of reproduction in these plants will differ in relation to the relative investment in male versus female function, as the female and the male sexual functions incur different costs. This different cost of reproduction may be translated into differences in other plant functions between the sexes as all functions are connected through trade-offs. Therefore, since sexes differ in resource needs and allocation patterns, and AM mediate resource acquisition and allocation patterns through imposing both costs and benefits to the plant, the sexes of dimorphic plant species may possess, at least theoretically, a different relationship with their AM roots symbionts. In this thesis, I have investigated whether the sexes in sexually dimorphic plant species differ in their mycorrhizal relationship, and if so, in which ways. Several plant life history traits were studied in the dioecious species Antennaria dioica and also in the gynodioecious Geranium sylvaticum using greenhouse, common-garden and field experiments. Resource acquisition, resource allocation, and both plant and fungal benefits from AM symbiosis were considered. Mainly beneficial effects of AM symbiosis were observed in both sexes of the two dimorphic plant species for most of the studied plant life history traits. Overall, both partners benefited from the AM association. However, several sex-specific benefits were detected which were not uniformly present in all experiments for any given trait. Moreover, the responses observed in certain life history traits were dependent on both the AM fungal and plant species involved in the symbiosis. Remarkably, plants gained sex-specific benefits from the same species of AM fungi and the fungal benefit differed depending on the sex of the host plant. In addition, mycorrhizal benefits were lost under certain environmental conditions. To summarise, the results obtained in this study highlight the complexity of AM interactions. My results suggest that the plant-mycorrhizal fungus relationship may differ depending on the sex of the host plant. Through sex-specific effects on survival, growth and reproduction of the hosts, AM fungi may play a role in the evolution of the life histories in the studied species. In addition, sex-specific relationships between plants and their mycorrhizal symbionts may have potential important consequences for the population dynamics of the sexual morphs and the coevolution of the mycorrhizal relationship.

La grande majorité des plantes à fleurs se reproduisent grâce à leurs pollinisateurs. L’évolution chez les plantes est pourtant souvent étudiée sans prendre en compte ces interactions, et cette thèse vise à mieux comprendre leur impact sur l’évolution des plantes. Dans un premier chapitre, je présenterai les effets connus des pollinisateurs sur le taux d’autofécondation des plantes et sur son évolution. Dans un second chapitre, j’ai modélisé l’évolution du taux d’autofécondation des plantes lorsque celui-ci affecte la démographie des plantes et des pollinisateurs, et l’investissement des plantes dans la pollinisation. Cette étude montre que l’évolution vers l’autofécondation peut mener à l’extinction des plantes. Dans un troisième chapitre, je m’intéresserai à l’évolution des caractéristiques florales pour des espèces qui dépendent obligatoirement du transfert de pollen entre individus : les espèces dioïques. Cette étude montre que l’attractivité des plantes peut évoluer différemment chez les individus mâles et femelles, surtout dans les grandes populations qui subissent peu de limitation en pollen. Ce résultat suggère que le dimorphisme sexuel ne menacerait pas le maintien des populations dioïques. Enfin, même si elles prennent en compte les pollinisateurs de manière sommaire, les études précédentes ont montré leur importance pour la démographie et l’évolution chez les plantes. La dernière étude de cette thèse a donc pour but de mieux décrire et quantifier les mécanismes sous-jacents au comportement du pollinisateur, en particulier concernant l’impact des traits floraux. Elle permettra une meilleure intégration des interactions plantes-pollinisateurs dans les modèles
The mode of pollination is often neglected regarding the evolution of plant traits, although the reproduction of most flowering plants is based on their interactions with pollinators. This thesis aims at a better understanding of the interplay between animal-pollination and the evolution of plant traits. First, I will present a detailed review on the interplay between plant mating system and pollinator behavior, which highlights the impact of pollinators on the immediate ecological selfing rate and on its evolution. Second, I modeled the evolution of plant selfing rate when it affects both the demography of plants and pollinators and the investment of plants in pollination. This study provides new theoretical evidence that evolution towards selfing can lead to an evolutionary suicide in some conditions. Third, I will present a modeling analysis of the impact of animal-pollination for species that compulsorily rely on outcross pollination: entomophilous dioecious species. This study revealed that under pollinator-mediated selection, attractiveness of males and females should evolve in large populations that do not suffer from pollen limitation. This result suggests that dimorphism may not be a threat for dioecious populations. Finally, although the previous models integrated pollinators in a basic way, they highlighted strong interplays between pollinators, plant demography, and the evolution of plant traits. The last study of this thesis, aims at defining and quantifying the mechanisms underlying pollinator foraging behavior, and especially the impact of plants floral traits on pollen transfer. This would allow for a better modeling of plant-pollinators interactions

Foliar functional traits have been shown to strongly co-vary with each other and with rates of litter decomposition, demonstrating an “after-life effect” of foliar traits on ecosystem processes. Leaf-litter traits are often used to indicate substrate quality in decomposition studies. Chemical traits have been studied more extensively in the context of decomposition than physical traits such as specific leaf area (SLA) and leaf toughness, which impart information on litter structure and decomposer access. I investigated relationships among foliar and litter traits, and between traits and early mass-loss, in 14 plant species native to British Columbia. Both physical and chemical traits were measured in foliage and leaf litter of each species. Foliar traits novel to this kind of study include cuticle thickness and distance to lumen (DTL); novel litter traits include leaching loss and water uptake after 2 and 24 hours. Decomposition, as net proportion of mass lost over time, was measured in litterbags installed in a temperate rain forest at the University of British Columbia Farm in Vancouver. Mass loss was divided into two phases: Phase I from 0 to 3 months, and Phase II from 3 to 12 months. Foliar traits co-varied in ways predicted by the leaf economics spectrum hypothesis, and litter traits similarly co-varied. Trait-based relationships among species differed when using foliar traits and using litter traits, suggesting that the same traits measured in foliar and litter impart different meaning in the context of decomposition. Phase I was best predicted by leaching loss and litter traits, suggesting that leaching dominates Phase I, and Phase II was best predicted by foliar functional traits such as leaf dry matter content and nitrogen that relate to relative mesophyll abundance, suggesting that decomposer activity dominates Phase II. Physical traits predicted mass loss as well or better than chemical traits, and using both types of traits in correlative studies may provide insights into the processes that underlie litter decomposition.
Forestry, Faculty of
Graduate

In pea, lodging changes canopy structure, increases disease pressure, reduces yield, and reduces harvest efficiency. In order to discover the quantitative trait loci (QTLs) influencing lodging resistance and other important agronomic traits in pea, a recombinant inbred line (RIL) population was created from a relatively wide cross between the commercial variety Delta and an unnamed pea variety. The RIL population was grown for 6 site-years in Bozeman and Moccasin, MT, USA, and phenotypic data was collected for 22 quantitative morphological traits and seven categorical traits which were thought to be associated with lodging resistance. Genotypic data was derived from genotype by sequencing, microsattelite markers, and cleaved amplified sequence tagged sites.

QTL analysis identified a total of 135 putative QTLs for the 22 traits examined in the study. There were 12 specific regions where 115 QTLs co-located, indicating that as few as 12 genes may be responsible for multiple pleiotropic effects. Ten QTLs were found for lodging resistance. Due to the large amount of phenotypic data collected, the putative mechanism of lodging resistance was determined for each QTL. In nearly every case, lodging resistance was associated with reduced plant height, a change in tendril number, or increased stem strength. This conclusion was supported by mathematical modeling. Branch number, which determines the number of tendrils per plant, was also positively associated with lodging resistance during all site-years, indicating that increasing tendril number also increases lodging resistance.

Yield was controlled by eight QTLs. All QTLs for yield had pleiotropic effects on lodging resistance and yield per plant. Seed size was not correlated with yield, and a model was created which explained why no association between yield and seed size was found.

The pleiotropic effects and utility of the QTLs discovered in this study are discussed. The results of this study further refine the ideotype for pea, and can be used for marker assisted selection in this crop.

There is critical need for studies on interspecific competition which enable general principles to be deduced that apply beyond the species and conditions of a particular study or site. Studies on plant traits are a key part of this search for general principles. I measured relative competitive ability in 63 terrestrial herbaceous plant species using the phytometer Trichostema brachiatum, to test whether competitive ability can be predicted from simple measurable plant traits. The test species utilised in this experiment represented a wide array of terrestrial vegetation types (e.g. rock. barrens, alvars, old fields), and an array of growth forms, from small rosette species (e.g. Saxifraga virginiensis) to large clonal graminoids (e.g. Agropyron repens). The experiment was carried out under both a "normal" and a "drought" treatment. Multiple linear regression showed that there was a strong relationship between plant traits and competitive ability (Normal treatment--r$\sp2$ = 0.54; Drought--treatment r$\sp2$ = 0.55). Total plant biomass explained 34% of the variation in competitive ability in the normal treatment and below-ground biomass explained 35% of the variation in the drought treatment. Leaf shape explained most of the residual variation. The competitive hierarchy for plants in the normal and drought treatment was compared. Rankings for individual species varied between treatments, however, when all species were compared simultaneously, competitive hierarchies in both treatments were highly correlated (r$\sb{\rm s}$ = 0.91). This suggests that invariant and variant views of competitive hierarchies are not mutually exclusive but instead depend on the scale at which competition is being addressed. On the broad scale, relative competitive abilities appear consistent across different environments. Thus, both traits and hierarchies show general repeatable patterns that allow us to generalize from one set of circumstances to another.

Les interaccions planta-pol·linitzador són un component essencial de la biodiversitat i la funció ecològica dels ecosistemes terrestres. Un dels principals objectius de l'ecologia de la pol·linització és descriure aquestes interaccions i comprendre els factors subjacents a la seva estructura. En aquesta tesi doctoral es presenten els resultats dels estudis duts a terme durant tres anys en una comunitat mediterrània de plantes i els seus insectes pol·linitzadors al parc natural del Garraf (NE Espanya). En el capítol 1 es van registrar les interaccions planta-pol·linitzador i es van mesurar diferents trets morfològics, fenològics i ecològics de les especies de plantes i pol·linitzadors en un intent d'establir quins d’aquest trets estructuren les relacions planta-pol·linitzador. Es van registrar 14.713 contactes entre les principals 23 espècies de plantes i 221 espècies de pol·linitzadors, que van representar 960 interaccions específiques. Trobem que un tret ecològic (densitat de flors) i un tret fenològic (temps de floració) de les plantes van ser els principals factors que expliquen les interaccions observades. Trets florals, com la restricció de la corol·la i el pol·len i la producció de nèctar per flor, van tenir un efecte menor. En el capítol 2 s’explora el paper d'un atribut floral diferent i complex, l’aroma floral, en l'estructuració de la variació temporal de les taxes de visites de pol·linitzadors en la mateixa comunitat. Trobem que les plantes que floreixen a principis de la temporada, en un moment en què les flors són més abundants però els pol·linitzadors són escassos, produeixen major quantitats de compostos volàtils que les plantes que floreixen més tard, quan els pol·linitzadors són molt més abundants en relació a les poques flors disponibles. Aquest és el primer estudi en el qual s'analitzen els patrons d'emissió de fragàncies florals a nivell comunitari. Finalment, al capítol 3 s'exploren amb més detall la importància d’aquestes fragàncies florals mitjançant un cas d’estudi realitzat en el Jardí Botànic i Ecològic de la Universitat de Bayreuth (Alemanya). En aquest estudi es va utilitzar una planta focal (la composta Cirsium arvense) i un dels seus pol·linitzadors principal (el sírfid Episyrphus balteatus). Mitjançant mesures de volàtils al laboratori, tècniques d’electroantenografia i bioassajos es va trobar que els senyals olfactius eren més importants que els senyals visuals com a atraients de E. balteatus cap a les inflorescències de C. arvense.
Plant-pollinator interactions are an essential component of biodiversity and ecological function in terrestrial ecosystems. One of the main objectives of pollination ecology is to describe these interactions and to understand the factors underlying their structure. In this PhD thesis we present the results of studies conducted over three years in a Mediterranean plant-pollinator community in the natural park of el Garraf (NE Spain). In chapter 1 we monitored plant-pollinator interactions and measured plant and pollinator traits in an attempt to establish the main drivers of plant-pollinator relationships. We recorded 14713 contacts between the main 23 plant species and 221 pollinator species, representing 960 specific interactions. We found that an ecological trait (flower density) and a phonological trait (flowering time) were the main factors explaining the observed interactions. Floral traits, such as corolla restrictiveness and pollen and nectar production per flower, had a lesser effect. In chapter 2 we explore the role of a different and complex floral attribute, floral scent, in structuring temporal variation in pollinator visitation rates in the same community. We found that plants blooming early in the season, at a time when flowers are most abundant but pollinators are scarce, produce larger amounts of volatiles than plants blooming later, when pollinators are plentiful for the few flowers available. This is the first study in which emission patterns are analysed at the community level. Floral fragrances are further explored in chapter 3, which describes a case study conducted at the Ecological Botanical Garden of the University of Bayreuth (Germany). This study involves a focal plant (the composite Cirsium arvense) and a focal pollinator (the syrphid fly Episyrphus balteatus), and uses laboratory volatile measurements, electroantennography techniques and biossays. We found that olfactory cues were more important than visual cues as attractants of E. balteatus to C. arvense inflorescences.

In order to understand how ecosystems are likely to respond to global anthropogenic change it is first necessary to identify general patterns and processes that can explain how they are created and maintained. Plant traits potentially provide a mechanistic explanation for the differences in growth and survival that explain a species niche that can scale up from individual to biome. In this thesis I investigate the relationships between grass functional traits and the biotic and abiotic environment, and test whether the predictions made by community ecological theory are more broadly applicable at continental and global scales. I provide evidence that at the global scale soil nutrients is more important than climate in explaining the distribution of traits that reflect different strategies of resource use but that evolutionary history provides a stronger explanation for global trait distribution than contemporary environment. I then show the functional traits that are associated with gradients of grazing and fire and identify functional groups that have diverging responses to grazing across Sub-Saharan Africa. Finally I investigate species response to drought and identify traits which can explain a species hydrological niche. The findings of this work provide evidence that trade-offs between carbon and nitrogen acquisition and use (leaf nitrogen content and C/N ratio) could provide a foundation for predicting plant responses to changes in climate, soil nutrients and disturbance at global scales. However, I also show that traits often used to reflect differences in leaf growth and longevity (ie. specific leaf area and leaf tensile strength) are not able to strongly predict response to either resource availability or disturbance at macro-ecological scales. This highlights the need to identify other axis of variation and organs beyond the leaf economic spectrum, for example root architecture, that are potentially important in explaining the differing aspects of a species niche and how vegetation may respond to global change.

Thesis (M.S.)--University of Missouri-Columbia, 2008.
The entire dissertation/thesis text is included in the research.pdf file; the official abstract appears in the short.pdf file (which also appears in the research.pdf); a non-technical general description, or public abstract, appears in the public.pdf file. Title from title screen of research.pdf file (viewed on August 12, 2009) Includes bibliographical references.

The tundra is currently warming twice as rapidly as the rest of planet Earth, which is thought to be leading to widespread vegetation change. Understanding the drivers, patterns, and impacts of vegetation change will be critical to predicting the future state of tundra ecosystems and estimating potential feedbacks to the global climate system. In this thesis, I used plant traits - the characteristics of individuals and species - to investigate the fundamental structure of tundra plant communities and to link vegetation change to decomposition across the tundra biome. Plant traits are increasingly used to predict how communities will respond to environmental change. However, existing global trait relationships have largely been formulated using data from tropical and temperature environments. It is thus unknown whether these trait relationships extend to the cold extremes of the tundra biome. Furthermore, it is unclear whether approaches that simplify trait variation, such as the categorization of species into functional groups, capture variation across multiple traits. Using the Tundra Trait Team database - the largest tundra trait database ever compiled - I found that tundra plants revealed remarkable consistency in the range of resource acquisition traits, but not size traits, compared to global trait distributions, and that global trait relationships were maintained in the tundra biome. However, trait variation was largely expressed at the level of individual species, and thus the use of functional groups to describe trait variation may obscure important patterns and mechanisms of vegetation change. Secondly, plant traits are related to several key ecosystem functions, and thus offer an approach to predicting the impacts of vegetation change. Notably, understanding the links between vegetation change and decomposition is a critical research priority as high latitude ecosystems contain more than 50% of global soil carbon, and have historically formed a long-term carbon sink due to low decomposition rates and frozen soils. However, it is unclear to what extent vegetation change, and thus changes to the quality and quantity of litter inputs, drives decomposition compared to environmental controls. I used two common substrates (tea), buried at 248 sites, to quantify the relative importance of temperature, moisture and litter quality on litter decomposition across the tundra biome. I found strong linear relationships between decomposition, soil temperature and soil moisture, but found that litter quality had the greatest effect on decomposition, outweighing the effects of environment across the tundra biome. Finally, I investigated whether tundra plant communities are undergoing directional shifts in litter quality as a result of climate warming. Given the importance of litter quality for decomposition, a shift towards more or less decomposable plant litter could act as a feedback to climate change by altering decomposition rates and litter carbon storage. I combined a litter decomposition experiment with tundra plant trait data and three decades of biome-wide vegetation monitoring to quantify change in community decomposability over space, over time and with warming. I found that community decomposability increased with temperature and soil moisture over biogeographic gradients. However, I found no significant change in decomposability over time, primarily due to low species turnover, which drives the majority of trait differences among sites. Together, my thesis findings indicate that the incorporation of plant trait data into ecological analyses can improve our understanding of tundra vegetation change. Firstly, trait-based approaches capture variation in plant responses to environmental change, and enable prediction of vegetation change and ecosystem function at large scales and under future growing conditions. Secondly, my findings offer insight into the potential direction, rate and magnitude of vegetation change, indicating that despite rapid shifts in some traits, the majority of community-level trait change will be dependent upon the slower processes of migration and species turnover. Finally, my findings demonstrate that the impact of warming on both tundra vegetation change and ecosystem processes will be strongly mediated by soil moisture and trait differences among vegetation communities. Overall, my thesis demonstrates that the use of plant traits can improve climate change predictions for the tundra biome, and informs the fundamental rules that determine plant community structure and change at the global scale.

The fragmentation of natural habitat caused by anthropogenic land use changes is one of the main drivers of the current rapid loss of biodiversity. In face of this threat, ecological research needs to provide predictions of communities' responses to fragmentation as a prerequisite for the effective mitigation of further biodiversity loss. However, predictions of communities' responses to fragmentation require a thorough understanding of ecological processes, such as species dispersal and persistence. Therefore, this thesis seeks an improved understanding of community dynamics in fragmented landscapes. In order to approach this overall aim, I identified key questions on the response of plant diversity and plant functional traits to variations in species' dispersal capability, habitat fragmentation and local environmental conditions. All questions were addressed using spatially explicit simulations or statistical models. In chapter 2, I addressed scale-dependent relationships between dispersal capability and species diversity using a grid-based neutral model. I found that the ratio of survey area to landscape size is an important determinant of scale-dependent dispersal-diversity relationships. With small ratios, the model predicted increasing dispersal-diversity relationships, while decreasing dispersal-diversity relationships emerged, when the ratio approached one, i.e. when the survey area approached the landscape size. For intermediate ratios, I found a U-shaped pattern that has not been reported before. With this study, I unified and extended previous work on dispersal-diversity relationships. In chapter 3, I assessed the type of regional plant community dynamics for the study area in the Southern Judean Lowlands (SJL). For this purpose, I parameterised a multi-species incidence-function model (IFM) with vegetation data using approximate Bayesian computation (ABC). I found that the type of regional plant community dynamics in the SJL is best characterized as a set of isolated “island communities” with very low connectivity between local communities. Model predictions indicated a significant extinction debt with 33% - 60% of all species going extinct within 1000 years. In general, this study introduces a novel approach for combining a spatially explicit simulation model with field data from species-rich communities. In chapter 4, I first analysed, if plant functional traits in the SJL indicate trait convergence by habitat filtering and trait divergence by interspecific competition, as predicted by community assembly theory. Second, I assessed the interactive effects of fragmentation and the south-north precipitation gradient in the SJL on community-mean plant traits. I found clear evidence for trait convergence, but the evidence for trait divergence fundamentally depended on the chosen null-model. All community-mean traits were significantly associated with the precipitation gradient in the SJL. The trait associations with fragmentation indices (patch size and connectivity) were generally weaker, but statistically significant for all traits. Specific leaf area (SLA) and plant height were consistently associated with fragmentation indices along the precipitation gradient. In contrast, seed mass and seed number were interactively influenced by fragmentation and precipitation. In general, this study provides the first analysis of the interactive effects of climate and fragmentation on plant functional traits. Overall, I conclude that the spatially explicit perspective adopted in this thesis is crucial for a thorough understanding of plant community dynamics in fragmented landscapes. The finding of contrasting responses of local diversity to variations in dispersal capability stresses the importance of considering the diversity and composition of the metacommunity, prior to implementing conservation measures that aim at increased habitat connectivity. The model predictions derived with the IFM highlight the importance of additional natural habitat for the mitigation of future species extinctions. In general, the approach of combining a spatially explicit IFM with extensive species occupancy data provides a novel and promising tool to assess the consequences of different management scenarios. The analysis of plant functional traits in the SJL points to important knowledge gaps in community assembly theory with respect to the simultaneous consequences of habitat filtering and competition. In particular, it demonstrates the importance of investigating the synergistic consequences of fragmentation, climate change and land use change on plant communities. I suggest that the integration of plant functional traits and of species interactions into spatially explicit, dynamic simulation models offers a promising approach, which will further improve our understanding of plant communities and our ability to predict their dynamics in fragmented and changing landscapes.
Die Fragmentierung von Landschaften umfasst die Zerschneidung und den Verlust von Flächen mit natürlicher Vegetationsentwicklung und ist eine der Hauptursachen für den gegenwärtigen drastischen Verlust an Biodiversität. Diese Dissertation soll zu einem besseren Verständnis der Vegetationsdynamik in fragmentierten Landschaften beitragen. Damit verbunden ist das Ziel, Vorhersagen über die Reaktion von Pflanzengemeinschaften auf Fragmentierung zu verbessern. Diese Vorhersagen sind notwendig, um gezielte Naturschutzmaßnahmen zur Verminderung eines weiteren Verlustes an Biodiversität umsetzen zu können. In Kapitel 2 der Dissertation wird mit einem Simulationsmodell untersucht, wie sich die Ausbreitungsdistanz von Samen auf die lokale Artenzahl von Pflanzengemeinschaften auswirkt. Dabei zeigte sich, dass längere Ausbreitungsdistanzen die lokale Artenvielfalt sowohl erhöhen, als auch verringern können. Der wichtigste Einflussfaktor war dabei die Artenvielfalt der über-geordneten Pflanzengemeinschaft, in der die betrachtete lokale Gemeinschaft eingebettet war. Im dritten Kapitel wird die Konnektivität zwischen Pflanzengemeinschaften in Habitat-fragmenten, d.h. der Austausch von Arten und Individuen durch Samenausbreitung, im Unter-suchungsgebiet in Israel analysiert. Dafür wurde ein zweites räumliches Simulationsmodell mit statistischen Verfahren an Felddaten angepasst. Der Vergleich des Modells mit den Daten wies auf eine sehr geringe Konnektivität zwischen den Habitatfragmenten hin. Das Modell sagte vorher, dass innerhalb von 1000 Jahren 33% - 60% der Arten aussterben könnten. In Kapitel 4 wird zuerst analysiert, welche Prozesse die Verteilung von funktionellen Eigenschaften in Pflanzengemeinschaften bestimmen. In einem zweiten Schritt wird dann unter-sucht, wie sich funktionelle Eigenschaften von Pflanzengemeinschaften mit dem Niederschlag und der Fragmentierung im Untersuchungsgebiet in Israel verändern. Der Zusammenhang zwischen den Eigenschaften Pflanzenhöhe, sowie spezifischer Blattfläche und der Fragmentierung änderte sich nicht entlang des Niederschlagsgradienten. Im Gegensatz dazu, änderte sich der Zusammenhang zwischen der Samenmasse bzw. der Samenzahl und der Fragmentierung mit dem Niederschlag. Aus den Ergebnissen der ersten Teilstudie wird deutlich, dass Naturschutzmaßnahmen, die natürliche Habitate stärker vernetzen sollen, die Diversität, sowie die Zusammensetzung der übergeordneten Artengemeinschaft berücksichtigen müssen, um Verluste an Biodiversität zu vermeiden. Die Verknüpfung eines räumlichen Simulationsmodells mit Felddaten in der zweiten Teilstudie stellt einen neuen und vielversprechenden Ansatz für die Untersuchung der Auswirkungen verschiedener Management-Szenarien dar. Die dritte Teilstudie ist die erste Analyse der gemeinsamen Auswirkungen von Klima und Fragmentierung auf funktionelle Pflanzen-eigenschaften und zeigt die hohe Bedeutung der Untersuchung von Synergie-Effekten verschiedener Umweltfaktoren. Für zukünftige Forschung legt diese Dissertation nahe, funktionelle Eigenschaften und Konkurrenz zwischen Arten in räumlichen Simulationsmodellen zu berücksichtigen, um das Verständnis von Artengemeinschaften in fragmentierten Landschaften noch weiter zu verbessern.

Una de les principals contribucions com ecòlegs forestals al segle XXI és proporcionar la teoria i aproximacions ecològiques per descriure i predir canvis dels ecosistemes forestals causats pel canvi global. En l'última dècada, l’ecologia basada en els trets funcionals ha sorgit com a una nova disciplina capaç de transformar l'ecologia en una disciplina més mecanicista i predictiva, i no només merament descriptiva. Tanmateix, algunes de les seves assumpcions fundacionals no s’han testat rigorosament. S’assumeix que els trets mesurats a nivell d’òrgan es poden escalar fàcilment a nivell de tota la planta, que la variabilitat intraespecífica dels trets (ITV) es pot ignorar en gran mesura i que els trets afecten les taxes demogràfiques dels individus i, per tant, són funcionals. A més, la majoria d’aproximacions estudien trets relativament fàcils i ràpids de mesurar per a un gran nombre de mostres, tot i que no estan directament relacionats amb mecanismes fisiològics específics. En aquesta tesis, mostrem que els trets hidràulics de les plantes poden ser de gran utilitat a l'hora d'entendre les principals estratègies ecològiques de les plantes. El transport d'aigua de les plantes afecta tant la seva taxa fotosintètica com el seu creixement. La hidràulica de les plantes permet incorporar l’aigua en l'economia del carboni i els nutrients, i determina la resistència de les plantes a la sequera esdevenint un factor clau a l’hora d’avaluar la vulnerabilitat dels boscos al canvi climàtic. L'objectiu principal d'aquesta tesi és integrar els trets hidràulics en el marc dels trets funcionals clàssics, i determinar-ne la variabilitat, relacions i compromisos a diferents escales, així com usar aquesta informació per definir estratègies de les plantes per fer front a la sequera. Per tal d’aconseguir aquest objectiu, es van seguir dues aproximacions diferents: una basada en la compilació d’un conjunt de dades global de 1149 espècies d’arreu del món (Capítol 2); i una altra basada en dades de trets foliars, del tronc i hidràulics mesurats al llarg d'un gradient de disponibilitat d'aigua, en sis de les espècies arbòries dominants a Catalunya (NE Espanya) (Capítol 3 i Capítol 4). Concretament, al Capítol 2 es testa un nou marc conceptual que relaciona els trets hidràulics amb els trets més clàssics a nivell global. En el Capítol 3 s’investiguen els ajustos i la coordinació dels trets hidràulics, foliars i del tronc al llarg d’un gradient de disponibilitat d'aigua a nivell interespecífic i intraespecífic. Finalment, al Capítol 4 s’avalua la importància funcional dels trets estudiats en el capítol anterior, explorant-ne les relacions amb el creixement dels arbres a nivell interespecífic i intraespecífic. Un resultat rellevant d'aquesta tesi és que no hem trobat evidències que donin suport a l’existència d’un espectre econòmic global de tota la planta que n’integri els diferents òrgans i recursos (carboni, nutrients i aigua). D'aquesta manera, escalar els trets mesurats a nivell d’òrgan a trets de tota la planta i estratègies en l’ús de recursos, pot ser més difícil del que es sol preveure degut a les respostes compensatòries que es donen dins d’un mateix individu. També mostrem que la ITV és especialment rellevant en trets integradors que involucren més d’un òrgan i que incorporar la ITV és un pas necessari per millorar la nostra comprensió dels ajustos de les plantes als canvis ambientals. Finalment, il·lustrem que la nostra comprensió de les relacions entre el creixement i els trets pot millorar considerablement mitjançant la selecció de trets estretament relacionats amb funcions fisiològiques i factors ambientals específics del context d’estudi, integrant els trets al llarg d’eixos comuns de variació, i reavaluant les variables que s’utilitzen per reflectir el funcionament de la planta.
One of the main contributions of forest ecologists, in the 21st century, is to provide ecological theory and tools to describe and predict forests ecosystem changes caused by the ongoing global change. Over the last decade, ‘functional trait-based ecology’ has emerged as a refreshed discipline with the promise to turn ecology from a primarily descriptive science into a more mechanistic and predictive discipline. However, several foundational assumptions of trait-based ecology have not been rigorously tested. It is presumed that organ-level traits can be easily scaled-up to whole-plant traits, that intraspecific trait variability (ITV) can be largely overlooked and that traits affect individual demographic outcomes and thus, are functional. Additionally, most trait-based approaches study ‘soft’ traits which are relatively easy and quick to measure for a large number of samples although they are not directly linked to specific physiological mechanisms. We argue that plant hydraulic traits can provide useful insights to the understanding of plant ecological strategies. Water transport throughout the plant affects both photosynthetic rate and growth. Plant hydraulics allow linking water to the carbon/nutrient economics and determine plants’ drought resistance and thus, are key factors when assessing forest vulnerability to climate change. The main aim of this thesis is to integrate plant hydraulics into a functional trait-based framework, to assess trait variability, relationships and trade-offs at different ecological scales and to use this information to define strategies to cope with drought stress. To achieve this objective, two different study approaches were followed: one based on compiling a global dataset for 1149 species worldwide (Chapter 2), and another based on field data collection of a set of leaf, stem and hydraulic traits along a water availability gradient for six of the dominant tree species in Catalonia (NE Spain) (Chapter 3 and Chapter 4). Specifically, in Chapter 2 we test a new framework relating hydraulic and more ‘standard’ traits across species at the global scale. In Chapter 3 we investigate the adjustments and coordination of hydraulic, leaf and stem traits along a water availability gradient at the interspecific and intraspecific levels. Finally, in Chapter 4 we test the functional importance of traits studied in the previous chapter, exploring the strength of the association between traits and tree growth also at the interspecific and intraspecific levels. A significant finding to emerge from this thesis is that we do not find support for a world-wide ‘fast-slow’ plant economics spectrum that integrates across organs and resources (carbon, nutrients and water). Thus, scaling-up from organ level traits to whole-plant traits and resource use strategies may be more challenging than commonly anticipated because of compensatory responses within individuals. We also show that the ITV is especially relevant for integrative traits that involve more than one organ and that accounting for ITV is a necessary step forward towards improving our understanding of plant adjustments to environmental changes. Finally, we also show that our understanding of trait-growth (and by extension trait-performance) relationships can be greatly improved by selecting traits closely related to physiological functions and context-specific environmental drivers, integrating them along common axes of variation, and re-assessing the variables that are used to reflect whole-tree performance

Co-flowering plants within communities typically share pollinators which can lead to the deposition of pollen grains from varying species onto stigmas; or heterospecific pollen transfer (HPT). It has been shown that HPT can have varying effects on plant reproductive success. These effects can range from an 80% reduction on seed production to no effect. However, to date, there are no studies that have evaluated the causes underlying variability of these effects. We investigated this variability through a greenhouse experiment. Hand-pollinations were conducted with a mix of conspecific and heterospecific pollen and a control (conspecific pollen only). We used six pollen recipient and four species as donors for the heterospecific pollen (5 treatments total) We conducted hand-pollinations on a minimum of 10 plants per species (584 total pollinations). After pollination seed set data was recorded for each treatment and the amount of conspecific and heterospecific pollen on stigmas was recorded. We evaluated if the effects of HPT can be explained by the recipient species, the donor species or the interaction between donor and recipient. The results show high variability in the magnitude of HPT(2-93) but this variability is not a result of donor characteristics or even recipient characteristics but a result of the interactions between donors and recipients (df=20, α=.05, p=0.015). We will further investigate if the interaction can be explained by stigma/pollen size ratio, degree of co-flowering, or phylogenetic distance between donor and recipient species. This study will contribute to advance our understanding of how co-flowering plant communities interact amongst themselves after pollination.

Development of winter wheat (Triticum aestivum L.) cultivars capable of more efficient uptake and utilization of applied nitrogen (N) has the potential to increase grower profitability and reduce negative environmental consequences associated with N lost from the plant-soil system. The first study sought to evaluate genotypic variation for N use efficiency (NUE) and identify lines consistently expressing high or low NUE under two or more N rates in a total of 51 N-environments. The results indicated that significant genotype by N rate interactions were frequently observed when trials utilized at least three N rates and identified wheat lines with high and stable yield potential that varied in performance under low N conditions. In addition, NUE was associated with above-ground biomass at physiological maturity were found to be both highly heritable across multiple N supplies. In the second study, two bi-parental mapping populations having a common low ('Yorktown') and two high (VA05W-151 and VA09W-52) NUE parents were characterized to dissect the genetics underlying N response. The populations were evaluated in eight N-environments and genotyped using single-nucleotide polymorphism data derived from a genotyping-by-sequencing protocol to identify quantitative trait loci (QTL) associated with high NUE. Six QTL for NUE were identified on chromosomes 1D, 2D, 4A, 6A, 7A, and 7D that were associated with N use efficiency. The QTL on 2D and 4A co-localized with known loci governing photoperiod sensitivity and resistance to Fusarium head blight (caused by the fungal pathogen Fusarium graminearum Schwabe), respectively. Three of the identified QTL (6A, 7A, and 7D) were associated with NUE in previous investigations, while the QTL on 1D was novel. The final experiment employed a small panel of soft red winter wheat lines to study the effects of photoperiod alleles on chromosome 1D (Ppd-D1) on yield-related traits under three or five N rates that were variably split over two growth stages in eight environments. The results validated the effect of a photoperiod sensitive allele (Ppd-D1b) that was associated with increased grain yield across N rates in half of the Virginia testing environments and under low N rates in all Ohio testing sites at the expense of grain N content. Yield advantages conferred by the Ppd-D1b allele were attributable to increased floret fertility and kernel number per spike. The findings from these studies have direct application for winter wheat breeding programs targeting NUE improvements.
Doctor of Philosophy
Wheat (Triticum aestivum L.) products account for a significant percentage of the total dietary calories and protein consumed globally. To meet production demands, wheat requires efficient nitrogen (N) management to ensure continued grower profitability and to reduce negative environmental impacts of N lost from agricultural systems. This dissertation sought to evaluate variation among wheat lines for N use efficiency (NUE), assess the performance of wheat lines under multiple N supplies, validate traits that are associated with NUE, investigate the role of photoperiod sensitivity genes on N response, and identify regions of the wheat genome associated with high N use efficiency. These studies were conducted using panels of winter wheat lines grown under two or more N conditions over a combined 32 location-years. Results of Chapter I identified variation in cultivar response to N rates was more frequently observed when a greater number of N rates were used in trials of wheat N response. The first chapter also identified variation among wheat lines for NUE and identified lines that consistently produce high grain yields over N-location-years. In addition, above-ground biomass at physiological maturity was found to be strongly associated with grain yield under all N rates and was highly heritable in both studies. Chapter II utilized a combination of genetic and observable trait data to perform genetic analysis in two bi-parental populations grown in eight Nlocation-years. The study identified reproducible and significant genetic markers associated with NUE for application in wheat breeding programs. Upon analysis of photoperiod sensitive versus insensitive wheat lines in Chapter III, photoperiod sensitive wheat lines had a significant yield advantage under N-limited conditions in Ohio and across N treatments in half of the Virginia testing location-years. This resulted from an increased number of kernels per spike and fertile florets in photoperiod sensitive wheat lines. Results from this dissertation suggest that active breeding and selection for N response may be achieved through the employment of high NUE genes and the continued identification of adapted high NUE wheat parental lines.

Includes bibliographical references
Erica makes up 7% of all species in the Cape flora. It is the most species-rich genus in the Cape Floristic Region (CFR), which has an area 0f 90 000km². Erica species have great inter- and intra-specific variation in floral form as well as in post-fire regeneration strategies. Previous studies of other plant groups (Barrett et al. 1996; Button et al. 2012) have illustrated changes in floral traits with a shift from outcrossing to selfing. The aim of this thesis was to determine whether similar changes occur in Erica. I thus analysed breeding systems in Erica in relation to floral traits, pollinators, and fire survivals strategies. Seed and fruit set data obtained from hand-pollination treatments suggested that self- fertilization occurs rarely. Autonomous selfing did not generally yield significant seed set. When comparing changes in floral traits with increased selfing ability and pollination syndromes weak relationships were observed. Average plant height showed a positive relationship with selfing ability but this correlation was not significant. Comparing traits within small and large flowered species separately yielded significant relationships between corolla size and selfing ability of small-flowered species.. Furthermore, general trends indicate that small-flowered species have increased ability to self-fertilise when corolla sizes are larger, corolla apertures larger and herkogamy reduced. Large-flowered species employ the same strategy but average corolla aperture is reduced. A trade-off between the size and the number of flowers was seen within the Erica genus. Small-flowered species had significantly more flowers compared to larger- flowered species that had markedly fewer flowers per unit height. This finding has implications for the selfing potential of small-flowered species as increased self- incompatibility may have evolved in order to reduce the effects of increased geitonogamy due to increased floral number. The prediction that self-fertilisation would be increased in seeders compared to resprouters, on the basis that seeders are more reliant on seeds for persistence than resprouters, was not realised when comparing the selfing ability of different fire- survival strategies. Erica mammosa, a species with morphs possessing both fire-survival strategies, shows no significant differences in selfing ability, this includes differences in pollen-ovule (P/O) ratios. However, indices suggest the resprouting form of E. mammosa to have an increased ability to self-fertilize while the seeder form has an increased ability for autonomous selfing. The 29 species analysed were divided into outcrossers and facultative outcrossers based on selfing indices but these did not fit neatly within Cruden’s proposed P/O ranges (facultative autogamy: P/Os= 32-397; facultative outcrossers: P/Os= 160.7 - 2258.6; outcrossers: P/Os= 1062 - 19525). This may be due to his classification of species into breeding systems being based on relatively few distantly related species per category with extremely variable P/O ratios per category. For example, outcrossers ranged an order of magnitude (from 1000+ to 20 000). It is also true that this ratio can be influenced by a variety of different factors, these include: habitat, evolutionary history and pollination syndrome. Consequently, P/O ratios in Erica do not seem to reflect pollination syndromes very well. Presumably, sex allocation theory may explain the relationship of breeding system with P/O ratios better. Histological studies of pollen tube growth for self- and cross-pollinated flowers of eight species suggested that Erica has late acting self-incompatibility (LSI). LSI is a barrier to selfing that occurs in the ovary. However, I could not determine if the rejection process occurs pre- or post-fertilization. Although, a large amount of knowledge is still lacking, this preliminary study provided insight into the reproductive biology of Erica.

The management of weed species Alopecurus myosuroides (black-grass) in arable agriculture is largely achieved through use of herbicides. However, resistant populations are increasingly commonplace and new modes of action are proving elusive. Growers use integrated weed management (IWM) strategies to manage the weed seedbank, such as rotational ploughing to bury seed and delayed drilling to reduce weed numbers within a crop. Competitive cultivars may contribute to IWM, but testing cultivars is a long, expensive process. The aims of this studentship were to identify the traits that confer enhanced crop competitive ability and determine if these can be used to predict competitive ability of new cultivars. This was investigated on outdoor sand-beds and in field trials. Commercial wheat cultivars were grown alongside A. myosuroides. Various wheat traits were measured throughout growth. The seed return of A. myosuroides was quantified at maturity, and yield was harvested in the field. Pearson’s correlations and multivariate analysis were used to identify traits related to competition, and Linear Mixed Models (LMM) were used to identify predictive traits. Two models of crop-weed interactions were parameterised for the cultivars. Potential interactions between cultivar choice and other IWM strategies (delayed sowing and increased sowing rate) was assessed experimentally and through simulation models. Cultivar differences in suppressive ability were most evident between the extreme ends. Various traits were related to a cultivar’s ability to suppress A. myosuroides seed return, such as early height and tillering parameters, though no traits were consistent across all experiments. Few traits could be related to tolerance to yield loss. Suppressive ability can be ascertained early in the growing season, but the relationship with individual traits can change direction, possibly depending on the availability of belowground resources. Generally, earlier maturity and a conserved tillering strategy appears to be more suppressive. Cultivar choice is largely compatible with delayed sowing and increased sowing date. The effect of environmental variability on relationships between traits and competitive ability requires further investigation before they can be employed as predictors, particularly in the context of belowground competition.

Although semi-natural grasslands in Europe are declining there is often a time delay in the local extinction of grassland species due to development of remnant populations, i.e., populations with an extended persistence despite a negative growth rate. The objectives of this study were to examine the occurrence of remnant populations after abandonment of semi-natural grasslands and to examine functional traits of plants associated with the development of remnant populations. We surveyed six managed semi-natural grasslands and 20 former semi-natural grasslands where management ceased 60-100 years ago, and assessed species response to abandonment, assuming a space-for-time substitution. The response of species was related to nine traits representing life cycle, clonality, leaf traits, seed dispersal and seed mass. Of the 67 species for which data allowed analysis, 44 species declined after grassland abandonment but still occurred at the sites, probably as remnant populations. Five traits were associated with the response to abandonment. The declining but still occurring species were characterized by high plant height, a perennial life form, possession of a perennial bud bank, high clonal ability, and lack of dispersal attributes promoting long-distance dispersal. Traits allowing plants to maintain populations by utilizing only a part of their life cycle, such as clonal propagation, are most important for the capacity to develop remnant populations and delay local extinction. A considerable fraction of the species inhabiting semi-natural grasslands maintain what is most likely remnant populations after more than 60 years of spontaneous succession from managed semi-natural grasslands to forest.

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The ornamental industry has become an important economic force in recent years, in the UK alone this industry is estimated to be around £2.1 billion, while the international trade is around £60-75 billion (Chandler and Tanaka, 2007). The continued success of the floriculture industry depends on the introduction of new species/cultivars with major alterations in key agronomic characteristics, such as resistance to pathogens, novel flower colour and patterns or control of male fertility. Lilium, one of the most important bulbous ornamental crops, is an attractive and popular cut flower. However, the production of vast quantities of pollen that stains easily and is toxic to animals is not always desirable. The control of pollen release without affecting the appearance of the flower is therefore an important breeding goal. Lilium is also susceptible to several fungal pathogens, including Botrytis cinerea, which infects leaves, stem and flowers leading to a reduction of yield. New cultivars have tended to rely upon selective breeding as a mechanism for trait development. However approaches that utilise transgenes to manipulate traits of interest provide alternative opportunities for the ornamental industry provided that transformation and regeneration can be achieved efficiently. A rapid, highly efficient and reproducible Agrobacterium-mediated transformation for Lilium has been developed. Successful transient GUS expression in callus, shoots and basal plate discs was achieved using A. tumefaciens strain AGL1 containing plasmid pBI121 harbouring intron-containing GUS and NPTII genes in cultivars "Beverly's Dream", "Star Gazer", "Night Flyer", "Acapulco", "Sweet Surrender" and Lilium leichtlinii. Based on the same transformation protocol, transgenic plants of cv. "Star Gazer" overexpressing the RCH10 chitinase gene from rice were generated. In vitro sporulation assays of these plants showed different levels of resistance to Botrytis cinerea correlated to the level of relative expression of the transgene. This is the first report of induced pathogen resistance in any Lilium cultivar by transgenic approach. Experiments were also conducted to modify fertility and pollen release in Lilium by translating regulatory gene information from Arabidopsis to Lilium. Transgenic plants of cv. "Star Gazer" either overexpressing or silencing the AtMYB26 gene, were generated. RNAi lines showed a delay in anther dehiscence suggesting that pollen development pathways could be conserved between Arabidopsis and Lilium. In addition, partial sequences of the putative orthologues of AtMS1 and AtMYB26 in Lilium were identified and cloned for future research.

Wheat is the third most widely consumed crop after rice and maize globally. The Green Revolution increased the Indian wheat production tremendously since the 1960s using semi-dwarf wheat varieties and subsequent trait-based breeding under non-hostile soils. In addition to grain yield, wheat is an important source of dietary zinc (Zn) and other mineral elements in many countries. Dietary Zn deficiency is widespread, especially in developing countries, and there are wide scale efforts to breed wheat with increased grain Zn concentrations in South Asia. It is not clear if further grain yield and quality traits such as grain Zn concentration improvements can be sustained due to 1) narrow genetic diversity in modern wheat, and 2) limited land availability e.g., many soils are marginal due to salinity, alkalinity, acidity and mineral nutrient imbalances. The first aim of this thesis was to quantify grain yield and yield components, including juvenile root traits, and grain Zn concentration of a panel of 36 Indian diverse wheat genotypes to explore the potential for site specific trait selection for hostile soils and characterise the baseline effect of genotype (G), site (E), and genotype x site interaction (G*E) under a wide range of soil conditions. Mean grain yields ranged from 1.0 to 5.5 t ha-1 at hostile and non-hostile sites, respectively. G*E interactions affected many yield and component traits, which support the value of site-specific traits selection for hostile soils. The mean grain Zn concentration of 36 genotypes ranged from 25 to 35 mg kg-1. Despite a relatively small overall contribution of G to the overall variation in grain Zn concentration, biofortifying wheat through breeding is likely to be effective at scale given that some genotypes (e.g. Kharchia 65) performed consistently across diverse soil types. Root angle and lateral root traits were associated with grain yield and some mineral composition traits. The second aim of this thesis was to study the performance of eight amphidiploids derived from Thinopyrum bessarabicum, a tall wheat grass, for yield, yield components and grain Zn concentration under saline soils. Reduction in GYD in amphidiploids were less than in Indian genotypes under saline soils and grain Zn concentration ranged from 36-43 mg kg-1. The third aim of this thesis was to explore wild wheat relatives, non-relatives and their derivatives to increase the genetic diversity for grain Zn concentration. The mean grain Zn concentration of 225 wild wheat accession ranged from 47 to 178 mg kg-1. Notably, Amblyopyrum muticum, derived amphidiploids and double haploid lines could be useful sources of grain Zn variation that can be used in breeding programmes to increase the grain Zn concentration in modern wheat varieties to alleviate the dietary Zn deficiency.

The dynamics of a plant-pathogen interaction vary both within and among species. Both spatial structuring and specific genetic and life-history characteristics will affect the interaction and the outcome of a potential co-evolution between the two organisms. In this thesis I have studied the interaction between the wild perennial herb Silene dioica and its automictic, obligate anther smut Microbotryum violaceum MvSd. From the plant perspective, I have examined different aspects of biochemical resistance in S. dioica to M. violaceum MvSd. From the pathogen perspective, I have focused on the breeding system of M. violaceum MvSd and its connection to fitness and distribution of genetic diversity. I have used varying methods; glasshouse trails involving inoculation of plants with the pathogen, classical Mendelian analysis involving controlled crosses between plants, microscopic studies of spores and molecular DNA-analysis. With the results I demonstrate that resistance to M. violaceum MvSd in S. dioica can be specific to the attacking pathogen strain and also spatially highly diverse both within and among populations within a metapopulation. Together, these factors are likely to delay the establishment of the disease within host populations and reduce the spread and amount of disease, once it has been established. The results also suggest that the specific resistance expressed against two different M. violaceum MvSd strains were determined by separate gene systems and that, in both cases, the resistance was simply inherited. This implies a potential for relatively rapid response to M. violaceum-induced selection in S. dioica populations variable for resistance. My results also show that automixis clearly is the predominating breeding system of M. violaceum MvSd, similarly to what earlier has been shown for M. violaceum MvSl. Furthermore, I found lower levels of neutral genetic diversity in M. violaceum MvSd in the northern parts of Sweden, compared to what has been found in populations in more southern Europe. This result is consistent with predictions that populations in the outer regions of a species distribution have lower levels of genetic variation. Moreover, populations were highly differentiated in northern Sweden, which could have been generated by high selfing rates, genetic drift and high population turnover rates, all factors that coincide with life-history and ecology of M. violaceum MvSd. However, despite the general low variability in neutral genetic markers, I did find variation in fitness related traits, both within and among populations, as well as differences in infection ability between strains, suggesting there is a potential for co-evolution between S. dioica and M. violaceum MvSd in the area. To summarize, this thesis reflect a plant-pathogen system that is highly influenced by constant colonisation-extinction dynamics, which is likely to have influenced both the genetics of resistance in the plant and the breeding system of the pathogen and thus also the interaction between the two organisms.

Mediterranean-type ecosystems (MTEs) are among the most vulnerable to land use and climate change and many attempts are in place to restore these ecosystems. Therefore, it is necessary to assess differences in plants’ ability to withstand water-stress, including biotic interactions. Such knowledge helps us understand community assembly, which is crucial for ecological intervention. This study involved: (1) reviewing the literature on traits that can differentiate functional types; (2) adapting the methodology to measure leaf water potential at turgor loss point (πtlp) for small-leaved species; (3) using these traits to quickly identify water-use strategies of adult plants from Southwest Australia; (4) identifying the water-use strategies that juveniles have to survive first summer drought; and (5) determining whether there is facilitation between a deep-rooted species and seedlings through hydraulic redistribution. The selection of functional response traits was based on their association with water-stress, with effect traits, and on methodologies that are easy, inexpensive and applicable for Mediterranean species. Relevant traits were identified from the literature, including: leaf carbon isotope composition, leaf nitrogen and phosphorus contents, leaf mass per area, πtlp, and xylem vessel morphology. Measurements of πtlp through osmometry of extracted sap and through Pressure-volume curves were compared. Selected traits were then measured for 15 species from different eco-hydrological habitats. Drought resistance of juveniles was assessed by measuring water relations, rooting depth/pattern and carbon reserves use of species from different eco-hydrological habitats. Lastly, seedlings were grown isolated or near donor plants. Water status and growth were measured, and stable isotopes were used to investigate water pathways within and between plants. A strong correlation between the methodologies for measuring πtlp was found. With analysis of these traits, it was possible to cluster adult species, from the Swan Coastal plain, into five functional groups that corresponded to their rooting depths. During drought, Banksia seedlings reduced stomatal conductance and appeared to use carbon reserves, whereas Gompholobium tomentosum seedlings tolerated higher water deficits, despite reduced stomatal conductance. Lastly, although seedlings were able to absorb hydraulically redistributed water, they grew, transpired and survived more when isolated from the deep-rooted plant. In the literature review, theoretical analyses on functional traits and speculations on functional groups were made through a conceptual diagram. The osmometry technique is a suitable replacement for Pressure-volume curves since its estimations of πtlp were accurate in small and large-leaved species. The functional traits approach can be transferable to other MTEs for application by restoration practitioners, as the traits selected were effective in determining functional groups, and were relatively easy and cost effective. The seedlings’ responses to summer drought were consistent with their habitats and root-depth, which is an important factor for niche differentiating and community assembly. Competition between seedlings and deep-rooted plants supported the updated stress-gradient hypothesis. In conclusion, analyses of water-use strategies of Mediterranean species during summer allow predictions of differences in drought resistance. When this functional approach is applied for ecological intervention, restoration practitioners can select species with a better match to future environmental conditions of MTEs, particularly in large species sets.

The evolution of disease resistance in plants occurs within a framework of interacting phenotypes, balancing natural selection for life-history traits along a continuum of fast-growing and poorly defended, or slow-growing and well-defended lifestyles. Plant populations connected by gene flow are physiologically limited to evolving along a single axis of the spectrum of the growth-defense trade-off, and strong local selection can purge phenotypic variance from a population or species, making it difficult to detect variation linked to the trade-off. Hybridization between two species that have evolved different growth-defense trade-off optima can reveal trade-offs hidden in either species by introducing phenotypic and genetic variance. Here, I investigated the phenotypic and genetic basis for variation of disease resistance in a set of naturally formed hybrid poplars. The focal species of this dissertation were the balsam poplar (Populus balsamifera), black balsam poplar (P. trichocarpa), narrowleaf cottonwood (P. angustifolia), and eastern cottonwood (P. deltoides). Vegetative cuttings of samples were collected from natural populations and clonally replicated in a common garden. Ecophysiology and stomata traits, and the severity of poplar leaf rust disease (Melampsora medusae) were collected. To overcome the methodological bottleneck of manually phenotyping stomata density for thousands of cuticle micrographs, I developed a publicly available tool to automatically identify and count stomata. To identify stomata, a deep con- volutional neural network was trained on over 4,000 cuticle images of over 700 plant species. The neural network had an accuracy of 94.2% when applied to new cuticle images and phenotyped hundreds of micrographs in a matter of minutes. To understand how disease severity, stomata, and ecophysiology traits changed as a result of hybridization, statistical models were fit that included the expected proportion of the genome from either parental species in a hybrid. These models in- dicated that the ratio of stomata on the upper surface of the leaf to the total number of stomata was strongly linked to disease, was highly heritable, and wass sensitive to hybridization. I further investigated the genomic basis of stomata-linked disease variation by performing an association genetic analysis that explicitly incorporated admixture. Positive selection in genes involved in guard cell regulation, immune sys- tem negative regulation, detoxification, lipid biosynthesis, and cell wall homeostasis were identified. Together, my dissertation incorporated advances in image-based phenotyping with evolutionary theory, directed at understanding how disease frequency changes when hybridization alters the genomes of a population.

Wheat (Triticum aestivum L.) grain yield potential is generally sink-limited under favourable conditions with grain growth limited mainly by the number of grains formed per unit area. In the CIMMYT program in NW Mexico, novel large-ear phenotype traits (e.g. high assimilate partitioning to ear, high fertile florets ear-1) have been developed and may offer scope for increasing grain number per unit area (Gaju et al., 2009). In this study, ear fertility traits and their genetic regulation were investigated in backcross lines derived from novel large-ear doubled-haploid lines (UK Rialto x novel large-ear CIMMYT L14 line cross) backcrossed into either UK spring wheat Ashby or UK winter wheat Humber. Forty four BC3 near isogenic lines (NILs) (7 spring and 37 winter wheat NILs, currently BC3S5 and BC3S6) and 34 BC1S7 lines (18 spring and 16 winter wheat NILs, currently BC1S7) and their recurrent parents (Ashby or Humber, respectively) were chosen for physiological analysis in field experiments at University of Nottingham, UK and KWS, Thriplow, Hertfordshire, UK for evaluating novel variation for ear fertility traits and grain yield and specific introgressed target QTL on ear fertility traits and grain yield in 2012/13 and 2013/14. In highest/lowest performing BC3 spring NILs, above ground dry matter (AGDM) per main shoot increased by 97%, grain dry weight (GDW) ear-1 by 95% and grain number (GN) ear-1 by 68%, but grain yield was decreased by 71% associated with fewer ears m-2 (-87%) compared to the Ashby recurrent parent. For BC3 winter NILs, results showed that there was variation above Humber, for grain yield 100% DM (+22%), grains m-2 (+16%), harvest index (HI) (+6%), spikelets ear-1 (+14%), fertile spikelets ear-1 (+15%), rachis length (cm) (+24%) and thousand grain weight (TGW) (g) (+21%) (P<0.10). In the experiment at KWS Thriplow, the effects of the Tin1A gene in pairs of BC1S7 NILs contrasting in tiller number were investigated in the Ashby and Humber backgrounds. Amongst five pairs of spring NILs contrasting for the tiller inhibition Tin1A locus, the Tin1A lines were reduced in tillers m-2 (-16%), grain yield (-9%) and ears m-2 (-19%) but increased in spikelets ear-1 (+12%). In two pairs of winter NILs contrasting for the Tin1A locus, the Tin1A lines reduced tillers m-2 (-18%), grain yield (-6%), ears m-2 (-16%) but increased GN ear-1 (+20%), spikelets ear-1 (+11%) and GN spikelets-1 (+6%). The extent of tiller reduction was overall too severe in the spring NILs with Ashby background to lead to increased yield in the lines carrying the L14 allele. In winter NILs, grain yield and biomass were increased with high canopy green area and better maintenance of green area during grain filling. This suggested grain growth may have been partly limited by source supply of assimilate during grain filling possibly during the latter stages of grain filling. A strong relationship between individual grain weight and rate of grain filling was consistent in BC3 spring NILs. Grain weight was increased in BC3 winter NILs with increasing rate of grain filling but duration of grain filling was decreased. DNA samples from each BC3S5 line were screened using 8 SSR markers for the introgressed ear fertility QTLs identified in the Rialto x CIMMYT L14 DH population. The genotyping results showed the CIMMYT L14 allele for a novel QTL on chromosome 3A was associated with increases in ear fertility traits (grain number ear-1, spikelets ear-1, and grain DM shoot-1) amongst the BC3S5-6 lines when compared to the Humber recurrent parent and confirmed the presence of Tin1A gene in the Ashby background determining ear fertility and grain yield effects.

The aim of the work presented in this thesis was to assess the genetic variation present within the wild tomato species Solanum pennellii that can be adapted to improve the texture of the domesticated tomato species. Using a population of S. pennellii introgression lines, 23 significant QTL supporting intervals were identified. Nine of the QTL were significant in two growing seasons. Three QTL were identified for pericarp firmness. Lines containing the firmness QTL F-Sp 2.1 were used to create BC1 populations. Sensory analyses were used to correlate the instrumental texture measurements to those perceived during mastication. Repeated texture measurements were conducted on lines representing similar chromosomal regions from another wild tomato species Solanum habrochaites introgression line population. To better understand the genetic basis of one of the firmness QTL identified, the Syngenta tomato Affymetrix GeneChip was used to quantify the differential expression of S. pennellii genes within the QTL-introgression line through development in comparison to the recurrent parent S. lycopersicum L. cv M82. The microarray analyses were extended to the ripening mutants Cnr, nor and rin. Differential gene expression between the ripening mutants and the wild type Ailsa Craig were compared through development. Candidate genes for the firmness QTL and fruit development were nominated.

Les interactions entre organismes ont des conséquences majeures sur la composition des communautés et le fonctionnement des écosystèmes. En écologie l'étude des interactions négatives, telles que la prédation et la compétition, a largement dominé la littérature. Des travaux récents ont souligné l’importance des interactions positives dans la nature, telles que la facilitation, mais ces interactions restent malgré tout peu intégrées dans les théories contemporaines en écologie. Cette thèse s’inscrit dans cette démarche et aborde deux questions centrales : (i) Comment la facilitation indirecte (via la protection contre le pâturage) affecte-t-elle la structure fonctionnelle (caractéristiques des distributions de traits) des communautés de plantes ? (ii) L'effet net des interactions facilitatrice-bénéficiaire identifiées à l’échelle d’une paire d’espèces restent-elles valides en présence d’une communauté entière d'espèces bénéficiaires potentielles ? Deux expérimentations in situ dans des environnements contrastés ont été mises en place : l’exclusion du pâturage dans des tourbières tropicales alpines et une transplantation de communautés de plantules sous des plantes adultes en milieu méditerranéen semi-aride. Nous avons montré que la facilitation indirecte affectait les caractéristiques du filtre environnemental, la dominance des espèces et la différenciation de niche au sein de la communauté. Nos travaux suggèrent également que la composition des communautés de plantules modifie les interactions adultes-plantules, remettant ainsi en cause la possibilité d’extrapolation des résultats entre paires d'individus à l’échelle de la communauté
Interactions between organisms are key drivers of community composition and ecosystem functioning. Ecology has a long history of studies on negative interactions, such as predation and competition. Recent studies have highlighted the importance of positive interactions, such as facilitation in nature. The integration of these interactions into modern ecological theory has nonetheless lagged behind. This thesis aims at contributing to this research effort and addresses two core questions : (i) How does indirect facilitation (through protection against grazing) affect the functional structure (characteristics of trait distributions) of plant communities? (ii) Does the net effect of the interactions between a species pair (benefactor-beneficiary) remain valid in the presence of several beneficiary species at community level? We set up two insitu experiments in contrasted environments: a grazing exclusion experiment in tropical alpine peatlands and a transplantation experiment of sapling communities beneath adult plants in a mediterranean environment. Our results showed that indirect facilitation affects the characteristics of the environmental filter, species dominance and niche differentiation in the community. Our results also suggested that the composition of sapling communities modifies adult-sapling interactions, thereby questioning the possibility of extrapolating results from pairs of individuals to the community scale

Oil palm (Elaeis guineensis) produces over five times more oil/year/hectare than oil seed rape and accounted for 33% of world vegetable oil production in 2011. Being a cross-pollinated perennial tree crop with long breeding cycles (typically 12 years) and a large planting area requirement (usually 143 palms/hectare), utilization of molecular technology could greatly improve the efficiency of oil palm breeding. In the present study, various approaches were used to develop molecular markers for genetic linkage mapping and QTL analysis, with the ultimate goal of marker-assisted selection in oil palm. Firstly, Representational Difference Analysis (RDA) and Amplified Fragment Length Polymorphism (AFLP) were coupled with Bulked Segregant Analysis (BSA) to try to identify marker(s) closely linked to the important shell-thickness gene. A novel combination of RDA with Roche 454 pyrosequencing enabled a more comprehensive study of the enrichment profiles compared to Sanger sequencing. Identification of >35% redundant sequences, repetitive sequences and organelle DNA suggested that subtractive hybridization and target enrichment of RDA were inefficient here, with the lack of elimination of common sequences masking the real difference products. The use of the AFLP method identified 29 primer pairs that yielded 49 putative shell-thickness related-polymorphic bands. A detailed analysis will need to be carried out to fully evaluate and validate these markers. The use of the relatively new Diversity Array Technology “Genotyping-By-Sequencing” (DArTSeq) platform through genotyping of two closely-related tenera self-pollinated F2 populations, 768 (n=44) and 769 (n=57), generated a total of 11,675 DArTSeq polymorphic markers of good quality. These markers were used in the construction of the first reported DArTSeq based high-density linkage maps for oil palm. Both genetic maps consist of 16 major independent linkage groups (total map length of 1874.8 and 1720.6 cM, with an average marker density of one marker every 1.33 and 1.62 cM, respectively), corresponding well with the 16 homologous chromosome pairs of oil palm (2n = 2x = 32; 14/16 chromosomes were confirmed by known location SSR markers). Preliminary quantitative trait loci (QTL) mapping of the yield and vegetative growth traits detected four significant and 34 putative as well as two significant and 30 putative QTLs for these small 768 and 769 populations, respectively. No common significant QTL were detected between the two closely-related controlled crosses which could have allowed combination of QTL across the two populations. Saturation of the shell-thickness (Sh) region with all available DArTSeq markers, as well as map integration around the Sh regions for both populations, identified 32 Single Nucleotide Polymorphism (SNP) and DArT markers mapped within a 5 cM flanking region of the Sh gene. Homology search of the DArTSeq marker sequence tag (64 bp) against the recently published oil palm genome assembly confirmed that 23 out of the 32 (72%) DArTSeq markers were located on the p5_sc00060 scaffold in which the SHELL gene was identified. The identified shell-thickness markers could be useful as molecular screening tools. This study demonstrated the potential and feasibility of using genomic resources available for genetic improvement of oil palm breeding programmes.

Species assembly into local communities from the surrounding region can be caused either by species failure to reach the site (i.e. seed limitation) or to establish (i.e. establishment limitation). The aim of this thesis was to investigate plant species assembly and to determine the relative importance of different factors in that process. In a cultivated landscape in southeast Sweden, plant community assembly was studied in grazed ex-arable fields. Community assembly from the surrounding region into the local community was explored using trait-based null models and seed sowing and transplanting experiments. The influence of local environmental factors and landscape history and structure on community assembly was also studied. In addition, differences in species assembly between ex-arable fields and semi-natural grasslands were explored. Seed limitation was the strongest filter on local community assembly. Only a fraction (36%) of species in a region dispersed to a local site and adding seeds/transplants increased species establishment. Species abundance at the regional scale, species dispersal method and seed mass strongly influenced which species arrived at the local sites. Establishment limitation also affected the assembly. Of species arriving at a site 78% did establish, seedling survival was low and which species established was influenced by species interactions, local environmental conditions and stochastic events. In addition, landscape structure that determined the species richness in the regional species pool influenced the local assembly. The comparison between assembly in ex-arable fields and semi-natural grasslands indicated that the main cause of difference in species assembly between them was difference in their age. The main conclusion of this thesis is that regional processes are more important than local factors in determining plant community assembly.

At the time of the doctoral defense, the following papers were unpublished and had a status as follows: Paper 3: Submitted. Paper 4: Submitted. Paper 5: Manuscript.

Winter wheat (Triticum aestivum L.) is one of the mostly widely grown arable crops worldwide, with a total annual global production of approximately 716 million tonnes. In the UK, around 14.5 million tonnes of wheat is produced annually on roughly 1.8 million hectares of land; however, 15-30% of this annual wheat yield production is lost to drought. Two field experiments were conducted in 2013-14 and 2014-15 to characterise a doubled-haploid (DH) population of 94 lines derived from a cross between the winter wheat cultivars, Rialto and Savannah, at the University of Nottingham Sutton Bonington Campus, UK (52o 50' N, 1o 15' W). This population was selected due to the genetic variation observed in previous field experiments in stay-green traits under drought and nitrogen stress in the UK and France (Foulkes et al., unpublished). A shovelomics methodology was developed for phenotyping wheat crown root traits of the mapping population and validation on soil core samples (extraction of roots by washing and root scanning using WinRHIZO software) was carried out on a subset of 14 DH lines and the two parents. In addition, two 50-cm soil column glasshouse experiments examining the two parental genotypes and the subset of 14 Rialto x Savannah DH population lines, and one 100 cm soil column glasshouse experiment examining the two parental genotypes and two Rialto x Savannah DH lines using micro-computed tomography (μCT) scanning, were carried out under well-watered and drought conditions. Two further glasshouse experiments were carried out to quantify root anatomical traits on the two parental genotypes under well-watered and drought conditions. The main objectives were to quantify genetic variation in root traits and associations with water uptake and drought tolerance in the Rialto x Savannah doubled-haploid population, to quantify mechanisms underlying associations between root traits and water capture and drought tolerance and to identify quantitative trait loci (QTL) associated with root traits and drought tolerance through genetic analysis in the Rialto x Savannah DH population. In the field experiments, drought reduced grain yield by 16.7% in 2014 and 14.9% in 2015. Amongst the DH lines, genetic variation for crown root angle, roots plant-1, roots shoot-1 and length was observed (p < 0.05). Under unirrigated conditions, root length density (RLD) at depth (40-60 cm) was positively associated with crown root angle and crown roots shoot-1 in 2014 and 2015. RLD at depth was also positively correlated with grain yield. Amongst the 94 R x S DH lines, crown root angle (greater angle = steeper root) and crown roots shoot-1 were positively associated with post-anthesis canopy stay-green as indicated by the Normalised Difference Vegetation Index (NDVI) spectral reflectance index and grain yield under unirrigated conditions. Later onset and end of flag-leaf senescence were associated with increased grain yield in 2014, but not in 2015. In the x-ray μCT soil column experiment, there were positive relationships amongst genotypes between steeper crown root angle at 5, 10 and 15 cm depths measured using μCT and RLD at 60-80 cm depth measured directly (WinRHIZO root scanning) under drought, but negative relationships under well-watered conditions. RLD at 60-80 cm was associated with water uptake and number of grains plant 1 under drought. There were positive associations between the total root length plant-1 measured using μCT and direct measurement of this trait (WinRHIZO root scanning) and between μCT root number and direct measurement of RLD in each soil horizon. In addition, there were associations between root angle in the μCT soil column experiment and crown root angle in the field measured using shovelomics techniques. Under drought, root cortical aerenchyma, the ratio of total stele area: total cortical area and cortical cell size were found to increase and total cortical area, cortical cell file number, xylem area and metaxylem area to decrease in the parental lines. Each of these anatomical traits was related to improved water uptake under drought. This indicated that root traits that may reduce the metabolic cost of soil exploration, or decrease water loss, may improve the acquisition of limiting soil resources under water-stressed conditions. For the QTL analysis in the Rialto x Savannah DH population, co-locating QTL for crown root angle and NDVI, HI and AGDM were identified under irrigated or unirrigated conditions in individual years on chromosomes 3B and 7A. QTL for stay green traits under both irrigated and unirrigated conditions were identified on chromosome 7D. Overall, these results indicated the potential for designing a winter wheat ideotype to enhance drought tolerance under UK drought with steeper crown root angle, increased crown roots shoot-1 and anatomical traits related to decreased metabolic cost, all of which increase RLD at depth, thereby improving water uptake at depth. Results from the shovelomics crown root assessments indicated scope for high-throughput field root phenotyping to quantify responses of crown root traits under drought and validate the relationship with root traits at depth, and identify QTL and candidate genes linked to these traits.

The research presented here focuses on the functional aspect of biodiversity of plant communities, with emphasis placed on the functions of species within biological communities and ecosystems, rather than their identity. The prominence of plant functional traits as major contributors to ecosystem functioning is based on underlying mechanisms whereby individual species interact with each other and with their abiotic environment to influence ecological processes on different spatial scales. In this study, particular attention is given to the modulating effects of functional diversity and composition on community dynamics and ecosystem processes (e.g., soil processes relevant to the cycles of carbon and nitrogen), as well as its response to disturbance. A number of green leaf functional traits considered to be pertinent to soil processes and the biogeochemical cycles of carbon and nitrogen were measured from vascular plant species growing in lowland fens in East Anglia, UK. Such habitats are widely recognised as areas of high conservation value for providing numerous benefits to society, including nutrient cycling and soil carbon storage. The set of analyses presented here reveals the implications of different degrees of management intervention for the functional composition of lowland fen plant communities. Overall, the functional diversity of such communities were found to respond strongly to changing disturbance intensity, to significantly interact with abiotic factors to contribute to the provision of ecosystem processes and to exert major effects on species coexistence within plant assemblages. These results confirm the wide applicability of the trait approach when investigating the effects of biodiversity on the stability of biological communities and ecosystems, and is potentially informative to conservation focused projects that aim to simultaneously enhance biodiversity and the provision of vital ecosystem services. In fact, management intervention was largely found to favour species with a set of traits conducive to enhancing soil carbon storage, lending support to current long term conservation projects that aim to positively influence soil carbon balance.

Fusarium head blight (FHB) is a devastating fungal disease of wheat and other small grain cereals worldwide caused by a complex of toxigenic Fusarium spp. and non-toxigenic Microdochium spp. Infection leads to a reduction of grain yield, loss of grain quality and the production of harmful mycotoxins. Control methods for FHB include both cultural and chemical strategies, however the development of cultivars with improved FHB resistance is considered as the most sustainable method for controlling the impact of this disease. Resistance to FHB is a polygenic trait and can be improved by stacking multiple resistance genes together, however there are currently no highly FHB resistant genotypes with acceptable agronomic characteristics available, therefore passive disease resistance can potentially make significant contributions to improved FHB resistance. The aim of this study was to identify novel physiological traits in wheat conferring passive resistance to FHB using ground inoculated field experiments to enable disease escape mechanisms to be expressed, and spray inoculated glasshouse experiments to test if the identified traits were associated with genetic resistance. The most consistent traits relating to FHB were flag leaf length, plant height and awn length. Since these relationships were present in both field and glasshouse experiments, they are likely caused by a genetic linkage or pleiotropy, with genes conferring FHB resistance or susceptibility. Remaining leaf area was less consistently related to FHB, however, since canopy leaf area showed a positive relationship with the development of FHB in ground inoculated field experiments, there is a basis to support the role of reduced canopy leaf area as conferring passive resistance to FHB. In general, relationships were poor between visual FHB symptoms and both pathogen DNA and grain mycotoxin contamination. This was theorised to be due to the use of a mixed species inoculation which introduced antagonism between FHB species and which included more than one producer of several mycotoxins quantified. Therefore the use of visual FHB assessments under mixed species inoculation is concluded to be a poor indicator of both pathogen infection and mycotoxin contamination.

Thesis (MSc)--Stellenbosch University, 2012.
ENGLISH ABSTRACT: Plant growth promoting substances (PGPS) are emerging as useful tools in the investigation of important plant growth traits. Two PGPS, smoke-water derived from burning plant material and a synthetic strigolactone analogue, GR24, have been reported to regulate a wide variety of developmental and growth processes in plants. These PGPS are beginning to receive considerable attention in the area of improving plant biomass yield and production. Variation in growth between plants is a major impediment towards the complete understanding of the intrinsic processes that control biomass production. Callus cultures of the model plant Arabidopsis thaliana could overcome some of these hindrances. However, the suitability of these callus cultures as a model system for plant biomass production must be established first. This study aimed at using A. thaliana callus cultures as a platform to study the plant growth promoting activities of smoke-water and GR24. The first part of this study was conducted to develop an optimal protocol for inducing A. thaliana callus formation. Wild-type A. thaliana Col-O, as well as strigolactone deficient and insensitive mutants (max1-1, max2-1, max2-2, max3-9 and max4-1) were cultured for callus induction. Hypocotyl and leaf explants were cultured onto MS media supplemented with different hormone concentrations of 2,4-D and kinetin (2:2 mg/L 2,4-D:kinetin and 0.5:0.05 mg/L 2,4-D:kinetin). Both media proved suitable for callus induction of all genotypes, with max1-1 showing the highest efficiency (83.33% and 92.22%) of callus induction. Calli were then used as a platform for future investigations into the effects of smoke-water and GR24. Secondly, this study examined the effects of smoke-water and GR24 on wild-type A. thaliana Col-O callus. Basic physiological studies were conducted to determine if these two compounds would positively affect callus growth, as was shown in previous studies using whole plants. Calli cultivated on MS media containing the two different hormone concentrations were transferred onto the same fresh MS medium, supplemented with either smoke-water or GR24. Growth promotion by smoke-water and GR24 in calli was characterized by a significantly increased mass (biomass). Calli were additionally transferred onto MS medium containing either auxin only or kinetin only and supplemented with GR24 or smoke-water. In the auxin only system, increased mass was recorded for both GR24 and smoke-water treatments, while these two compounds seemed to reduce growth in the kinetin only system. The positive growth stimulatory effect observed for the auxin only system could be attributed to the synergistic relationship between auxin and strigolactones, whilst the reduced mass in the latter system could be due to the antagonistic interaction between strigolactones and cytokinins. Finally, this study has discovered a dual role of strigolactones in biomass accumulation and adventitious root formation for Arabidopsis thaliana callus. On an auxin- and cytokinin-free MS medium supplemented with GR24, calli of Arabidopsis thaliana strigolactone deficient mutants (max1-1 and max4-1) and the wild-type Col- O, but not the strigolactone response mutant (max2-2), showed enhanced biomass accumulation. In addition to this, the max4-1 mutant and wild-type Col-O demonstrated enhanced adventitious rooting, which was not apparent in max2-2. Together these data suggested that the biomass accumulation and the adventitious rooting activities of GR24 in Arabidopsis thaliana calli are controlled in a MAX2- dependent manner. The interaction between strigolactone, auxin and cytokinin signalling pathways in regulating these responses appears to be complex. Gene expression profiling showed regulation of stress-related genes such as B-box transcription factors, CALCINEURIN B-LIKE and RAP4.2 Genes encoding hormones associated with stress (ABA, ethylene) and defence mechanisms (JA) were upregulated. Expression of stress related genes indicated clues on some kind of stress mediation that might be involved during the regulation of the rhizogenic response. Conversely, smoke-water treatment could not enhance the biomass of the calli and nor could it induce adventitious rooting in the absence of auxin and cytokinin. This observation strongly emphasized the distinct roles of these two compounds, as well as the importance of the interaction and ratio of auxin and cytokinin in callus growth. This study has demonstrated a novel role of strigolactones in plant growth and development, i.e. enhancement of biomass production in callus cultures. Secondly the enhanced adventitious rooting ability is in agreement with recently published literature on the role of strigolactones in regulating root architecture. In vitro callus production is advantageous to plant sciences. It creates an opportunity for increasing plant material for cultivation and offers the use of cell cultures that accurately mimic specific growth responses. It could greatly contribute to the study of intricate regulatory and signalling pathways responsible for growth and development in plants. Because the regulation of plant biomass production is very complex and the molecular mechanisms underlying the process remain elusive, it is of paramount importance that further work be done in order to gain more in-depth insights and understanding of this aspect and subsequently improve efficiency and returns when applying biotechnology tools on commercially important crop plants.
AFRIKAANSE OPSOMMING: Verbindings wat plantgroei bevorder (PGBV) het as nuttige alternatief ontstaan om plant groei te ondersoek. Rook-water, afkomstig van verbrande plant material, en ‘n sintetiese strigolaktoon analoog, GR24, wat ‘n α, β-onversadigde furanoon funksionele groep in gemeen het, is vir die regulering van ‘n wye verskeidenheid ontwikkelings- en groei prosesse in plante verantwoordelik. Tans ontvang hierdie PGBVs aansienlik aandag in die area van die verbetering van plant biomassa opbrengs en -produksie. Die variasie in groei tussen plante is ‘n groot hindernis om die intrinsieke prosesse wat biomass produksie beheer, volledige te verstaan. Deur gebruik te maak van kallus kulture van die model plant Arabidopsis thaliana kan van hierdie hindernisse oorkom word. Tog moet die geskiktheid van kallus kulture as ‘n model sisteem vir plant groei biomass produksie eers gevestig word. Die doel van hierdie studie was om A. thaliana kallus kulture as ‘n platform vir die studie van die plantgroei bevorderingsaktiwiteite van rook-water en GR24 te gebruik. Die eerste deel van die studie is uitgevoer ten einde ‘n optimale protokol vir die induksie van A. thaliana kallus produksie te ontwikkel. Wilde tipe Col-0, asook strigolaktoon afwesige en onsensitiewe mutante (max1-1, max2-1, max2-2, max3-9 en max4-1) is vir kallus induksie gekultiveer. Hipokotiel en blaar eksplante is op MS medium wat verskillende hormoon konsentrasies van 2,4-D en kinetien (2:2 mg/L 2,4-D:kinetien en 0.5:0.05 mg/L 2,4-D:kinetien) bevat, oorgedra. Beide media was geskik vir kallus induksie van al die genotipes, met max1-1 wat die hoogste effektiwiteit (83.33% en 92.22%) van kallus induksie getoon het. Kalli is daarna as ‘n platform vir toekomstige navorsing i.v.m die effek van rook-water en GR24 gebruik. Tweedens ondersoek die studie die effek van rook-water en GR24 op wilde tipe Col-0 kallus. Basiese fisiologiese studies is uitgevoer om te bepaal of die twee verbindings ‘n positiewe effek op kallus groei toon soos aangedui in vorige studies waar intakte plante gebruik is. Kallus wat op MS medium wat die twee verskillende hormoon konsentrasies bevat gekultiveer was, is op dieselfde vars MS medium, wat addisioneel óf rook-water óf GR24 bevat, oorgedra. Die stimulering van groei van kalli deur rook-water en GR24 is deur ‘n merkwaardige toename in massa (biomassa) gekenmerk. Kallus is additioneel op MS medium wat slegs óf ouksien óf kinetin bevat (gekombineer met GR24 of rook-water behandeling), oorgedra. In die sisteem waar slegs ouksien toegedien is, is ‘n toename in massa waargeneem vir beide GR24 en rook-water behandelinge. In teenstelling hiermee, het die twee verbindings in die sisteem waar slegs kinetin toegedien is, ‘n vermindering in groei meegebring. Die positiewe groei stimulerende effek wat waargeneem is vir die sisteem waar slegs ouksien toegedien is, kan toegedra word aan die sinergistiese verhouding tussen die ouksien en strigolaktone; terwyl die verlaagde massa in die laasgenoemde sisteem aan die antagonistiese interaksie tussen strigolaktone en sitokiniene toegedra kan word. Laastens het hierdie studie het ‘n gelyktydige rol van strigolaktone vir biomassa akkumulasie en bywortelvorming in Arabidopsis thaliana kallus ontdek. Kallus van A. thaliana strigolaktoon afwesige mutante (max1-1 en max4-1) en die wilde tipe Col-0 (maar nie die strigolaktoon reagerende mutant (max2-2) het op ‘n ouksien en sitokinien vrye MS medium wat GR24 bevat ‘n verhoogde biomassa akkumulasie getoon. Die max4-1 mutant en wilde tipe Col-0 het verhoogde bywortelvorming getoon, wat nie so opmerklik by max2-2 was nie. Hierdie data het tesame voorgestel dat die biomassa akkumulasie en die bywortelvormingsaktiwiteite van GR24 in Arabidopsis thaliana kallus op ‘n MAX2-afhanklike wyse beheer word. Die interaksie tussen strigolaktoon, ouksien en sitokinien sein transduksie paaie vir die regulering van hierdie reaksies blyk kompleks te wees. Die geen uitdrukkingsprofiel het die regulering van stres verwante gene soos B-boks transkripsie faktore, CALCINEURIN B-LIKE en RAP4.2, getoon. Gene wat vir hormone wat aan stres (ABA, etileen) en verdedigingsmeganismes (JA) verwant is, is opgereguleer. Die uitdrukking van stress verwante gene dui op tekens van ‘n ander tipe stres bemiddeling wat dalk by die regulering van die risogeniese reaksie betrokke kan wees. In teenstelling, rook water behandeling kon nie die kallus biomassa verhoog nie en dit kon ook nie die bywortelingvorming in die afwesigheid van ouksien en sitokiniene induseer nie. Hierdie waarneming is ‘n sterk bevestiging vir die uitsonderlike rol van die twee verbindings, asook die belang van die interaksie en verhouding van ouksien en sitokinine vir die groei van kallus. Hierdie studie toon op ‘n nuwe rol van strigolaktoon in plant groei en ontwikkeling, d.w.s die verhoogde biomassa produksie in kallus kulture. Tweedens, die verhoogde bywortelvormingsvermoë is in ooreenstemming met literatuur wat onlangs gepubliseer is i.v.m die rol van strigolaktone in die regulering van wortel argitektuur. Die in vitro produksie van kallus is voordelig in plant wetenskappe. Dit skep ‘n geleentheid vir die vermeerdering van plant materiaal vir kultivering en bied die gebruik van selkulture wat spesifieke groei reaksies op ‘n merkwaardige wyse akkuraat namaak. Dit kan grootliks bydra tot die studie van die delikate regulatoriese en sein transduksie paaie wat vir groei en ontwikkeling van plante verantwoordelik is. Aangesien die regulering van plant biomassa produksie baie kompleks is en die molekulêre meganismes vir die proses onbekend bly is dit van grootskaalse belang dat meer werk gedoen word om ‘n meer in diepte insig en kennis van die aspekte en gevolglike verbetering van effektiwiteit en wins te kry deur die toepassing van biotegnologiese metodes op die gewas plante wat van kommersiêle belang is.

Wheat (Triticum spp.) is a particularly important crop for food security, providing 20% of worldwide calorie intake. Food production is not meeting the projected global demand of an increase of 2.4% p.a. Improvement of resource capture in wheat could help meet this demand. Nitrogen (N) is an essential macronutrient for plant growth and development; however, nitrogen use efficiency (NUE) for cereal production is only 33%. Domestication of modern varieties of wheat may have lost potentially beneficial agronomic traits, particularly in the root system. Optimisation of root system architecture could profoundly improve nitrogen uptake efficiency (NUpE) and in turn increase the yield potential of the crop. Using ancestral wheat germplasm and mapping populations, desirable traits may be identified and bred back into commercial wheat varieties to increase yield potential. Using a high-throughput hydroponic root phenotyping system, N-dependent root traits have been identified in wheat mapping populations. Using transcriptomic analyses, the gene expression profile of a candidate N-dependent root QTL has been identified. Using a new root phenotyping system, X-ray micro-computed tomography (μCT), a three-dimensional representation of wheat roots can now be imaged in soil. A selection of the same mapping lines have been used for 3D μCT analysis based on field NUpE parameters to identify promising root traits in both seedlings and mature plants.

Master of Science
Department of Biology
Jesse B. Nippert
The Konza Prairie in northern Kansas, USA contains over 550 vascular plant species; of which, few have been closely studied. These species are adapted to environmental stress as imposed by variable temperature, precipitation, fire, and grazing. Understanding which plant traits relate to drought responses will allow us to both predict drought tolerance and potential future shifts in plant community composition from changes in local climate. Morphological and physiological measurements were taken on 121 species of herbaceous tallgrass prairie plants grown from seed in a growth chamber. Gas exchange measurements including maximum photosynthetic rate, stomatal conductance to water vapor, and intercellular CO[subscript]2 concentration were measured. All plants were exposed to a drought treatment and were monitored daily until stomatal conductance was zero. At this point, critical leaf water potential (Ψ[subscript]crit), an indicator of physiological drought tolerance was assessed. Other measurements include root length, diameter, volume, and mass, leaf area, leaf tissue density, root tissue density, and root to shoot ratio. Traits were compared using pair-wise bivariate analysis and principal component analysis (PCA). A dichotomy was found between dry-adapted plants with thin, dense leaves and roots, high leaf angle, and highly negative Ψ[subscript]crit and hydrophiles which have the opposite profile. A second axis offers more separation based on high photosynthetic rate, high conductance rate, and leaf angle, but fails to provide a distinction between C[subscript]3 and C[subscript]4 species. When tested independently, grasses and forbs both showed drought tolerance strategies similar to the primary analysis. Matching up these axes with long term abundance data suggests that species with drought tolerance traits have increased abundance on Konza, especially in upland habitats. However, traits that relate to drought tolerance mirror relationships with nutrient stress, confounding separation of low water versus low nutrient strategies. My results not only illustrate the utility of morphological and physiological plant traits in classifying drought responses across a range of species, but as functional traits in predicting both drought tolerance in individual species and relative abundance across environmental gradients of water availability.

Studies of the inheritance of morphological traits contribute to the understanding of peanut genetics. Investigations of the fertility and cytogenetics of interspecific progenies between Arachis hypogaea and wild Arachis species have provided invaluable information on the phylogenetic relationships within the genus Arachis and on the amphidiploid nature of peanut. However, the inheritance of morphological traits using interspecific progenies has not been elucidated to date. The objective of this study was to identify and to analyze genetic factors controlling growth habit, stem color, root nodulation, and leaflet size in peanut. F1 and F2 progenies were obtained from diallel crosses between A. hypogaea cvs. Argentine and T2442, and A. monticola. Fz progenies and parents were grown at the Tidewater Agricultural Experiment Station in 1985. F1 plants were grown in the greenhouse in 1986. Five, six, and seven phenotypic classes, respectively, were assigned to characterize growth habit, stem color, and leaflet size. Root nodulation was indirectly determined through leaf color. Chi-squares were computed to test homogeneity of reciprocal crosses and genetic ratios for growth habit, stem color, and root nodulation. Leaflet size distributions were analyzed graphically and independence of inheritance was tested among all traits studied. Analysis of results indicates that: 1) growth habit may be determined by four genes having two types of isoalleles, 2) the relationship between and within these four genes may be essentially additive, 3) all loci may not contribute with the same weight to growth habit phenotype, 4) purple and green pigmentations may be determined by two distinctive sets of epistatic genes, 5) the two genes responsible for green pigmentation may be duplicate, 6) more than two types of alleles may have been involved for one or more loci responsible for stem color, 7) root nodulation may be determined by three independent non-duplicate genes, 8) leaflet size may be quasi-quantitatively determined in peanut, 9) extranuclear factors may interact additively and/or epistaticly with nuclear factors determining growth habit, stem color, and leaflet size, 10) the relatively high number of segregating loci observed for all the traits studied may have resulted from the use of A. monticola as one of the parents, and 11) extranuclear factors may induce or modify relationships between traits when they interfere with nuclear genes determining these traits.
M.S.