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Root system architecture (RSA) and morphology are important for plant productivity as many soil resources are unevenly distributed. RSA varies widely between species, individuals in a species and even within individual root systems. In recent years, the structure and function of plant root systems has received increasing attention. Many cultivated plants have undergone a reduction in genetic variability from ancestral forms, and this is particularly obvious in tomato whose history of domestication has significantly reduced the variation available in the cultivated tomato gene pool. However, substantial variation for root architecture and other traits still exists in related wild Solanum species. This root variability can be potentially used to breed new and improved tomato varieties. Quantitative Trait Loci (QTL) for root architecture and other important traits can be identified using available sets of tomato introgression lines, which were developed through a succession of backcrosses. The small green-fruited species Solanum pennellii is a distant sexually compatible relative of S. lycopersicum (domesticated tomato) native to the Andes mountains of South America. S. pennelli was used as a founding donor parent of the first tomato introgression (IL) population made available for interspecific QTL identification, cloning, and plant breeding. In this project, the S. pennellii IL population was used as the starting point to fine map QTL involved in the control of tomato root architecture. A large effect QTL was identified on the top of tomato chromosome 4. The QTL region enhanced root length and number of lateral roots. To fine map the underlying gene(s), approximately 8000 IL 4-1-1 F2 plants were screened to identify recombinants, leading to the generation of two small ILs (Q1120 and Q2173) harbouring the root system architecture (RSA) QTL. These recombinants delineated a mapping interval of 177kb containing 26 gene models. Analysis of the genes in the mapping interval indicated that several showed expression depending on the presence of an M82 or S.pennellii allele. Based on these and other criteria two genes were selected as RSA QTL candidates. These included a transcription factor belonging to the bHLH class and the gibberellin receptor GID1. Functional studies in Arabidopsis and tomato are in progress to validate the link between these genes and improved RSA.

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Plant seeds progress through specific stages during germination, from quiescence in the dry state through water uptake, testa rupture and finally endosperm rupture. The stages of seed germination are fairly well classified but the underlying biochemical and mechanical processes are unknown. The ability to control a seeds progression through the stages of germination has implications on farming efficiency and so the following thesis explores Arabidopsis thaliana and Lepidium sativum seeds during the germination process. A systematic approach to analysing the shape of cells within the radicle (embryonic root tissue) is developed, using confocal imaging, in order to characterise the shape of cells in the different tissues of the radicle. The cell shape approximations are not refined enough to characterise the different cell tissues. With more data, this approach would hope to find the region in which cells alter through the germination process. Change in the activity of cell wall modifying enzymes within the endosperm, that surrounds the emerging embryo, is a key part of the germination process and temporally and spatially defined high resolution transcriptomics data-sets are available to inform models. Through the course of this thesis, biochemical networks are developed, with ordinary and partial differential equation models being constructed and analysed. The models highlight elements for further investigation as well as differences between the two species considered. The mathematical models, along with data from biomechanical experiments on the endosperm, inform discussion on how the cell wall biochemistry of a cell wall alters the cell wall properties. These discussions focus on cell wall permeability, extensibility and the final cell separation event associated with germination. From the considered proteins, polygalacturonase and pectin lyase arise as the only viable candidates to cause the cell separation event with the model framework.

Stomata open in response to light allowing CO2 uptake for photosynthesis and they close in response to abiotic stress, such as drought, to prevent transpirational water loss from the plant. A pair of guard cells surrounds each stoma and stomatal movements depend on K+ fluxes across the guard cell plasma membrane. These fluxes are mediated by inward and outward rectifying K+ channels (K+in and K+out). The SNARE SYP121 was originally identified in association with ion channel regulation in guard cells. SNARE proteins mediate vesicle fusion and facilitate delivery of membrane proteins to target membranes. They are also linked to a variety of physiological responses. In particular, the plasma membrane SNARE SYP121 has been attributed a role in immune response and K+ nutrition. I have used the Arabdopsis loss-of-function mutant syp121 and uncovered a set of mutant phenotypes associated with impaired stomatal opening. In the syp121 mutant stomatal reopening was delayed and incomplete following Ca2+-induced closure, and increase in stomatal transpiration was slowed in the light. Incomplete reopening was rescued by complementation with wild-type SYP121 and was not observed in the syp122 mutant, lacking the homologous gene product. Guard cell K+ in current, necessary for K+ uptake during stomatal reopening, was reduced in syp121 mutant guard cells. Analysis of current gating characteristics suggested an impaired delivery of K+in channels to the plasma membrane, which was consistent with inhibition of stomatal reopening by the trafficking inhibitor Brefeldin A in wild-type plants. Impaired stomatal reopening in the syp121 mutant was phenomenologically similar to a Ca2+-encoded form of ‘programmed closure’ and my results suggest that endocytosis and delayed recycling of K+in channels may underly this phenomenon. Impaired stomatal function manifested in a conditional syp121 mutant growth phenotype dependent on high light and low humidity, characterised by reduced stomatal conductance and photosynthetic CO2 assimilation. My results suggested the necessity for SYP121-dependent K+in channel traffic during stomatal reopening. My results revealed a novel syp121 stomatal phenotype that was linked to K+in channel recycling in guard cells and had consequences for whole-plant water use and biomass production.

Trees are exposed to many stresses over their lifetime and withstand them due to their woody skeleton which provides excellent mechanical support. Wood has therefore been one of the most used materials throughout the history of humanity. However, the mechanical properties of wood vary considerably depending on wood anatomy and also show significant differences between and within trees. Wood is a cellular solid, characterised by a high degree of anisotropy at all levels of organisation and is formed by cells which are oriented largely in the longitudinal and radial directions, making wood mechanics rather complicated. Therefore, there is a need for an understanding of the mechanical properties of wood in different species and in different parts of the tree and its relationship to wood anatomy. This study began with two investigations into the transverse toughness of green trunk wood in different tree species including both hardwood and conifers. Double-edge notched tensile tests were conducted on the specimens to quantify their specific fracture energies and evaluate their failure fashions. The influence of wood anatomy on the toughening mechanism of wood was observed using both electron microscopy and light microscopy. It was found that the fracture properties of woods were mainly affected by the wood density and anatomy. Hardwoods were found to have higher fracture energies than conifers due to their denser woods and higher volume fraction of rays. The results also found that the specific fracture energies of RL and RT systems were around 1.5-2 times greater than TL and TR systems. This difference was mainly explained by the presence of rays which provided toughness in the radial direction, at least in hardwoods, as breaking across rays resulted in spiral fractures of the cell walls. The mechanical properties of green branches and coppice shoots of three temperate tree species (chestnut, sycamore and ash), were then investigated at three distances from the tip. The study also investigated how bending failure was influenced by the morphology and anatomy of branches and coppice shoots. Coppice shoots were shown to be more likely to buckle in bending, whereas branches failed with a clean fracture. It was shown that ash and sycamore had greater properties in their coppice shoots than their branches, while chestnut showed better properties in their branches. It was suggested that this occurred because increasing the leaf node frequency resulted in a decrease in mechanical properties; ash and sycamore had more leaf nodes in their branches, thus lower properties in their branches, while chestnut had more leaf nodes in its coppices. The mechanical properties also decreased from base to tips of branches and coppice shoots because of falls in diameter of shoots and wood density. The results also suggested why coppice shoots can act as a useful structural material. Finally, this thesis investigated how and why the fracture properties vary around the structure of tree forks. The fracture properties of green hazel forks were examined using double-edge notched tensile tests in the RT and TR directions. The fracture surfaces were also observed using scanning electron microscopy in both fracture systems. The results showed that the central apex of forks were considerably tougher than other locations, suggesting they provide the load-bearing capacity of tree forks. It was shown that the increased toughness was related to both higher wood density and an interlocking wood grain pattern. Interestingly, the TR fracture system was found to be tougher than the RT fracture system at the central apex of forks, probably related to the orientation of the fibres. These results provide insight into the relationship between wood mechanics and anatomy, particularly showing the importance of rays. They can also help us understand how our ancestors shaped wood and designed tools and how we could design better structures.

En forêt tropicale humide Amazonienne, les facteurs gouvernant l'évolution des espèces d'arbres restent peu connus et continuellement débattus. En particulier, les micro-variations environnementales attirent beaucoup d'attention car elles induisent de profondes modifications de structure et composition des communautés. Les variations micro-environnementales associées à la topographie ont couramment été évoquées comme facteur de radiations adaptatives chez les espèces d'arbres. Cependant, l'hypothèse de l'adaptation locale n'a jamais été testée au niveau intra-spécifique chez les arbres de forêt amazonienne alors que l'on sait que la diversité génétique des arbres tropicaux est couramment structurée à faibles échelles spatiales par des processus neutres (en particulier du fait de restrictions de flux de gènes). Dans cette étude, j'ai étudié le processus de différentiation génétique d'une espèce d'arbre (Eperua falcata, Fabaceae) dans les paysages forestiers de Guyane française grâce à la combinaison d'une approche phénotypique (génétique quantitative) et d'une approche moléculaire (génétique des populations). Je me suis attachée à répondre à trois questions principales : 1) Comment se distribue la diversité génétique dans les paysages forestiers de Guyane française ? 2) Quelles forces évolutives sont impliquées dans le processus de différentiation génétique à faible échelle spatiale ? 3) Est-ce que le processus d'adaptation locale contribue à structurer la diversité génétique à faible échelle spatiale ? / In the tropical rainforest of Amazonia, the factors driving the evolution of tree species remain poorly understood, and the relative influence of neutral and adaptive processes is continuously debated. In particular, local habitat patchiness draws much attention, as profound changes in the structure and composition of forest communities occur among micro-habitats. Thus, micro-environmental variations related to topography have frequently been invoked as drivers of adaptive radiation leading to sympatric speciation in Neotropical trees. On one hand, the hypothesis of local adaptation has never been investigated at the intra-specific level, i.e. within species currently undergoing population differentiation; on the other hand, many tree species are genetically structured over local scales due to neutral processes, mainly limited gene flow (caused by restricted pollen and seed dispersal). In this study, I used populations of a common tree species of the Guiana Shield - Eperua falcata (Fabaceae) - to study how neutral and adaptive processes shape the distribution of genetic diversity across forest landscapes characterized by local micro-habitat patchiness. I asked three main questions by combining both phenotypic (quantitative genetics) and molecular (population genetics) approaches: 1) How is the genetic diversity structured in forest landscapes of French Guiana? 2) Which evolutionary drivers are relevant to explain the structure of genetic diversity at local scale? 3) Does local adaptation contribute to structure genetic diversity within continuous populations?