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

Factors affecting flowering time have been extensively studied for decades. Greater understanding of flowering time has wider implications in agriculture and ecology as the trait is crucial to optimising reproductive success. It is best understood in the genetic model Arabidopsis thaliana (Arabidopsis), in which loss and gain of function mutations have identified several pathways that regulate flowering and its response to the environment. This has been complemented by studies of natural variation in flowering. Worldwide accessions of Arabidopsis have been used to identify additional flowering regulators and to examine the evolution of these genes and their potential involvement in adaptation to different environments. One of the most extensively studied pathways is responsible for accelerated flowering in response to an extended period of cold (vernalization). Several studies have attributed a substantial proportion of worldwide variation to the genes FRIGIDA (FRI) and FLOWERING LOCUS C (FLC), both of which are instrumental in conferring sensitivity to vernalization, though other genes have also been found. This study examines flowering time variation locally in populations of Arabidopsis from in and around Edinburgh. It identifies substantial, genetically determined variation in flowering time and in sensitivity to photoperiod and vernalization between local accessions. Variation in FRI and FLC sequences and in their levels of expression were detected in local accessions, but these were able to explain little of the phenotypic variation observed. Hybrids between local accessions showing extreme differences in flowering time or responses to photoperiod and vernalization were therefore used to map genes underlying their differences as quantitative trait loci (QTL). This analysis identified a locus in chromosome 5 that could account for differences in vernalization sensitivity. This region includes the VERNALIZATION INSENSITIVE 3 (VIN3) gene. Sequence differences between VIN3 alleles and their expression in response to vernalization supported the potential involvement of this gene in local flowering time variation.

This thesis describes the natural variation and influence of aspen harvesting on stream chemical concentration and flow-weighted export from catchments typical of the Western Boreal Plain, Alberta, Canada. The catchment stream discharge and stream chemical concentrations presented are taken from a subset of a five-year paired catchment (2005-2010) HEAD2 NSERC-CRD study. Nutrients, major anions, major cations and two minor ions were monitored from second-order streams draining a 18.3 sq km reference catchment (R1) and compared to a 9.9 sq km experimental catchment (H1) for two years of pre-harvesting (2005-2006) and two years of sequential harvesting (2007-2008). Preliminary analyses showed that non-harvest high flows had a total average instantaneous export greater than 10 times that of low flows. In addition, summer storms and beaver dam breakages had stream export equivalent to or greater than spring melt. Intensive upland aspen harvesting showed no significant differences in major cation and anion export post-harvest with the exception of increased sulfate. / Ecology

No description available.

<p>Trichome formation in Arabidopsis lyrata is a naturally occurring trait with phenotypic polymorphisms within wild populations. In Swedish accessions of A. lyrata, three genetic polymorphisms situated in the coding region of GL1, an important transcription factor in trichome production, have been identified, and these are candidates for being the cause of a glabrous phenotype. In this study a complementation test has been performed to clarify which mutation/mutations that are detrimental for trichome formation. A set of constructs has been transformed into A. thaliana, a close relative to A. lyrata, and subsequent generations of plants were examined for phenotype, genotype and gene expression. A SNP (Single Nucleotide Polymorphism) in the R3 MYB domain of GL1, resulting in a change of an alanine to aspartic acid, was identified as the critical polymorphism. The other two mutations, two indels, were harmless to protein function. The inserted constructs were under control of the native GL1 promoter. Plants that, because of the SNP, lacked trichome production, became totally glabrous.</p>

The use of Arabidopsis thaliana populations to understand the genetic basis for natural variation has been highlighted in recent years. The role of adaptation in natural variation remains of key interest. Here, natural variation in growth rate, flowering time and seed production were examined in local populations of A. thaliana from the Edinburgh area using a common garden approach. Growth rate and seed production were found to be highly genetically determined and sometimes correlated, and some genotypes were found to perform consistently better as winter annuals and others as summer annuals, suggesting that adaptation to different seasons might maintain natural variation locally. In order to dissect the environmental factors that could affect growth, these genotypes were also grown under controlled conditions. Photoperiod and temperature were identified as two of the seasonal variables to which different genotypes may be adapted. The relationship between growth rate and competition was also examined. In general, competition exaggerated the differences in performance between genotypes, although the identity of neighbours was observed to have an effect on both growth rate and fitness of A. thaliana in competition. To understand the genetic basis of growth rate variation, the genetic relationships between local populations was examined. Local accessions were usually found to be more closely related to each other than to world-wide accessions, suggesting that their variation did not reflect recent immigration. To examine the genetic architecture of growth rate variation, hybrids between local genotypes with different growth rates were used in QTL analysis. Four chromosomal regions were detected; these regions represent potential growth-rate associated QTL.

Modifying root architecture is a strategy that aims to develop plants, which capture nutrients more efficiently and thus suitable for sustainable agriculture with fewer fertilizer inputs. The focus is on nitrate, since it is a major nutritional determinant of root morphology and because of its importance in determining yield. Low concentrations of nitrate in soil stimulate the development of lateral roots, thereby increasing the root surface available for the uptake. Conversely, uniformly concentrations of nitrate inhibit the elongation of lateral roots. The aim of the thesis was to study the natural variation of the root morphological responses to nitrate in Arabidopsis thaliana. First, the manuscript starts with the screening of a core collection of twenty-four accessions, which maximize the genetic diversity within the species, on agar medium at low and moderate nitrate levels. Our results showed that the variability for production and allocation of biomass and root architecture traits exists within the species. Second a detailed characterization is done with eleven accessions showing contrasting root morphological responses to nitrate supply. We demonstrated that at an early development stage, the nitrate uptake efficiency is not implicitly correlated with root system architecture. Third, the genetic determinism of the natural variation of the root system architecture is studied. A combination of genome-wide association mapping on a larger number of accessions (> 300), a linkage mapping with existing recombinant inbred lines and a bulk segregant analysis was carried in order to identify candidate genes involved in root morphological responses to nitrate. The perspectives of this work would be, through a model species to crop pipeline, to translate knowledge from Arabidopsis to Brassica crops that would have a root architecture redesigned to increase the acquisition of nutrients. / Doctorat en Sciences / info:eu-repo/semantics/nonPublished

Photoperiodism refers to the organism’s ability to detect and respond to seasonal changes in the daily duration of light and dark and thus constitutes one of the most significant and complex examples of the interaction between the organism and its environment. This thesis attempts to describe the prevalence of variation in a photoperiodic response, its adaptive value, and its putative genetic basis in a common cruciferous weed, Capsella bursa-pastoris (Brassicaceae). Furthermore, the thesis presents a first comprehensive comparative overview of the circadian clock mechanism in an early land plant, Physcomitrella patens (Bryophyta), thus providing insights into the evolution of the plant circadian system. In an introductory survey of global gene expression changes among early- and late flowering accessions of C. bursa-pastoris we found an enrichment of genes involved in photoperiodic response and regulation of the circadian clock. Secondly, by phenotyping circadian rhythm variation in a worldwide sample of accessions with known flowering time, we detected robust latitudinal clines in flowering time and circadian period length, which constitute strong indications of local adaptation to photoperiod in the shaping of flowering time variation in this species. In an attempt to elucidate putative genetic causes for the correlated variation between circadian rhythm and flowering time, we found that sequence variation and diverged expression in components regulating light input to the clock, PHYTOCHROME B (PHYB) and DE-ETIOLATED 1 (DET1) make them strong candidate genes. Finally, we present a comparative study of circadian network topology in the moss P. patens. Phylogenetic analyses and time series expression studies of putative clock homologues indicated that several core clock genes present in vascular plants appeared to be lacking in the moss. Consequently, while the clock mechanism in higher plants constitutes at least a three-loop system of interacting components, the moss clock appears to comprise only a single loop. We conclude that C. bursa-pastoris is a highly suitable model system for the further elucidation of the molecular variation that influences adaptive change in natural plant populations. Furthermore, we believe that the continuing study of the seemingly less complex circadian network of P. patens not only can provide insights into the evolution of the plant circadian system, but also may help to clarify some of the remaining issues of the circadian clock mechanism in higher plants.

The environment can exert strong selective pressures on an organism. When selective pressures on traits differ between environments local adaptation may occur. If there is gene flow between the environments, local adaptation may be slowed or prevented. In plants, particularly weedy ephemerals, germination is a life-history trait that can be a strong determinant on fitness. In this dissertation, I explore the germination traits of two weedy Brassicaceae species, Arabidopsis thaliana and Sinapis arvensis, having populations in different habitats to determine whether germination traits within and between populations vary based on environmental conditions and to assess the extent of local adaptation. In Chapter 1, I assessed which genomic regions of A. thaliana were associated with differences in germination traits due to genotype-by-environment interactions. I performed a genome-wide association study using 100 natural accessions of A. thaliana under four light and nutrient combinations. I found 20 single nucleotide polymorphisms significantly associated with different environments, but none associated specifically with genotype-by-environment interactions. In Chapter 2, I assessed germination traits of S. arvensis collected from agricultural and non-agricultural habitats in the Bitterroot Valley of Montana. I discovered that the agricultural collection studied exhibited significantly different germination timing and amounts than the non-agricultural collections, which were statistically indistinguishable from each other. I also found evidence of a strong maternal effect on germination traits. In Chapter 3, I tested whether patterns of genetic variation between agricultural and non-agricultural collections of S. arvensis supported local adaptation to the two habitats even in the face of gene flow. While I expected to see some genetic differentiation between habitats, as seen in Chapter 2, no genetic differentiation was detected and markers putatively under selection were not associated with a particular habitat. I discuss why this might have occurred even though I have evidence for genetically-based phenotypic differentiation between agricultural and non-agricultural populations of S. arvensis. / text

Hybrid plants and animals, like corn and the domestic dog, grow larger and more vigorously than their parents, a common phenomenon known as hybrid vigor or heterosis. In hybrids between Arabidopsis ecotypes or species (in allotetraploids), altered expression of circadian clock genes leads to increased starch and chlorophyll content and greater biomass. In plants and animals, circadian clock regulation plays a key role in optimizing metabolic pathways, increasing fitness, and controlling responses to biotic and abiotic stresses. In the allotetraploids, the increased level of heterosis is likely caused by interspecific hybridization as well as genome doubling. However, it is unknown how genome dosage and allelic effects influence heterosis, and whether additional clock output traits, such as stress responses, are altered in hybrids. In three related projects, the effects of genomic hybridization (including parent-of-origin effects) and genome dosage on heterosis were elucidated. In my first project, I found that although ploidy influenced many traits, including seed and cell size, biomass and circadian clock gene expression were most strongly influenced by hybridization. Additionally, parent-of-origin effects between reciprocal hybrids were frequently observed for many traits. In my second project, I described a unique role for RNA-directed DNA methylation (mainly CHH methylation) in mediating the parent-of-origin effect on expression of the circadian clock gene CCA1 in reciprocal hybrids. Altered CCA1 expression peaks were associated with heterosis of biomass accumulation in the reciprocal hybrids. Lastly, I used transcriptome sequencing in hybrids at different times of day to examine changes in downstream clock-regulated pathways. In the hybrids, many genes in photosynthetic pathways were upregulated, while many genes involved in biotic and abiotic stresses were repressed during the morning and afternoon, respectively. Additionally, natural variation between parents in stress-responsive gene expression was found to be crucial for producing vigorous hybrids. These conceptual advances increase the mechanistic understanding of heterosis, and may guide selection of parents for making better hybrids. / text