Syngenta-PSC Fellow Abstracts

Epigenetic Contributions to Hybrid Vigor in Apomictic Offspring Prof. Bernhard Schmid, Institute of Evolutionary Biology and Environmental Studies, UZH Prof. Ueli Grossniklaus, Institute of Plant Biology, UZH In the 1930es it was proposed that fixation of hybrid vigor through apomixis would have a tremendous impact on agriculture. Apomixis, the asexual propagation through seeds, completely preserves the genotype2). However, the clonal fixation of heterosis will only be possible if there is no major epigenetic contribution to the hybrid phenotype. In fact, it was never tested whether phenotypes are faithfully conserved during apomictic reproduction. This, it is not clear whether heterosis could indeed be fixed through apomixis. In mammals, the lack of epigenetic reprogramming during reproduction is the major cause for developmental abnormalities in clones derived from somatic nuclear transfer (3). Similarly, the absence of such reprogramming events during apomixis could also results in phenotypic variability. Furthermore, epigenetic changes occur upon hybridization (4) and if these are inherited to some extent, they may lead to me.This complex mechanism potentially manipulates host gene expression and enhances cellsusceptibility before invasion. To gain insight into this process, we propose to use RNA deepsequencing and RNAseq to profile small RNAs and corresponding mRNA targets during thespread of GFP-tagged TMV infection sites in Nicotiana benthamiana. Respective profiles ofcells ahead, within, and behind the leading front of infection w cellular and tissue level.

Causes and consequences of epigenetic variation in plant interactions with pollinators and herbivores Prof. Ueli Grossniklaus, Institute of Plant Biology, UZH Prof. Florian Schiestl, Institute of Systematic Botanic, UZH Post doc Heather Kirk, Institute of Systematic Botanic, UZH Most flowering plants use animals for pollination, and interactions between plants and their pollinators are key components of agricultural and natural ecosystems. For instance, pollination success is of great importance for the production of canola seed (Brassica napus) , a close relative of the species we propose to investigate here (B. rapa). In order to maintain beneficial mutualisms with their pollinators, plants have evolved floral signals, such as color and fragrance, which advertise rewards such as nectar. However, floral signals can also attract antagonists such as herbivores that have detrimental effects on plant fitness. Classical evolutionary models incorporate only genetic variation and changes in populationwide allele frequencies as mechanisms for diversification and adaptation. However, epigenetic variation is generated at a much higher frequency than genetic variation (1,2), and these epigenetic changes can be faithfully inherited (3,4). Epigenetic variation may therefore also be subject to selection and could contribute to evolutionary change (1,2,3), particularly in rapidly fluctuating environments. The role of epigenetic variation in individual and population level adaptive responses to pollinators and herbivores has never been investigated. This project will investigate the role of heritable epigenetic variation in response to selection by pollinators and herbivores. First, we will characterize the degree of genome-wide epigenetic variation between floral and vegetative tissues in B. rapa, and we will assesswhether herbivores drive epigenetic changes in floral and vegetative tissues within individuals and across generations. Second, in an extension of an ongoing project in the Schiestl lab, epigenetic variation will be characterized before and after several generations of herbivore- and pollinator-mediated selection in a Brassica rapa population. Floral signaling and plant defense traits will be measured over successive generations, and phenotypic selection on these traits will be quantified. Epigenomic changes associated with different selection pressures will be tracked. Post doc (12 months) Novel chimeric receptors inducing programmed cell death for resistance against the plant pathogenic Xanthomonas genera in model and tropical crop species Oberassistent Hervé Vanderschuren, Institute of Agricultural Sciences, ETH Post doc Emily McCallum, Institute of Agricultural Sciences, ETH Oberassistent Delphine Chinchilla, Botanical Institute, UniB In the proposed project, we will generate novel chimeric receptors for broad spectrum and sustainable Xanthomonas disease resistance in a variety of model and tropical crop species (Arabidopsis, cassava and rice). Using the Xanthomonas-specific pattern recognition receptor Xa21, we will replace the intracellular kinase domain (cleaved after bacterial recognition) with proteins known to trigger programmed cell death (PCD) in plants. Transgenic plants containing these chimeric receptors should induce a rapid, localized PCD response at the site of Xanthomonas infection, preventing bacterial replication and systemic infection of the host plant. Transient expression assays will be performed to verify appropriate cleavage, subcellular localization and PCD-induction of each chimeric receptor in planta, before and after exposure to Xanthomonas pathogens. Transgenic plants will be generated, and experiments undertaken to determine PCD responses and resistance to Xanthomonas infection. We seek funding for a postdoctoral fellow to undertake this research, which will be performed in collaboration between two laboratories with the necessary combined experience in plant-pathogen biology at the ETH Zürich and Basel University. Taking advantage of the skills and resources already available in each laboratory, the proposed research can be completed within 1.5 years. Post doc (12 Month) Start Spring 2010: Understanding and exploiting diversity in plant storage carbohydrates Prof. Samuel C Zeeman, Institute of Plant Sciences, ETHZ Prof. Wilhelm Gruissem, Institute of Plant Sciences, ETHZ We rely on the carbohydrates (sugars and starches) stored by plants. The work proposed here aims to discover novel protein factors that control how much and in what form carbohydrates are stored. Most plants store starch, but its metabolism is not fully understood. Unanswered questions surround the initiation of insoluble starch granules, the structure of the constituent polymers, and how amount is controlled. We will take two new approaches to tackle these questions, the results of which may enable the improvement of starch crops. First, we will analyze starch using proteomics to identify granule-bound proteins that may be involved in biosynthesis. The cooperation between our labs means that we have the combination of skills to do this. Through preparatory work and external collaborations, we have obtained the biological materials we need. Second, we will analyze the unique features of the tropical tree Cecropia peltata, which makes starch in its leaves, but soluble glycogen in other tissues. We have obtained C. peltata plants and established an EST library through 454 sequencing. Quantitative transcript and protein data will be obtained in this project through Illumina sequencing and mass spectrometry, respectively. This will tell us how the enzymatic machinery can be reconfigured for different polymer biosynthesis. Contact person: Dr. Sylvain Bischof sylvain.bischof@ipw.biol.ethz.ch Start Spring 2010: EPIGENOMICS: Characterization of Epigenetic Changes in Systems under Selection Prof. Ueli Grossniklaus, Institute of Plant Biology, UZH Prof. Bernhard Schmid, Institute of Environmental Sciences , ETHZ Dr. Lindsay A. Turnbull, Institute of Environmental Sciences, ETHZ Variation in plant traits and patterns of co-variation between these traits and environmental conditions are of great interest in ecology and agriculture. Disturbance of suitable conditions pose major problems for yield security, in particular given the current climate change. Whether species contain the necessary adaptive potential to respond to these changes, and which genetic or epigenetic changes are involved, are crucial to predicting crop performance in a changing environment. It has become increasingly clear that epigenetic changes could play a role in plant adaptation to a changing environment. In this project, we propose to investigate genome-wide epigenetic changes in experimental Arabidopsis populations that have undergone 5 generations of selection. This pilot study will establish the molecular and bioinformatic methods necessary to study epigenetic changes at the genome level and thus contribute to the two Target Areas “Plant Growth” and “Innovation and Technology”. A selection experiment was performed on Arabidopsis populations and phenotypic traits relevant to fitness were recorded. Quantitative analyses of allele distributions identified loci that were selected under specific conditions. Unexpectedly strong changes were found at both the phenotypic and genotypic levels under dynamic landscape selection for just 5 generations. In this proposal, we ask for further support to analyze the changes that occurred at the epigenetic level in the most divergent experimental and parental populations. Genomewide analyses of DNA methylation have become possible using bisulfite treatment in combination with next-generation sequencing technology. Contact person: Dr. Christian Heichinger christian.heichinger@live.com Start Spring 2010: Exploring unreduced male gamete formation for plant breeding Prof. Claudia Köhler, Institute of Plant Sciences, University ETH Zürich Prof. Lynette Brownfield, Institute of Plant Sciences , University ETH Zürich Our proposed research project is designed to explore molecular mechanisms governing unreduced gamete formation in plants and to exploit this knowledge to generate tools for plant breeding. Specifically, we would like to test whether unreduced male gametes can be produced by virus induced gene silencing of an important regulator of male meiosis in Arabidopsis and whether homologs of this gene perform a similar function in monocots. For this purpose we like to establish the genetically tractable model organism Brachypodium distachyon as a model for studying meiosis in monocots. Furthermore, we like to identify novel regulators of male meiosis in Arabidopsis by applying forward and reverse genetic screens with the aim to illuminate the underlying molecular mechanisms governing meiosis in plants. We plan to apply modern deep sequencing technology to map and isolate the affected genes. Apart from advancing our currently scarce knowledge on the molecular basis of meiosis in plants, the identified genes will provide important tools for the targeted generation of unreduced gametes in economically important crops. Interploidy crosses are rarely successful, posing a major problem for breeding of polyploid crop species like hexaploid wheat. Therefore, developing tools allowing the targeted generation of unreduced gametes at high frequency holds great promise for plant breeding programs. Contact person: PhD student David Kradolfer davidkra@ethz.ch Start Spring 2010: Integration of transcriptomics and genome-wide association study for identification of genes responsible for natural quantitative variation: A “multi-omics” approach Dr. Takashi Tsuchimatsu, Istitute of Plant Biology, UZH Prof. Ass. Kentaro Shimizu, Institute of Plant Biology, UZH Dr. Thomas Städler, Institute of Integrative Biology, ETHZ Most agriculturally important phenotypes are quantitative traits regulated by polygenes. Exploring the genes responsible for uantitative traits has long been a challenge in genetics; however, the resolution of classical quantitative-trait loci (QTL) apping is low, despite the labor-intensive and timeconsuming work involved in this approach. Recently, as sequencing and single-nucleotide polymorphism (SNP) typing costs continue to decrease, genome-wide association (GWA) studies are emerging as a powerful tool for the identification of genes responsible for quantitative natural variation (Nordborg & Weigel, 008 Nature; Atwell et al., 2010 Nature). GWA studies seek to screen genes underlying variable phenotypes, based on associations between phenotypes of interest and genome-wide genetic markers, such as SNPs. However, the large number of false-positive estimations has been a major obstacle. In this project, we will exploit the genome-wide SNP data in Arabidopsis thaliana to identify genes responsible for several reproductive traits that are known to be highly variable in this species. To avoid false-positive results, we propose the novel idea of “multi-omics mapping” by combining GWA studies and transcriptomics data obtained by microarrays. We will confirm these in silico predictions using transgenic experiments. The integration of computational and molecular genetic analyses will allow us to assess this approach and to propose improved statistical algorithms. These algorithms will be implemented and distributed as software that can be applied to other species, including crops. Contact person: Dr. Takashi Tsuchimatsu Start Spring 2010: The mechanisms of volatile-mediated plant growth promotion: A focus on indole Dr. Laure Weisskopf, Institute of Biology, UZH Prof. Thomas Boller, Botanical Institute, UniBs Prof. Leo Eberl, Institute of Biology, UZH Mounting evidence indicates that rhizosphere bacteria can promote the growth of plants through the emission of volatile organic compounds (VOCs). We have identified five bacterial VOCs which strongly promote the growth of Arabidopsis thaliana. This project aims at determining how plants perceive these bacterial VOCs and at elucidating the mechanisms underlying the observed growth promotion. We will use well-established bioassays to analyze the perception of our bacterial volatiles by A. thaliana. We will then further investigate one bacterial compound of particular interest: indole, a metabolite with multiple functions in bacterial communities. Based on its structural similarity to auxin, we hypothesize that plants can use indole as a precursor for this phytohormone. We will use available biochemical and molecular tools to test this hypothesis. The putative function of indole in priming defense responses will also be assessed. Despite numerous reports of plant growth promotion by bacterial volatiles, nothing is yet known of the perception of these compounds by plants and of the mechanisms involved in the observed growth promotion. This project will provide first insights into the plant’s perception of microbial VOCs and into the mode of action of these compounds. This will have significant impact on the understanding of volatilemediated plant-microbe interactions and also provide useful information for the prospective use of microbial VOCs as plant-growth promoting compounds. Contact person: NN Start Spring 2009: Decision making in plants: resource allocation to mycorrhizal hyphal networks Prof. Bernhard Schmid, Institute of Environmental Sciences, UZH Prof. Andres Wiemken, Institute of Botany, Uni Basel In contrast to animals, plants have no central nervous system with which to integrate deci-sion-making when foraging for resources. Nevertheless, intuitively, integration of information must be important for plants. This is particularly evident in the case of symbioses such as the mycorrhizal symbiosis, where the plant invests photosynthetic products (chiefly carbon) into a fungal partner in order to get access to mineral nutrients foraged for by the fungus. If part A of a plant root system has a connection with an arbuscular mycorrhizal fungus (AMF) that takes more resources than it returns and part B has an AMF connection that takes less than it returns, the plant should favor part B over part A to maximize its fitness. However, can a plant indeed select between the two AMF connections and display an "intelligent" integrated response? To answer this question we will construct experimental systems with split plant root systems of which one side has a more beneficial AMF connection than the other side. This will be done in two ways: (i) the two sides contain two AMF species differing in their ability to supply mineral resources to the plant, (ii) the two sides contain the same beneficial AMF species, but this AMF species is connected on one side to a different plant species known to disproportionately draw mineral resources from the mycorrhizal network while contributing relatively little carbon. The plant response will be assessed via growth analysis and tissue concentrations of N15 and P33 provided to the AMF on the two sides. The allocation of carbon to the AMF will also be assessed by isotopic analysis. Because we expect that plants are more selective when resources are scarce, we will use low or high levels of N and P in our experimental systems. Finally, we will expand the experimental systems to include two plants mutually limited by either N or P to test if resource sharing via a common AMF will occur to a greater extent than if the limitation is not mutual. The results of our research will contribute to the fundamental question of “decision-making” in plants and to the applied question of how interactions between plants and AMF affect plant performance in the wild and in agro-ecosystems. Contact person: PhD student Alicia Argüello García Start Spring 2008: Impacts of EXtreme CLIMatic Events on ecosystem functioning in alpine grasslands Dr. Michael Scherer-Lorenzen, Institute of Plant Sciences, ETHZ Dr. Eva Spehn, Institute of Botany, Uni Basel PD Dr. Andreas Lüscher, Grassland Systems and Forage Production, Agroscope Reckenholz-Tänikon Human induced climate change is unequivocal and ongoing, with the European Alps being a hotspot of warming. The future summer climate in Switzerland is predicted to be drier and warmer, with an increased probability of extreme events such as high intensity rainfall. In this project, we propose to study the impacts of prolonged summer drought and intensive rainfall on key ecosystem processes and services of alpine grasslands. At three sites representing the most contrasting extremes in macroclimate and geology we will simulate drought with rainout shelters, combined with a rainfall experiment. Replication of the experiment along steep altitudinal gradients will allow us to estimate the influence of different temperature regimes. Adopting an integrated and process-orientated approach, we propose to study (i) changes in sward structure and productivity, (ii) susceptibility to erosion and surface runoff, (iii) species-specific water stress responses, and (iv) litter decomposition, mineralisation and soil respiration in complementary work packages. Our project will contribute to predictions of the consequences of the most likely climate change scenario for the Swiss Alps. Because vegetation integrity of alpine grasslands reduces risk of erosion and secures slope stability, knowledge on vulnerability of these grasslands to climate change is crucial for the welfare and safety of many people. Contact person: PhD student Samuel Schmid samuel.schmid@ipw.agrl.ethz.ch Start Summer 2008: Relationship between the success of establishment of invasive plants and their mode of reproduction Prof. Ueli Grossniklaus, Institute of Plant Biology, UZH PD Dr. Jürg Stöcklin, Institute of Botany, Uni Basel Invasive plants pose a great problem to many natural ecosystems. Moreover, invasiveness and transgene spread are two of the major perceived dangers associated with genetically modified organisms (GMOs). The goal of this interdisciplinary project is the experimental simulation of the spread, establishment, and potential persistence of a typical transgenic trait. However, we will not analyze the spread and ecological behavior of a transgene in a GMO, but rather of apomixis, a trait that has all the typical characteristics of commonly used transgenes. Much of the perceived danger of GMOs has to do with their potential ability to spread rapidly in a population after out-crossing. This is based on the genetic nature of many commonly used transgenic traits, which (i) are dominant, (ii) can cross via pollen to related species, and (iii) have a potential advantage for the plants carrying the trait. All these characteristics are shared by the apomixis trait, which we will use as a model to experimentally simulate the short- and long-term ecological behavior of a transgene. Shortterm spread in different agricultural situations will be experimentally simulated in common garden plots using different landscape models. Long-term establishment and persistence of such traits will be studied by analysing the relative contribution of sexual and apomictic individuals on a glacier foreland that has been de-glaciated for various periods of time. The latter will allow us to infer the population dynamics of traits with the above characteristics over a period of 100-150 years, which can currently not be done with any other system. Contact person: PhD student Christian Sailer christian.sailer@access.uzh.ch Start Summer 2008: Structural and Functional Analysis of Ultraconserved Elements (UCEs) in Plants Dr. Thomas Wicker, Institute of Plant Biology, UZH Dr. Célia Jäger-Baroux, Institute of Plant Biology, UZH Prof. Ueli Grossniklaus, Institute of Plant Biology, UZH Three years ago, the first report on Ultraconserved Elements (UCEs) in mammals was published. UCEs are sequences of ≥200 bp that are nearly 100% conserved between orthologous regions of the human, rat and mouse genomes (Bejerano et al., 2004). Until now, no satisfactory explanation for this astounding finding has been proposed as no biological process is known that would require such an extreme sequence conservation. Some UCEs have been shown to have enhancer activity in mouse transgenic assays (Pennacchio et al., 2006). However, all protein-DNA interactions known to date do tolerate significant sequence divergence without dramatically affecting binding and no mechanism can be envisioned that would lead to such a high degree of sequence conservation. Our preliminary studies have shown that UCEs are also present in plant genomes and that some are evolutionary ancient (conserved between Arabidopsis, rice, and Physcomitrella). We propose to use a combination of bioinformatic, cytological, and population genetic approaches to study the structure and function of UCEs in plants as these offer unique opportunities due to the availability of insertional mutants and the large number of offspring produced. We will analyze UCEs in all available plant genomes and study their number and distribution within these genomes to detect possible peculiarities. Cytogenetic studies will reveal whether these sequences play structural roles in nuclear organization or chromosome pairing, and transmission studies using insertional mutants disrupting UCEs will reveal even slight effects on fitness traits. This interdisciplinary project is only possible through the cooperation of scientist with diverse expertise in experimental and computational biology. Contact person: PhD student Konstantinos Kritsas kokrits@gmail.com Start Summer 2008: Volatile mediated impact of bacteria on plant growth and disease resistance Dr.Laure Weisskopf, Institute of Plant Biology, UZH Prof. Thomas Boller, Institute of Botany, Uni Basel Prof. Leo Eberl, Institute of Plant Biology, UZH Increasing evidence indicates that bacteria can interact with other organisms (e.g. plants or fungi) through the emission of volatile organic compounds (VOCs). Of these VOCs, 2-3 butanediol was recently shown to induce changes in growth, auxin homeostasis and disease resistance of Arabidopsis thaliana. Interestingly, production of 2,3 butanediol is regulated by a quorum-sensing (QS) mechanism in various bacteria. QS regulates many bacterial functions important for plant-microbe interactions but a direct link between QS and VOCsmediated plant growth promotion has not yet been established. In this project, we will investigate the VOCs-mediated plant-bacteria interactions from both the plant’s and the bacteria’s perspective. We will test a wide range of bacterial strains for VOCs-mediated effects on growth of Arabidopsis thaliana in a compartmental Petri dish assay. A collection of mutants defective in QS-regulation will be used to assess the role of QS in bacteria-plant interaction. VOCs profiles of bioactive strains will be analyzed by GC-MS and active compounds will be identified. On the plant side, the perception of the bacterial VOCs will be studied using bioassays that are well-established in the group of Thomas Boller. Furthermore, mutants impaired in disease resistance will be used and the expression of relevant genes monitored to gain insights into the mechanism underlying the action of bacterial VOCs on plants. The collaboration between the Basel and the Zurich laboratories will enable us to investigate VOCs-mediated bacteria-plant interactions using an interdisciplinary approach. In addition to the gained basic knowledge on bacteria-plant interactions, this project may also lead to the discovery of new plant growth-promoting or biocontrol strains that could be of economical interest in crop science. Contact person: PhD student Dirk Blom Dirk.Blom@access.uzh.ch 2003-2008: Constraints to plant tissue formation in the cold Prof. Fred Meins, FMI Prof. Christian Körner, Botanical Institute, UniBS Dr. Andrew Fleming, Group Prof. Nikolaus Amrhein, Institute of Plant Sciences, ETHZ We propose that organisms selected to thrive in the cold are primarily limited by developmental constraints (i.e. meristemic activity, cell differentiation, and organogenesis), rather than stress resistance or carbon acquisition, conventionally the central themes in this field. We plan a gene identification approach with Arabidopsis thaliana ecotype Columbia to gain an understanding of molecular mechanisms important for regulating development in low temperatures. This will involve RNA profiling of Arabidopsis grown under low and high temperature to identify candidate genes, expression studies of these genes in high and low temperature ecotypes, and functional characterization of genes by T-DNA insertion mutagenesis combined with knock-down or over-expression in transgenic plants. Overall, the results of this project should help answering classical ecological questions with molecular techniques and the use of model organisms. The cooperation between the FMI, the ETH-Institute for Plant Sciences and the ecology unit at Botany in Basel is seen as an ideal opportunity for a PhD student interested in interdisciplinary problems. The laboratory work will be performed at the FMI, but the candidate will attend seminars in all three institutions and in the PSC program. Contact person: Fred Meins 2003-2008: Chemical signaling in the mutualistic arbuscular-mycorrhizal symbiosis in plants Dr. Marcel Bucher, Group Prof. Nikolaus Amrhein, Institute of Plant Sciences, ETHZ Prof. Thomas Boller, Botanical Institute, UniBS Prof. Enrico Martinoia, Institute of Plant Biology, UZH Although plants do not have sensory organs like animals, they can perceive chemical signals, such as e.g. nutrient concentrations or microbial substances, with a high specificity. Upon perception of the signal, a transduction mechanism eventually leads to the molecular response in the nucleus of a cell, i.e. induction or repression of gene expression. This project focuses on the molecular interaction between the fungus and the host plant in the mutualistic arbuscular mycorrhizal (AM) symbiosis. This symbiosis is more than 400 Mio years old and is thought to have been essential for the colonisation of land by plants. A central aspect of the AM symbiosis is bidirectional transfer of nutrients between both organisms, including phosphate (Pi) transport from the fungus to the plant at the fungus/root interface including structures such as arbuscules or coiled hyphae colonizing root cells. We have recently identified a Pi transporter gene named StPT3 which is specifically expressed at this interface. The fungal signal(s) and the subsequent signal transduction mechanisms involved in induction of the StPT3 gene are at present unknown. Recently, we have shown that these signaling mechanisms leading to mycorrhiza-specific Pi transport are well conserved in evolutionary distant plant species. Moreover, the signal transduction pathway is selectively activated by fungi from the phylum Glomeromycota. A primary goal of this project is the establishment of an in vivo screening system which eventually allows the identification of regulatory compounds in StPT3 expression. The proposed collaboration is promising with respect to signaling in the AM symbiosis. Secondly, this project contributes to an already existing project which aims at large-scale genomic screening to isolate AM-symbiosis signal-transduction mutants in the model plant Petunia. Contact person: Marcel Bucher marcel.bucher@ipw.biol.ethz.ch 2003-2008: Molecular and phenotypic diversity of wheat landraces for winter hardiness Prof. Beat Keller, Institute of Plant Biology, UZH Prof. Peter Stamp, Institute of Plant Sciences, ETHZ Dr. Jörg Leipner, Group Prof. Peter Stamp, Institute of Plant Sciences, ETHZ Wheat is worldwide one of the most important crops and, together with maize and rice, forms the basis of human and animal nutrition. In order to breed for crop plants required for the future, the optimised use and the availability of genetic resources are essential. For wheat, there are considerable numbers of accession available in gene banks, but they are not well characterised for many phenotypic traits, and it is not clear to which extent they contain valuable resources for a specific breeding goal. In addition, very little is known about the molecular polymorphisms at agronomically important genetic loci and their contribution to phenotypic variability. Here, we propose to study genetic resources of wheat for abiotic stress resistance, specifically for winter hardiness. A set of landraces will be phenotypically analysed for cold adaptation and freezing tolerance and groups of lines with different responses will be made. At the molecular level, we propose to identify candidate genes, which might be involved in the traits studied. This will be done based on physiological knowledge of freezing tolerance in wheat (obtained in this project) and other grasses as well as molecular studies in the model plant Arabidopsis (studies in the literature and databases). Haplotypes of a selected number of candidate genes will be analysed at the molecular level in wheat. We will investigate whether linkage disequilibria can be observed at these loci and specific haplotypes can be found in the freezing-tolerant lines. This work should contribute to a better molecular characterisation of winter hardiness in wheat using commonly available genetic resources. Contact person: Peter Stamp peter.stamp@ipw.agrl.ethz.ch 2004-2007: Genetic dissection of seed and fruit development in Arabidopsis thaliana Dr. Claudia Köhler, former group of Prof. Ueli Grossniklaus, Institute of Plant Biology, UZH Dr. Lars Hennig, Group Prof. Wilhelm Gruissem, Institute of Plant Sciences, ETHZ The development of fruits follows fertilization and occurs simultaneously with seed maturation. The fertilized gametophytes develop into seeds, whereas the carpels and, in some species, also other flower organs develop into the fruit. In apomictic species the formation of viable seeds and fruits occurs in the absence of fertilization, whereas parthenocarpic species form fruits without seeds. Thus it is possible to uncouple seed and fruit formation from the fertilization process, and also the formation of fruits can occur independently from seed formation. In Arabidopsis thaliana, several mutants have been identified forming fruits and seed-like structures independent of fertilization. The genes affected in these fertilization-independent seed (fis) class mutants encode proteins of the Polycomb group that are required to maintain the stable transcriptional repression of target loci. The msi1 mutant belongs to the fis class mutants displaying silique development in the absence of fertilization. We propose to perform a mutant screen using the msi1 mutant as a tool to dissect the genetic networks governing seed and fruit development. By searching for suppressors of the fis phenotype in a msi1 mutant background it will be possible to uncover the molecular events controlling the initiation of seed and fruit development and their link to plant hormone signal transduction processes. Furthermore, this study will allow us to dissect the role of MSI1 during seed and fruit development and toidentify downstream target genes of MSI1. Contact person: Claudia Köhler claudia.koehler@ipw.biol.ethz.ch 2004-2008: Identification and Characterisation of Tonoplast Transport Systems Using Proteomic Approaches Dr. Ulrike Schmidt, Group Prof. Enrico Martinoia, Institute of Plant Biology, UZH Dr. Sacha Baginsky, Group Prof. Wilhelm Gruissem, Institute of Plant Sciences, ETHZ Membrane proteins are responsible for the exchange of solutes between the cell and the surrounding medium as well as within different cellular compartments. In Arabidopsis thaliana the function of at least 2/3 of the predicted membrane proteins is unknown. The expression pattern and subcellular localization of these proteins can provide useful information for the understanding of their function in planta. A closer look at the literature reveals that among the different organelles only few vacuolar proteins have been investigated. To elucidate the function of vacuolar membrane proteins we will isolate tonoplast fractions from Arabidopsis cell cultures and cauliflower to identify vacuolar transport proteins by high-throughput mass spectrometry. Vacuolar localization of the identified proteins will be verified by GFP fusion constructs. Next, we will conduct a detailed functional characterization of putative transporters by the analysis of knock-out mutants, antisense/RNAi and overxpression plants, flux analysis using isolated vacuoles or tonoplast vesicles, and characterisation of vacuolar proteins in heterologous expression systems. Contact person: Ulrike Schmidt ulrike.schmidt@botinst.unizh.ch 2005-2008: Neutral versus niche-structured communities: testing for resource partitioning by plants Prof. Nina Buchmann, Institute of Plant Sciences, ETHZ Prof. Andrew Hector, Institute of Environmental Sciences, UZH Dr. Pascal Niklaus, Institute of Botany, UniBS At the large scale, 'neutral' models that assume species to be identical show surprising success in reproducing community patterns. In contrast, small-scale experiments have shown that complementary niche partitioning may allow species to coexist and cause biodiversity effects on ecosystem functioning. However, it is unclear if such complementarity is ubiquitous in all ecosystems and whether it is generally due to such resource-based niche partitioning. This interdisciplinary project experimentally tests whether plant species in temperate grasslands occupy different resource-based niches. Replicated experimental mixtures of plant species that are known to commonly co-occur in grasslands, plus replicated monocultures of all of the constituent species will be established. Furthermore, differences in traits related to resource capture and link these to resource uptake, and resource availability mediated by soil microorganisms, using stable isotope analyses (15N) will be tested. Contact person: Nina Buchmann nina.buchmann@ipw.agrl.ethz.ch Start Fall 2007: Discovering the mechanism of sucrose export from plant cells Prof. Samuel Zeeman, Institute of Plant Sciences, ETHZ Prof. Enrico Martinoia, Insitute of Plant Biology, UniZH The aim of the research proposed here is to discover the mechanisms by which plant cells release sugars that are assimilated during photosynthesis. This is crucial to the functioning of a plant, which contains both autotrophic and heterotrophic tissues. There are several sites at which sugars are unloaded into the extracellular space for uptake by neighbouring cells. This includes phloem loading, seed development and pollen development. Sugar export is also vital for the interactions between plants and mutualistic or parasitic fungi, (mycorrhizas and biotrophic pathogens, respectively). In all cases, little is known about the transport mechanisms mediating export, or their regulation. Most studies of metabolite transporters to date have identified sugar uptake systems. New techniques are required to isolate and study those involved in export. Understanding this process could be a key to optimise assimilate partitioning in crops. The major approach will focus on sucrose, the major transported sugar in plants, and will seek to identify carriers capable of mediating sucrose export using experimental and bioinformatic approaches. The functions of candidate proteins will be evaluated using a functional genomic approach in Arabidopsis. Contact person: PhD student HsiangChun Lin linh@ethz.ch Epigenetic Contributions to Hybrid Vigor in Apomictic Offspring Prof. Bernhard Schmid, Institute of Evolutionary Biology and Environmental Studies, UZH Prof. Ueli Grossniklaus, Institute of Plant Biology, UZH In the 1930es it was proposed that fixation of hybrid vigor through apomixis would have a tremendous impact on agriculture. Apomixis, the asexual propagation through seeds, completely preserves the genotype of the mother, resulting in clonal offspring (1). Unfortunately, progress in apomixis research has been slow and the transfer of apomixis to crops has not been achieved so far (2). However, the clonal fixation of heterosis will only be possible if there is no major epigenetic contribution to the hybrid phenotype. In fact, it was never tested whether phenotypes are faithfully conserved during apomictic reproduction. This, it is not clear whether heterosis could indeed be fixed through apomixis. In mammals, the lack of epigenetic reprogramming during reproduction is the major cause for developmental abnormalities in clones derived from somatic nuclear transfer (3). Similarly, the absence of such reprogramming events during apomixis could also results in phenotypic variability. Furthermore, epigenetic changes occur upon hybridization (4) and if these are inherited to some extent, they may lead to variation in the offspring, even if clonal in nature. It is currently unclear to what extent epigenetic information is inherited from one generation to the next in plants. However, a better understanding of transgenerational inheritance in plants is central to plant development, ecology, and agriculture. In this project, we propose to compare phenotypic and epigenetic changes that occur in hybrid progeny that was either produced sexually or clonally. Sexually produced seeds undergo normal reprogramming events during gametogenesis and early seed development (5-7), while asexually produced, clonal seeds short-circuit gametogenesis (1) and thus fail to be reprogrammed. A comparison of genetically identical populations, created sexually or clonally, will allow us to investigate the importance of epigenetic reprogramming. By combining ecological with genome-wide molecular approaches we will be able to determine not only the nature of inherited epigenetic information but also its relevance for phenotypic variation and its interaction with the environment. PhD student (3 years) Temporal analysis of the regulatory activities of small RNAs during the cell-to-cell spread of tobamovirus infection Prof. Manfred Heinlein, Institute of Botany, Uni Basel Dr. Franck Vazquez, Institute of Botany, Uni Basel Prof. Thomas Boller, Institute of Botany, Uni Basel Plant viruses spread their genomes through infected tissues by cell-to-cell movementthrough plasmodesmata (PD) and replication in each infected cell. During spread the virusesencounter the efficient host RNA silencing antiviral defense response. As a counter-defenseviruses generally protect their genomes by producing specialized RNA silencing suppressorproteins. Strikingly, several plant viruses, like Tobacco mosaic virus (TMV), encode proteinsthat enhance RNA silencing, rather than block it. This indicates that interaction of the viruswith the host silencing machinery is more complex than previously thought. In the case ofTMV, the silencing suppressor acts behind the spreading infection front whereas at the frontthe movement protein (MP) of the virus spreads small RNAs as well as the viral genome.This complex mechanism potentially manipulates host gene expression and enhances cellsusceptibility before invasion. To gain insight into this process, we propose to use RNA deepsequencing and RNAseq to profile small RNAs and corresponding mRNA targets during thespread of GFP-tagged TMV infection sites in Nicotiana benthamiana. Respective profiles ofcells ahead, within, and behind the leading front of infection will be evaluated and furtherverified by Northern blots, RACE analysis, and innovative reporter constructs. These datawill provide important knowledge about the role of RNA silencing-mediated gene regulationduring viral invasion of plants. Post doc (18 months) Characterization of the purine permease (PUP) family of genes in Arabidopsis as candidates for a cytokinin transport system controlling signaling activities and domains Dr. Bruno Müller, Institute of Plant Biology, UZH Prof. E. Martinoia, Institute of Plant Biology, UZH Prof. Ueli Grossniklaus, Institute of Plant Biology, UZH Cytokinins control numerous and essential processes throughout the plant life cycle viaactivating a phosphorelay signaling cascade in signal-receiving cells. Various lines ofevidence suggest the existence of a cytokinin transport system, which enables signalingactivity at the cellular level, and contributes to define the signaling domains at the tissuelevel. However, the molecular nature of such a transport system has not been elucidated.The plant-specific purine permease gene PUP1, which belongs to a gene family comprising21 members in Arabdiopsis, has been characterized in yeast as low-affinity cytokinin cellularimporter in yeast cells. To identify novel PUP genes that could affect cytokinin signaling atphysiological cytokinin concentrations in planta, we cloned a representative set of previouslyuncharacterized family members and assayed the consequences of transient overexpressionon the cytokinin signaling response, both in a cellular system and in planta. These assayshave identified previously uncharacterized PUP family members that can strongly affect thecytokinin response at physiological cytokinin concentrations. These initial results motivate amore detailed functional analysis of the PUP genes as transporters of cytokinin, and wepropose a comprehensive analysis of relevant PUP family members, which includes thedetermination of their transcription patterns, subcellular localization, analyses of mutants,and cytokinin transport assays to establish a coherent logic of how PUP functions controlcytokinin signaling at the cellular and tissue level. PhD student (3 years) Causes and consequences of epigenetic variation in plant interactions with pollinators and herbivores Prof. Ueli Grossniklaus, Institute of Plant Biology, UZH Prof. Florian Schiestl, Institute of Systematic Botanic, UZH Post doc Heather Kirk, Institute of Systematic Botanic, UZH Most flowering plants use animals for pollination, and interactions between plants and their pollinators are key components of agricultural and natural ecosystems. For instance, pollination success is of great importance for the production of canola seed (Brassica napus) , a close relative of the species we propose to investigate here (B. rapa). In order to maintain beneficial mutualisms with their pollinators, plants have evolved floral signals, such as color and fragrance, which advertise rewards such as nectar. However, floral signals can also attract antagonists such as herbivores that have detrimental effects on plant fitness. Classical evolutionary models incorporate only genetic variation and changes in populationwide allele frequencies as mechanisms for diversification and adaptation. However, epigenetic variation is generated at a much higher frequency than genetic variation (1,2), and these epigenetic changes can be faithfully inherited (3,4). Epigenetic variation may therefore also be subject to selection and could contribute to evolutionary change (1,2,3), particularly in rapidly fluctuating environments. The role of epigenetic variation in individual and population level adaptive responses to pollinators and herbivores has never been investigated. This project will investigate the role of heritable epigenetic variation in response to selection by pollinators and herbivores. First, we will characterize the degree of genome-wide epigenetic variation between floral and vegetative tissues in B. rapa, and we will assesswhether herbivores drive epigenetic changes in floral and vegetative tissues within individuals and across generations. Second, in an extension of an ongoing project in the Schiestl lab, epigenetic variation will be characterized before and after several generations of herbivore- and pollinator-mediated selection in a Brassica rapa population. Floral signaling and plant defense traits will be measured over successive generations, and phenotypic selection on these traits will be quantified. Epigenomic changes associated with different selection pressures will be tracked. Post doc (12 months) Novel chimeric receptors inducing programmed cell death for resistance against the plant pathogenic Xanthomonas genera in model and tropical crop species Oberassistent Hervé Vanderschuren, Institute of Agricultural Sciences, ETH Post doc Emily McCallum, Institute of Agricultural Sciences, ETH Oberassistent Delphine Chinchilla, Botanical Institute, UniB In the proposed project, we will generate novel chimeric receptors for broad spectrum and sustainable Xanthomonas disease resistance in a variety of model and tropical crop species (Arabidopsis, cassava and rice). Using the Xanthomonas-specific pattern recognition receptor Xa21, we will replace the intracellular kinase domain (cleaved after bacterial recognition) with proteins known to trigger programmed cell death (PCD) in plants. Transgenic plants containing these chimeric receptors should induce a rapid, localized PCD response at the site of Xanthomonas infection, preventing bacterial replication and systemic infection of the host plant. Transient expression assays will be performed to verify appropriate cleavage, subcellular localization and PCD-induction of each chimeric receptor in planta, before and after exposure to Xanthomonas pathogens. Transgenic plants will be generated, and experiments undertaken to determine PCD responses and resistance to Xanthomonas infection. We seek funding for a postdoctoral fellow to undertake this research, which will be performed in collaboration between two laboratories with the necessary combined experience in plant-pathogen biology at the ETH Zürich and Basel University. Taking advantage of the skills and resources already available in each laboratory, the proposed research can be completed within 1.5 years. Post doc (12 Month) Start Spring 2010: Understanding and exploiting diversity in plant storage carbohydrates Prof. Samuel C Zeeman, Institute of Plant Sciences, ETHZ Prof. Wilhelm Gruissem, Institute of Plant Sciences, ETHZ We rely on the carbohydrates (sugars and starches) stored by plants. The work proposed here aims to discover novel protein factors that control how much and in what form carbohydrates are stored. Most plants store starch, but its metabolism is not fully understood. Unanswered questions surround the initiation of insoluble starch granules, the structure of the constituent polymers, and how amount is controlled. We will take two new approaches to tackle these questions, the results of which may enable the improvement of starch crops. First, we will analyze starch using proteomics to identify granule-bound proteins that may be involved in biosynthesis. The cooperation between our labs means that we have the combination of skills to do this. Through preparatory work and external collaborations, we have obtained the biological materials we need. Second, we will analyze the unique features of the tropical tree Cecropia peltata, which makes starch in its leaves, but soluble glycogen in other tissues. We have obtained C. peltata plants and established an EST library through 454 sequencing. Quantitative transcript and protein data will be obtained in this project through Illumina sequencing and mass spectrometry, respectively. This will tell us how the enzymatic machinery can be reconfigured for different polymer biosynthesis. Contact person: Dr. Sylvain Bischof sylvain.bischof@ipw.biol.ethz.ch Start Spring 2010: EPIGENOMICS: Characterization of Epigenetic Changes in Systems under Selection Prof. Ueli Grossniklaus, Institute of Plant Biology, UZH Prof. Bernhard Schmid, Institute of Environmental Sciences , ETHZ Dr. Lindsay A. Turnbull, Institute of Environmental Sciences, ETHZ Variation in plant traits and patterns of co-variation between these traits and environmental conditions are of great interest in ecology and agriculture. Disturbance of suitable conditions pose major problems for yield security, in particular given the current climate change. Whether species contain the necessary adaptive potential to respond to these changes, and which genetic or epigenetic changes are involved, are crucial to predicting crop performance in a changing environment. It has become increasingly clear that epigenetic changes could play a role in plant adaptation to a changing environment. In this project, we propose to investigate genome-wide epigenetic changes in experimental Arabidopsis populations that have undergone 5 generations of selection. This pilot study will establish the molecular and bioinformatic methods necessary to study epigenetic changes at the genome level and thus contribute to the two Target Areas “Plant Growth” and “Innovation and Technology”. A selection experiment was performed on Arabidopsis populations and phenotypic traits relevant to fitness were recorded. Quantitative analyses of allele distributions identified loci that were selected under specific conditions. Unexpectedly strong changes were found at both the phenotypic and genotypic levels under dynamic landscape selection for just 5 generations. In this proposal, we ask for further support to analyze the changes that occurred at the epigenetic level in the most divergent experimental and parental populations. Genomewide analyses of DNA methylation have become possible using bisulfite treatment in combination with next-generation sequencing technology. Contact person: Dr. Christian Heichinger christian.heichinger@live.com Start Spring 2010: Exploring unreduced male gamete formation for plant breeding Prof. Claudia Köhler, Institute of Plant Sciences, University ETH Zürich Prof. Lynette Brownfield, Institute of Plant Sciences , University ETH Zürich Our proposed research project is designed to explore molecular mechanisms governing unreduced gamete formation in plants and to exploit this knowledge to generate tools for plant breeding. Specifically, we would like to test whether unreduced male gametes can be produced by virus induced gene silencing of an important regulator of male meiosis in Arabidopsis and whether homologs of this gene perform a similar function in monocots. For this purpose we like to establish the genetically tractable model organism Brachypodium distachyon as a model for studying meiosis in monocots. Furthermore, we like to identify novel regulators of male meiosis in Arabidopsis by applying forward and reverse genetic screens with the aim to illuminate the underlying molecular mechanisms governing meiosis in plants. We plan to apply modern deep sequencing technology to map and isolate the affected genes. Apart from advancing our currently scarce knowledge on the molecular basis of meiosis in plants, the identified genes will provide important tools for the targeted generation of unreduced gametes in economically important crops. Interploidy crosses are rarely successful, posing a major problem for breeding of polyploid crop species like hexaploid wheat. Therefore, developing tools allowing the targeted generation of unreduced gametes at high frequency holds great promise for plant breeding programs. Contact person: PhD student David Kradolfer davidkra@ethz.ch Start Spring 2010: Integration of transcriptomics and genome-wide association study for identification of genes responsible for natural quantitative variation: A “multi-omics” approach Dr. Takashi Tsuchimatsu, Istitute of Plant Biology, UZH Prof. Ass. Kentaro Shimizu, Institute of Plant Biology, UZH Dr. Thomas Städler, Institute of Integrative Biology, ETHZ Most agriculturally important phenotypes are quantitative traits regulated by polygenes. Exploring the genes responsible for uantitative traits has long been a challenge in genetics; however, the resolution of classical quantitative-trait loci (QTL) apping is low, despite the labor-intensive and timeconsuming work involved in this approach. Recently, as sequencing and single-nucleotide polymorphism (SNP) typing costs continue to decrease, genome-wide association (GWA) studies are emerging as a powerful tool for the identification of genes responsible for quantitative natural variation (Nordborg & Weigel, 008 Nature; Atwell et al., 2010 Nature). GWA studies seek to screen genes underlying variable phenotypes, based on associations between phenotypes of interest and genome-wide genetic markers, such as SNPs. However, the large number of false-positive estimations has been a major obstacle. In this project, we will exploit the genome-wide SNP data in Arabidopsis thaliana to identify genes responsible for several reproductive traits that are known to be highly variable in this species. To avoid false-positive results, we propose the novel idea of “multi-omics mapping” by combining GWA studies and transcriptomics data obtained by microarrays. We will confirm these in silico predictions using transgenic experiments. The integration of computational and molecular genetic analyses will allow us to assess this approach and to propose improved statistical algorithms. These algorithms will be implemented and distributed as software that can be applied to other species, including crops. Contact person: Dr. Takashi Tsuchimatsu Start Spring 2010: The mechanisms of volatile-mediated plant growth promotion: A focus on indole Dr. Laure Weisskopf, Institute of Biology, UZH Prof. Thomas Boller, Botanical Institute, UniBs Prof. Leo Eberl, Institute of Biology, UZH Mounting evidence indicates that rhizosphere bacteria can promote the growth of plants through the emission of volatile organic compounds (VOCs). We have identified five bacterial VOCs which strongly promote the growth of Arabidopsis thaliana. This project aims at determining how plants perceive these bacterial VOCs and at elucidating the mechanisms underlying the observed growth promotion. We will use well-established bioassays to analyze the perception of our bacterial volatiles by A. thaliana. We will then further investigate one bacterial compound of particular interest: indole, a metabolite with multiple functions in bacterial communities. Based on its structural similarity to auxin, we hypothesize that plants can use indole as a precursor for this phytohormone. We will use available biochemical and molecular tools to test this hypothesis. The putative function of indole in priming defense responses will also be assessed. Despite numerous reports of plant growth promotion by bacterial volatiles, nothing is yet known of the perception of these compounds by plants and of the mechanisms involved in the observed growth promotion. This project will provide first insights into the plant’s perception of microbial VOCs and into the mode of action of these compounds. This will have significant impact on the understanding of volatilemediated plant-microbe interactions and also provide useful information for the prospective use of microbial VOCs as plant-growth promoting compounds. Contact person: NN Start Spring 2009: Decision making in plants: resource allocation to mycorrhizal hyphal networks Prof. Bernhard Schmid, Institute of Environmental Sciences, UZH Prof. Andres Wiemken, Institute of Botany, Uni Basel In contrast to animals, plants have no central nervous system with which to integrate deci-sion-making when foraging for resources. Nevertheless, intuitively, integration of information must be important for plants. This is particularly evident in the case of symbioses such as the mycorrhizal symbiosis, where the plant invests photosynthetic products (chiefly carbon) into a fungal partner in order to get access to mineral nutrients foraged for by the fungus. If part A of a plant root system has a connection with an arbuscular mycorrhizal fungus (AMF) that takes more resources than it returns and part B has an AMF connection that takes less than it returns, the plant should favor part B over part A to maximize its fitness. However, can a plant indeed select between the two AMF connections and display an "intelligent" integrated response? To answer this question we will construct experimental systems with split plant root systems of which one side has a more beneficial AMF connection than the other side. This will be done in two ways: (i) the two sides contain two AMF species differing in their ability to supply mineral resources to the plant, (ii) the two sides contain the same beneficial AMF species, but this AMF species is connected on one side to a different plant species known to disproportionately draw mineral resources from the mycorrhizal network while contributing relatively little carbon. The plant response will be assessed via growth analysis and tissue concentrations of N15 and P33 provided to the AMF on the two sides. The allocation of carbon to the AMF will also be assessed by isotopic analysis. Because we expect that plants are more selective when resources are scarce, we will use low or high levels of N and P in our experimental systems. Finally, we will expand the experimental systems to include two plants mutually limited by either N or P to test if resource sharing via a common AMF will occur to a greater extent than if the limitation is not mutual. The results of our research will contribute to the fundamental question of “decision-making” in plants and to the applied question of how interactions between plants and AMF affect plant performance in the wild and in agro-ecosystems. Contact person: PhD student Alicia Argüello García Start Spring 2008: Impacts of EXtreme CLIMatic Events on ecosystem functioning in alpine grasslands Dr. Michael Scherer-Lorenzen, Institute of Plant Sciences, ETHZ Dr. Eva Spehn, Institute of Botany, Uni Basel PD Dr. Andreas Lüscher, Grassland Systems and Forage Production, Agroscope Reckenholz-Tänikon Human induced climate change is unequivocal and ongoing, with the European Alps being a hotspot of warming. The future summer climate in Switzerland is predicted to be drier and warmer, with an increased probability of extreme events such as high intensity rainfall. In this project, we propose to study the impacts of prolonged summer drought and intensive rainfall on key ecosystem processes and services of alpine grasslands. At three sites representing the most contrasting extremes in macroclimate and geology we will simulate drought with rainout shelters, combined with a rainfall experiment. Replication of the experiment along steep altitudinal gradients will allow us to estimate the influence of different temperature regimes. Adopting an integrated and process-orientated approach, we propose to study (i) changes in sward structure and productivity, (ii) susceptibility to erosion and surface runoff, (iii) species-specific water stress responses, and (iv) litter decomposition, mineralisation and soil respiration in complementary work packages. Our project will contribute to predictions of the consequences of the most likely climate change scenario for the Swiss Alps. Because vegetation integrity of alpine grasslands reduces risk of erosion and secures slope stability, knowledge on vulnerability of these grasslands to climate change is crucial for the welfare and safety of many people. Contact person: PhD student Samuel Schmid samuel.schmid@ipw.agrl.ethz.ch Start Summer 2008: Relationship between the success of establishment of invasive plants and their mode of reproduction Prof. Ueli Grossniklaus, Institute of Plant Biology, UZH PD Dr. Jürg Stöcklin, Institute of Botany, Uni Basel Invasive plants pose a great problem to many natural ecosystems. Moreover, invasiveness and transgene spread are two of the major perceived dangers associated with genetically modified organisms (GMOs). The goal of this interdisciplinary project is the experimental simulation of the spread, establishment, and potential persistence of a typical transgenic trait. However, we will not analyze the spread and ecological behavior of a transgene in a GMO, but rather of apomixis, a trait that has all the typical characteristics of commonly used transgenes. Much of the perceived danger of GMOs has to do with their potential ability to spread rapidly in a population after out-crossing. This is based on the genetic nature of many commonly used transgenic traits, which (i) are dominant, (ii) can cross via pollen to related species, and (iii) have a potential advantage for the plants carrying the trait. All these characteristics are shared by the apomixis trait, which we will use as a model to experimentally simulate the short- and long-term ecological behavior of a transgene. Shortterm spread in different agricultural situations will be experimentally simulated in common garden plots using different landscape models. Long-term establishment and persistence of such traits will be studied by analysing the relative contribution of sexual and apomictic individuals on a glacier foreland that has been de-glaciated for various periods of time. The latter will allow us to infer the population dynamics of traits with the above characteristics over a period of 100-150 years, which can currently not be done with any other system. Contact person: PhD student Christian Sailer christian.sailer@access.uzh.ch Start Summer 2008: Structural and Functional Analysis of Ultraconserved Elements (UCEs) in Plants Dr. Thomas Wicker, Institute of Plant Biology, UZH Dr. Célia Jäger-Baroux, Institute of Plant Biology, UZH Prof. Ueli Grossniklaus, Institute of Plant Biology, UZH Three years ago, the first report on Ultraconserved Elements (UCEs) in mammals was published. UCEs are sequences of ≥200 bp that are nearly 100% conserved between orthologous regions of the human, rat and mouse genomes (Bejerano et al., 2004). Until now, no satisfactory explanation for this astounding finding has been proposed as no biological process is known that would require such an extreme sequence conservation. Some UCEs have been shown to have enhancer activity in mouse transgenic assays (Pennacchio et al., 2006). However, all protein-DNA interactions known to date do tolerate significant sequence divergence without dramatically affecting binding and no mechanism can be envisioned that would lead to such a high degree of sequence conservation. Our preliminary studies have shown that UCEs are also present in plant genomes and that some are evolutionary ancient (conserved between Arabidopsis, rice, and Physcomitrella). We propose to use a combination of bioinformatic, cytological, and population genetic approaches to study the structure and function of UCEs in plants as these offer unique opportunities due to the availability of insertional mutants and the large number of offspring produced. We will analyze UCEs in all available plant genomes and study their number and distribution within these genomes to detect possible peculiarities. Cytogenetic studies will reveal whether these sequences play structural roles in nuclear organization or chromosome pairing, and transmission studies using insertional mutants disrupting UCEs will reveal even slight effects on fitness traits. This interdisciplinary project is only possible through the cooperation of scientist with diverse expertise in experimental and computational biology. Contact person: PhD student Konstantinos Kritsas kokrits@gmail.com Start Summer 2008: Volatile mediated impact of bacteria on plant growth and disease resistance Dr.Laure Weisskopf, Institute of Plant Biology, UZH Prof. Thomas Boller, Institute of Botany, Uni Basel Prof. Leo Eberl, Institute of Plant Biology, UZH Increasing evidence indicates that bacteria can interact with other organisms (e.g. plants or fungi) through the emission of volatile organic compounds (VOCs). Of these VOCs, 2-3 butanediol was recently shown to induce changes in growth, auxin homeostasis and disease resistance of Arabidopsis thaliana. Interestingly, production of 2,3 butanediol is regulated by a quorum-sensing (QS) mechanism in various bacteria. QS regulates many bacterial functions important for plant-microbe interactions but a direct link between QS and VOCsmediated plant growth promotion has not yet been established. In this project, we will investigate the VOCs-mediated plant-bacteria interactions from both the plant’s and the bacteria’s perspective. We will test a wide range of bacterial strains for VOCs-mediated effects on growth of Arabidopsis thaliana in a compartmental Petri dish assay. A collection of mutants defective in QS-regulation will be used to assess the role of QS in bacteria-plant interaction. VOCs profiles of bioactive strains will be analyzed by GC-MS and active compounds will be identified. On the plant side, the perception of the bacterial VOCs will be studied using bioassays that are well-established in the group of Thomas Boller. Furthermore, mutants impaired in disease resistance will be used and the expression of relevant genes monitored to gain insights into the mechanism underlying the action of bacterial VOCs on plants. The collaboration between the Basel and the Zurich laboratories will enable us to investigate VOCs-mediated bacteria-plant interactions using an interdisciplinary approach. In addition to the gained basic knowledge on bacteria-plant interactions, this project may also lead to the discovery of new plant growth-promoting or biocontrol strains that could be of economical interest in crop science. Contact person: PhD student Dirk Blom Dirk.Blom@access.uzh.ch 2003-2008: Constraints to plant tissue formation in the cold Prof. Fred Meins, FMI Prof. Christian Körner, Botanical Institute, UniBS Dr. Andrew Fleming, Group Prof. Nikolaus Amrhein, Institute of Plant Sciences, ETHZ We propose that organisms selected to thrive in the cold are primarily limited by developmental constraints (i.e. meristemic activity, cell differentiation, and organogenesis), rather than stress resistance or carbon acquisition, conventionally the central themes in this field. We plan a gene identification approach with Arabidopsis thaliana ecotype Columbia to gain an understanding of molecular mechanisms important for regulating development in low temperatures. This will involve RNA profiling of Arabidopsis grown under low and high temperature to identify candidate genes, expression studies of these genes in high and low temperature ecotypes, and functional characterization of genes by T-DNA insertion mutagenesis combined with knock-down or over-expression in transgenic plants. Overall, the results of this project should help answering classical ecological questions with molecular techniques and the use of model organisms. The cooperation between the FMI, the ETH-Institute for Plant Sciences and the ecology unit at Botany in Basel is seen as an ideal opportunity for a PhD student interested in interdisciplinary problems. The laboratory work will be performed at the FMI, but the candidate will attend seminars in all three institutions and in the PSC program. Contact person: Fred Meins 2003-2008: Chemical signaling in the mutualistic arbuscular-mycorrhizal symbiosis in plants Dr. Marcel Bucher, Group Prof. Nikolaus Amrhein, Institute of Plant Sciences, ETHZ Prof. Thomas Boller, Botanical Institute, UniBS Prof. Enrico Martinoia, Institute of Plant Biology, UZH Although plants do not have sensory organs like animals, they can perceive chemical signals, such as e.g. nutrient concentrations or microbial substances, with a high specificity. Upon perception of the signal, a transduction mechanism eventually leads to the molecular response in the nucleus of a cell, i.e. induction or repression of gene expression. This project focuses on the molecular interaction between the fungus and the host plant in the mutualistic arbuscular mycorrhizal (AM) symbiosis. This symbiosis is more than 400 Mio years old and is thought to have been essential for the colonisation of land by plants. A central aspect of the AM symbiosis is bidirectional transfer of nutrients between both organisms, including phosphate (Pi) transport from the fungus to the plant at the fungus/root interface including structures such as arbuscules or coiled hyphae colonizing root cells. We have recently identified a Pi transporter gene named StPT3 which is specifically expressed at this interface. The fungal signal(s) and the subsequent signal transduction mechanisms involved in induction of the StPT3 gene are at present unknown. Recently, we have shown that these signaling mechanisms leading to mycorrhiza-specific Pi transport are well conserved in evolutionary distant plant species. Moreover, the signal transduction pathway is selectively activated by fungi from the phylum Glomeromycota. A primary goal of this project is the establishment of an in vivo screening system which eventually allows the identification of regulatory compounds in StPT3 expression. The proposed collaboration is promising with respect to signaling in the AM symbiosis. Secondly, this project contributes to an already existing project which aims at large-scale genomic screening to isolate AM-symbiosis signal-transduction mutants in the model plant Petunia. Contact person: Marcel Bucher marcel.bucher@ipw.biol.ethz.ch 2003-2008: Molecular and phenotypic diversity of wheat landraces for winter hardiness Prof. Beat Keller, Institute of Plant Biology, UZH Prof. Peter Stamp, Institute of Plant Sciences, ETHZ Dr. Jörg Leipner, Group Prof. Peter Stamp, Institute of Plant Sciences, ETHZ Wheat is worldwide one of the most important crops and, together with maize and rice, forms the basis of human and animal nutrition. In order to breed for crop plants required for the future, the optimised use and the availability of genetic resources are essential. For wheat, there are considerable numbers of accession available in gene banks, but they are not well characterised for many phenotypic traits, and it is not clear to which extent they contain valuable resources for a specific breeding goal. In addition, very little is known about the molecular polymorphisms at agronomically important genetic loci and their contribution to phenotypic variability. Here, we propose to study genetic resources of wheat for abiotic stress resistance, specifically for winter hardiness. A set of landraces will be phenotypically analysed for cold adaptation and freezing tolerance and groups of lines with different responses will be made. At the molecular level, we propose to identify candidate genes, which might be involved in the traits studied. This will be done based on physiological knowledge of freezing tolerance in wheat (obtained in this project) and other grasses as well as molecular studies in the model plant Arabidopsis (studies in the literature and databases). Haplotypes of a selected number of candidate genes will be analysed at the molecular level in wheat. We will investigate whether linkage disequilibria can be observed at these loci and specific haplotypes can be found in the freezing-tolerant lines. This work should contribute to a better molecular characterisation of winter hardiness in wheat using commonly available genetic resources. Contact person: Peter Stamp peter.stamp@ipw.agrl.ethz.ch 2004-2007: Genetic dissection of seed and fruit development in Arabidopsis thaliana Dr. Claudia Köhler, former group of Prof. Ueli Grossniklaus, Institute of Plant Biology, UZH Dr. Lars Hennig, Group Prof. Wilhelm Gruissem, Institute of Plant Sciences, ETHZ The development of fruits follows fertilization and occurs simultaneously with seed maturation. The fertilized gametophytes develop into seeds, whereas the carpels and, in some species, also other flower organs develop into the fruit. In apomictic species the formation of viable seeds and fruits occurs in the absence of fertilization, whereas parthenocarpic species form fruits without seeds. Thus it is possible to uncouple seed and fruit formation from the fertilization process, and also the formation of fruits can occur independently from seed formation. In Arabidopsis thaliana, several mutants have been identified forming fruits and seed-like structures independent of fertilization. The genes affected in these fertilization-independent seed (fis) class mutants encode proteins of the Polycomb group that are required to maintain the stable transcriptional repression of target loci. The msi1 mutant belongs to the fis class mutants displaying silique development in the absence of fertilization. We propose to perform a mutant screen using the msi1 mutant as a tool to dissect the genetic networks governing seed and fruit development. By searching for suppressors of the fis phenotype in a msi1 mutant background it will be possible to uncover the molecular events controlling the initiation of seed and fruit development and their link to plant hormone signal transduction processes. Furthermore, this study will allow us to dissect the role of MSI1 during seed and fruit development and toidentify downstream target genes of MSI1. Contact person: Claudia Köhler claudia.koehler@ipw.biol.ethz.ch 2004-2008: Identification and Characterisation of Tonoplast Transport Systems Using Proteomic Approaches Dr. Ulrike Schmidt, Group Prof. Enrico Martinoia, Institute of Plant Biology, UZH Dr. Sacha Baginsky, Group Prof. Wilhelm Gruissem, Institute of Plant Sciences, ETHZ Membrane proteins are responsible for the exchange of solutes between the cell and the surrounding medium as well as within different cellular compartments. In Arabidopsis thaliana the function of at least 2/3 of the predicted membrane proteins is unknown. The expression pattern and subcellular localization of these proteins can provide useful information for the understanding of their function in planta. A closer look at the literature reveals that among the different organelles only few vacuolar proteins have been investigated. To elucidate the function of vacuolar membrane proteins we will isolate tonoplast fractions from Arabidopsis cell cultures and cauliflower to identify vacuolar transport proteins by high-throughput mass spectrometry. Vacuolar localization of the identified proteins will be verified by GFP fusion constructs. Next, we will conduct a detailed functional characterization of putative transporters by the analysis of knock-out mutants, antisense/RNAi and overxpression plants, flux analysis using isolated vacuoles or tonoplast vesicles, and characterisation of vacuolar proteins in heterologous expression systems. Contact person: Ulrike Schmidt ulrike.schmidt@botinst.unizh.ch 2005-2008: Neutral versus niche-structured communities: testing for resource partitioning by plants Prof. Nina Buchmann, Institute of Plant Sciences, ETHZ Prof. Andrew Hector, Institute of Environmental Sciences, UZH Dr. Pascal Niklaus, Institute of Botany, UniBS At the large scale, 'neutral' models that assume species to be identical show surprising success in reproducing community patterns. In contrast, small-scale experiments have shown that complementary niche partitioning may allow species to coexist and cause biodiversity effects on ecosystem functioning. However, it is unclear if such complementarity is ubiquitous in all ecosystems and whether it is generally due to such resource-based niche partitioning. This interdisciplinary project experimentally tests whether plant species in temperate grasslands occupy different resource-based niches. Replicated experimental mixtures of plant species that are known to commonly co-occur in grasslands, plus replicated monocultures of all of the constituent species will be established. Furthermore, differences in traits related to resource capture and link these to resource uptake, and resource availability mediated by soil microorganisms, using stable isotope analyses (15N) will be tested. Contact person: Nina Buchmann nina.buchmann@ipw.agrl.ethz.ch Start Fall 2007: Discovering the mechanism of sucrose export from plant cells Prof. Samuel Zeeman, Institute of Plant Sciences, ETHZ Prof. Enrico Martinoia, Insitute of Plant Biology, UniZH The aim of the research proposed here is to discover the mechanisms by which plant cells release sugars that are assimilated during photosynthesis. This is crucial to the functioning of a plant, which contains both autotrophic and heterotrophic tissues. There are several sites at which sugars are unloaded into the extracellular space for uptake by neighbouring cells. This includes phloem loading, seed development and pollen development. Sugar export is also vital for the interactions between plants and mutualistic or parasitic fungi, (mycorrhizas and biotrophic pathogens, respectively). In all cases, little is known about the transport mechanisms mediating export, or their regulation. Most studies of metabolite transporters to date have identified sugar uptake systems. New techniques are required to isolate and study those involved in export. Understanding this process could be a key to optimise assimilate partitioning in crops. The major approach will focus on sucrose, the major transported sugar in plants, and will seek to identify carriers capable of mediating sucrose export using experimental and bioinformatic approaches. The functions of candidate proteins will be evaluated using a functional genomic approach in Arabidopsis. Contact person: PhD student HsiangChun Lin linh@ethz.ch