1. Call Fellows

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PLANT FELLOWS gets off to a good start

Eleven young plant scientists were chosen from the first call of the PLANT FELLOWS international post doc fellowship programme. To learn more about their interesting research projects see the table below and click on the links to their principal investigators and host organisations.

Dr. Firas Talas


ETH Zurich, Institute of Integrative Biology, Group of Plant Pathology

Principal Investigator: Prof. Dr. Bruce McDonald


Project title: Population genetics of fungicide resistance in the wheat head scab pathogen Fusarium graminearum

Fusarium head blight is a destructive disease of wheat and other cereals caused by F. graminearum. My PhD research was oriented around resistance breeding in wheat.        I focused on the environmental factors that may select for higher aggressiveness in Fusarium graminearum populations, enabling this pathogen to overcome existing resistance in wheat. At the ETH I will study the development of resistance to several groups of fungicides in F. graminearum populations. The rapidly decreasing cost of Next Generation Sequencing (NGS) makes it possible to obtain genomic information across multiple populations.

My goal is to identify candidate genes, and possibly specific point mutations, associated with fungicide resistance. Identification of these genes will increase our understanding of the mechanisms that underlie resistance in this filamentous fungus and may provide insight into more effective anti-resistance strategies.

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Dr. Javier Martin Sanchez


University of Zurich, Institute of Plant Biology

Principal Investigator: Prof. Dr. Beat Keller


Project title: Molecular analysis of wheat disease resistance against powdery mildew and glume blotch

The best approach to fight pathogens in the context of a sustainable agriculture is through the use of the resistant cultivars. The awarded project is an ambitious project covering the molecular characterization of two important diseases affecting wheat in Switzerland: Powdery mildew, caused by Blumeria graminis f. sp. tritici and Stagonospora nodorum glume blotch (SNGB). We aim, through genomic, functional genomics and molecular biology approaches to 1) molecularly clone and characterize two powdery mildew resistance genes, Pm1a and Pm4, and 2) identify and validate candidate genes conferring resistance against SNGB identified and genetically studies as a QTL.



Dr. Ruben Gutzat


Gregor Mendel Institute of Molecular Plant Biology (GMI), Vienna

Principal Investigator: Dr. Ortrun Mittelsten Scheid


Project title: Stability of epigenetic information in the shoot apical meristem

Epigenetic inheritance refers to the stability of gene expression states during cell divisions and between generations. For the latter, epigenetic information has to be transmitted faithfully through the germ line.

While the germ line of animals is set aside very early during development, the germ line of plants is defined out of cells of the shoot apical meristem (SAM) only after a long growth period, in which plants have to continuously adjust to highly variable environmental conditions. This includes epigenetic mechanisms, as exemplified by the chromatin changes after temperature-induced vernalization control of flowering time. However, the vernalization response on the chromatin level is reset in every generation, arguing either for germ line cells being exempt from the response to the exogenous stimulus, or for a genome-wide epigenetic re-formatting in the germ line. These possibilities must differ with regard to molecular mechanism, and likely also in fidelity and accuracy of maintenance. We aim to characterize epigenetic features and their stability in the shoot apical meristem of Arabidopsis upon stressful environmental conditions and their link with the transmission of phenotypic changes. The results will give insights into how robust epigenetic states are in the shoot apical stem cells. The identification of epigenetic regulators, either in maintenance or flexibility, might also pave the way to intentionally enhance epigenetic diversity in plant breeding and conservation biology.

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Dr. Heather Kirk

University of Zurich, Institute of Systematic Botany

Principal Investigator: Prof. Dr.  Florian  Schiestl


Project title: Evolution of floral signallig

Most flowering plants use animals for pollination, and plant- pollinator interactions are important components of natural and agricultural ecosystems. Plants use floral signals such as color and fragrance to advertise rewards such as nectar. However, floral signals can also attract antagonists such as herbivores that have detrimental effects on plant fitness. Additionally, defense mechanisms in plants that are induced by herbivore attack may compromise plants’ attractiveness to pollinators, resulting in reduced reproductive success. The research project will investigate potential tradeoffs between attraction and defense in a model system (Brassica rapa) that is highly relevant for agriculture. The functions and evolution of floral signals in response to selection by mutualists and antagonists will be investigated.

This multidisciplinary project will include an experimental evolution study that will incorporate approaches from chemical ecology, genomics, and epigenetics.



Dr. Dominique Arnaud

Pohang University of Science and Technology (POSTECH), Divison of Molecular and Life Sciences

Principal Investigator: Associate Professor Il-Doo Hwang


Project title: Unraveling the role of cytokinin in stomatal immunity

Stomata are critical during the plant innate immune response by limiting bacterial entry into plant tissues and subsequent disease symptoms. A rapid stomatal closure occurs upon perception of PAMPs and it was demonstrated that the ABA, ethylene and SA signaling pathways are required for PAMP-triggered stomatal closure. However, the role of cytokinin (CK) hormones in stomatal immunity is still unknown. Recent studies have showed that CKs play an important role in PAMP-triggered immunity (PTI) by promoting the SA signaling pathway.

Moreover, elements of the two-component CK signaling pathway such as the Arabidopsis cytokinin histidine kinase receptors (AHKs) and response regulators (ARRs) are required for apoplastic defense response. The main objective of the research proposal is to elucidate the underlying molecular mechanisms on the cytokinin-mediated regulation of stomatal immunity by conducting integrative approaches that include molecular genetics, cellular biology, functional genomics, biochemistry and system biology.

For this purpose, research activities will be conducted 1) to characterize the modulation of stomatal immunity by CKs, 2) to identify components of the CK signaling pathway and their downstream target genes involved in the regulation of PAMP-triggered stomatal closure and 3) to analyze the molecular and physiological mechanisms involved in the regulation of stomatal immunity by CKs and AHK/ARR proteins.



Dr. Ezequiel Lentz


ETH Zurich, Institute of Agricultural Sciences, Group of Plant Biotechnology

Principal Investigator: Prof. Dr. Wilhelm Gruissem


Project title: Molecular approaches to investigate and enhance drought tolerance in cassava

This project focuses on the molecular mechanisms underlying the drought response of cassava (Manihot esculenta). Genes differentially regulated during water stress will be identified by transcriptomics and proteomics studies in roots and leaves of drought tolerant cassava cultivars, under drought situations representative of field conditions. Expression patterns of candidate genes for an enhanced drought tolerant phenotype will be validated, and their function will be further studied employing transgenic cassava and virus induced gene silencing. These studies will certainly contribute to the understanding of the molecular mechanisms underlying drought tolerance in cassava and will lead to its genetic improvement, in order to cope with the more frequent drought episodes due to climatic change that affect crop yields worldwide.

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Dr. Daniela Liebsch


Umea Plant Science Center (Sweden), Department Forest Genetics and Plant Physiology

Principal Investigator: Dr. Urs Fischer


Project title: Cambial function of KNAT1 and STM

Plant growth is mediated by meristems, specialized regions that contain stem cell populations giving rise to all postembryonically formed organs. Consequently, an intricate balance between organogenesis and differentiation on the one hand and meristem maintenance on the other hand is of the utmost importance to sustain proper plant development. To understand the complex regulatory mechanisms acting to ensure this vital balance is one of the major and most fascinating challenges in plant biology.

Among the key regulators involved in these processes are class-I KNOX (KNOTTED1-like homeobox) transcription factors. In Arabidopsis thaliana (Arabidopsis), the homeodomain transcription factors SHOOTMERISTEMLESS (STM) and KNOTTED1-LIKE FROM ARABIDOPSIS THALIANA 1 (KNAT1) regulate meristem maintenance in the shoot apical meristem (SAM) by preventing cell differentiation.

Both STM and KNAT1 also influence cell differentiation in the hypocotyl, where another meristem - the vascular cambium - gives rise to cambial daughter cells which subsequently differentiate into secondary xylem and phloem, respectively. However, rather than preventing cell differentiation as in the SAM, STM and KNAT1 are positively required for the differentiation of cambial derivatives into xylem fibers, an effect that seems to be local for KNAT1 and potentially mediated by a mobile signal in case of STM.

As a PLANT FELLOW, I will be working in the group of Dr. Urs Fischer at the Umeå Plant Science Centre, on elucidating the molecular mechanisms underlying this cambial function of KNAT1 and STM as well as on the molecular basis for the apparent functional difference with regard to the SAM.

For this purpose, I will analyze tissue specific differences in protein interaction and target gene spectra as well as in target regulation for KNAT1 by comparative ChIP-seq, gene expression analysis, and yeast-2-hybrid screening. To get insight into the nature of the potential mobile signal mediating the effect of STM on the differentiation of cambial derivatives, a candidate approach involving tissue specific expression and grafting will be pursued.

This work will allow us to better comprehend how the delicate balance of differentiation in the cambium and the SAM is regulated and increase our understanding of plant development in general.



Dr. Timothy Paape

University of Zurich, Institute of Evolutionary Biology and Environmental Studies

Principal Investigator: Prof. Dr. Kentaro Shimizu


Project title: Population genomics, gene expression and evolutionary rates in allopolyploid species

Allopolyploid species in Brassicaceae have broad geographic distribution and inhabits many highly variable climates. Using next-generation sequencing I am identifying homeologous gene copies whose haplotypes are traceable to each of the diploid ancestors. I will use polymorphism and divergence data from single nucleotide polymorphisms (SNP’s) to characterize genome wide patterns of diversity, and signatures of positive and purifying selection between homeologs. Using A. thaliana orthologs to orient as an outgroup, I will estimate genome wide patterns of selection using allele-frequency based statistics and adaptation (α) by using ingroup polymorphism vs. outgroup divergence. After identifying ancestral homoelogous gene identities, differential signatures of positive and purifying selection.

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Dr. Lars Götzenberger


Institute of Botany ASCR, Section of Plant Ecology

Principal Investigator: Prof. Dr. Jitka Klimesova


Project title: Exploring the role of functional diversity in community assembly across scales

The general aim of our research project is to analyse functional trait diversity patterns in a variety of plant communities, integrating the latest available methods and theoretical advances, to test for the relative importance of different assembly processes: limiting similarity, environmental filtering and dispersal processes. This will be achieved by spanning a range of different scales and environmental conditions, involving own field surveys as well as existing databases at local, regional and national scales. Functional diversity will be decomposed at different levels (within and between species, within and between communities) and assessed in connection with taxonomical and phylogenetic diversity. In particular, we will follow three research topics within our project.

  1. 1. Functional composition of small scale patches within wet-grassland communities across 22 meadows with different productivity and grassland management regimes.
  1. 2. Assembly patterns in a large set of vegetational data (Czech National Phytosociological Database) using a novel method that compares functional diversity of the species in the community with that of the regional species pool.
  2. 3. Functional diversity and its turnover across large scale grid cells (approximately ten by ten kilometres) at the national scale in Germany and Czech Republic.

We anticipate that results from all three objectives will help to improve our understanding of plant community assembly across a range of geographical and environmental scales. The research project will thus help to recognize how biotic and abiotic processes govern the maintenance of species diversity and make an important contribution to improving the predictability of future changes in vegetation.



Dr. Cornelia Eisenach


University of Zurich, Institute of Plant Biology

Principal Investigator: Prof. Dr. Enrico Martinoia


Project title: Regulation of vacuolar anion transport in stomatal response

Plant CO2 and water relations are crucial for biomass production and are regulated by stomata. Stomatal aperture is regulated by a pair of guard cells, which swell to open and shrink to close a stoma. Swelling and shrinkage depend on the uptake and loss of osmotically active substances, mainly K+, Cl- and malate2-. In this process solute transport in and out of the vacuole is of central importance. Although we know a lot about the regulation of solute fluxes across the plasma membrane our knowledge about the transporters and ion channels involved in mediating these solute fluxes across the vacuolar membrane, the tonoplast, is scarce.

In the recent past my host lab headed by Prof. Enrico Martinoia has made important advances in characterising proteins that are responsible for mediating malate2- and Cl- fluxes: members of the AtALMT family of Arabidopsis thaliana have been shown to be tonoplast-localised ion channels. During the next three years I plan to further elucidate the role of these channels in stomatal response. Using a combination of electrophysiology, biochemistry, and gas exchange measurements I aim to understand how these channels are placed in the guard cell signalling network especially with regard to CO2 signalling. On a molecular level I aim to further analyse the regulation and electrophysiological characteristics of selected members of the ALMT family.

In toto, my research shall elucidate new properties of ALMT-channel regulation in response to environmental signals and set vacuolar anion fluxes in the context of guard cell signaling.

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Dr. Gavin George


ETH Zurich, Institute of Agricultural Sciences, Group of Plant Biochemistry

Principal Investigator: Prof. Dr. Samuel C. Zeeman


Project title: Understanding how fluxes in carbohydrate metabolism control plant growth using an integrated, cross-species analysis

Society depends on plant biomass for its food, fuel and materials. Biomass accumulation is underpinned by the photosynthetic production of carbohydrates, which are partitioned for growth and for temporary storage as leaf starch. This leaf starch is used to sustain growth at night. Recently, a broad study of Arabidopsis ecotypes identified leaf starch as the factor with the tightest correlation to plant biomass production. Fast-growing ecotypes make less leaf starch than slow growing accessions. However, mutations affecting enzymes of starch synthesis, which abolish leaf starch altogether, lead to dramatic reductions in growth. Mutations that affect enzymes of starch degradation, preventing starch mobilization at night, also cause strong reductions in growth. Thus, it appears that leaf starch metabolism is critical, but needs to be optimized to deliver the highest growth rates. My project will discover whether leaf starch is generally important for plant growth using existing genetic resources. I will use next-generation sequencing to detect carbon starvation in other species, based on starvation reporter genes identified in Arabidopsis. Overall, my work will extrapolate from pioneering Arabidopsis studies to generate a cross-species picture of the control of carbon allocation and growth coordination – critical for subsequent crop improvement.

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