The Graduate School Experimental Plant Sciences (EPS)

Research Themes

Research Themes2023-08-28T12:45:51+01:00

EPS Theme 1 – Developmental Biology of Plants

The research within this theme aims at elucidating the molecular and cellular bases of the pro­cesses that govern plant development. During development of plants, the genetic inform­ation contained in the zygote is passed to successive generations of cells by cell division. During this process the cells become arranged in tissues and organs with different specific functions. In seed plants, the zygote develops first into an embryo that is stored in the seed, and only after seed germination the post-embryonic development of the plant body starts. A key role in the deve­lopment of plants is played by the primary meristems, which are laid down in the embryo. They produce new cells that differentiate into tissues and organs, depending on the position of the meristem in the plant. During the vegetative stage of the plant, the primary meristems and secondary meristems form organs such as roots, stems, leaves, and with the transition to flower­ing, floral organs. In addition to the genetic information carried by the meristematic cells, internal signal molecules such as growth regulators, and external factors such as light, temperature and availability of nutrients also contribute to the embryonic and/or post-embryonic development of the plant.

  • dr. G.C. Angenent (Molecular Biology, WU; Bioscience, PRI, WUR): Plant developmental systems
  • J.W. Borst (Biochemistry, WU): Biomolecular imaging
  • K. Boutilier (Bioscience, PRI, WUR): Haploid embryogenesis.
  • G.W. van Esse (Molecular Biology, WU): Plant architecture and development
  • R. Geurts (Molecular Biology, WU): Nodulation Engineering
  • R. Heidstra (Molecular Biology, WU): Stem cell specification and regeneration
  • dr. R.G.H. Immink (Molecular Biology, WU; Bioscience, PRI, WUR): Molecular control of flowering and reproduction of plants
  • T. Ketelaar (Cell Biology, WU): The cytoskeleton in plant cell growth and division, intracellular organization and signaling
  • W. Kohlen (Molecular Biology, WU): De novo meristem formation
  • dr. R. Koes (Plant Development & (Epi)Genetics, UvA): Genetic control and evolution of inflorescence and flower development.
  • E.H.M. Limpens (Molecular Biology, WU): Molecular development of Arbuscular Mycorrhizal symbiosis
  • R. de Maagd, Prof dr. G.C. Angenent (Molecular Biology, WU; Bioscience, PRI, WUR): Tomato fruit development.
  • T. Munnik (Cell Biology, UvA): Role of phospholipids in plant signalling and development.
  • M.D. Nodine (Molecular Biology, WU): RNA Biology of Plant Embryos
  • R. Offringa (Plant Sciences and Natural Products, LU): The role of the phytohormone auxin in patterning and organ development.
  • M.C.G. Proveniers (Molecular Plant Physiology, UU): Control of plant architecture – The role of TALE
  • homeodomain proteins
  • E.E. Smakowska-Luzan (Biochemistry, WUR): Redox Cell Surface Signaling
  • dr. D. Weijers (Biochemistry, WU): Plant development
  • V. Willemsen (Molecular Biology, WU): Plant architecture in relation to the environment
  • dr. J. Xu (Plant Systems Physiology,RU): Systems biology

EPS Theme 2 – Interactions between Plants and Biotic Agents

Plants dynamically interact with a wide range of organisms, some of these are harmful (e.g. pathogens, pests and even parasitic plants) while others are beneficial (e.g. growth- or resilience inducing microbes, pollinators, natural enemies of pests) for the plant. These interactions are not only interesting objects for study, but they are also highly relevant as plant pathogens and pests destroy nearly 35% of the world’s annual crop harvest. Researchers in this theme study wild and cultivated accessions of economically important crops, such as potato, tomato, barley, tobacco and Brassicaceae, next to model species such as clover and Arabidopsis thaliana. The ecological, physiological and molecular interactions of these plants with a wide range of biotic agents, such as viruses, bacteria, fungi, oomycetes, nematodes, plants, insects, and mites are investigated. The main research focus lies on: (a) pathogenicity and virulence factors from the invader, (b) resistance and susceptibility of the hosts, (c) multitrophic interactions in which a plant is exposed simultaneously to various stresses and (d) how plants balance interactions with both antagonists and mutualists. Understanding the ecological context that shapes plant adaptations to various stresses will unravel evolution of plant resilience to the myriad of stresses they are exposed to. Elucidation of the molecular mechanisms underlying these intricate interactions will contribute to the development of disease resilient crops that retain compatibly with beneficial organisms.

Theme Coordinator : Erik H. Poelman

My research team studies the interactions between plants and insects addressing curiosity driven questions on how plants defend themselves against the numerous insects they harbour, what shapes the composition of these insect communities and how insect behaviour is adapted to the complexity of the ecological communities they are part of. Fundamental understanding of these interactions is key in development of sustainable and resilient agriculture in which pest insect occurrence is kept below an economic threshold using plant traits and insect interactions such as biological control to reduce pesticide use.

Our research focuses on the mechanisms and community-wide consequences of the induced responses of plants to insect herbivore damage as a major component of plant defence strategies. A central theme in our studies are induced plant responses to herbivory that initiate interaction networks among many members of plant-insect communities, such as herbivores, parasitoids, hyperparasitoids, and pollinators.

Theme Coordinator : Frank Takken

My main research interest is elucidating of the molecular and biochemical mechanisms underlying disease-resistance and -susceptibility in plants. I want to understand how the immune system of a plant functions and translates pathogen recognition into effective defence responses. Furthermore, I want to know how pathogens manipulate their hosts and manage to evade its immune system. Thereto, I am keen on developing new technologies, which can also be applied to convert knowledge into novel strategies for disease resistance.\

  • G. van den Ackerveken (Plant-Microbe Interactions, UU). Molecular basis of disease susceptibility in Arabidopsis
  • Y. Bai, Dr. A.W. van Heusden, Prof.dr. R.G.F. Visser (Plant Breeding, WUR): Resistance breeding
  • dr. M. Dicke (Entomology, WU): Chemical and molecular ecology of tritrophic interactions
  • M.H.A.J. Joosten (Phytopathology, WU): Resistance and (a)virulence in the interaction between Solanaceous plants and their pathogens
  • L. Fokkens (Phytopathology, WU): Comparative genomics
  • J.A.L. van Kan (Phytopathology, WU): Molecular genetic analysis of Botrytis species
  • M.R. Kant (Population Biology, UvA): Exploring how herbivore variability leads to adaptation against host-plant defenses
  • dr. G.H.J. Kema (Phytopathology, WU): tropical phytopathology
  • dr. G.H.J Kema, Dr. H.J.G. Meijer, Dr. T.A.J. van der Lee, Dr. C. Waalwijk (Biointeractions, PRI, WUR): Mycosphaerella and Fusarium research
  • dr. P.G.L. Klinkhamer (Ecology and Phytochemistry, LU): Ecology and evolution of herbivory and plant defence systems
  • R.J.M. Kormelink, Dr. E. Matsumura (Virology, WU): Plant viruses
  • dr. J.J.A. van Loon (Entomology, WU): Ecophysiology of insect-plant interactions
  • dr. C.M.J. Pieterse, Prof. dr. A.C.M. van Wees, Dr. R. de Jonge, Dr. R. Berendsen (Plant-Microbe Interactions, UU): Exploring the immune response of Arabidopsis
  • E. Poelman (Entomology, WU): Mechanisms and community-wide consequences of the induced responses of plants to herbivore damage
  • W.H. van der Putten, Dr. A. Biere (NIOO): Interactions aboveground-belowground induced responses
  • J.M. Raaijmakers (NIOO): Molecular and functional analysis of biosurfactant production in beneficial and plant pathogenic Pseudomonas species
  • dr. M. Rep (Plant Pathology, UvA): Identification and functional analysis of pathogenicity factors of Fusarium oxysporum
  • A. Schots (Nematology, WU): Oral immune regulation of inflammatory bowel diseases.
  • dr. G. Smant, Dr. A. Goverse, Dr. J. Helder, Dr. R. Wilbers, Dr. J. Lozano Torres, Dr. M. Sterken (Nematology, WU): Plant-nematode interactions
  • dr. R.C. Schuurink, Prof.dr. M.A. Haring (Plant Physiology, UvA): The role of plant volatiles in airborne communicatio
  • F.L.W. Takken (Plant Pathology, UvA): Uncovering the molecular mechanisms of R protein function.
  • V.G.A.A. Vleeshouwers, Prof.dr. R.G.F. Visser, (Plant Breeding, WUR): In search for durable resistance against the potato pathogen Phytophthora infestans

EPS Theme 3 – Metabolism and Adaptation

EPS theme 3 combines two fields of plant biology that are intimately connected, Metabolism and Adaptation. Metabolism underlies the functioning of plants, ranging from the fundamental primary processes of photosynthesis and respiration to the synthesis of, sometimes species-specific, secondary metabolites that are responsible for an enormous diversity in traits in the plant kingdom. At the same time, plants are plastic: they continuously sense their environment and adjust their metabolism, growth and development to deal with external changes. This ability to acclimate is a key determinant of their fitness. Over evolutionary time, natural selection has resulted in the great variation in constitutive and inducible environmental adaptation strategies that are found within and among plant species. Insight into the metabolism and adaption of plants helps us to understand how biological processes are regulated and supports the breeding for novel traits, such as those necessary to sustainably maintain yield in the face of climate change and resource limitations.

Theme Coordinator : Ivo Rieu

Dr Ivo Rieu is interested in the physiological basis of plant stress responses and tolerance traits, in particular those related to the effect of high temperature on plant fertility. With a combination of approaches, from cytology and physiology to genomics and genetics, he aims to understand which processes become rate limiting in times of stress and which responses are adaptive. By targeting both, model and crop species, the research generates fundamental as well as urgently needed applicable knowledge and contributes to the development of sustainable, climate-smart agriculture.

Theme Coordinator : Leónie Bentsink

Professor Dr Leónie Bentsink is intrigued by the potential of seeds to survive storage and to time their germination to appropriate moments that allow successful establishment of the seedling. Her research focusses on the regulation of seed germination and includes traits like seed dormancy and seed longevity. The research group has a strong background in the physiological and genetic analyses of these important seed traits and combines these approaches with investigating cellular processes, for example the translational regulation of mRNAs that appears to be strongly regulated during seed germination. All research is being performed in relation to the ecological importance of seed germination and its application prospective for the industry.

  • dr. M.G.M. Aarts (Genetics, WU): The genetics of complex traits in Arabidopsis thaliana and related Brassicaceae species
  • dr. H. van Amerongen, Dr. J. Hohlbein, Dr. E. Wientjes (Biophysics, WU): Primary steps in plant photosynthesis
  • dr. L. Bentsink (Plant Physiology, WU): Seed science
  • P.M. Bleeker, Prof. dr. M.A. Haring (Plant Physiology, UvA): Production of secondary compounds in tomato glandular tissues
  • A.B. Bonnema, Prof.dr. R.G.F. Visser (Plant Breeding, WUR): Quality and Development research in crop plants
  • dr. H.J. Bouwmeester (Plant Hormone Biology, UvA): The role of plant hormones in the communication between plants and other organisms
  • dr. T.M. Elzenga (Ecophysiology of Plants, RUG): Membrane transport processes in plants
  • C.M.M. Gommers (Plant Physiology, WUR): Chloroplast development and chloroplast function and signalling in light and abiotic stress responses
  • dr. R.D. Hall, (Plant Physiology, WU): Metabolomics in plant science
  • R. Karlova (Plant Physiology, WU): Stress resilience in crops
  • L.J. de Kock (Ecophysiology of Plants, RUG): Plants’ Sulfur Metabolism and its Significance in Adaptation to the Environment
  • dr. R.E. Koes, Dr. F.M. Quattrocchio (Plant Development & (Epi)Genetics, UvA): Regulation of vacuolar pH in flower epidermal cells
  • dr. J. Memelink (Plant Cell Physiology, LU): Plant responses to jasmonic acid
  • V. Mironova (Plant Systems Physiology, RU): Genomics and systems biology
  • T. Munnik (Plant Cell Biology, UvA): Phosphatidic acid signaling in Arabidopsis ethylene and salt stress responses
  • I. Rieu (Plant Cell Biology, RU): Biotic and a-biotic stress responses in Solanaceae Dr. H. Schluepmann (Molecular Plant Physiology, UU): Trehalose metabolism in plants.
  • dr. R.C. Schuurink, Prof.dr. M.A. Haring (Plant Physiology, UvA): Molecular control of fragrance biosynthesis in higher plants
  • dr. C.S. Testerink (Plant Physiology, WU): Abiotic stress tolerance
  • L.M. Trindade, Prof.dr. R.G.F. Visser (Plant Breeding, WUR): Bioengineering of metabolic pathways in food and industrial crops
  •  Prof. dr. R. Pierik, Dr. R. Sasidharan (Plant Ecophysiology, UU): Regulation of environmentally induced elongation growth
  • J. Xu (Plant Systems Physiology, RU): Physiology in plant systems

EPS Theme 4 – Genome Biology and Gene Regulation

The central research topic of this theme is the organization of the genome, which is studied at all levels, including the molecular structure, nuclear and cellular organisation and genetic transmission, as well as at the level of populations, phylogeny and evolution. The major disciplines involved include; Genetics, Biosystematics, Genomics and Bioinformatics. The four are closely related with numerous connections and opportunities for co-operations within Theme 4 and with research groups in the other themes.

Theme Coordinator : Aalt-Jan van Dijk

My research focuses on the development and application of machine learning approaches to analyze plant -omics data. Recently, this includes for example the development of protein-structure based machine learning to analyze protein function and interaction. This allows to get insight into the molecular mode of action of e.g. important transcription factors such as MADS domain proteins. Other examples of applying machine learning include prediction of meiotic crossovers in various plants based on genome sequence data, prediction of gene regulatory interactions or modelling genotype-phenotype relationships.

  • F.T. Bakker , Prof. dr. M.E. Schranz (Biosystematics, WU): Evolution and phylogenetics of plant species, including wild relatives of crop plants
  • P. Bourke (Plant Breeding, WUR): Genetics
  • dr. P.W. Crous (Phytopathology, WU): Host specificity and speciation in the Dothideomycetes
  • H.J. van Eck, Prof.dr. R.G.F. Visser (Plant Breeding, WUR): Genetic and Physical mapping of the Potato Genome
  • N. Fatouros (Biosystematics, WU): evolution of insect-microbe-plant interactions
  • P. Fransz, Dr. M.E. Stam (Plant Development & (Epi)Genetics, UvA): Regulation of the chromatin structure in Arabidopsis and maize
  • J. Keurentjes (Genetics, WU): Plant genetics
  • dr. D. de Ridder, Dr. Marnix Medema, Dr. Sandra Smit, Dr. H. Nijveen, Dr. A.J. van Dijk, Dr. A. Kupczok (Bioinformatics, WU)
  • dr. E. Schranz (Biosystematics, WU): Comparative and Ecological genomics in the Brassicaceae
  • K. Verhoeven (NIOO) Ecological epigenetics
  • E. van de Weg, Dr. P. Arens, Dr. C. Maliepaard (Plant Breeding, WUR): Crop genomics.
  • M. van Zanten, Prof. dr. J.C.M. Smeekens (Molecular Plant Physiology, UU): Mechanisms of plant high temperature acclimation