The research within this theme aims at elucidating the molecular and cellular bases of the processes that govern plant development.


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.

With the completion of genome sequences of Arabidopsis, soybean, rice, maize, and the increasing genome sequence information available for other plant species, among which the important crop species potato and tomato, a major part of the research on plant development involves a genome wide search for genes involved in various developmental processes in these plant species. The identification and functional characterisation of these genes, and the availability of novel bio-informatics tools to build genetic networks will provide crucial new insights on the dynamic regulatory control of the formation of a particular plant organ, and its functioning in the whole plant. Key regulatory genes and their products can also be used as molecular markers for the identity of specific cell types. Such markers are of pivotal importance to determine spatial and temporal factors controlling development, for example to study to what extent cells differentiate in an autonomous manner and how long and short range communication between cells and tissues contributes to developmental decisions. Insight in molecular mechanisms controlling development opens new possibilities to study the evolution of developmental processes.

The molecular and cell biology research of the EPS Theme 1 groups requires development of novel techniques and the use of ever faster and more precise methods in the omics and microscopy field to keep abreast with international competition. A powerful approach that is recognized by several Theme 1 EPS researchers is the combination of multi-disciplinary experimental science and mathematics, which should result in a systems biology approach of iterative modelling and experimentation. Such an approach comes into reach of EPS researchers, since key regulators of processes have been identified, and are presently being studied in living cells with in vivo chemistry techniques. The Molecular Systems Biology approach is rapidly applied for improving human health, but has as much potential for agriculture and its applications. EPS Theme 1 participants are currently employing molecular systems biology approaches to generate mathematical models of cell wall dynamics (Emons/Mulder, Plant Cell Biology, WU), polar auxin transport (Offringa, Molecular and Developmental Genetics, LU), flowering time specification (Angenent, Molecular Biology, WU) and root (Scheres, Molecular Genetics, UU) and nodule (Bisseling/Mulder, Molecular Biology and Plant Cell Biology, WU) patterning.

The following subthemes are in place:

Subtheme 1a - Signaling and Cell Development

Development and morphogenesis of plants are controlled by internal signals such as plant hor­mones including peptides and by plant growth stimulating bacteria that interfere with internal signaling pathways. The perception of these signals and their transduction play a role in almost every aspect of plant development. The research in this subtheme aims at the identification of signal molecules and the receptors involved in signal perception, and at the study of downstream pathways followed in signal transduction, that finally result in specific gene expression and morphogenesis. Apart from the classical plant hormones auxin, ethylene, cytokinins and gibberellins, hormone-like peptides and other molecules are involved in embryogenesis, organogenesis, flower senescence, shoot and lateral root formation. Also microbial signal molecules (lipo-oligosaccharides and peptide elicitors) are investigated. The isolation and characteriz­ation of developmental mutants disturbed in signal perception or transduction are key to this subtheme. Receptors are identi­fi­ed and their function investigated by genetic and bio­chemical approaches, including modern proteomics techniques. More frequently, proteins and protein complexes are studied in their natural environment within cells. For this purpose proteins are tagged with various fluorescent probes or antigenic tags enabling in vivo studies using microspectroscopical techniques such as Fluorescence Correlation Spectroscopy (FCS) and Fluorescence Lifetime Imaging Microscopy (FLIM) making use of Förster Resonance Energy Transfer (FRET) and immunocytochemical techniques. Development and use of FRET biosensors is performed to examine in a time resolved way the molecular mechanism of the ATP effects on FRET sensors fluorescence spectroscopy techniques. Arabidopsis thaliana and the legume models Medicago trunculata and Lotus japonica are used to study plant cell signaling, such as in the interaction between legume plants and Rhizobium bacteria, signaling pathways served by somatic embryogenesis receptor- like kinases, and phospholipid signaling. Other participants investigate the cellular changes that underlie the processes of organogenesis and embryogenesis, with studies on the role of cytoskeleton dynamics, cell division, cell elongation and cell wall formation. Here, advanced fluorescence light microscopy techniques are utilized to study the mechanisms of single protein complexes.

Contributors to Subtheme 1a:
  • Prof.dr. M.E. Janson, Dr. T. Ketelaar, Prof.dr. A.M.C. Emons (Plant Cell Biology, WU): The cytoskeleton in plant cell growth and division, intracellular organization and signaling.
  • Prof.dr. B.M. Mulder, Prof.dr. A.M.C. Emons (Plant Cell Biology, WU): The biophysics of cellulose synthesis.
  • Prof.dr. S.C. de Vries (Biochemistry, WU): Multiple signaling pathways served by the SERK receptors.
  • Dr. J.W. Borst (Biochemistry, WU): ATP effects on FRET biosensors.
  • Dr. T. Munnik, Dr. C. Testerink, Prof.dr. M.A. Haring (Plant Physiology, UvA): Role of phospholipids in plant signalling and development.
  • Prof.dr. T. Bisseling, Dr. H.G.J.M. Franssen, Dr. R. Geurts, Dr. E.H.M. Limpens (Molecular Biology, WU): Legume-Rhizobium interaction.
  • Dr. A.R. van der Krol, Prof.dr. R. Bino (Plant Physiology, WU), Dr. A.H.P. America (Bioscience, PRI, WUR): Cell specific proteomics in plants.

Subtheme 1b - Patterning and Differentiation

Plants have an amazing developmental plasticity, which allows them as sessile organisms to adapt to their environment, but at the same time specific parts of plant development occur according to fixed patterns that are under strict genetic control. This subtheme aims to study these controlled developmental programs. During embryogenesis, the basic body plan is laid down in the embryo with shoot and root meristem at opposing ends. Following germination, the seedling develops into the adult plant through organogenesis from the shoot meristem and root pericycle, which involves the induction of organ primordia that usually arise at specific positions. The research on plant organ development aims at understanding how positional information controls the generation of an organ. A good example of this research is the control of floral meristem initiation and the determination of floral organ iden­tity in the appropriate whorls in Arabidopsis and Petunia flowers. Participants of the sub-theme Patterning and Differentiation focus on the evolution of inflorescence and flower development, and the molecular action of floral specific MADS box proteins, and MADS box genes involved in female gametophyte development. Arabidopsis is the main model to study development at the organ and whole plant level. Studies focus on the role of the plant hormone auxin and its transport generated maxima and gradients in plant embryogenesis, organogenesis (flower and fruit), and plant architecture. The role of auxin is also studied as being part of the genetic network that establishes and maintains root meristem patterning. Auxin as well as cytokinin play a key role in legume root nodule formation and insight in the evolutionary origin of root nodule formation is studied Furthermore, the role of TALE homeodomain proteins in the control of the shoot meristem phase identity (vegetative vs. generative) is studied.

Contributors to Subtheme 1b:

  • Prof.dr. B.J.G. Scheres (Molecular Genetics, UU): Stem cell programming and Developmental gradients.
  • Dr. D. Weijers (Biochemistry, WU): Cell specification and cell communication in the Arabidopsis embryo.
  • Dr. M.C.G. Proveniers, Prof.dr. J.C.M. Smeekens (Molecular Plant Physiology, UU): Control of plant architecture - The role of TALE homeodomain proteins.
  • Dr. R. Offringa (Molecular and Developmental Genetics, LU): The role of the phytohormone auxin in patterning and organ development.
  • Prof.dr. R. Koes (Genetics, VU): Genetic control and evolution of inflorescence and flower development.
  • Prof.dr. G.C. Angenent, Dr. R.G.H. Immink, Dr. Kerstin Kaufmann (Molecular Biology, WU; Bioscience, PRI, WUR): Analysis of floral specific MADS box proteins.
  • Prof.dr. T. Gerats (Plant Genetics, RU): The ABC of floral development.
  • Dr. K. Boutilier (Bioscience, PRI, WUR): Haploid embryogenesis.
  • Dr. R. de Maagd, Prof dr. G.C. Angenent (Molecular Biology, WU; Bioscience, PRI, WUR): Tomato fruit development.


Subtheme 1c - Developmental Plasticity

Plants are able to adapt and grow in a wide range of different environments. The fundamental life processes that are at the basis of this tremendous developmental adaptive potential of plants are hardly understood and require further study. This is especially urgent in view of the rapidly changing climatic conditions due to anthropogenic factors. The responsive adaptations of plant species to their environments lead to differences in growth rate and productivity and to diffe­rences in light, water or nutrient use efficiency ('plant plasticity'). Ultimately adaptation will result in increased survival and reproduction.

Research within this subtheme is focused at unraveling the mechanisms involved in adaptation to changes in non-stress environmental conditions, such as light and temperature, at the ecological, biophysical and molecular level. A thorough under­standing of the genetic and physiological background of plant performance in different environments is crucial for nature conservation, and is essential for breeders to select the proper crop varieties for optimal yield under sustainable growth conditions.

Participants in this subtheme study for example the effect of elevated levels of light signaling on development of the green house crop tomato. An important anthropogenic factor is elevated temperatures (global warming), and how this affects fertility and fruit set is studied in field-grown tomatoes. Furthermore, the natural variation among Arabidopsis ecotypes is used to study the parental influence (tissue micro-environment) on seed size, or how sugar signaling acts in concert with plant hormones and environmental signals to control plant developmental processes, such as seed dormancy.

Contributors to Subtheme 1c:

  • Dr. A.R. van der Krol (Plant Physiology, WU): Exploring the potential of light signalling in tomato, petunia and Arabidopsis.
  • Dr. T. de Jong, Prof.dr. P.G.L. Klinkhamer (Ecology and Phytochemistry, LU): Paternal conflicts in seed size determination.
  • Dr. J. Hanson, Prof.dr. J.C.M. Smeekens (Molecular Plant Physiology, UU): Sugar sensing and natural variation in seed dormancy.
  • Dr. R. Offringa (Molecular & Developmental Genetics, LU): Auxin transport, and plant growth in response to environmental signals.
  • Dr. S.C.P. Groot (Bioscience, PRI, WUR): Shoot meristem determinacy and environment.

Graduate School Experimental Plant Sciences