The global demand for plant-derived products such as feed and food is increasing dramatically. It is hard to fathom, but in the coming decades three billion additional people will have to be fed while less arable land is available. Plants also start to play a major role in supplying a sustainable, CO2-neutral source for the ever-increasing energy needs.
There is an obvious and urgent need to further increase crop productivity. As yield is the most important trait for breeding, a considerable amount of (eco)physiological research has been conducted on yield performance of crops. In contrast, surprisingly little is known about the molecular networks underpinning crop yield and plant organ size, partly because of its multifactorial nature in which many physiological processes, such as photosynthesis, water and mineral uptake, mobilization of starch and lipid reserves, and stress tolerance determine the resources available to produce new cells, tissues, and organs.
Albeit plant growth and stress tolerance are obviously complex processes, novel approaches collectively called "systems biology" allow us to better understand this complexity. It is our ambition to decipher the molecular networks underpinning yield and organ growth both under standard as well as mild drought stress conditions in Arabidopsis and the C4 crop maize. Systems biology will ultimately provide a holistic view enabling the optimization of plant productivity.
Molecular mechanisms regulating organ size
Understanding the mechanisms that control tissue, organ and organism size are amongst the most mysterious and fascinating open questions in biology.
A key concept in “size biology” is that both, in animals and plants, size itself is regulated. Our long term goal is to unravel the molecular pathways that govern leaf size in Arabidopsis. One of our approaches is based on studying the action mechanisms of so-called intrinsic yield genes (IYGs) which, when mutated or overexpressed, enlarges leaf size. In all cases examined so far enlarged leaf size results from an increased cell number without significantly affecting cell size, pinpointing to a central role of cell proliferation in size control. A detailed kinematic analysis as well as transcript and metabolome profiling is undertaken on various IYG lines. Crosses between lines with enlarged leaves reveal unexpected additive and synergistic phenotypes. Detailed computational as well as functional analysis has shed new light on how organ size is governed in plants. As cell proliferation plays an important role in the control of final size, genome-wide transcript profiling is performed on leaves primordia throughout the transition from proliferation to expansion in order to identify temporally and spatially regulated genes involved in the control of these processes. In addition, novel image analysis algorithms are developped to visualize and quantify the size and shape of the cells along the proximal-distal axis of these leaves primordia.
Systems biology of drought tolerance in Arabidopsis
Despite the recognized importance of drought in limiting plant growth and biomass production, little is known about the underlying molecular mechanisms.
However it is now clear that plants reduce their growth as a primary adaptation response to stress rather than as a secondary consequence of resource limitation (Skirycz and Inzé, 2010). In unpredictable environments, growth reduction enables plants to re-distribute and save resources, ensuring reproduction even when the stress becomes extreme. However when the episode of stress does not threaten plant survival and from the agricultural point of view growth reduction can be seen as counter-productive leading to unnecessary yield loss. Limiting growth reduction may thus provide a strategy to boost plant productivity under stress. Certainly a better understanding of the mechanisms that determine growth under stress conditions such as those involved in shutting down meristem activity will be vital in the development of new technologies that increase plant growth during stress and are also of main interest to our group. Whilst stress responses of mature organs are relatively well characterized what happens in the growing zones is much less understood. To address this gap in knowledge, physiological (growth analysis) and molecular (e.g. transcript, metabolite and protein profiling) analyses have been undertaken to understand how growing (fully proliferating and fully expanding) Arabidopsis leaves regulate their growth in response to water deficit (Skirycz et al., 2010). Candidate biological processes, genes and metabolites are further investigated using an automated phenotyping platform (WIWAM) and targeted molecular approaches.
Translational research: from Arabidopsis to maize
The major aim of our maize research is to identify strategies to increase its yield under normal and adverse conditions by affecting growth processes.
To reach this objective, we take different approaches: on one hand we take advantage of the plethora of knowledge affecting growth obtained in Arabidopsis thaliana (intrinsic yield genes, stress tolerance genes and the molecular yield networks) and assess its translatability to maize. On the other hand we also examine growth characteristics and stress growth responses in the maize plant itself to identify monocot specific traits.
Similar as the approaches in Arabidopsis, we sample within the relative small growth zone of the leaf in which cell division and cell expansion take place, responsible for the growth of the plant.
Up to now, we gathered a substantial toolbox to perform the maize biotech research varying from efficient transformation, optimized growth conditions (normal, mild drought and mild cold conditions), kinematic analysis (to assess the contribution of cell division and cell expansion to the observed phenotypes), bio-informatics and computational tools, genome-wide technologies to an automated system to phenotype the plants (under development).
Exemplified is one pathway identified through the translational approach to enhance the growth of maize plants by overexpression of the Arabidopsis gene compared to the controls. In addition, mutants in the same pathway have a negative effect on plant growth.
Computational approaches to unravel leaf growth
High-throughput technologies generate huge amounts of data representing the active components of the cell, e.g. genes, proteins, metabolites, and the interactions between them in particular developmental stages, tissues or environments.
We develop and apply computational approaches to construct networks of these players that are relevant to growth control. For instance, we have developed the tool CORNET which allows the interrogation of currently available microarray and protein-protein interaction data, flexible co-expression analysis and comprehensive network visualization. In addition, we are applying state-of-the-art computational approaches to the analysis and integration of transcriptomics, interactomics and functional genomics data to pinpoint candidate genes for further experimental studies. With the advent of molecular profiling technologies such as nCounter and RNA-seq, the scale of transcriptomics studies can be increased significantly, allowing the identification of transcript abundancy landscapes. These landscapes describe the relative gene activities necessary to obtain specific phenotypes.