Plant form and function

In the Plant form and function theme we analyse the relationships between plant traits, architecture, and functioning in crop stands as influenced by the abiotic environment (e.g., crop-microclimate feedbacks). Key in this theme are also plant-plant interactions. CSA is currently a world leader in 3D functional-structural plant modelling of crops, that allows analyzing plant-environment relationships in realistic crop settings.


Root anatomy responses to nutrient stress


Root anatomical traits have important roles in soil resource capture, especially in environments with suboptimal water and nutrient availability. The maize root system consists of three major root classes: seminal axial (or seed-borne) and nodal axial (shoot-borne) roots which all produce lateral (root-borne) roots of the first and second order. Lateral roots typically constitute the major portion of root systems, accounting for approximately 90% of the total root length.

Phenotypic plasticity is the ability of an organism to alter its phenotype in response to the environment and may involve changes in physiology, anatomy, or development. Plasticity has been observed for a number of root anatomical traits and is important for adaptation to environments with drought or suboptimal nutrient availability. Lateral root growth and behavior has been shown to be plastic in response to the microenvironment that the root is experiencing. Lateral roots can proliferate and even branch further when the roots encounter resources, such as water or nutrients, that a plant needs to grow. However, little is understood about anatomical trait plasticity of lateral roots in response to nutrient stress. The expression of anatomical traits in lateral roots presumably has a direct influence on plant growth and nutrient acquisition and therefore plant performance.

Types of work:

You will conduct a series of experiments in the growth chamber using a set of diverse genotypes. Plants will be grown under various nutrient regimes and lateral root responses to nutrient stress will be assessed. Anatomical phenotypes of lateral roots in different environments will be mapped based on root order and position on the axial root. Projects will involve microscopy, image analysis, and development of a conceptual framework for root adaptation to nutrient stress.


Wageningen (WUR Crop Systems Analysis)


Dr Hannah Schneider (

3D modelling of plant species coexistence under light competition


A key question in understanding the structure of a natural vegetation is how plants of different heights within the canopy can co-exist. An exciting hypothesis is that taller plants may have the advantage of higher light interception; but taller plants sway more with wind, forming a gap between canopy crowns. This gap has important consequences for within-canopy light environment and performance of subordinate plants. This project aims to reconstruct the 3D light environment within canopies by considering canopy gaps, in order to understand global canopy structure and species co-existence in vegetations such as forests and agroforestry systems.

Types of work:

This work is an FSP modelling study. There is flexibility in which exact questions will be explored using a model, but it will be limited to competition for light. The model can be built from scratch, or be based on existing FSP models. The topic is suitable for students who are interested in plant-plant interaction and community ecology, but also for those who wish to develop FSP modelling skills.


Wageningen (WUR Crop Systems Analysis)


Niels Anten (, Jochem Evers (

Building the first Dutch model on grape


In the Netherlands and Belgium grape production for wine making is getting more professional by the year. Yet, physiological knowledge on growth of the used genotypes in response to local climate conditions is limited. For better prediction of crop performance and timely pruning actions, a growth model is a good tool. Currently some vineyards monitor the development of growth, Veraison and ripening in detail. Apart from crop growth, climate is registered by temperature, humidity and radiation sensors in the city vineyard in The Hague. Detailed knowledge on fruit development and associated sugar production is available at French research institutes. When current knowledge and new monitoring data are integrated, all elements for a model for Dutch grapes are available. As easy as, like we say in Dutch, harvesting low hanging fruit.

Type of research:

The proposed MSc work consists of construction of a growth model for grape plants and its fruits. Since this model is new, elements of other plant models will be used to make a quick start. The programming environment (Matlab, C#, Java, etc.) is free of choice. The calibration of model parameters will be facilitated by the data collected by the growers and by known relationships from academic research in Bordeaux (France) and Geisenheim (Germany). It is recommended to visit some Dutch vineyards to get more insight in crop management in practice.


Wageningen UR Greenhouse Horticulture 


Pieter de Visser (, Jochem Evers (

The dilemma of plants: growth or defend? Understanding the growth-defense trade-off


Plants that grow in competition and that are attacked by herbivores face a dilemma: grow or defend? This dilemma arises because a plant can either invest its resources in defense or in growth, and a plant should prioritize one over the other. Evidence is mounting that plants downregulate their defense in favour of competitive strength. A plant that receives a low red:far-red ratio  - an indication of forthcoming competition for light - becomes less sensitive for hormones involved in defense (jasmonic acid and salycic acid).

The adaptive significance of this downregulation is not well understood. And although this downregulation may be advantageous in an ecological setting, it may be disadvantageous in agricultural setting. In agriculture, plants grow at high density and hence they maybe be sub defended. Thus, compromising defense over competitiveness may be a disadvantage in this context. Therefore, one outstanding question is whether plants vary in the extent to which they downregulate defences upon reception of lower red:far-red ratios. For example, do genotypes that are less sensitive to a decreased red:far-red ratio have higher defense levels compared to genotypes that are responsive to a decreased red:far-red ratio? Another questions is more fundamental: what are the consequences in terms of fitness if a plant downregulation its defenses by far-red in high density? This question could be answered through modelling.

We are looking for a highly motivated student with good experimental skills or an interest in modelling. We offer a challenging thesis project supervised by enthusiastic and creative supervisors.


Bob Douma (, +31(0)317 482140)

Modelling crop-weed interactions in 3D


Weeds are a serious biotic production constraint in most agricultural production systems. Acting at the same trophic level as the crop, weeds capture resources that cannot anymore be used by the crop. A sustainable way to suppress weed growth in a crop canopy is by improving crop competitiveness. This can be achieved by changing architectural traits of the crop plants that enhance its competitive strength, such as early soil cover, as well as optimized leaf orientation and branching patterns. Crop competitiveness can also be improved by changing population characteristics such as crop population density, presence of secondary competitive crops or the uniformity of crop plant arrangement. In all cases, the balance between competition with weed plants (interspecific competition) and competition among crop plants (intraspecific competition) will determine whether the increased crop competitiveness will result in improved weed suppression.

Experimental and modelling work conducted in recent years has shown that substantial gain in crop competitiveness is to be expected by combined optimization of plant and canopies characteristics. The focus of this thesis work is to explore the balance between inter- and intraspecific competition for light in crop-weed canopies, in relation to plant and canopy characteristics. Potential questions to be addressed are: how does canopy uniformity relate to weed suppression? Which crop traits make a crop more competitive with weeds and how does this depend on population density? What is the influence of the moment of weed emergence in this? Which crop plant architecture is optimal for weed suppression? To address such questions, a 3D functional-structural plant (FSP) model of crop-weed interactions is available that simulates growth and development of individual crop and weed plants in a specific arrangement.

Types of work

This work is a modelling study. There is flexibility in which questions will be explored using the FSP model, but it will be limited to competition for light. The model available can be used as it is, requiring only parameter value adjustments, or it can be adapted and modified to accommodate simulation of processes it is currently lacking – this is up to the student’s learning goals. The topic is suitable for students who are interested in plant-plant interactions and ecological weed control, but also for those who wish to develop FSP modelling skills.


Wageningen (WUR Crop Systems Analysis)


Jochem Evers (, Lammert Bastiaans (

Does a plant need multiple light cues to cope with shade effectively?


Plants use a number of cues to retrieve information about their environment and to respond optimally to the conditions they are exposed to. For example, plants use the ratio of far-red versus red light to sense impending competition, and respond by increasing stem and petiole extension, reducing branching and increasing leaf angle. In addition, plants can use other cues such a blue or green light, or overall light intensity to obtain information on future and current shading conditions. These signals are generated by neighbouring plants during canopy development, change in strength over time and do not operate simultaneously. We would like to explore whether plants that integrate multiple cues are better able to cope with their environment than plants that use a single cues, and what is the relative contribution of the individual cues to plant performance.

Type of research:

The proposed work consists of constructing or extending a plant simulation model, based on the principles of functional-structural plant (FSP) modelling, to include multiple light cues, the response of plants to those cues, and the consequences for plant performance. The study is not limited a priori to a specific species. The model can be used to test a range of different cues and responses, and to evaluate to what extent these affect plant performance when combined.

If you are enthusiastic for this topic and you want model plant-plant interactions please contact us.


Jochem Evers (, Bob Douma (

Plant-plant communication through volatiles


Plant volatiles provide information on the status of the volatile emitting plant. For example, plants that are attacked by pathogens or insects release a different blend of volatiles compared to non-attacked individuals. Volatiles that signal attack do for example attract the natural enemies of the attackers and can prime neighbour plants for defense. The priming leads to a stronger and faster response to attacker than non-primed plants. Volatiles released by healthy individuals affect a growth response in neighbour plants in this way affecting competition between the neighbour and emitter plants. Despite this knowledge there is a large number of questions to be answered to get further insight in the role of volatiles in plant-plant interactions. For example,

1.     Is volatile communication impaired when plants grown in competition?

2.     Is the plant response to volatiles dose dependent?

3.     How are different volatiles or other cues of plant-plant communication such as light reflection, brief touching, integrated?

4.     Do some volatile signals have priority over others?

5.     How do volatiles affect performance of species mixtures?

6.     How do volatiles interaction between plants affect performance of herbivore insects and their natural enemies?

This research will be done in close collaboration with Velemir Ninkovic from the Swedish University of Agricultural Sciences (SLU, He has good experimental facilities to test these and related questions. A compensation of a part of the costs of living may be covered by the Erasmus program (

We are looking for highly motivated students with good experimental skills that are willing to stay in Sweden for at least three to four months. In case of an MSc thesis, writing of the proposal and report is possible in Wageningen and examination will take place in Wageningen. Experiments can be done from February until November.


Bob Douma, Centre for Crop Systems Analysis,, +31 (0)317 482140

Velemir Ninkovic,

Plant-plant communication through volatiles: which compound is responsible?


Plants emit tens to hundreds of volatile organic compounds when subjected to insect herbivory of which only a small number of compounds is sufficient to attract natural enemies or prime neighbour plants. We have little knowledge why plants emit so many compounds and whether the individual compounds have different functions. Progression on the function of individual VOCs in the ecosystem is limited because it is common practice to classify VOCs by the chemical class they belong to, while compounds within a class can for example differ substantially in their life time in the atmosphere or in the emission dynamics upon feeding – characteristics which are thought to influence the signalling ability of a compound. In addition, experimentally testing which blend of compounds act as attractants to herbivores and natural enemies presents a logistical difficulty since the number of combinations that can be made from a blend is enormous.

A promising approach that has recently been explored is to describe volatiles by their traits (a small number of physico-chemical and physiological characteristics specific to that compound) and to explore through a model analysis if the signalling ability of a compound in terms of predicting herbivore presence/absence depend on the characteristics of the volatile organic compound. The model predicted some compounds to be good predictors of herbivory and others poor predictors.

A next step that could be taken is to test the model predictions by creating two artificial blends; one composed of compounds that are indicated by the model to have high predictive power in terms of presence/absence of insect herbivores, and another blend composed of compounds that were predicted to have a low predictive power and to test if plants or parasitoids respond stronger to the good blend compared to the poor blend.  


We are looking for highly motivated students with good experimental skills that are willing to stay at the Max Planck Institute in Jena (Germany) for at least three to four months to carry out the experiments (in collaboration with Dr. Sybille Unsicker). In case of an MSc thesis, writing the proposal and/or report is possible in Wageningen and examination will take place in Wageningen. Start September or October possible.

Contact person

Bob Douma (

Modelling pixel cropping


Pixel cropping (or pixel farming) is the practice of growing multiple crop species in complex arrangements in which communities of plants are spatially allocated at a fine resolution. The goal is to create diverse configurations of multiple crop species in which the right plant community is allocated to the right location, at the right time, and at the optimal resolution. The concept is grounded in the diversity—productivity theory, and evidence that diversification in agro-ecosystems is necessary to reduce damaging externalities caused by industrial monocultures.

We are currently conducting a preliminary pixel cropping experiment in the field at the Droevendaal Organic Experimental farm in Wageningen. Because we do not yet have the scientific knowledge to design ecologically optimal pixel cropped fields, in the experiment we have implemented superficial design rules: limiting the number of crop species, and allocating all plant communities to a uniform pixel size and shape (50 cm  x 50 cm) within a fixed grid. Crops are randomly assigned to each pixel in equal proportion.

The challenge of designing a good pixel cropping plan brings up many questions, such as:

  • How do plants selected for monocultures respond (in terms of morphology, yield, service provision, etc.) to being grown in heterogeneous communities?
  • What is the optimal pixel resolution for each crop?
  • Which crop combinations make good and bad neighbors?
  • Which particular plant traits make a species suitable for pixel cropping?

Acquiring the knowledge needed to design optimal pixel plots could involve conducting field experiments in which the complexity of the experimental setup is exponentially amplified to accommodate all possible neighbor and pixel size/shape combinations for the crops of interest. Alternatively, modeling offers a platform to explore designs and interactions out of the field. Our goal is to develop a simulation model that can capture the spatial heterogeneity and species diversity typical for pixel crop designs. The modelling approach to be used here is called functional-structural plant (FSP) modelling, in which individual plants are simulated in inter- and intraspecific competition with neighbouring plants. Ultimately, such a model will allow to address questions on plant response, traits, pixel resolution and optimal neighbour combinations.

The specific aim of this Master thesis is to develop a pixel cropping FPS model that captures the main components of a typical pixel crop system, using data from the pixel cropping field experiments and the modelling tools already available.

Type of work

Modelling, data analysis




Lenora Ditzler (FSE, or Jochem Evers (

Stealth games in vegetations – can plants make themselves invisible to their neighbours?


Plants are capable of shaping their developmental pattern to the competitiveness of the environment. For example, plants growing at a high population density can divert resources towards height growth to prevent being shaded by their neighbours. To be able to do so, plants make use of light signals they perceive through light-sensitive molecules such as phytochrome. Such light signals can already be perceived before the actual shading takes place. A well-known example of such a light signal is the ratio between red and far-red light (R:FR). The value of R:FR of the light reflected off neighbouring plants is relatively low compared to light coming from the sky. The reason for this is that plants absorb red light for photosynthesis, but reflect far-red light. The decreased ratio between the two reveals their presence to neighbours.

The aim of this thesis project is to find out to what extent plants may exploit this mechanism, by weakening or masking the light signals that give away their presence. Such ‘cheating’ behaviour by plants is well known to occur, for example orchids deceiving their pollinators by the morphology of their flowers, but has not been reported for light signals. If a plant would be able to manipulate the spectrum of the light it reflects, it would gain a competitive advantage over neighbouring plants who do not.

Therefore, the operational objectives of this thesis will be 1) to screen a range of plant genotypes for the spectral properties of their leaves, to get a quantification of the variation in the composition of the light they reflect; 2) to apply an FSP model to explore potential benefits of stealth behaviour by modifying light signals, and to find out what the level of signal masking should be in order for it to make a difference for competitive outcomes.

Type of research:

Preferably the student combines experiments and modelling. However, only modelling or experiments are possible depending on the learning goals of the student.


Bob Douma (, Jochem Evers (

How dynamic is light inside canopies? Intercepting light in the real world


The conversion of light into biomass and harvestable product is one of the key processes that drive yield. Not only the amount of light intercepted by a crop canopy, but also the distribution of light is of great importance to maximize this so-called light use efficiency. Leaves within a canopy are exposed to a constantly changing light intensity, not only by the incoming sunlight, but also the movement of leaves in the upper part of the canopy. Even though this phenomenon is well known, it has not been well characterized. In theory, an optimal distribution of light within a canopy should increase the light use efficiency. However, these estimates have been made using a static light environment. So, it is the question to what extent the variability of light inside a canopy is of influence to the light use efficiency.

We have developed a methodology to quantify the light environment in a crop canopy and its variability over time. For this, a new open-source, low cost, rugged light sensor (ceptometer) is used to measure light inside a canopy (DOI: 10.3791/59447). The low construction cost of this ceptometer allows measurement with a number of these rugged ceptometers at multiple levels inside a canopy, where the dynamic light environment can be measured and logged under real-world conditions in the field. A field experiment is planned in Cambridge (UK), in collaboration with Dr Johannes Kromdijk (Cambridge University).

With these data, the light environment and its variation inside a canopy can be analysed. Further, this light environment can be modelled using Functional Structural Plant modelling and studied to find ways for optimization of light distribution inside a canopy.

Methods and expectations:

This project will involve hands-on (construction), field work and theoretical work (variation analysis and FSP modelling):

  • Measuring light intensity at a range of levels in a crop canopy in the field (Cambridge, UK)
  • Analysing collected data for variability and FSPmodelling.

Please note:

  • this project, or parts of this project, can be done as a BSc thesis, MSc thesis or an internship
  • aspects of this project (e.g. field work, data analysis or FSP modelling) can be done as separate thesis projects

Do not hesitate to contact us to discuss the possibilities or aspects of your interest!


Dr Steven Driever, Dr Alejandro Morales and Dr Jochem Evers (Crop Physiology Chair, Centre for Crop Systems Analysis – CSA;,,