Crop systems biology

Crop systems biology analyses and models complex phenotypic traits expressed at crop level - the hierarchical level relevant to real-life agricultural production – by using information from “omics”, underlying biochemical and molecular-physiological understanding and linking that information in a coherent and scale logical way to yield determining, crop physiological component processes. By doing so crop systems biology aims to assist in orchestrating the knowledge chain from molecule and gene through cell and tissue or organ all the way up to plant and plant community in order to predict crop phenotype and crop performance.

Thesis subjects

Making cereals more nutritious: zinc translocation and allocation in major cereals


There is a world-wide effort to enhance micro-nutrient density in staple crops in order to improve the nutritional quality of foodstuffs eaten by the poorer majority of the world population. Zinc is among the target micro-nutrients for this effort. A theme the Centre for Crop Systems Analysis, the Soil Quality Group and Human Nutrition and Epidemiology from Wageningen University all work on, partly in joint research efforts.

Studies carried out within this framework have established methods to grow zinc deprived rice, wheat and cowpea and have shown differences between these species that support the need for more studies of these inter specific differences next to cultivar (intra specific) differences. Recently the interaction between crop nitrogen nutrition and Zn allocation has been shown to be of importance. This might also explain why under enhanced CO2 predicted for 2050 both protein and Zn levels are decreased, showing a looming aggravation of so-called hidden-hunger.

There are a number of major research question for this work.

  • What is the relative role of re-allocation and direct uptake during grain formation as source of zinc in cereal or legume grains in dependency of plant mineral and nitrogen nutrition, genotype and their interactions.
  • Where and how is Zn stored in cereal or legume grains in relation to the role in human nutrition and the role in plants and as a function of plant mineral nutrition, genotype and their interactions.
  • Can we model mineral allocation and re-allocation within plants to provide a tool for a more targeted breeding.
  • Can we use models to link the vast body of subcellular level understanding of transport and sequestration processes to whole plant  crop level and allocation under field conditions.
  • This may vary between purely experimental to purely modelling, to relevant combinations of these.
  • .... you may obviously formulate other research questions a try to convince me about their scientific relevance ....


Wageningen or in collaboration with partners like IRRI in the Philippines.


Experiments in Wageningen need to be carried out at decent light levels so between April and September.


Tjeerd Jan Stomph (

Come and prove our models wrong: Shining light on the real differences between C4 and C3 photosynthesis with theory-based experiments


C4 species (e.g. maize and sorghum) have a higher photosynthetic capacity than C3 species (e.g. rice and wheat), because C4 crops can maintain a higher CO2 concentration at the site of Rubisco – the enzyme binding CO2 during photosynthesis. However, this comes at a cost of extra ATP; photosynthetic light use efficiency under limiting lights may not be higher in C4 than in C3 species. Our  theoretical models predict that C4 photosynthesis has a more linear light response curve than C3 photosynthesis, and that such a difference in shape has a direct consequence on the optimum vertical light and nitrogen distribution in canopies for a maximized canopy photosynthesis. For instance, compared with C4 species, C3 plants would benefit more from a more uniform light distribution and from the optimum nitrogen distribution in canopy.


  • In this project, you will be challenged to prove whether or not our models are wrong by addressing questions in both theory and reality: Theory: what are the consequences of the theoretical model predictions for the canopy photosynthesis of C3 and C4 species?
  • Reality: are these theoretical predictions found in comparable C3, C4 and C3-C4 intermediate species (e.g. Panicum, Moricandia, Flaveria and Alloteropsis semialata) in actual experiments and measurements of photosynthesis?


You will design and conduct a set of simultaneous photosynthesis measurements (gas exchange and chlorophyll fluorescence) under various temperature, CO2 and light conditions on leaves of these plants. At canopy levels, you will measure light and nitrogen profiles once canopy is established. The collected data will be combined with biochemical leaf-photosynthesis models for quantifying critical model parameters and sub-processes. These parameters will be incorporated into a canopy photosynthesis model considering light and N profiles.


In the end, you will be able to use these models as a research tool, for example, (i) to predict leaf photosynthesis for different environment scenarios, and (ii) to conduct a sensitivity analysis for identifying options with which leaf and canopy photosynthesis can be further enhanced. The obtained quantitative understanding of photosynthesis in general may have strong implications for crop production of both sustainable food and bio-energy supply.


Dr. Xinyou Yin, and Mr. Peter van der Putten (Crop Physiology Chair, Centre for Crop Systems Analysis – CSA;;

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.

The first step is to develop 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) has been developed that can be used to measure light inside a canopy (DOI: 10.3791/59447). The low cost 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.


To develop an open-source measurement method to quantify dynamic light environment in a crop canopy.

Methods and expectations:

This project will involve both hands-on and theoretical work (analysis):

  • Measuring light intensity at a range of levels in a crop canopy in the field
  • Analysing collected data to determine e.g. number of ceptometers, canopy depths, etc. as well as the observed variability.


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

Assessment of genetic variation in photosynthetic temperature response in wheat


The response to temperature is a key trait for breeding more resilient crops for future climates, where temperatures are predicted to rise by 2-4 °C by the end of the 21st century (Le Quere et al., 2009, Stocker et al., 2013). The impact of this temperature change on crop production has been estimated to be as much as a 6% reduction per °C (Zhao et al., 2017). 

One of the main physiological processes affected by temperature is photosynthesis. There is emerging evidence that leaf and canopy photosynthesis acclimate to changing temperature and that photosynthetic temperature responses vary considerably between genotypes. This variation can potentially be exploited, if the genetic and physiological variation can be characterized. However, there is currently no rapid, comprehensive method for assessment of photosynthetic temperature responses, something required for characterizing this genetic variation.


To develop a rapid screen for wheat, focused on CO2 assimilation rate in response to dynamic temperature change.

Methods and expectations:

This project will involve hands-on and theoretical work:

  • Design a rapid screening method for wheat, based on gas exchange and chlorophyll fluorescence techniques
  • Measure the variation of the photosynthetic temperature response in a number of wheat genotypes under controlled conditions
  • Evaluate the most varying parameter(s) of the photosynthetic temperature response among wheat genotypes


Dr. Steven Driever (Crop Physiology Chair, Centre for Crop Systems Analysis – CSA;

Quantitative analysis of photosynthesis of a super-performer


During photosynthesis, light energy is converted into chemical energy, which is then mainly used for the fixation of carbon dioxide. Insight into the quantitative aspects of photosynthesis and CO2 exchange has been very much advanced by experimentation and modelling. The classical biochemical model of Farquhar, Von Caemmerer and Berry has paved the way and this model has since been elaborated and improved. Making use of their concepts, it is possible to estimate a wide diversity of biologically relevant photosynthesis-related parameters based on a specific measuring protocol followed by several steps of curve fitting.

Plants of different natural habitats differ in their response to increases in the amount of light intercepted, i.e. plants differ in the decrease of light use efficiency with an increase in incoming radiation. A very good example of a species with a high light use efficiency even at very high levels of incoming light is shortpod mustard (Hirschfeldia incana; formerly Brassica geniculata). It is known for its large environmental plasticity and it grows well at elevated temperatures. It is therefore worthwhile to investigate in great detail the responses of this species to environmental factors influencing the rate of photosynthesis and to quantify in great detail what factors contribute to its high rate of photosynthesis. Equally important it is necessary to compare it with a crop species that is closely related. Based on such a quantitative comparison based on, supported by and enhanced by modelling, we can identify avenues for crop improvement.

Plants performing well under high light intensity may demonstrate a relatively high electron transport efficiency, a large proportion of electrons following more efficient alternative electron pathways, and/or a high Rubisco carboxylation efficiency. In all cases they also require a high rate of physical transport of CO2 to the carboxylation site and a low rate of loss of CO2 that arises from (photo)respiration. The latter aspects are very strongly influenced by biochemistry, leaf anatomical factors and the positioning of different organelles within the mesophyll cells of C3 plants. However, which of these (photochemical, biochemical, physical and anatomical) aspects (co)contribute most to the high photosynthetic productivity and plasticity of Hirschfeldia incana is yet to unravelled.

Methods and expectations:

We offer MSc students the opportunity to work on various aspects of photosynthesis of Hirschfeldia and other Brassicaceae, mainly related to their responses to environmental factors. We offer opportunities for experimental work, modelling topics and combinations of the two methodologies. We prefer combined modelling and experimental approaches. Depending on availability of facilities, the work can take place throughout the year. In most cases, collaboration with other chair groups will be part of the practical arrangements.


Prof. Dr Paul Struik ( and Dr Steven Driever (