Crop photosynthesis

In the Crop photosynthesis theme we aim to understand the drivers of photosynthesis and seek for avenues to improve photosynthesis. It thus quantifies the link between the regulation of photosynthesis at cellular level and the ultimate growth of crops. It addresses a key question for future food production: to what extent can improved photosynthesis result in increased yields.

Thesis subjects

Photosynthesis under investigation: how different are potato plants grown from true botanical seeds and seed tubers?


With the introduction of the novel hybrid potato technology, potato nowadays can be produced from both true potato seeds (TPS) and commonly used seed tubers. There are morphological differences observed between the two plant types, especially in development of the number of stems and types of lateral branches, which form the basic components comprising overall plant architecture. Also, potato tuber yield and tuber number differ between TPS and tuber-grown plants, which can be the result of feedback between source-sink relationships and plant architecture. Source organs, such as leaves, perform photosynthesis which can convert solar energy into chemical energy and produce assimilates; while sink organs such as potato tubers can import and store biomass that make economic products. The source-sink relations influence the development of plant architecture, specifically the lateral branching behaviour, in which feedback mechanisms are involved to regulate the whole plant development and growth. However, for the newly-developed hybrid potato plants, it is still unknown whether the assimilates productivity is different in source organs for different planting materials. A better understanding of photosynthetic traits in different materials of hybrid potato helps us further investigate whole plant source-sink relations, and therefore seeking the beneficial plant architecture for high yielding potato crop.

Objectives and methods:

The aim of this study is to examine the photosynthetic characteristics of leaves at different positions on the potato plant and compare TPS and seed tuber grown plants. Light response of photosynthesis will be measured on leaves situated at different positions on the plant for two planting materials. Also, whole plant photosynthesis will be determined in the photosynthes-lab using a custom-built gas-exchange system. Leaf traits such as leaf area, leaf shape and biomass will be quantified. Plant architectural variables including the number of branches developed, branch length over time will be measured. More information to be explored if you have more interesting ideas!


  • Gain insights in the principles of photosynthesis at the leaf and whole plant level, from both theoretical and practical trainings.  
  • Perform greenhouse experiments and get to work with our excellent researchers and facilities in the photosynthesis-lab
  • Develop skills in data analysis and scientific writing and more

Starting time:

2022, April - September


If you are interested in the topics of photosynthesis, hybrid potato or source-sink relations, please feel free to contact us!

Jiahui Gu (, Jochem Evers (, Steven Driever (, Paul Struik (

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 boththeoryandreality:

  • 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,FlaveriaandAlloteropsis semialata) in actual experiments and measurements of photosynthesis?



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;;

Is triose phosphate utilization limitation on photosynthesis regulated by the whole-plant sink-source relationships during the life cycle of rice?


Photosynthesis is the primary physiological process that determines the productivity of crops and ecosystems? Are you interested in understanding the processes that limit photosynthetic rates and crop productivity? Do you like to challenge yourself to learn combined experimental and modelling research? Here is a subject that you might consider to work for your thesis.

The process that drives the synthesis of sucrose and starch from sugar precursors in the photosynthetic Calvin–Benson cycle is called triose phosphate utilization (TPU). It is one of the three canonical biochemical limitations of photosynthesis in gas exchange analysis of C3 plants, which can give feedback inhibition on photosynthesis when carbon exports from the cycle cannot keep pace with carbon fixation. From CO2 response curves of conventional gas exchange and chlorophyll fluorescence measurements, TPU-limited photosynthesis rate (Ap) behave like no response to CO2, or sometimes, an inhibition under increasing CO2. Currently, in a biochemical photosynthesis model, either Rubisco carboxylation capacity (Vcmax) or electron transport rate (Jmax) is widely accepted as the main limiting factor to photosynthesis, while TPU received less attention, since an observable TPU limitation is only occasional and highly variable, depending on genotypes and growth conditions. However, inclusion of TPU limitation in models is important to understand the basic principles of photosynthetic mechanisms.

Recently, an apparent TPU limitation from leaf photosynthesis was observed in our leaf-colour variants from two backgrounds of rice genotypes. We hypothesise that these leaf-colour variant genotypes differ from their default counterparts in photosynthetic capacity and thus, in the extent of TPU limitation. We plan to conduct a greenhouse experiment on four rice genotypes under two or three nitrogen treatments to: 1) identify the occurrence of the TPU limitation; 2) explore the whole-plant physiological regulating mechanisms of TPU limitation, and 3) quantify the effect of TPU limitation on photosynthesis.


  • Measuring CO2response curves on adaxial and abaxial surfaces of leaves by Li-Cor
  • Analysing collected data and modelling the rate of triose phosphate utilization
  • Investigate the link between TPU limitation and the whole-plant source-sink ratio and nitrogen status

Supervisors and contact:

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

Starting time:

As soon possible (preferably before March 2022)

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):

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


Dr Steven Driever, Dr Alejandro Morales and Dr Jochem Evers (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;

Open-Abs: an open source method to quickly measure leaf absorbtance


Visible light is readily absorbed by leaves and used in photosynthesis. This light varies greatly in intensity over time and e.g. within a canopy. As leaves acclimate to light, their absorbtion of light is altered. Not only the total amount of light absorbed is changed, but also the absorbtion of different colours of light may change. In order to assess the changes that occur in light acclimation, a quick and easy measurement is needed. Up to date, leaf absorbtance measurements have only been possible with expensive and rare specialist equipment, such as a Taylor integrating sphere. As a result, this type of measurement is rarely performed in plant science. Moreover, there is currently no off-the-shelf equipment that can do this measurement in a simple manner.

These type of spheres used to be quite expensive, as well as spectrometers of sufficient resolution and accuracy. With the emergence of 3D printing and low-cost miniature spectrometers, this is no longer the case. These advances open the opportunity to develop an affordable open source integrating sphere system that can measure spectral leaf absorbance. The low cost of such system can increase the number of systems and in turn allow for more (rapid) leaf absorbtance measurements to be taken over time and space, providing opportunity to collect large amounts of data that can give new insight into the development and acclimation of leaves to light.


In this thesis you will develop, build and test a reliable, easy to use, open source method to instantly measure spectral leaf reflectance, transmittance and absorbtance, that can be operated under a range of conditions (e.g. in the field).

Methods and expectations:

This project will involve both hands-on and theoretical work

  • Design and build a dual-integrating sphere set-up
  • Test and improve set-up for spectral leaf absorbance measurements, using miniature spectrometers, on a range of different leaf types in a laboratory environment
  • Develop a proto-type integrating sphere system
  • Test the proto-type system in a greenhouse and field environment, to study leaf acclimation to light in a canopy

This thesis topic or parts thereof are suitable for BSc, MSc or internship projects.

Part of the work can be carried out at Cambridge University (UK), as this project will be done in close collaboration with Dr. Johannes (Wanne) Kromdijk at the Department of Plant Sciences, Cambridge University (UK).


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

Does climate change affect photosynthesis and nitrogen fixation activity in soybean?


In the near future, the concentration of CO2 is predicted to further increase and this will have implications for crop production. Elevated [CO2] has been predicted to potentially enhance photosynthesis and increase productivity. In some species this has already been partly shown to be the case. However, the predicted levels of increase in yield, especially in biomass, are currently not achieved.

A vital requirement for crop productivity is the availability of nutrients such as organic nitrogen. High organic nitrogen input can greatly enhance crop productivity, but a too great supply is detrimental to both plant development and the environment. It is possible that organic nitrogen is a limiting factor for reaching the full potential of increased crop yield in future climates, especially under elevated [CO2].

When organic nitrogen is not readily available, legumes such as soybean have the ability to acquire it through a symbiosis with Rhizobium. This symbiosis is energetically costly for the plant, however, with elevated [CO2] and increased photosynthesis, legumes might perform better compared to other plant species since there should be more carbohydrates available to invest in this symbiosis. Nevertheless, it is only possible to increase overall productivity if a plant is able to wisely allocate its resources like nitrogen, carbohydrates, etc.

This project will look into the effects of elevated [CO2], organic nitrogen availability and resource allocation in soybean, an important crop species. The project is a collaboration between Crop Systems Analysis and Molecular Biology.

Methods and expectations:

This project looks into the interaction between elevated [CO2], organic nitrogen, photosynthesis, nodulation and nitrogen fixation activity in soybean. Potential thesis topics within this project are, for instance:

  • Does the plant allocate its carbon and nitrogen differently under elevated [CO2] in the presence or absence of nodulation?
  • How much does photosynthesis need to increase to increase the plant’s N content through nodulation?
  • Does increased photosynthesis under elevated [CO2] enhance nitrogen fixation activity?

Please note that these topics are examples, do not hesitate to contact us to discuss a topic or area of your interest related to this!


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

Dr Wouter Kohlen (Laboratory of Molecular Biology,

Does nitrogen supply affect the light use efficiency of photosynthesis?


Crops such as maize with so-called C4 photosynthesis are among the most productive and the benefits are such, that there are currently efforts to realize C4 photosynthesis in crops with C3 photosynthesis like rice. Because of this turbo-charged C4 photosynthesis, the water-use efficiency and nitrogen use efficiency are already quite high, especially under warm conditions. However, when temperatures are low, C4 photosynthesis decreases in efficiency. This is where C3 crops have a benefit over C4 crops. However, light use efficiency seems to depend partly on the nitrogen supply in both C3 and C4 crops. Some crops are able to maintain their photosynthesis even under lower temperatures due to an increase in the abundance of their most important photosynthetic enzymes. Increasing these enzymes requires quite some nitrogen, potentially reducing their nitrogen use efficiency.

At the same time, the light use efficiency of photosynthesis is reduced under low temperature. However, the cause of this reduction is not quite known. One of the causes may be the nitrogen metabolism, the reduction of nitrate to ammonia, which is energetically quite costly. This could potentially benefit the plant, by making more nitrogen available, for instance for the formation of additional photosynthetic enzymes and increase its productivity.

In this project, we will focus on the effects of the availability of different forms of nitrogen (nitrate and ammonia) to young C4 and C3 plants and assess the role of nitrate reduction in relation to photosynthesis to unravel what causes reductions in light use efficiency.

Methods and expectations:

This project will involve a combination of a growth experiment in a controlled environment with different nitrogen treatments and experimentation with physiological measurements (gas exchange of CO2 and O2 and chlorophyll fluorescence). Additionally, leaf material will be analyzed for its (different forms of) nitrogen content.

Depending on the chosen duration of the thesis, research interest and background of the candidate, the thesis topic can focus on any or part of the following topics:

  • What is the effect of nitrate and ammonia on the leaf N composition of young leaves?
  • What is the relation between growth temperature, nitrate and photosynthetic light use efficiency of young leaves?
  • Does net O2 exchange increase compared to CO2 exchange in response to limiting ammonia availability?

Please note that these topics are examples, do not hesitate to contact us to discuss a topic or area of your interest!


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

Improving crop light-use efficiency: Exploiting differences in the energy budget among subtypes of C4 plants to boost crop productivity


C4 crops of agricultural importance all belong to the NADP-ME subtype, and this subtype has been the template for C4 introductions into C3 crops to improve their productivity. However, the ATP cost for the C4 cycle in both NADP-ME and NAD-ME subtypes accounts for >40% of the total ATP requirement for CO2 assimilation. These high ATP costs, and the associated need for intense cyclic electron transport (CET) and low intrinsic quantum efficiency of CO2-assimilation, are major constraints in realising strong improvements of canopy photosynthesis and crop productivity. Based on mathematical modelling, we have recently proposed a C4 ideotype with low chloroplastic ATP requirements present as in the non-domesticated PEP-CK subtype. The ideotype is a mixed form of NAD(P)-ME and PEP-CK types, requires no CET, and its theoretical quantum efficiency is much higher than that of a crop C4 type. Its cell-type-specific ATP and NADPH requirements can be fulfilled by local energy production. The ideaotype is projected to have ca. 10% yield advantage over current C4 crops, and >50% advantage over C3 counterparts. The ideotype provides a unique (theoretical) case of improved quantum efficiency, thereby paving a new avenue for improving photosynthesis in both C3 and C4 crops. This thesis work aims to first identify whether there are C4 species in nature, super CO2-assimilators, that are identical or close to the designed C4 ideotype. We then apply a set of experimental approaches, which will be combined with model analysis. This combined approach can identify the key physiological requirements for the C4 ideotype. The ideotype key-requirements and any super CO2-assimilators can be exploited for improvement of the photosynthetic performance and boost productivity of crops.


Based on our recent Viewpoint ( in this area, you will screen C4 species of different subtypes and then conduct a set of simultaneous photosynthesis measurements (gas exchange and chlorophyll fluorescence) under O2 and light conditions on leaves of these plants. The collected data will be combined with biochemical C4 leaf-photosynthesis models for quantifying critical model parameters and sub-processes. This information will be used to identify if there are species identical or close to the theoretical ideotype.


In the end, you will be able to use the models as a research tool for identifying options with which leaf photosynthetic light-use efficiency can be improved. The obtained quantitative understanding of differences in photosynthesis among C4 subtypes may have strong implications for improving production of both C3 and C4 crops.


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

Comparative analysis of photosynthetic CO2 re-fixation using Oxygen response of photorespiration


Hirschfeldia incana (Grey mustard) is used in the Extremophile programme of Wageningen University as a model species with a very high rate of photosynthesis under high light. Initial gas exchange measurements show higher rate of Hirschfeldia incana under high light conditions in comparison to Brassica nigra, Brassica rapa and Arabidopsis thaliana. Several factors may contribute to the high photosynthesis performance. High biochemical capacity influenced by high leaf nitrogen content, efficient electron transport and efficient gas transport are some of the potential factors. In this research, it is hypothesized that efficient re-fixation of (photo)respired CO2 contributes significantly to the high photosynthesis rate of H. Incana. Effective re-fixation of (photo)respired CO2 is influenced by leaf anatomy as chloroplast-mitochondria arrangement and chloroplast coverage of mesophyll surface area exposed to intercellular airspaces influence the fate of the released CO2. The extent  of re-fixation of (photo)respired CO2 and anatomical factors are examined using experiment and mathematical modelling.


Hirschfeldia incana, Brassica rapa and Arabidopsis thaliana are grown in climate chamber. The light and CO2 responses of photosynthesis are measured at several oxygen levels using combined gas exchange and chlorophyll fluorescence measurements. The extent of re-fixation of (photo)respired CO2 is then estimated using mathematical modelling using the method reported here ( The anatomy of the leaf is examined using light and electron microscopy.


You will be able to generate insights on how to improve leaf photosynthesis rate through efficient gas diffusion and leaf anatomy. You will be able to identify leaf anatomical traits contributing to efficient re-fixation and hence photosynthesis. These insights has strong implication on improving crop yield through efficient photosynthesis.

This thesis topic is suitable for MSc.


Dr Moges Retta (Crop Physiology Chair, Centre for Crop Systems Analysis – CSA;

The photosynthesis lab: towards next-generation plant and crop photosynthesis research and teaching


The photosynthesis lab is an initiative by the Centre for Crop Systems Analysis (CSA) and the Horticulture and Product Physiology group (HPP) to jointly advance the level of photosynthesis research in Wageningen. In this lab, expertise and experimentation on photosynthesis come together to develop the next generation of plant and crop photosynthesis research and teaching.

If you are interested in photosynthesis, at leaf and/or crop scale, and like to develop new approaches for research or teaching, then this is the lab for you!

The lab very much welcomes students that wants to do their BSc- or MSc thesis, research practice or a teaching based project. Within the lab there are a number of possibilities to do your own project, broadly within the following categories:

  • Development and use of novel photosynthesis measuring techniques

When you are interested in novel measuring techniques, you have an ease to work with technical stuff and are familiar (or not afraid to start) with R and/or Python, a project on one of the many novel techniques being developed in the lab may be for you! For example,  integrating multiple optical measurement techniques (Chlorophyll Fluorescence (PSII), absorbance changes (PSI) and Electrochromic Shift) with gas exchange for simultaneous measurements of CO2, H2O, electron and proton-fluxes in photosynthesis.

  • Do in-depth physiological research on climate-plant-interactions

Are you fascinated by how plants adapt their photosynthesis to the climate they grown in? Are you interested in effects of climate change? Then you can investigate that in the lab with state-of-art measurement equipment to unravel the physiological basis of these interactions and effects. You can think of interaction of photosynthesis with light (including spectrum and LED!), temperature, humidity and CO2, for leaves, plants or even small canopies!

  • Develop video’s/manuals/course material for using equipment and methods for photosynthesis research

When you have an interest or passion for teaching and/or science communication, then we have an opportunity for you! The lab aims to train the next generation of scientists in all things photosynthesis. We have a number of opportunities to develop instruction video’s, manuals or entire readers about photosynthesis and how to measure it!


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

Dr Wim van Ieperen (Horticulture and Product Physiology – HPP;