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.

How does wheat photosynthesis respond to climate change variables?

Theory:

Climate change has led to the global warming and extreme climatic events (ECEs) such as heat waves and drought. Photosynthesis respond to such environmental variables, however, quantitative information about which components of photosynthesis (e.g. light conversion, CO2 capture, metabolic activities, etc.), and to what extent they are affected by these variables is generally lacking. The classical steady-state biochemical model of Farquhar, Von Caemmerer and Berry (FvCB model) has been widely used to analyze leaf photosynthesis and this model has been elaborated and improved. In our previous study, the thermal responses of wheat photosynthesis and its components have been changed by different water regimes. For instance, drought plants had lower optimum temperature than those grown under well-watered conditions.

Challenges:

In this project, you will be challenged to assess whether or not the thermal responses of wheat leaf photosynthetic components could be altered by the contrasting growth temperatures and water regimes.

Methods:

We offer the interested MSc student the opportunity to conduct a set of photosynthesis measurements (gas exchange and chlorophyll fluorescence) under various temperature, CO2 and light levels on wheat leaves. Afterwards, the data will be used to quantify the essential parameters of the FvCB model and to examine if a dynamic version of the FvCB model based on the optimum nitrogen partitioning is required to predict leaf photosynthesis under contrasting growth environments.

Expectations:

In the end, the MSc student will be able to use the LI-6800 (the most advanced equipment for gas exchange measurement), and use the model as a research tool to predict leaf photosynthesis under various environment scenarios. The insights generated from this thesis research on photosynthesis responses to various environmental variables are expected to have strong implications for crop production and breeding programs in the context of future climate change.

Contact:

Dr. Xinyou Yin, Mr. Peter van der Putten, and Mr. Liang Fang (Crop Physiology Chair, Centre for Crop Systems Analysis – CSA; Xinyou.yin@wur.nlpeter.vanderputten@wur.nl; liang.fang@wur.nl)

Quantifying wheat source-sink relationships during grain filling in response to drought

Theory:

Wheat is one of the most important cereal crops in the world. Grain yield in wheat is dependent not only on the availability of photosynthetic assimilates (source), but also on the capacity of grains to utilize available assimilates (sink). The source strength and sink size are both affected by environmental changes, such as drought and heat. A quantitative model by using grain filling dynamics and biomass produced during grain filling has been used in our previous studies to quantify the source-sink relationships. Such approach may help to identify the environmental factors involved in the alteration of grain yield in the context of global climate change, such as water deficit, high temperature and CO2 elevation, and their influences on source-sink balance.

Challenges:

In this project, the MSc student will be challenged to examine whether or not the source-sink relationships during grain filling will be altered by different water regimes and if this alternation is regulated by or associated with photosynthetic acclimation to the contrasting environmental variables.

Methods:

We offer the interested MSc student the opportunity to conduct a pot experiment on wheat in the greenhouse at Unifarm. The yield data will be collected for several times during the grain filling period. Afterwards the data will be used in a quantitative model to quantify changes in the balance between source supply and sink demand and to identify the environmental variables involved in regulating these changes under contrasting water regimes.

Expectations:

In the end, the MSc student will be able to use the model as a research tool to analyze how the source-sink balance during grain-filling will be affected by various growth environmental conditions. The quantitative insights generated on the response of source-sink relationships to various environmental variables may have strong implications for crop production and breeding programs in the context of future climate change.

Contact:

Dr. Xinyou Yin, Mr. Peter van der Putten, and Mr. Liang Fang (Crop Physiology Chair, Centre for Crop Systems Analysis – CSA; Xinyou.yin@wur.nlpeter.vanderputten@wur.nl; liang.fang@wur.nl)

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

Description:

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 ....

Location:

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

Period:

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

Contact:

Tjeerd Jan Stomph (tjeerdjan.stomph@wur.nl)

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

Theory:

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.

Challenges:

  • 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?

Methods:

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.

Expectations:

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.

Contact:

Dr Xinyou Yin, and Mr Peter van der Putten (Crop Physiology Chair, Centre for Crop Systems Analysis – CSA; Xinyou.yin@wur.nl; peter.vanderputten@wur.nl)

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

Description:

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!

Contact:

Dr Steven Driever, Dr Alejandro Morales and Dr Jochem Evers (Crop Physiology Chair, Centre for Crop Systems Analysis – CSA; steven.driever@wur.nl, alejandro.morales@wur.nl, jochem.evers@wur.nl)

Assessment of genetic variation in photosynthetic temperature response in wheat

Description:

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.

Challenge:

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

Contact:

Dr Steven Driever (Crop Physiology Chair, Centre for Crop Systems Analysis – CSA; steven.driever@wur.nl)

Quantitative analysis of photosynthesis of a super-performer

Description:

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.

Contact:

Prof. Dr Paul Struik (paul.struik@wur.nl) and Dr Steven Driever (steven.driever@wur.nl)

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

Description:

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.

Challenge:

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).

Contact:

Dr Steven Driever and Dr Alejandro Morales (Crop Physiology Chair, Centre for Crop Systems Analysis – CSA; steven.driever@wur.nl, alejandro.morales@wur.nl)

Effects of elevated CO2 and nitrogen availability on growth, photosynthesis and resource allocation

Description:

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 under elevated [CO2].

When organic nitrogen is not readily available legumes 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 (such as nitrogen, carbohydrates, etc.).

This project will look into the effects of elevated [CO2], organic nitrogen availability and resource allocation in the model legume Medicago truncatula. 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, growth and photosynthesis in the model species Medicago truncatula. Potential thesis topics within this project are, for instance:

  • How does the plant allocate its carbon/nitrogen under elevated [CO2] in the presence or absence of symbiosis?
  • At which available organic N level (NO3- and/or NH4) is symbiosis beneficial to the plant’s productivity?
  • How much does photosynthesis need to increase to increase the plant’s N content through symbiosis?

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

Contact:

Dr Steven Driever (Crop Physiology, Centre for Crop Systems Analysis – CSA; steven.driever@wur.nl)

Dr Wouter Kohlen (Laboratory of Molecular Biology, wouter.kohlen@wur.nl)

What are the effects of nitrogen on the light use efficiency of C4 photosynthesis?

Description:

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 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. There are some C4 crops, such as Miscanthus x giganteus, that maintain their photosynthesis 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 due to a phenomenon called alternative electron transport. This is a form of photosynthetic electron transport (as part of the so-called light reactions) that is not used for the assimilation of CO2, but for something else. The alternative electron can be quite substantial and reduces the light use efficiency of photosynthesis which is detrimental to the growth and production of the plant. However, this alternative electron transport could potentially be used to provide energy for processes in the leaf other than CO2 assimilation. One of such processes is 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 maize plants and assess the role of nitrate reduction in relation to photosynthesis and alternative electron transport. If effects of different nitrogen forms are found, this will be investigated further in response to stress, such as low growth temperature.

Methods and expectations:

This project will involve a combination of a growth experiment in a controlled environment and physiological experimentation with gas exchange and chlorophyll fluorescence techniques. 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 maize leaves?
  • What is the relation between growth temperature, nitrate and photosynthetic light use efficiency of young maize leaves?
  • Does alternative electron transport increase in response to limiting ammonia availability in young maize leaves compared to Miscanthus leaves?

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

Contact:

Dr Steven Driever (Crop Physiology, Centre for Crop Systems Analysis – CSA; steven.driever@wur.nl)

Dr Xinyou Yin (Crop Physiology, Centre for Crop Systems Analysis – CSA; xinyou.yin@wur.nl)