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

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)

Dynamic photorespiration under fluctuating light

Description:

CO2 fixation in leaves is the basis of plant growth, and is facilitated by the enzyme Rubisco (Ribulose-1,5- bisphosphate carboxylase oxygenase). However, Rubisco can also fix O2 instead of CO2, which reduces photosynthesis. This wasteful side-reaction, photorespiration, depends on the CO2/O2 ratio. In fluctuating light intensities, a condition that leaves in nature are often subjected to, the CO2 concentration in the chloroplast often fluctuates, because of a temporal mismatch between CO2 diffusion into the leaf and the rate of CO2 fixation. These fluctuations should translate into fluctuations in the rate of photorespiration. However, we do not know how strongly photorespiration changes in leaves exposed to rapid changes in light intensity, and what the exact role of photorespiration under these circumstances is. It is the objective of this thesis to shed light onto the interplay of photorespiration and photosynthesis during light fluctuations. This project will be performed in collaboration with Horticultural and Product Physiology chair group (Elias Kaiser).

Type of research:

Performing short-term experiments using a gas exchange and chlorophyll fluorescence system (LI-6400 or LI-6800). Manipulating O2 and CO2 concentrations. Performing growth experiments under controlled/measured light intensity fluctuations. A mathematical modelling component can be included if the student wishes to do so.

Location:

Wageningen

Period:

To be scheduled after consulting with the supervisors.

Contact:

Alejandro Morales (alejandro.moralessierra@wur.nl)

Dynamic stomatal limitations using epf mutants

Description:

In nature, leaves are often exposed to fluctuations in light intensity. These fluctuations directly impact on photosynthesis rates, as they cannot react instantaneously. One of the major limitations of photosynthesis in fluctuating light intensities is stomatal conductance, i.e. the capacity for CO2 flux into the leaf. Stomata are microscopic pores on the leaf surface that exchange water vapour for CO2, and are dynamically regulated: for example, they open in high light intensities and partially close in the shade. After a transition from shade to high light, stomatal opening is slow (30-60 minutes), which reduces the diffusion of CO2 into the leaf and therefore photosynthesis. What is unclear at the moment is how strongly stomatal conductance limits photosynthesis in fluctuating light, and whether the stomatal limitation of photosynthesis in fluctuating light actually translates into reductions in growth. To test this, in this project, epidermal patterning factor (epf) mutants (Arabidopsis thaliana) will be used, which have changed stomatal density compared to the wildtype. These mutants are thus ideal in studying how a larger, or smaller, stomatal conductance (due to more, or fewer, stomata) will impact on plant growth in fluctuating light. This project will be performed in collaboration with Horticultural and Product Physiology chair group (Elias Kaiser).

Type of research:

Performing short-term experiments using a gas exchange and chlorophyll fluorescence system (LI-6400 or LI-6800). Measuring stomatal density by silicone imprints and microscopy. Performing growth experiments under controlled light intensity fluctuations.

Location:

Wageningen

Period:

To be scheduled after consulting with the supervisors.

Contact:

Alejandro Morales (alejandro.moralessierra@wur.nl)

Chloroplast movements under fluctuating light

Description:

In nature, leaves are exposed to fluctuations in light intensity. These fluctuations have a negative effect on photosynthetic rates, partly due to the low speed at which photosynthesis responds to changes in light. In plants acclimated to shade, chloroplast move to the side of the cells when the leaf is exposed to high light, in order to reduce light absorption and photodamage. However, the speed at which the chloroplast return to their original position in low light may reduce photosynthesis after a transition from high light to shade. Although this effect is expected from theory and may be predicted from mathematical models, it has never been quantified experimentally. To perform this quantification this project will measure dynamic gas exchange and leaf optical properties on leaves of Arabidopsis thaliana exposed do light transients. In order to induce different levels of chloroplast movements, mutants (e.g. phot2) and/or different blue light intensities (as chloroplast movements only respond to blue light) will be used. The data may also be used to improve current models of chloroplast movements in Arabidopsis. This project will be performed in collaboration with Horticultural and Product Physiology chair group (Elias Kaiser).

Type of research:

Performing short-term experiments using a gas exchange system (LI-6400 or LI-6800). Measuring changes in leaf optical properties with spectrometers. Performing growth experiments under controlled/measured light intensity fluctuations. A mathematical modelling component can be included if the student wishes to do so.

Location:

Wageningen

Period:

To be scheduled after consulting with the supervisors.

Contact:

Alejandro Morales (alejandro.moralessierra@wur.nl)

Comparative ecophysiology of Setaria viridis and Brachypodium distachyon

Description:

Research in plant physiology is often accelerated by the use of model organisms rather crops. The reason is that model organisms are more convenient to work with in the lab (small stature, short cycle) and more amenable to genetic studies and transformation than crops. Setaria viridis and Brachypodium distachyon are being used as model organisms for cereals and grasses. However, little is known about the ecophysiology of these species and how they compare to crops.

B. distachyon uses the C3 photosynthesis pathway and is related to barley and wheat, whereas S. viridis uses a C4 photosynthesis pathway as is it is a type of millet, but also used as model organism for other C4 crops. In this project, B. dystachion and S. viridis will be grown alongside a C3 and C4 crop (e.g. wheat and maize) under greenhouse conditions. The goal is to characterize differences in photosynthesis, biomass accumulation, seed yield as well as basic plant morphology and development among the model organisms and the crops. These differences will be analysed to evaluate to what extent B. distachyon and S. viridis are useful model organisms for the ecophysiology of C3 and C4 crops.

Type of research:

Perform plant growth experiments under greenhouse conditions, accompanied with measurements of photosynthesis, morphology and development of the crops. Statistical analysis of the different traits.

Location:

Wageningen

Period:

Spring to Summer 2019.

Contact:

Alejandro Morales (alejandro.moralessierra@wur.nl)