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)

Seeking drought tolerance in wild coffee populations

Description:

Coffee is grown in 52 mostly low-income countries. In Uganda, it contributes 20-25% to foreign trade, and its production sustains about 8 million Ugandans. However, global coffee production is under serious threat from climate change, i.e. warming and shifts in rainfall patterns, particularly in East Africa for which 2 – 4 ºC warming and increased occurrence of droughts have been predicted. Potentially climate change could result in severe reductions in Ugandan coffee growing areas raising important concerns for the future of the Ugandan coffee industry.

The ability of crops to adapt to climate change strongly depends on the genetic variation that exists within a crop. For coffee much of that variation can be found in wild populations that still grow in natural forest. Uganda is one of the centers of diversity for wild C. canephora (one of the two major coffee species) being at the drier end of this distribution. In order to improve the resilience potential of C. canephora production in Uganda, there is thus an urgent need to assess the genetic diversity in drought and high temperature tolerance, their underlying traits and subsequently conserve this diversity.  This research therefore addresses two questions:

  1. What is the genotypic variaton in drought tolerance among wild coffee populations (experimental work being conducted in Uganda)
  2. To what extend does this variation in candidate genes (molecular work in Montpellier France)

Location:

Uganda or Montpellier, France

Contact:

Niels Anten (niels.anten@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)

Modelling yield penalty of Early Bligh infection on potato

Description:

The Early Blight complex, caused by several species of the fungal genus Alternaria, has been known for many years as a foliar disease of potato crops. In latest years, increased incidence and aggressiveness of the disease has given it the title of an “emerging” disease. Several factors are hypothesized to have contributed to this increased emergence, such as reduced fungicide use, different climatic conditions, reduced fertilizer inputs, mutations within the species and more susceptible cultivars being grown, among others.

There is little information on the actual yield penalty caused by the disease. Especially interesting is the fact that it appears on older, lower leaves on potato plants. Given the fact that the yield loss caused is probably directly correlated with the decrease in the photosynthetic potential of the plant, there is a need for a better understanding of the underlying mechanism of disease spread on a single plant and how this affects the plant yield.

In this topic the selected student will start developing a functional-structural plant model of potato with the purpose of simulating how the disease spreads on the plant over time, how it can potentially impact total photosynthesis and as a result plant yield.

Types of research:

Mainly modelling and potentially some plant experiments (climate room) to increase the student’s understanding of how the disease develops on live tissue.

Location:

Wageningen

Contact:

Ioannis Baltzakis (ioannis.baltzakis@wur.nl)

Studying Alternaria spp. responsible for the Early Blight disease on potato

Description:

The Early Blight complex, caused by several species of the fungal genus Alternaria, has been known for many years as a foliar disease of potato crops. In latest years, increased incidence and aggressiveness of the disease has given it the title of an “emerging” disease and is causing more interest in the industry as well as the scientific world.

Originally attributed to the species Alternaria solani and Alternaria alternata, advancements in molecular identification techniques and in taxonomy have revealed as many as 6 species that exist in symptomatic lesions of Early Blight on potato plants. Little is known as to which of those species are the most aggressive and which are just opportunistic and weak pathogens that are simply causing secondary or no infections at all.

In this topic we will study the pathogenicity of many Alternaria species on potato plants. Several infection characteristics need to be quantified and experimental methods standardized. Some of the measurements will include, lesion growth rate, time of onset of symptoms on inoculated plants, latent and infectious periods, time to sporulation after initial infection, quantification of sporulation. Those measurements will be mainly done on detached leaf assays, but whole plant experiments will also be conducted.

Types of research:

Mainly, controlled environment (climate rooms) work. Data obtained will be used for designing a plant-disease functional structural model of potato-early blight, if the student also wishes to participate in this area of the research it can be further discussed.

Location:

Wageningen

Contact:

Ioannis Baltzakis (ioannis.baltzakis@wur.nl)

The interaction between potato canopy architecture and light interception, in the context of yield loss from foliar diseases

Description:

Potato (Solanum tuberosum) is one of the most economically important crops globally, with a significant role in maintaining food security and providing accessible food for developing countries.

Potato yields can be severely undermined by a plethora of plant pathogens that affect the canopy, and therefore directly reducing the photosynthetic potential of the crop. Early blight of potato, caused by certain species of the Alternaria genus of fungi, is the disease of interest for this thesis topic.

The student, will help obtain data that will help construct a potato FSPM model, currently in development in the C.S.A. group. The student will be involved in the modelling process and gain a deeper understanding of what is required to plan and develop an FSPM model.

The goal of developing the potato FSPM, is to investigate what the impact of a foliar disease, such as Early Blight, can be in the final crop yield. Said model can potentially allow us to answer this question by simulating a reduction in leaf area of the crop canopy while taking into account the timing of infection onset.

Type of research:

The successful applicant will be tasked with obtaining architectural and light interception data of potato plants growing in field conditions. He or she will also be part of the team developing the FSPM, providing insights on how the plants grow and what kind of measurements are most important for the final model.

Location:

Wageningen UR

Contact:      

Ioannis Baltzakis (ioannis.baltzakis@wur.nl), Jochem Evers (jochem.evers@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)