In the Plant form and function theme we analyse the relationships between plant traits, architecture, and functioning in crop stands as influenced by the abiotic environment (e.g., crop-microclimate feedbacks). Key in this theme are also plant-plant interactions. CSA is currently a world leader in 3D functional-structural plant modelling of crops, that allows analyzing plant-environment relationships in realistic crop settings.
Root system architecture (RSA) is the results of the genetic make-up of the plant and environmental factors such as soil nitrogen and water, and changes as the plant develops. Differences in RSA can affect plant nutrient capture which may have consequences for grain biomass accumulation. Being able to adapt RSA in response to these environmental factors enables the plant to shape its RSA to optimize resource capture. Such plasticity of RSA-related traits, such as the distance between side branches along a main branch, can help plant survive under resource-limited environments. However, there are still gaps in our understanding on these plastic responses contribute to plant performance and productivity across environments.
Functional structural plant (FSP) modelling is a plant simulation approach combining plant 3D structure and carbon & nitrogen sink-source relations. This approach can be used to understand how changes in RSA traits in response to environmental factors affect plant growth. Currently, our modelling of RSA changes in response to local nitrogen availability in maize still needs further development. Therefore, further understanding of possible mechanisms driving plasticity in RSA based on available data, and implementing this in current FSP modelling efforts are necessary. This will enable quantifying the relevance of plasticity in RSA traits for maize performance.
Objectives and methods:
The aim of this project is to understand and quantify maize RSA characteristics in response to nitrogen, which can be further used to develop whole plant FSP model. Data from a hydroponic maize experiment is available. In this thesis, you mainly focus on image analysis, data analysis and modelling.
Types of research:
Data analysis (root traits as a function of nitrogen level), FSP modelling (implementation of relations between nitrogen and RSA; simulations of maize growth and development)
For further information on this thesis subject, please contact us.
The plant structure of potato is highly plastic. Environmental factors like light and temperature, genotype and age determine the overall plant branching pattern. In addition, the novel hybrid potato technology makes it realistic to grow potato tubers from various starting materials, namely true potato seed, seedling tuber and seed tuber. While there are morphological differences existing in potato plants grown from different starting materials, especially in development of number of stems and types of branches. For example, plants grown from true potato seeds develop a single main stem and normally basal branches are only produced from above ground nodes, whereas more than one main stems can be developed in tuber-grown plants and several basal branches grow from below ground.
Various crop simulation models have been developed for tuber-grown potato crops to simulate total light interception, dry matter accumulation and partitioning at the population level. However, such models do not well represent the development of apical and basal branches and their contributions to canopy leaf area varied at different stem density and temperature conditions. Their roles in determining tuber yield and size distribution is still unknown. It is necessary to study the dynamics of development and growth of individual organs as regulated by source-sink relations under different environments, across developmental stages and for different propagules.
Objectives and methods:
The aim of this thesis is to develop a plant model for potato, based on the principle of functional-structural plant (FSP) modelling. The purpose of this model will be to explore how genetic, management and environmental factors are linked to plant morphology, notably branching pattern, and how this relates to tuber production. Data from an extensive field trail from 2021 is available, and additional data will be collected in 2022. Within this thesis, you will focus primarily on the development of the potato plant model, and there are possibilities to also be involved in the field work, depending on the timing of the thesis.
Types of research:
FSP modelling, data analysis, possibly field work
If you are interested to know the growth and development of hybrid potato plants and FSP modelling, please feel free to contact us!
Root anatomical traits have important roles in soil resource capture, especially in environments with suboptimal water and nutrient availability. The maize root system consists of three major root classes: seminal axial (or seed-borne) and nodal axial (shoot-borne) roots which all produce lateral (root-borne) roots of the first and second order. Lateral roots typically constitute the major portion of root systems, accounting for approximately 90% of the total root length.
Phenotypic plasticity is the ability of an organism to alter its phenotype in response to the environment and may involve changes in physiology, anatomy, or development. Plasticity has been observed for a number of root anatomical traits and is important for adaptation to environments with drought or suboptimal nutrient availability. Lateral root growth and behavior has been shown to be plastic in response to the microenvironment that the root is experiencing. Lateral roots can proliferate and even branch further when the roots encounter resources, such as water or nutrients, that a plant needs to grow. However, little is understood about anatomical trait plasticity of lateral roots in response to nutrient stress. The expression of anatomical traits in lateral roots presumably has a direct influence on plant growth and nutrient acquisition and therefore plant performance.
Types of work:
You will conduct a series of experiments in the growth chamber using a set of diverse genotypes. Plants will be grown under various nutrient regimes and lateral root responses to nutrient stress will be assessed. Anatomical phenotypes of lateral roots in different environments will be mapped based on root order and position on the axial root. Projects will involve microscopy, image analysis, and development of a conceptual framework for root adaptation to nutrient stress.
Wageningen (WUR Crop Systems Analysis)
Dr Hannah Schneider (email@example.com)
A key question in understanding the structure of a natural vegetation is how plants of different heights within the canopy can co-exist. An exciting hypothesis is that taller plants may have the advantage of higher light interception; but taller plants sway more with wind, forming a gap between canopy crowns. This gap has important consequences for within-canopy light environment and performance of subordinate plants. This project aims to reconstruct the 3D light environment within canopies by considering canopy gaps, in order to understand global canopy structure and species co-existence in vegetations such as forests and agroforestry systems.
Types of work:
This work is an FSP modelling study. There is flexibility in which exact questions will be explored using a model, but it will be limited to competition for light. The model can be built from scratch, or be based on existing FSP models. The topic is suitable for students who are interested in plant-plant interaction and community ecology, but also for those who wish to develop FSP modelling skills.
Wageningen (WUR Crop Systems Analysis)
Niels Anten (firstname.lastname@example.org), Jochem Evers (email@example.com)
In the Netherlands and Belgium grape production for wine making is getting more professional by the year. Yet, physiological knowledge on growth of the used genotypes in response to local climate conditions is limited. For better prediction of crop performance and timely pruning actions, a growth model is a good tool. Currently some vineyards monitor the development of growth, Veraison and ripening in detail. Apart from crop growth, climate is registered by temperature, humidity and radiation sensors in the city vineyard in The Hague. Detailed knowledge on fruit development and associated sugar production is available at French research institutes. When current knowledge and new monitoring data are integrated, all elements for a model for Dutch grapes are available. As easy as, like we say in Dutch, harvesting low hanging fruit.
Type of research:
The proposed MSc work consists of construction of a growth model for grape plants and its fruits. Since this model is new, elements of other plant models will be used to make a quick start. The programming environment (Matlab, C#, Java, etc.) is free of choice. The calibration of model parameters will be facilitated by the data collected by the growers and by known relationships from academic research in Bordeaux (France) and Geisenheim (Germany). It is recommended to visit some Dutch vineyards to get more insight in crop management in practice.
Wageningen UR Greenhouse Horticulture
Pieter de Visser (firstname.lastname@example.org), Jochem Evers (email@example.com)
Plants that grow in competition and that are attacked by herbivores face a dilemma: grow or defend? This dilemma arises because a plant can either invest its resources in defense or in growth, and a plant should prioritize one over the other. Evidence is mounting that plants downregulate their defense in favour of competitive strength. A plant that receives a low red:far-red ratio - an indication of forthcoming competition for light - becomes less sensitive for hormones involved in defense (jasmonic acid and salycic acid).
The adaptive significance of this downregulation is not well understood. And although this downregulation may be advantageous in an ecological setting, it may be disadvantageous in agricultural setting. In agriculture, plants grow at high density and hence they maybe be sub defended. Thus, compromising defense over competitiveness may be a disadvantage in this context. Therefore, one outstanding question is whether plants vary in the extent to which they downregulate defences upon reception of lower red:far-red ratios. For example, do genotypes that are less sensitive to a decreased red:far-red ratio have higher defense levels compared to genotypes that are responsive to a decreased red:far-red ratio? Another questions is more fundamental: what are the consequences in terms of fitness if a plant downregulation its defenses by far-red in high density? This question could be answered through modelling.
We are looking for a highly motivated student with good experimental skills or an interest in modelling. We offer a challenging thesis project supervised by enthusiastic and creative supervisors.
Bob Douma (firstname.lastname@example.org), +31(0)317 482140)
Weeds are a serious biotic production constraint in most agricultural production systems. Acting at the same trophic level as the crop, weeds capture resources that cannot anymore be used by the crop. A sustainable way to suppress weed growth in a crop canopy is by improving crop competitiveness. This can be achieved by changing architectural traits of the crop plants that enhance its competitive strength, such as early soil cover, as well as optimized leaf orientation and branching patterns. Crop competitiveness can also be improved by changing population characteristics such as crop population density, presence of secondary competitive crops or the uniformity of crop plant arrangement. In all cases, the balance between competition with weed plants (interspecific competition) and competition among crop plants (intraspecific competition) will determine whether the increased crop competitiveness will result in improved weed suppression.
Experimental and modelling work conducted in recent years has shown that substantial gain in crop competitiveness is to be expected by combined optimization of plant and canopies characteristics. The focus of this thesis work is to explore the balance between inter- and intraspecific competition for light in crop-weed canopies, in relation to plant and canopy characteristics. Potential questions to be addressed are: how does canopy uniformity relate to weed suppression? Which crop traits make a crop more competitive with weeds and how does this depend on population density? What is the influence of the moment of weed emergence in this? Which crop plant architecture is optimal for weed suppression? To address such questions, a 3D functional-structural plant (FSP) model of crop-weed interactions is available that simulates growth and development of individual crop and weed plants in a specific arrangement.
Types of work
This work is a modelling study. There is flexibility in which questions will be explored using the FSP model, but it will be limited to competition for light. The model available can be used as it is, requiring only parameter value adjustments, or it can be adapted and modified to accommodate simulation of processes it is currently lacking – this is up to the student’s learning goals. The topic is suitable for students who are interested in plant-plant interactions and ecological weed control, but also for those who wish to develop FSP modelling skills.
Wageningen (WUR Crop Systems Analysis)
Plant volatiles provide information on the status of the volatile emitting plant. For example, plants that are attacked by pathogens or insects release a different blend of volatiles compared to non-attacked individuals. Volatiles that signal attack do for example attract the natural enemies of the attackers and can prime neighbour plants for defense. The priming leads to a stronger and faster response to attacker than non-primed plants. Volatiles released by healthy individuals affect a growth response in neighbour plants in this way affecting competition between the neighbour and emitter plants. Despite this knowledge there is a large number of questions to be answered to get further insight in the role of volatiles in plant-plant interactions. For example,
1. Is volatile communication impaired when plants grown in competition?
2. Is the plant response to volatiles dose dependent?
3. How are different volatiles or other cues of plant-plant communication such as light reflection, brief touching, integrated?
4. Do some volatile signals have priority over others?
5. How do volatiles affect performance of species mixtures?
6. How do volatiles interaction between plants affect performance of herbivore insects and their natural enemies?
This research will be done in close collaboration with Velemir Ninkovic from the Swedish University of Agricultural Sciences (SLU, http://www.slu.se/cv/velemir-ninkovic/). He has good experimental facilities to test these and related questions. A compensation of a part of the costs of living may be covered by the Erasmus program (https://www.wur.nl/en/article/Final-call-exchange-spots-.htm)
We are looking for highly motivated students with good experimental skills that are willing to stay in Sweden for at least three to four months. In case of an MSc thesis, writing of the proposal and report is possible in Wageningen and examination will take place in Wageningen. Experiments can be done from February until November.
Bob Douma, Centre for Crop Systems Analysis, Bob.Douma@wur.nl, +31 (0)317 482140
Velemir Ninkovic, email@example.com
Pixel cropping (or pixel farming) is the practice of growing multiple crop species in complex arrangements in which communities of plants are spatially allocated at a fine resolution. The goal is to create diverse configurations of multiple crop species in which the right plant community is allocated to the right location, at the right time, and at the optimal resolution. The concept is grounded in the diversity—productivity theory, and evidence that diversification in agro-ecosystems is necessary to reduce damaging externalities caused by industrial monocultures.
We are currently conducting a preliminary pixel cropping experiment in the field at the Droevendaal Organic Experimental farm in Wageningen. Because we do not yet have the scientific knowledge to design ecologically optimal pixel cropped fields, in the experiment we have implemented superficial design rules: limiting the number of crop species, and allocating all plant communities to a uniform pixel size and shape (50 cm x 50 cm) within a fixed grid. Crops are randomly assigned to each pixel in equal proportion.
The challenge of designing a good pixel cropping plan brings up many questions, such as:
- How do plants selected for monocultures respond (in terms of morphology, yield, service provision, etc.) to being grown in heterogeneous communities?
- What is the optimal pixel resolution for each crop?
- Which crop combinations make good and bad neighbors?
- Which particular plant traits make a species suitable for pixel cropping?
Acquiring the knowledge needed to design optimal pixel plots could involve conducting field experiments in which the complexity of the experimental setup is exponentially amplified to accommodate all possible neighbor and pixel size/shape combinations for the crops of interest. Alternatively, modeling offers a platform to explore designs and interactions out of the field. Our goal is to develop a simulation model that can capture the spatial heterogeneity and species diversity typical for pixel crop designs. The modelling approach to be used here is called functional-structural plant (FSP) modelling, in which individual plants are simulated in inter- and intraspecific competition with neighbouring plants. Ultimately, such a model will allow to address questions on plant response, traits, pixel resolution and optimal neighbour combinations.
The specific aim of this Master thesis is to develop a pixel cropping FPS model that captures the main components of a typical pixel crop system, using data from the pixel cropping field experiments and the modelling tools already available.
Type of work
Modelling, data analysis
Lenora Ditzler (FSE, firstname.lastname@example.org) or Jochem Evers (email@example.com)
Plants are capable of shaping their developmental pattern to the competitiveness of the environment. For example, plants growing at a high population density can divert resources towards height growth to prevent being shaded by their neighbours. To be able to do so, plants make use of light signals they perceive through light-sensitive molecules such as phytochrome. Such light signals can already be perceived before the actual shading takes place. A well-known example of such a light signal is the ratio between red and far-red light (R:FR). The value of R:FR of the light reflected off neighbouring plants is relatively low compared to light coming from the sky. The reason for this is that plants absorb red light for photosynthesis, but reflect far-red light. The decreased ratio between the two reveals their presence to neighbours.
The aim of this thesis project is to find out to what extent plants may exploit this mechanism, by weakening or masking the light signals that give away their presence. Such ‘cheating’ behaviour by plants is well known to occur, for example orchids deceiving their pollinators by the morphology of their flowers, but has not been reported for light signals. If a plant would be able to manipulate the spectrum of the light it reflects, it would gain a competitive advantage over neighbouring plants who do not.
Therefore, the operational objectives of this thesis will be 1) to screen a range of plant genotypes for the spectral properties of their leaves, to get a quantification of the variation in the composition of the light they reflect; 2) to apply an FSP model to explore potential benefits of stealth behaviour by modifying light signals, and to find out what the level of signal masking should be in order for it to make a difference for competitive outcomes.
Type of research:
Preferably the student combines experiments and modelling. However, only modelling or experiments are possible depending on the learning goals of the student.
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):
- Building and testing PARbars (https://www.jove.com/video/59447/parbars-cheap-easy-to-build-ceptometers-for-continuous-measurement) and waterproof Cave Pearl dataloggers (https://thecavepearlproject.org/)
- Measuring light intensity at a range of levels in a crop canopy in the field (Cambridge, UK)
- Analysing collected data for variability and FSPmodelling.
- 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!
The influence of crop management practices and seedling “treatments” on yield and yield components of hybrid potato
Hybrid breeding in potato is a relatively novel and very promising technology, through which new potato cultivars can be developed and propagated much more rapidly. Hybrid ware can be established in the field through different pathways such as field transplanting of nursery generated seedlings, direct sowing and use of seedling tubers. Field transplanting of hybrid potato seedlings involves production of seedlings in a greenhouse nursery and transplanting into the field. The establishment and development of a hybrid ware crop from field transplanted seedlings is influenced by various factors including transplanting shock and crop management practices.
As part of the PhD project to develop a resilient cropping system for field transplanted hybrid potato, studies will be conducted on the influence of various seedling sizes as well as other seedling conditions on seedling establishment and their influence on transplant shock. Additionally, we will define the influence of crop management factors on yield and yield components of field transplanted hybrid potato. The crop management factors include, but are not limited to, fertiliser application and management, tillage practices as well as weeding.
The project work will mainly involve managing of field trials, lab work (processing plant biomass during destructive harvests), data collection and analysis. The work will start from May 2021 till the end of the project in 2024 and various topics on transplant growth and development as well as transplant crop management will be explored. We are therefore looking for enthusiastic Plant Sciences students (or students from other related studies programmes) to support our research through an MSc thesis during the trial period. Our ideal candidate is one who is keen on conducting field trials on agronomy research and has experience in field work and knowledge in data collection and analysis.
If you are interested, please get in touch with Olivia Kacheyo (firstname.lastname@example.org).
A digital twin is more than just a simulation model. The digital twin of tomato we are developing, is a 3D digital representation of a real tomato crop that grows and provides updated information for the model in real time. This data is used to update the model as the real crop grows, which will improve its predictions. This is important, because the output of the model is used to steer the growth of the real crop through management and greenhouse settings. This creates a closed feedback loop between the real and the digital twin members.
We are setting up a digital twin called the Virtual Tomato Crop, details here and here. For that we will conduct a large experiment in the new NPEC greenhouse facilities in which the plants and climate will be measured automatically (phenotyped) in great spatial and temporal detail. An important aspect in this regard is the ‘ground-truthing’ of the phenotyping data, using reliable manual measurements on the plants. This includes 3D morphological and physiological plant traits, as well as environmental conditions like the 3D distribution of light. This data will be used to parameterize the tomato simulation model.
Types of work
Within this project, we are looking for students who are interested in making a comprehensive study on the development over time of tomato in the NPEC greenhouse and make a comparison to the data coming from the phenotyping. For this the student will get involved in the experimental work in the greenhouse. An additional component of the thesis could be the development of a dataset of light distribution in the tomato canopy to verify the predictions of light distribution by the model that is currently under development.
This thesis topic is interesting for students who want to work on the cutting edge of phenotyping and plant model development. The exact contents of the thesis can be defined taking into account the wishes of the student and the requirements of the project.
Due to the reliance on the experiment in the NPEC greenhouse, the thesis can start September 2021 and be finished mid 2022.
Wageningen (WUR Crop Systems Analysis)