Plant form and function

The theme Plant form and function focuses on the relationships between architecture of plants and crops and physiological processes determining plant functioning and yield in interaction with environmental factors. An important tool within this theme is functional-structural plant modelling (FSPM). FSPM explicitly captures the development over time of the 3D architecture or structure of plants as governed by physiological processes which, in turn, depend on environmental factors. Topics include, but are not limited to, plant growth and development in relation to environmental drivers, above and below-ground plant-plant interactions, resource foraging in monocultures and mixed-species stands, and plant-climate feedbacks.

Thesis subjects

Shade avoidance in Arabidoposis thaliana

Description:

Plants are able to respond and adjust their phenotype in response to neighbour plants. In competition for light, plants invest more in height growth, by adjusting their leaves in a more vertical position and increasing the elongation of the stem, internode or petiole. These responses are an example of phenotypic plasticity and are part of the “shade avoidance syndrome (SAS)”. The key driver of these shade avoidance responses is the ratio between red and far-red light that the plants perceive. Light reflected from neighbouring plants is enriched in far-red and decreased in red light, by which the red to far-red (R:FR) ratio decreases. It has been shown that the right specific response should occur at the right time otherwise it is not beneficial during competition. The aim of this topic is to unravel the fine-tuned organ responses of Arabidopsis thaliana in dense vegetation stand, and study if a certain combination of responses is most beneficial while competition for light. In this topic various Arabidopsis genotypes and mutants will be used to study the variation within the fine-tuned shade avoidance responses. Finally, competition experiments should be able to help understand the importance of fine-tuned organ specific responses.

Types of research:

Both plant experiments (greenhouse) and plant modelling can be used in this topic.

Location:

Wageningen

Contact:

Jochem Evers (jochem.evers@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 variation in drought tolerance among wild coffee populations (experimental work being conducted in Uganda)
  2. To what extent does this variation correlate with variation in candidate genes (molecular work in Montpellier France).

Location:

Uganda or Montpellier, France

Contact:

Niels Anten (niels.anten@wur.nl)

The border effect in plant canopies

Description:

Small experimental plant plots are often used in ecophysiology, plant ecology and crop science, e.g. to compare yields between crop cultivars or crop management practices, analyse competition between plants or determine neighbour-induced responses. A key assumption underlying the use of such small plots is that the light environment experienced by the plants that are measured is respresentative of that in a much larger vegetation stand. However, plants that grow near the edge of such experimental plots experience less neighbour-induced shading or alterations of the spectral composition of the light. Together with other (belowground) factors, this border effect results in increased yields of the border plants.

This MSc thesis topic aims at quantifying the border effect in plots of field-grown crop plant species (e.g. wheat, rapeseed, mustard) in relation to population density, plot configuration and orientation, and to find out how far from the edge of a plot the border effect can still be observed. Variables to be analyzed are radiation intensity and quality, plant growth, leaf and branch development, as well as biomass and yield at the level of the plant in relation to the location within the plot.

Types of research:

This study includes a field experiment, which has consequences for the timing of the thesis period. If desired, the study can be extended with a modelling component.

Location:

Wageningen

Contact:

Jochem Evers (jochem.evers@wur.nl)

Do plants respond to neighbour-produced insect induced volatiles by changing their growth strategy?

Description:

As a response to insect herbivory, plants emit volatile compounds. These compounds serve as a cry for help for the plant because they attract the natural enemies of the insect herbivores. However, neighbour plants has also been shown to respond to these volatiles by priming their defence, and herewith preparing for attack. What has not been shown, but what is likely to occur is that neighbour plants also adjust their growth strategy in response to an attacked neighbour. To escape possible herbivore attack, flowering onset may be advanced. The response of the neighbour plants may depend on the growing conditions (number of (affected) neighbours, amount of volatiles received). In this thesis you will test how plants respond to neighbour produced volatiles and how this depends on the conditions plants grow in.

We are looking for a highly motivated student with good experimental skills. We offer a challenging thesis project supervised by enthusiastic and creative supervisors. This experiment can be done in Sweden (SLU, Uppsala, Sweden) in collaboration with Velemir Ninkovicz. He has ample experience with these kind of experiments. Performing these experiments under his supervision is a unique possibility.

Location:

Sweden (SLU, Uppsala, Sweden)

Contact:

Bob Douma (bob.douma@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)

3D modelling of plant species coexistence under light competition

Description:

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.

Location:

Wageningen (WUR Crop Systems Analysis)

Contact:

Niels Anten (niels.anten@wur.nl), Jochem Evers (jochem.evers@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)

Building the first Dutch model on grape

Description:

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.

Location:

Wageningen UR Greenhouse Horticulture 

Contact:

Pieter de Visser (pieter.devisser@wur.nl), Jochem Evers (jochem.evers@wur.nl)

The dilemma of plants: growth or defend? understanding the growth-defense trade-off

Description:

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.

Contact:

Bob Douma (bob.douma@wur.nl & +31(0)317 482140)

Improving homogeneity in cut chrysanthemum production

Description

Chrysanthemum is one of the most important horticultural ornamental crops worldwide. Much research has been done on the response of chrysanthemum to environmental factors such as temperature, light, and their interaction. This research is being used to optimize chrysanthemum production. However, the single most persistent issue in production of this ornamental crop is the variation within the product: individual chrysanthemum plants grown simultaneously in the same conditions differ from one another in terms of stem extension, branching, leaf area, biomass, and flower number and size. Adding to this complexity is the rapid introduction of new varieties, each with their own particular responses to environmental signals.

This MSc thesis topic aims at improving the homogeneity of chrysanthemum production by finding optimal plant traits for production. This entails mapping the suit of responses chrysanthemum shows to environmental signals (notably light), quantifying those responses, and formulating management protocols as well as directions for chrysanthemum breeding. This research will be done in collaboration with Deliflor, the largest chrysanthemum breeder worldwide (www.deliflor.nl).

Types of work

This study will include one or more of the following components: measurements in current chrysanthemum production situations, performing small-scale experiments to quantify crop responses to manipulation of environmental variables, and integration of new and existing knowledge in a simulation model of chrysanthemum growth and development based on the principles of functional-structural plant modelling. The exact contents of the work can be tailored towards the learning goals of the student to a certain extent.

Location

Wageningen (WUR Crop Systems Analysis; WUR Horticulture and Product Physiology) and Maasdijk (Deliflor)

Contact

Jochem Evers (jochem.evers@wur.nl), Ep Heuvelink (ep.heuvelink@wur.nl)

Modelling crop-weed interactions in 3D

Description

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.

Location

Wageningen (WUR Crop Systems Analysis)

Contact

Jochem Evers (jochem.evers@wur.nl), Lammert Bastiaans (lammert.bastiaans@wur.nl)

Modelling branching regulation by hormones and light

Description

Strigolactones are a newly discovered plant hormone which regulates plant shoot branching and secondary stem growth. We have found a new pathway in SL signaling, which links light signalling with strigolactone activity and carbohydrate transport in the phloem. The classical and novel SL signaling pathways interact and together provide a new conceptual model for the regulation of branching and secondary growth. The novel model aims to integrate SL action with light signaling through phytochromes and through plastid redox state. This project is a collaboration with the Laboratory of Plant Physiology.

Types of work

This work is a modelling study. It will consist of development of the underlying conceptual model (analysis of literature and datasets) as well as the actual implementation, calibration and testing of the model using simulation software and programming language of choice. Experience in modelling is a requirement.

Location

Wageningen (WUR Crop Systems Analysis)

Contact

Jochem Evers (jochem.evers@wur.nl) or Sander van der Krol (sander.vanderkrol@wur.nl)

Compensatory growth responding to branch bending and pruning in cut-rose

Description:

Pruning and bending are common crop management practices in cut-rose production.

Pruning leads to branch loss which can have a negative effect on plant growth due to the loss of branches and leaves as providers of assimilates. Previous studies showed that while partial defoliation results in a loss of photosynthetic area, this rarely leads to a proportional reduction in biomass production. Partially defoliated plants show compensatory growth through active responses such as increasing nitrogen concentration in the remaining leaves and reallocation of biomass to newly formed leaves, and through reducing self-shading in the canopy. Plants that endure loss of branches may show similar compensatory growth responses through adjusting architectural traits of the remaining branches to increase light interception, increasing leaf photosynthetic capacity of the remaining leaves, and producing new branches.

In rose branches can be bent and remain attached to the plant. Leaves on bent branches may have a low photosynthetic capacity due to the damage of the branch by bending or adaptation to the relatively low light level, but the actual photosynthesis of the bent branches may not be proportionally decreased, since these bent branches grow at better light conditions away from the dense upright canopy.

In this study, we are interested in knowing whether plants show compensatory growth in response to branch bending and pruning, and which processes are relevant to the compensatory growth responses.

Type of research:

Experimental work in the greenhouse. Type of measurements include plant architectural traits (e.g. internode length, leaf length and width, leaf area, etc.), light interception, and plant fresh and dry weight.

Contact:

Ningyi Zhang (ningyi.zhang@wur.nl)

Does a plant need multiple light cues to cope with shade effectively?

Description:

Plants use a number of cues to retrieve information about their environment and to respond optimally to the conditions they are exposed to. For example, plants use the ratio of far-red versus red light to sense impending competition, and respond by increasing stem and petiole extension, reducing branching and increasing leaf angle. In addition, plants can use other cues such a blue or green light, or overall light intensity to obtain information on future and current shading conditions. These signals are generated by neighbouring plants during canopy development, change in strength over time and do not operate simultaneously. We would like to explore whether plants that integrate multiple cues are better able to cope with their environment than plants that use a single cues, and what is the relative contribution of the individual cues to plant performance.

Type of research:

The proposed work consists of constructing or extending a plant simulation model, based on the principles of functional-structural plant (FSP) modelling, to include multiple light cues, the response of plants to those cues, and the consequences for plant performance. The study is not limited a priori to a specific species. The model can be used to test a range of different cues and responses, and to evaluate to what extent these affect plant performance when combined.

If you are enthusiastic for this topic and you want model plant-plant interactions please contact us.

Contact

Jochem Evers (Jochem.Evers@wur.nl), Bob Douma (Bob.Douma@wur.nl)

Plant-plant communication through volatiles

Description

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.

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.

Contact

Bob Douma, Centre for Crop Systems Analysis, Bob.Douma@wur.nl, +31 (0)317 482140

Velemir Ninkovic, velemir.ninkovic@slu.se

Understanding how pruning affects flowering and fruiting intensity and pattern in cocoa trees (Theobroma cacao L.)

Description

Cacao is the most important export crop in west African countries such as Ivory Coast and Ghana and an essential source of income for millions of small older farmers. Realized yield however falls way below the potential value calculated for the region. Better managements practise are required to improve yield.

Among other practises pruning, the selected removal of foliar and branch biomass, is essential to ensure to efficacy of fertilizer and pesticide applications and it balances the reproductive and vegetative production in order to maximize the efficacy of the tree canopy.  However it impacts  the physiology and  the resource allocation pattern of the plant, causing  in the short term a reduction in yield. To design effective pruning practises that would minimize this yield reduction an understanding of pruning effect on cacao physiology and resource allocation is needed but still lacking.

Theobroma cacao is a cauliflorous species with flower appearing both on the main stem and in the canopy and a very low fruit to flower ratio. The resource status of the plant is known to influence both the flowering intensity and the fruit abortion that occurs during the first phase of fruit development,  both important determinant of final yield. Since pruning intervention deeply affect the resource status and allocation in the plant we aspect that flowering and fruit abortion will be affected as well.

This project aims to understand and quantify those changes in order to obtain precious insight in resource dynamic in cacao plants under different pruning regimes.

Type of work

The project Comprise a field work of the duration of 2/3 months in the research station of  CNRA in Divo, Ivory coast.

Prefered Requirement

We are looking for an enthusiastic student, with very good adaptation skills and a working knowledge of French since in the research stations very few people speak English.

Location

Divo, Ivory coast

Starting time

April/May 2018 , Field work June- August 2018.

Contact

Ambra.tosto@wur.nl