Topics:
1. Open Canopy: open-source monitoring of whole-canopy water use
This thesis investigates an open-source, low-cost sensor system designed to monitor water vapour dynamics throughout a plant canopy and evaluate its usefulness for studying whole-canopy transpiration. Plant transpiration is a major component of ecosystem water fluxes and strongly influences climate, energy balance, and crop performance. Traditional methods—such as sap flow sensors, eddy-covariance towers, or commercial gas-exchange systems—provide high-quality data but are expensive, technically demanding, and poorly suited for large-scale screening or fine-scale spatial resolution within the canopy. Recent improvements in inexpensive humidity sensors create an opportunity to measure vertical patterns of water vapour and infer transpiration in a more accessible way. In this project, the student will deploy vertical arrays of humidity, temperature, and potentially light sensors in crop or greenhouse systems to collect time-series microclimate data. The work will test whether the system can distinguish differences in transpiration patterns across genotypes or environmental treatments, and assess its suitability for breeding programs targeting improved water-use efficiency and drought resilience. By advancing open-source microclimate monitoring, this thesis contributes to more scalable, affordable tools for both environmental research and sustainable agricultural management.
For more information, please contact Ludovico Caracciolo (ludovico.caracciolo@jii.org)
2. Miniature sensor for real-time photosynthesis tracking
This thesis focuses on improving and validating a miniature open-source leaf-clip sensor capable of monitoring plant photosynthetic activity in real time. Enhancing agricultural sustainability requires crops that produce more with fewer resources, yet measuring photosynthetic efficiency—one of the best predictors of plant productivity—remains a major bottleneck. Existing tools such as fluorometers and absorbance-based devices are costly, difficult to deploy at scale, and not optimized for continuous field use or large breeding trials. The project aims to expand the capabilities of a low-cost sensor that measures chlorophyll fluorescence signals linked to electron transport, providing an accessible proxy for photosynthetic performance. The student will collaborate with engineers, plant scientists, and programmers to build and refine hardware, develop simple firmware or software for data collection, and test the device in greenhouse or field conditions. No prior electronics experience is needed, but motivation and curiosity are essential. By enabling high-throughput, real-time measurements of photosynthetic efficiency, this work supports the development of crop varieties better suited to climate-resilient food production. The thesis merges engineering with plant physiology and contributes to democratizing advanced research tools for scientists and breeders worldwide.
For more information, please contact Ludovico Caracciolo (ludovico.caracciolo@jii.org)
As a step to explore possibilities for photosynthetic improvement in diploid potato, we explore the use of segregating populations, i.e. biparental populations, as a source of natural genetic variation. The objective of this research is to quantify the proportion of photosynthetic variation that can be explained by quantitative trait loci (QTL) in diploid potato biparental populations. Specifically, this study will first evaluate the extent of natural genetic variation for these traits in the population and then seek to map the loci underlying the observed phenotypic variation.For more information, please contact Olivia Kacheyo (olivia.kacheyo@jii.org) or Tom Theeuwen (tom.theeuwen@jii.org).
The effects of both sowing rate (sowing density) and plot size and their contribution to variation in photosynthetic traits as well as physiological traits including yield and yield components in barley will be explored in this study. Our aim is to optimize sowing density (number of plants per m2) as well as plot size (area in m2) in our field trials. This will help tailor decisions on reliability of various types of data collected under varying densities or plot sizes as well as help define optimal densities and plot sizes for various research trials.
For more information, please contact Olivia Kacheyo (olivia.kacheyo@jii.org) or Tom Theeuwen (tom.theeuwen@jii.org).
This study will assess genetic variation in physiological and agronomic traits including growth, development and flowering traits in large panels of diverse barley genotypes utilized in our project. This assessment will provide a means for grouping genotypes into various classes based on phenology, maturity type or other traits for a more targeted selection of candidate genotypes for further assessment of photosynthetic variation in future trials. Additionally, genetic loci linked to the various physiological and agronomic traits will be identified to further define genetic classes based on allelic variation.
For more information, please contact Olivia Kacheyo (olivia.kacheyo@jii.org) or Tom Theeuwen (tom.theeuwen@jii.org).
6. What are all these extra ATP synthases doing?
Photosynthesis is one of the most fundamental biological processes on Earth, supplying the energy that sustains nearly all life and shaping global carbon and oxygen cycles. Within this intricate system, the chloroplast ATP synthase plays a central regulatory role, and understanding how this complex is regulated is key for future efforts to engineer plants with improved resilience and productivity. Interestingly, ATP synthase appears to accumulate at levels far higher than needed under controlled conditions, suggesting that a large fraction of ATP synthase is inactivated by post-translational modifications. This project aims to uncover the environmental conditions under which this ‘inactive’ pool becomes activated. To achieve this, the student will use high-throughput phenotyping of transgenic tobacco plants engineered to accumulate roughly half the wild-type amount of ATP synthase. During the project, the student will gain hands-on experience with chlorophyll a fluorescence imaging, quantitative assays of ATP synthase activity in intact leaves and isolated thylakoids, and protein quantification techniques. A student with a strong interest in biochemistry, plant physiology, or a related field, along with enthusiasm for data analysis in Python or similar tools, will be a great fit. The preferred (but not fixed) start date is in the second quarter of 2026.
For more information, please contact Thekla von Bismarck (thekla.von.bismarck@jii.org) or Deserah Strand (dez@jii.org).
7. What do stop grains do to grow bigger?
Increased photosynthetic efficiency represents a promising frontier for achieving substantial improvements in crop yield and agricultural sustainability. However, the underlying mechanisms that link photosynthesis to yield remain unclear. Grain yield is thought to be limited by the amount of carbohydrates a plant assimilates and is allocated to the grain (source limitation). If so, increased photosynthesis could drive increased yields. Alternatively, grain yield can be limited by the capacity of the grain to grow any bigger (sink limitation), in which case increased photosynthesis will have limited effects on yield. A better understanding of the role of source and sink limitations to grain yield is key for breeding strategies.
The field experiment will be based on simple experimental manipulation of barley spikes to alter grain sink capacity for carbohydrates. Leveraging on, we aim to test the genetic variability on the degree of source/sink limitations to grain yield and its potential effects on photosynthesis.
The aim of this project is to quantify the genetic variability on the degree of source/sink limitations to grain yield and its potential effects on photosynthesis. The field experiment will be based on ongoing Barley breeding trails and simple experimental manipulation of barley spikes to alter grain sink capacity for carbohydrates. Within the project, you have the opportunity to expand on the physiological link between photosynthesis and grain mass, the compensatory effects of grain number and grain mass, and/or genetic variability across genotypes, depending on their own interests.
For more information, please contact Mauricio Tejera (mauricio.tejera@jii.org).
8. Genetic Diversity in Miscanthus Photosynthesis and Carbon Partitioning Perennial grasses, like Miscanthus, play a key role as sustainable biomass feedstock for the upcoming bioeconomy. Reduced photosynthesis during the growing season has been suggested as a potential driver of Miscanthus long-term productivity decline, however, the underlying mechanisms behind these declines are still unknown.
Previous research has identify decreased carbon allocation to belowground storage as a potential limitation to photosynthesis, however, these results are based on only one genotype and limited environmental conditions. We hope to expand this approach to a larger variety of Miscanthus genotypes. Data from this project will help breeding programs to better associate photosynthesis and final yield.
The aim of this project is to characterize Miscanthus genetic diversity in seasonal photosynthesis and its interaction with development. Within the project, you will have the opportunity to expand on the physiological and developmental response to the environment, the underlying biochemical limitations, and/or genetic variability across genotypes, depending on their own interests.
For more information, please contact Mauricio Tejera (mauricio.tejera@jii.org).
9. Quantifying Sink Limitations in Photosynthesis
While photosynthesis is the primary driver of plant growth and yield, it is not always the main limiting process. During plant development and under certain environmental conditions, photosynthetic performance can become constrained by the downstream consumption of carbohydrates—so-called sink limitations—rather than by carbon assimilation itself. Identifying when sink limitations become the primary bottleneck is key for efficiently improving photosynthetic performance.
To address this challenge, the JII aims to develop fast, reliable, and scalable instrumentation capable of measuring relevant photosynthetic traits and diagnosing sink limitations. Such tools could facilitate the integration of photosynthetic traits into breeding programs and accelerate the development of higher-yielding, climate-resilient crops.
The aim of this project is to test and validate fast protocols to quantify downstream metabolic limitations of photosynthesis (sink limitations) and identify key developmental stages. The project will investigate how sink limitations change during plant development and how different environmental or weather conditions influence the balance between carbon assimilation and carbohydrate utilization.
For more information, please contact Mauricio Tejera (mauricio.tejera@jii.org).
10. Genetic Diversity in Barley Photosynthesis and Radiation Use Efficiency
Increased photosynthetic efficiency represents a promising frontier for achieving substantial improvements in crop yield and agricultural sustainability. However, the underlying mechanisms that link photosynthesis to yield remain unclear. A better understanding of this link has large implications in crop production, management and breeding.
Grain yield is the result of the seasonal integration of light interception, the efficiency of the plant to convert light energy into biomass, and carbon allocation to grain, however, these processes are rarely studied together in the context of genetic variability. Within this project we seek to characterize how the genetic variability in radiation use efficiency and grain yield affect photosynthesis during the season.
The aim of this project is to characterize the relationship between photosynthesis and radiation use efficiency across a wide range of Barley genotypes. Within the project, you have the opportunity to expand on the physiological link between photosynthesis and RUE, the interactions with development, and/or genetic variability across genotypes depending on their own interests.
For more information, please contact Mauricio Tejera (mauricio.tejera@jii.org).
11. Spectroscopic Signals Beyond the light reactions: Capturing Biochemical Limitations and Photorespiratory Capacity
Increased photosynthetic efficiency represents a promising frontier for achieving substantial improvements in crop yield and agricultural sustainability. However, the lack of reliable high-throughput tools limits its integration into breeding programs. To address this challenge, the JII aims to develop fast, reliable, and scalable instrumentation capable of measuring relevant photosynthetic under field conditions.
The aim of this project is to test and validate fast protocols to quantify biochemical limitations and photorespiratory capacity. Within the project, you will have the opportunity to expand on sensor design, the environmental and developmental effects on the photosynthetic processes, or the genetic variability across barley and potato genotypes, depending on your interests.
For more information, please contact Mauricio Tejera (mauricio.tejera@jii.org).
12. Response of cyclic electron transfer to dynamic environmental conditions
Cyclic electron flow (CEF) is an alternative electron transport pathway that is thought to be important for plants due to its role in balancing the production of ATP and NADPH by the thylakoid electron transport chain. While CEF is well studied in the steady state, the response of CEF to dynamic environmental conditions is undefined. This is due to the laborious nature of measuring this process. In this project, we aim to develop a method to measure CEF under dynamic conditions using 1) high-throughput imaging systems to identify changes in CEF in response to user defined environmental changes and 2) hand-held systems and/or plant mounted sensors to identify changes in CEF to natural environments.
This project will involve learning chlorophyll fluorescence methods applied within a variety of approaches. An interest in method development is required, and a background in plant physiology and data analysis in Python (or another language) is preferred.
For more information, please contact Deserah Strand (dez@jii.org).
Location
Campus Wageningen, Radix
Type of Employment
Thesis or Internship (BSc./MSc.)
Starting Date
N/A
Status Vacancy
Open
Salary
-
