Topics:

1. Short- and long-term acclimation of plants to water stress

Drought stress has multiple compounding effects on plant physiology and biochemistry. Drought stress has consequences for plant growth and grain yield, threatening food security. With regards to photosynthesis, the anatomical response to water stress of stomatal closure has a secondary effect of limiting CO2 supply to rubisco. Water stress leads to the downregulation of both the carbon reactions and the electron transport chain, but the exact mechanisms and timing is unclear. The project aims to answer three questions: 1) is the downregulation of photosynthesis due to source or sink limitations arising from water stress, and 2) when do the long-term water stress responses occur, and 3) can we determine if the long-term responses are triggered by leaf water potential, or time under water stress? The project will involve learning the measurements of leaf level photosynthesis and leaf water status in controlled environments (i.e., growth cabinets and greenhouse), as well as biochemical methods for protein detection. The project will use tobacco and common bean as model plant systems and focus on the vegetative growth stage. A student with a strong background in plant physiology and data analysis in Python (or another language) is preferred.

For more information, please contact Mauricio Tejera-Nieves (mauri.tejera@jii.org) or Deserah Strand (dez@jii.org).

2. 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)

3. 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)

4. Measuring how leaves breathe and save water on both sides

This thesis explores how plants regulate water loss through stomata by using a new handheld porometer capable of measuring stomatal conductance simultaneously on both sides of a leaf. Stomata control the exchange of water vapour and CO₂ between the plant and the atmosphere, influencing everything from leaf-level photosynthesis to global water cycles. Understanding stomatal behaviour is especially important for breeding crops resilient to drought and heat. Traditional porometers measure only one leaf surface at a time. Because upper and lower leaf surfaces can differ substantially in stomatal density and aperture, sequential measurements risk altering stomatal behaviour due to handling and time delays, leading to incomplete or inconsistent data. The novel dual-sided porometer used in this project overcomes this limitation and allows more accurate characterization of whole-leaf water-use strategies. The student will apply this device to compare stomatal conductance across cultivars of the same species, generating insights into natural variation in water-use regulation. The instrument also integrates additional photosynthetic measurements, enabling a broader physiological assessment. The project provides hands-on experience in plant physiology, experimental setup, and data analysis while supporting breeding efforts for improved yield and drought tolerance.

For more information, please contact Ludovico Caracciolo (ludovico.caracciolo@jii.org)

5. How are leaf level photosynthesis measurements influenced by the physiological status of the whole plant? Key words: Photosynthesis, sink limitations, gas exchange measurements, chlorophyll a fluorescence, PAM, linking biochemistry with physiology Photosynthesis is the driver of all plant growth, yet the factors that limit this process remain incompletely understood. One possible limitation is the capacity of the plant to use photosynthetically fixed carbon, the so-called sink limitation. The Farquhar–von Caemmerer– Berry model and its extensions describe how photosynthesis can be limited by light availability, CO₂ supply, or triose phosphate utilization, and these frameworks are widely used to assess photosynthetic limitations at the leaf level. In this project, we aim to determine how whole- plant physiological status shapes these biochemical limitations locally within a leaf. A deeper understanding of how plant carbon sink strength regulates photosynthetic capacity may reveal new strategies for crop improvement pipelines. To address this the student will combine chlorophyll a fluorescence, CO₂ assimilation measurements and leaf sugar quantifications of plants exposed to different environmental conditions applied either to a single leaf section or to the entire plant to assess how whole-plant source–sink balance influences leaf level limitations. The student will gain hands-on experience in plant physiological measurements, molecular techniques, as well as data analysis in Python and/or R. For more information, please contact Simon Mall (simon.mall@jii.org)

6. What are all these extra ATP synthases doing? Possible methods: high-throughput phenotyping, chlorophyll a fluorescence, spectroscopy, Western blotting and immunodetection, data analysis in Python. 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. Identifying genetic variation in photosynthetic traits in heterozygous Bi parental diploid potato populations?

Exploiting natural genetic variation for photosynthetic traits in various crops is one way of improving crop photosynthesis. Various studies have assessed diverse panels of genotypes (including elite material bred over the years) in various crops including barley and wheat and indicate the high potential of utilizing this untapped resource for crop improvement. However, for some crops, specifically diploid potato, there are hardly any elite genotypes available, limiting the possibility of creating diverse panels of diploid genotypes to explore diversity in natural photosynthetic variation. Our goal is to utilize genomic selection methods to improve photosynthesis and to achieve this, we must first determine whether the observed phenotypic variation can be reliably attributed to specific QTLs, or whether a substantial proportion of the variation remains unexplained.

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. Bi parental populations are developed from crosses between two individual parental lines, which in this case are highly heterozygous diploid potato genotypes. This implies that the resulting population will segregate for various traits including and not limited to photosynthetic traits. A biparental population can be a useful tool for unraveling the genetic basis of various photosynthetic traits as well as plant responses to environmental conditions. The objective of this research is to quantify the proportion of photosynthetic variation that can be explained by quantitative trait loci (QTL). 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).

8. Are photosynthetic traits, yield and yield components influenced by sowing density and plot size in Barley?

Current field photosynthesis measurements are heavily influenced by environmental factors especially light intensity. In crop canopies, a light gradient is expected, with lower light intensities at lower levels of the canopies with variability also influenced by the sowing density (number of plants/m2). A canopy gradient holds a significant effect on photosynthetic measurements by influencing the amount of ambient light at the various levels of the canopy. While we can control this effect by defining where to measure within a canopy, various other factors can still lead to high light variation even in upper levels of the canopy. Additionally, yield and yield components are also influenced by sowing rate, with significant effects on crop growth and development (including influence on leaf traits) as well as yield and yield component traits due to the competition or lack thereof for resources including light.

Sowing rate is a critical factor to consider when conducting field trials to assess the availability of natural genetic variation in photosynthetic traits due to the need to minimize variation (i.e. random, spatial and environmental variation) as well as experimental error in our barley field trials. Another factor influencing the choice of sowing rate is the availability of seeds for trials, which also influences plot size. For some elite material currently on the market, seeds are accessible but for landraces and other genotypes the number of seeds limits both plot size and sowing rate. An optimal plot size is critical for reducing random variation between plots as well as reducing spatial variation between and within plots. While larger plots result in higher precision (often required in yield trials), they are less economical than smaller plots which are nonetheless prone to more error and border effects. Even so, due to the small quantities of seeds available for some genotypes, the choice of smaller plot sizes is unavoidable.

The effects of both sowing rate 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. This will help tailor decisions on reliability of various types of data collected under increasing 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).

9. Assessing genetic variation in physiological traits in diverse panels of barley genotypes under field conditions

Photosynthesis remains the last major untapped resource for improving crop yield. A promising route to unlocking this potential is the use of natural genetic variation. However, progress has been limited due to the complex interactions between photosynthesis and the environment, but also the agronomic and physiological properties of each genotype. Traits such as flowering time can have large indirect effects on photosynthesis, making it difficult to study photosynthetic variation in isolation. To overcome this challenge, we aim to develop methods that disentangle true photosynthetic variation from confounding agronomic and physiological influences. This study will assess genetic variation in physiological and agronomic traits including growth and 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. Diverse genotypes of barley including landraces and elite materials will be assessed in this study under field conditions during the 2026 growing season.

For more information, please contact Olivia Kacheyo (olivia.kacheyo@jii.org) or Tom Theeuwen (tom.theeuwen@jii.org).