Education

Climate change is increasing the frequency and unpredictability of extreme weather events, including late spring and early autumn frost, which pose significant threats to potato (Solanum tuberosum) cultivation.

Potatoes are particularly susceptible to frost, leading to damage that affects yield and crop quality. Despite its importance, the genetic variation underlying potato's response to frost events remains poorly characterized.

This project aims to establish a comprehensive understanding of the genetic variation in potato frost responses by integrating plant physiology, advanced phenotyping techniques, and molecular phenotyping through gene expression analysis. By evaluating diverse potato genotypes under controlled frost conditions, we will identify key physiological traits and gene expression patterns associated with frost tolerance. The findings from this research will enhance our understanding of the mechanisms underlying frost susceptibility in potato and may guide the development of frost-resistant potato varieties.

Supervisor

Natalia Rodriguez (n.y.rodriguezgranados@uu.nl, Kruyt Building, Room O201)

Potato (Solanum tuberosum)  is the most consumed non-cereal crop worldwide. However, its productivity is severely affected by anthropogenic climate change.

The current climate emergency has led to an increase in severity and frequency of flooding events. Waterlogging (i.e. root flooding) poses a significant threat to potato cultivation, leading to substantial yield losses. The primary consequence of waterlogging is soil hypoxia, where reduced oxygen availability severely impacts plant metabolism and survival. However, the molecular mechanisms underlying potato's response to waterlogging, particularly its ability to sense and acclimate to hypoxia, remain poorly understood. This project aims to explore the role of oxygen sensing in potato plants during waterlogging stress. For this purpose, we conducted a reverse genetic approach and created knock-down (RNAi) mutant of a key protein involved in the oxygen sensing pathway. Through a combination of genetic, molecular, and physiological approaches, we will investigate the role of hypoxia sensing in waterlogging responses, thereby paving new venues for improved resilience in this vulnerable, yet essential crop for food security.

Supervisor

Natalia Rodriguez (n.y.rodriguezgranados@uu.nl Kruyt Building, Room O201)

Stresses in nature seldom occur in isolation and effects of multiple stresses on phenotypic output (i.e. plant appearance/responses) usually differs from responses that are induced by single stresses.

For instance, in response to high temperature plants induce a suite of traits collectively termed thermomorphogenesis, which comprises of architectural and physiological traits that are induced by plants to aid cooling capacity by enhancing evaporation. However, under drought conditions, water loss must be limited and therefore drought counteracts thermomorphogenesis on the shoot level. However, belowground, high temperature and drought act additive on root elongation, which is a strategy to reach deeper soil water. Also, on the molecular level we see that the transcriptome response under combined drought and high temperature stress are unique and fundamentally differs from changes in gene expression induced by only high temperature or only drought.

Arabidopsis occurs throughout the Northern hemisphere in the wild, from the tropics to the arctic circle, and Arabidopsis varieties (called accessions) evolved different strategies to cope with their local temperature and precipitation conditions. We thus can directly learn from nature’s solutions to deal with combined stresses that evolved to deal with very different local environments. In the framework of the national PlantXR consortium, together with the National Plant Eco-Phenotyping Center (NPEC), we are currently assessing a large panel of natural Arabidopsis accessions under a combination of 3 high temperature x 3 drought conditions, to disclose the strategies that natural accessions evolved to deal with combined high temperature and drought stress. After identifying accessions with different strategies, we will phenotype these in even greater detail using the NPEC sensory systems, together with collaborators develop computational functional plant models to understand why the accessions behave under these adverse conditions as they do, and design experiments to understand the underlying molecular genetic networks that are involved. We are looking for one or two enthusiastic and motivated Msc student(s) interested in environmental and/or molecular biology, phenotyping and natural genetic variation, who would like to explore these accessions and help us disclosing the diverse strategies. There are many possibilities for students that can be tailored depending on the expertise and wishes.

Supervisors

Jelle Keijzer, Martijn van Zanten

Contact

m.vanzanten@uu.nl

Many plant biology studies involve Arabidopsis thaliana as model plant. Together with all first year Biology students and staff members we obtained a large collection (seeds, leaf material and soil samples) of >650+ wild Arabidopsis plants from all over the Netherlands in the springs of 2023 and 2024.

We are looking for one or two enthusiastic and motivated Msc student(s) interested in environmental biology, phenotyping and natural variation, who would like to explore this new collection. There are many possibilities with these samples and the available lines from an ecological to a bioinformatic and a molecular viewpoint. For example, we plan to phenotypically characterize the plant lines in the new NPEC-facility to observe phenotypical differences across environments. Also, we plan to grow the collection in the botanical garden and assess variation in phenology, growth and development. Using the soil samples of each site, we plan to assess parameters like pH, C/N ratio, soil type etc. Moreover, we plan to classify the samples according to their collection site (based on vegetation captured on photo’s that are available for each accession). We aim to correlate the environment to genetics and morphology to estimate the natural genetic variation in the species and to map traits that mediate resilience to environmental stress conditions.

We are interested in elucidating the molecular mechanisms regulating cold and warm temperature signalling, sensing and response in plants in many facets.

Our primary focus lies on deciphering thermomorphogenesis, which is a suite of architectural and physiological traits that are induced by plants under high temperatures. The resulting open rosette structure (due to e.g. upward leaf movement, elongation of leaf stalks etc) contributes to cooling capacity, which allows the acclimated plants to better withstand high temperature conditions. For long, studies on mild high temperature acclimation, heat stress, cold acclimation and freezing stress have been four separate fields of research. We now become more and more aware that many proteins that were previously considered to play a role in either heat stress or cold acclimation in fact control plant growth throughout the temperature gradient. In our group we aim to understand how proteins can have promiscuous roles at different temperatures using the model system Arabidopsis thaliana. We focus among others on the transcription factors INDUCER OF CBF EXPRESSION 1, better known as ICE1.

ICE1 is a well-known transcription factor being responsible for acclimation to cold conditions. However, we identified ICE1 in a phosphoproteomics experiments based on differential phosphorylation of the protein in different temperatures and found that ICE1 is also differentially phosphorylated at warm temperatures. In a follow-up experiment, we found that ice1 mutants surprisingly are largely insensitive to high temperature as well and we strive to elucidate the molecular basis of this. To this aim we are generating constructs in which the differentially phosphorylated residues are mutated to test the influence of these residues on the response. This explorative internship will allow diving deeper into the molecular mechanisms how ICE1 affects temperature responses across the temperature spectrum from cold to warmth. Experiments that should be conducted include Western blotting to test the protein abundance in different temperatures, testing marker genes to probe the molecular networks that are affected by ICE1 and making crosses and analysing ice1 mutants/overexpression lines with (mutants of) known temperature regulators to position ice1 in the molecular framework of known temperature signalling cascades.

Supervisors

Martijn van Zanten, Jelle Keijzer

Contact

m.vanzanten@uu.nl

Salinity affects plant growth by simultaneously causing ionic and osmotic stress, leading to both general and specific signaling responses (Lamers et al., 2020; van Zelm et al., 2020).

Some salt-tolerant plant species have evolved mechanisms to compartmentalize and excrete excess salt, enabling them to thrive in saline environments. High salinity stress can significantly reduce crop yields, emphasizing the importance of developing salt-resistant plant varieties and implementing better soil management practices. Salinity also induces changes in the structure of cell walls (Gigli-Bisceglia et al., 2022), triggering responses that are independent of its toxicity.

Our research group focuses on understanding the factors responsible for cell wall modifications and the molecular pathways that sense and initiate these responses. Recently, we made the discovery that salt application in plants leads to an increase in cell wall thickness. This increase appears to be regulated by an enzyme known as EXAD, which stands for EXTENSIN ARABINOSE DEFICIENT TRANSFERASE. EXAD adds arabinose residues to cell wall-localized proteins known as Extensins.

Figure 1. Impact of Salt on Cell Wall Thickness. The cell wall (depicted by yellow lines) undergoes a significant increase in width in response to salt, with this effect being dependent on EXAD.

Project Goal

Identification of Extensins that are targeted by salt stress and by EXAD.

What You Can Learn

Cell Wall extraction, Protein extraction, Immuno-Precipitation, Western blot

Further reading

Arabidopsis root responses to salinity depend on pectin modification and cell wall sensing. Gigli-Bisceglia et al., 2022 Development. Cell wall extensin arabinosylation is required for root directional response to salinity. Zou, Gigli-Bisceglia et al., 2023 Plant Cell.

Supervisor

Nora Gigli-Bisceglia (n.giglibisceglia@uu.nl)

Introduction

Climate change is taking a devastating toll on crop production. In the Netherlands and Northern Europe, heat waves and drought have been occurring more frequently and with higher intensities. Crops currently grown in the region are prone to yield losses under drought. To ensure food security we need to consider cultivation of drought tolerant crops. As such, sorghum offers a great alternative to maize, as it is drought and heat tolerant and requires less fertilizers. The main obstacle for sorghum cultivation in Northern Europe is that the growing season is too short, as the species is typically grown in areas with long, warm seasons. Hence, planting would need to occur early in the year when soil temperature is still low. Sorghum shows poor establishment in cold soils which motivates the study of mechanisms of cold tolerance of sorghum roots. Previous research focused mostly on sorghum cold tolerance at the reproductive stage, but little is known about the role of the roots therein.

The research questions we address are

1. How does cold affect sorghum root system architecture and root cellular patterning?
2. Which genes control sorghum root responses to drought?
3. What is the natural variation in sorghum in terms of root responses to cold?

Projects’ goals

You will get an opportunity to establish a method to study the effect of cold and warmth on sorghum root morphology and physiology. You will use our state-of-the-art temperature gradient table, which has been successfully used to study the effects of cold and higher temperatures. Once the conditions are optimized you will assess how cold is reshaping sorghum roots and ultimately the underlying molecular mechanisms.

What can you learn?

Plant growth and cultivation; temperature assays in plants, root system architecture analysis, root histology, confocal, fluorescent microscopy

Further reading 

Praat, M., Jiang, Z., Earle, J. et al. Using a thermal gradient table to study plant temperature signalling and response across a temperature spectrum. Plant Methods 20, 114 (2024). https://doi.org/10.1186/s13007-024-01230-2

Supervisors

Dr. Dorota Kawa (d.kawa@uu.nl) and Dr. Martijn van Zanten (M.vanZanten@uu.nl)