PhD Council Members

PhD candidate, Molecular Plant Physiology, Utrecht University
Project title: Plants grow with a foot on the brake: How a single kinase represses acclimation to high and low temperatures signals.

About my research
Plants are sensitive to small changes in ambient temperature and respond to both cold and warm temperatures by adjusting their growth, architecture and physiology. Acclimation to warm ambient temperatures is called thermomorphogenesis and includes the elongation of the stem and petioles. Together with an upward leaf movement this leads to an open rosette structure that aids the cooling capacity of plants. On the other end of the temperature spectrum cold stress can cause severe irreversible damage to plants. However, plants can become cold tolerant after an acclimation period at low temperatures by a process called cold acclimation. Although the molecular regulation of thermomorphogenesis and cold acclimation are increasingly well understood, none of the identified molecular factors have an apparent role in acclimation to both cold and warm ambient temperatures, despite being part of the same temperature continuum.

We have identified a kinase that functions in both thermomorphogenesis and cold acclimation pathways. A knockout of this kinase leads to an increased thermomorphogenesis and cold acclimation responses. Therefore this kinase could be considered a universal molecular break on acclimation to different ambient temperatures. I aim to unravel how this kinase simultaneously controls thermomorphogenesis and cold acclimation by using (phospho)proteomic and transcriptomics approaches.

PhD student, Molecular Biology, Wageningen University & Research
Project Title: ‘The art of multitasking: flowering time genes and their relation with seed dormancy‘

About my research

The life cycle of annual plants can be divided in different phases that include vegetative growth, reproductive adult phase, seed set and senescence. Since plants are organisms that cannot migrate when the external conditions are not favourable, the transition between the different life phases needs to be strictly controlled. In fact, the basis of an adaptive life relies on the ability to respond in different ways to environmental and/or internal cues in different developmental stages. From all the external variables, temperature is one of the strongest signals that plants sense and adapt to. For this reason, the current context of climate change is altering the timing of crucial transitions such as the transition to flowering.

In this project we aim to study two temperature-regulated traits, flowering time and seed dormancy, that have been separately researched for several years but that have been recently proposed to be interconnected. Both traits are fundamental for the reproductive success and survival of any plant specie. Therefore, knowledge of plant plasticity and adaptation to temperature fluctuations is vital for a sustainable global food security. In my PhD project we will combine techniques such as CRISPR-Cas9, molecular cloning or yeast-two-hybrid to understand the complex multitasking role of temperature-responsive key regulatory members that link timing of flowering and seed dormancy.

PhD candidate, Plant Ecophysiology, University of Groningen
Project title: Regulation of sulfur metabolism in C4 plants

About my research
Sulfur is an essential macronutrient for the proper physiological functioning of plants. It is important to understand how the metabolism of sulfur is regulated, since sulfur availability limits agricultural yield in many areas. Knowledge on the regulation of sulfur metabolism can help to improve sulfur fertilizer levels as well as the sulfur use efficiency of crops. Presumably, in the future more C4 plants will be cultivated in agriculture, since C4 plants can grow with a high productivity. However, until now research into the regulation of sulfur metabolism has mostly focused on C3 plants. How sulfur metabolism is regulated in C4 plants and how it responds to changes in sulfur supply has hardly been investigated. Since C4 plants differ significantly in leaf morphology and physiology from C3 plants, findings from C3 plants cannot simply be extrapolated to C4 plants. Therefore, we investigate the consequences of C4 photosynthesis for the regulation of sulfur metabolism. We study both the C4 crop plant maize (Zea mays) and species from the genus Panicum. This genus contains evolutionary-related C3 and C4 plants as well as C3/C4 intermediates. Assessing the regulation of sulfur metabolism in an evolutionary gradient within the same plant genus will provide important insights into differences in sulfur metabolism that can be attributed solely to a C3 or C4 photosynthetic mechanism. With this research we aim to improve our understanding of the links between C4 photosynthesis and sulfur nutrition in order to optimize sulfur fertilization for C4 plants and to inform breeders on breeding targets for efficient sulfur use.

PhD candidate, Plant Microbe Interactions, Utrecht University
Project title: Selecting soybean-specific consortia of beneficial microbes for sustainable yield improvement

About my research
Current agricultural practices call for innovative solutions towards more sustainable crop production. Reducing the use of fertilizers and pesticides is part of this challenge, where a solution can be found in plant-beneficial microbes that promote plant growth and health. Plants are able to recruit such beneficial microbes in the root environment upon infection, as shown recently in Arabidopsis thaliana infected with the oomycete Hyaloperonospora arabidopsidis or the bacterium Pseudomonas syringae. In my project, we study this disease-induced recruitment of beneficial microbes in soybean plants. We employ infection with different pathogens to select, isolate and characterize soybean-specific consortia of beneficial microbes. To explore the mechanisms underlying this recruitment, metabolite profiles of soybean roots and exudates will be compared between healthy and diseased plants. By combining metabolite profiling with microbiome analysis, we aim to commercialize soybean-specific beneficial microbes, providing soybean growers with a novel biocontrol product effective in the field.

PhD candidate, Molecular Developmental Genetics, Leiden University
Project title: Enhanced somatic embryogenesis by bacterial protein translocation

About my research
Many plant species are dependent on sexual reproduction to reproduce. In zygotic embryogenesis the fusion of two sexual cells forms a diploid zygote and then develops into an embryo. Apart from sexual reproduction embryos can be formed asexually e.g. by induction in vitro in various plant tissues. The application of in vitro embryogenesis is widely accepted as a biotechnical tool in industry as well as academic research. In plant breeding somatic embryogenesis (SE) is a popular tool for clonal propagation.
It has been shown that SE can be induced by overexpression of genes involved in embryogenesis. Since this relies on the modification of the plant genome, it is not suitable for plant breeding. In this work we will investigate the possibility to induce somatic embryos by translocation of various proteins involved in the induction of SE. Furthermore, we will try to better understand how the process of embryogenesis in induced by these proteins. This research might give more detailed knowledge on the role of certain proteins in embryogenesis induction and this could be eventually utilized in the field of plant breeding.

PhD candidate, Virology, Wageningen University & Research
Project title: Unravelling Tsw-mediated resistance and the interplay with the innate immunity modulator NSs of Tomato spotted wilt virus, a plant-infecting bunyavirus

About my research:
Tospoviruses are members of the arthopod-borne Bunyavirales, comprising one of the few genera whose members infect plants rather than animals. Tomato spotted wilt virus (TSWV), the type species of the tospoviruses, is one of the most important plant viruses worldwide with a large host range of more than 80 different plant families. Currently, two single dominant resistance (R) genes are available for commercial resistance breeding. The first, Sw5 from Solanum lycopersicon, confers resistance to TSWV and a few additional tospoviruses. The second, Tsw, from Capsicum chinense confers resistance to TSWV only. Although their mode of action is still largely unknown R genes, besides the actual resistance response, trigger a concomitant hypersensitive response. This is based on a programmed cell death and leads to the formation of necrotic spots that prevents further spread of the pathogen from the primary site of infection. Recently we have identified the viral NSs protein as the effector of the Tsw-mediated programmed cell death response. This protein, moreover, also suppresses antiviral RNAi, the first line of the innate immunity response against viruses in plants and insects. This project aims to support developments towards durable resistance against TSWV by unraveling the resistance mechanism of Tsw, and understand how NSs (in)directly triggers the intracellular innate immunity sensor Tsw leading to resistance and modulates innate immunity responses in its plant host and insect vector.

PhD student, Molecular Plant Physiology, Radboud University
Project title: Characterizing the molecular-physiological basis of pollen abortion upon prolonged high temperature stress.

About my research
Pollen development is a key heat-sensitive process in a variety of plant species, including mono- and dicots, and is pivotal for yield in many crop species. The cause of lowered pollen viability under elevated temperature conditions has not yet been identified, but literature suggests an important role for the tapetum, phytohormone signaling and carbohydrate metabolism.
In this project, we will combine phytohormone analyses and transcriptomics with modification of genetic backgrounds to establish in detail how the hormone, RNA-interference and anther-identity pathways and carbohydrate metabolism in tomato and rice interact, and are impacted by elevated temperature. Finally, we will address how the classical heat-shock-protein system interact with these pathways. Based on the results, we will propose a molecular-physiological model for high temperature-induced pollen defects.

PhD candidate, Plant physiology, Wageningen University & Research
Project title:  Unravelling the elusive sodium perception mechanism in plants

About my research
Soil salinization leads to massive decreases in crop yield and threatens 7% of arable land and 30% of irrigated soil. Plants experience two types of stress due to increased sodium concentrations in the soil. The immediate effect is the reduced water uptake by the root. Later on, sodium accumulation in the plant inhibits essential cellular processes like photosynthesis. Over the years, it has been proven that plants respond to sodium in a specific way that is not observed by solely osmotic stress or application of other ions. Meaning that sodium ions must be perceived specifically by the plant. The existence of such proteins is not surprising as studies already showed sodium sensors in mammals, bacteria and nematodes. However, no homologues have been found in plants. Although, studies have identified responses within 10 seconds after sodium application, the sensing mechanism and earliest responses remain elusive and finding it will be my main goal.

PhD candidate, Molecular Biology, Wageningen University & Research
Project title: Transient Induction of Plant Regeneration

About my research
One of the major bottlenecks in plant breeding programs is the recalcitrance for in vitro embryogenesis in some species or genotype of common crops, which limits the use of modern biotechnology tools.  Progress in tissue culture procedures by using growth regulators and culture media combinations have been time consuming and inefficient for a large number of crops, which is why there is an urgent need to develop novel, generic tools to improve plant regeneration processes in a germplasm-independent manner. Embryo-expressed transcription factor like the AP2 domain protein BABY BOOM and CAAT-box binding factor LEAFY COTYLEDON1 have been used to enhance plant regeneration in a range of crops when expressed from a constitutive promoter, resulting in transgenic lines.

This project aims to examine the extent to which BBM and LEC1 can be used to transiently promote in vitro regeneration without genomic integration of nucleic acids and without genomic DNA mutation. Different approaches will be used to transiently induce BBM/LEC1 protein in plant cells. One approach is to use cell-penetrating peptides to introduce those proteins into the plant. Additionally, we aim to activate endogenous BBM/LEC1 gene expression by using CRISPR-dCas9 technology and small chemical compounds. The overall focus lies on improving in vitro regeneration in haploid embryo induction for doubled-haploid production as well as somatic embryogenesis for clonal propagation.

PhD candidate, SILS UvA, Plant Hormone Biology
Project title: Plants calling for help: elucidating the mechanism by which tomato recruits its rhizosphere microbiome during phosphate deprivation.

About my research
From both a societal and an economic perspective, there is an increasing need for improved resilience in crops to biotic and abiotic stresses, which require less input of pesticides and fertilizers. Plants can deal with stresses in multiple ways, one of which is through the microbiome. Research shows that, just as in humans, a suitable microbiome is vital to plant health and functioning. It is becoming clear that plants can actively shape their microbiome. However, the mechanisms underlying this remain largely unknown. To understand the interaction between plants and their microbiome, I will explore unknown signaling relations to elucidate the mechanism by which tomato actively adjusts its microbiome under stress and how this relates to plant health. To this end, I will investigate genotypic variation in, and plasticity of, microbiome recruitment by tomato. The latter I will study using phosphate deprivation, which is known to affect the root transcriptome, exudate profile, and microbiome composition. I will use time-series experiments on plant transcriptomics, root exudate metabolomics and microbiome metagenomics. I will link these datasets and predict causal relations between them. From this, candidate genes will be identified which confer the ability to recruit certain groups of organisms in the microbiome. I will validate the candidate genes using VIGS and test their involvement in shaping the microbiome.

PhD Candidate, Plant Breeding, Wageningen University and Research
Project title: Potato genome editing for late blight resistance

About my research
Late blight, caused by the oomycete Phytophthora infestans, is the most devastating disease in potato. Moreover, most of the currently used elite potato cultivars are susceptible to late blight. In order to control P. infestans, growers rely on biocide application, which is expensive, time consuming and non-environmentally friendly. In many wild potato relatives, resistance (R) genes have been identified to confer resistant against P. infestans. The introgression of R genes from wild potato relatives into susceptible potato cultivars is very laborious and most of the times negative traits, such as lower yield or higher alkaloid content complicate the process. As an alternative, more advance techniques such as CRISPR-Cas have been developed in the last decade to modify plant genomes. In this project, we focus on the R gene editing of susceptible potato varieties to make them resistant to P. infestans. Additionally, we want to optimise and develop new genome editing approaches which will allow us to modify very precisely the target sequence. Therefore, this research also contributes to the general knowledge and to the discovery of new potential applications of genome editing for any plant species.