Members of the PhD Student Council of EPS

Vera Veltkamp Vera Veltkamp (Chair)

PhD student, Business Unit Bioscience - Plant Developmental Systems & Molecular Biology, Wageningen University & Research
Project Title: Enjoying the fruits of knowledge: cracking the Cis-regulatory code of gene regulation

About my research
Tomato is a model species for fleshy fruit development and an important economical crop. Its appeal to consumers is important for the competitiveness of Dutch breeders and growers as well as for consumer health. A trait generally liked by consumers is sweetness. Fruit sugar content is partly determined by the fruits ability to import and accumulate sugars during growth and release sugars during ripening. For this research I propose to focus on three genes involved in these steps: LIN5, AGPS1 and TIV1. These genes all underlie known QTLs for sugar accumulation in tomato fruits. We will study their transcriptional regulation, in particular their Cis-regulatory elements (CREs). CREs are recognition sites for transcription factors that control transcription and define spatial and/or temporal expression of a gene. It has as been proposed that by targeting this part of genes transcriptional regulation new phenotypes can be developed without harmful pleiotropic effects. A major hurdle in this endeavor is the lack of detailed knowledge on how CREs work. I propose to perform a comprehensive study on CREs of sugar-related genes during tomato fruit sugar accumulation. I will use a novel CRISPR/Cas9 multiplex system for tomato genome targeting to create variation in putative CRE regions by systematically deleting parts. By studying mutants for their effect on the target gene expression, we intend to discover new types of CRE functionalities in an in vivo system. By combining the mutagenesis method with proven methods for studying CRE function, we will work towards a comprehensive model explaining the transcriptional regulation of the three target genes.

Tieme Helderman Tieme Helderman (Secretary)

PhD student, Molecular Plant Pathology, University of Amsterdam
Project Title: Towards durable susceptibility (S) gene-based Tospovirus resistance in crops

About my research
Tomato spotted wilt virus (TSWV) and other members of the tospovirus family are among the most devastating plant viruses worldwide. TSWV has an extensive host range and can infect over 1000 different plant species. This RNA virus evolves quickly and has therefore already broken the few known dominant resistance genes used in plant breeding. To better understand how TSWV is so successful in infecting such a broad host range detailed knowledge on the infection process is needed. The goal of my work is to identify host genes that are essential for TSWV replication using different experimental methods. Upon host-factor identification, a more in-depth characterization will be performed to obtain detailed knowledge on the role of the gene product for the host and in viral proliferation. Such knowledge can be utilized by breeders to design new forms of tospovirus resistance in crops

  Martina Huber (Council member)

PhD student, Plant Ecophysiology, Utrecht University
Project Title: Towards sustainable weed management solutions for the aggressive rice weed Cyperus rotundus: a crop-weed perspective.

About my research
Weed infestation is a major constraint for agricultural productivity. In rainfed lowland rice, the flooding of fields is an effective manner for controlling weed growth, as most terrestrial plants do not grow well on waterlogged soils while flood tolerant rice growth is unaffected. This makes it an effective and and eco-friendly method for weed control. However the recent emergence of flood- tolerant weeds, such as one ecotype of the notorious rice weed Cyperus rotundus, has reduced the efficacy of this traditional weeding method, resulting in major losses in yields of lowland rice. In this project we investigate on a two-pronged approach to new management options for this weed.
First: identification of weed competitive traits in rice to improve its shading ability, leading to reduced weed growth. We will screen a collection of rice landraces to identify traits that make rice more competitive against weeds like C. rotundus. When growing close together, as in agricultural fields, the ability of a plant to outcompete its neighbour is dependent on certain morphological characteristics such as the ability to grow faster and cast shade on slower growing species. The identification of competitive shade-casting traits and its genetic basis will provide the knowledge needed to breed weed competitive rice varieties.
Second: In a parallel investigation we will investigate on a comparative basis, the flooding tolerant and sensitive ecotypes of C. rotundus to unravel the mechanisms underlying the evolved flooding tolerance, which could uncover an alternative flooding regime that suppresses its growth
Ultimately, the combination of flooding and strongly competitive rice phenotypes is likely to result in an effective reduction in C. rotundus populations in rice fields. Thereby this research will not only aid the design of a sustainable weed management strategy but also provide tremendous insight into crop-weed competition.

Irene van Grinsven (Council member)

PhD student, 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 unravelling 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.

Nikita Sajeev Nikita Sajeev (Council member)

PhD student, Plant Physiology, Wageningen University & Research
Project Title: Genome-wide association mapping for hemp breeding

About my research
Seed germination is crucial for the survival of a plant. At the time of seed imbibition, translation is initiated from being completely inhibited in the dry seed. Therefore the seed provides an exclusive system to study translation and its regulation. The abundance of mRNA and the fraction of mRNA that is being translated into protein are the main factors that impact translation. This relationship is not always linear and can vary per gene or condition. In previous research we employed Translatome profiling to separate mRNAs based on their association to ribosomes. This resulted in the identification of two time shifts during seed germination at which translation is extensively regulated(Bai, Peviani et al. 2017). These changes in ribosomal association could be regulated by various mechanisms. Independent of all mechanisms, the mRNA must contain a specific signal within its transcript which when recognized, determines the fate of the mRNA. We hypothesize that special RNA binding proteins (RBPs) are involved in this signal recognition. I aim to identify those RBP’s and their role in germination.

Octavina Sukarta Octavina Sukarta (Council member)

PhD student, Laboratory of Nematology, Wageningen University & Research
Project Title: Insight inside: identifying and characterizing novel interactors of the potato CC-NB-LRR immune receptor Rx1

About my research
The potato Rx1 is an intracellular Nucleotide-binding Leucine Rich Repeat (NLR) immune receptor with an archetypical N-terminal coiled-coil (CC) domain. It confers extreme resistance against Potato Virus X (PVX) by gene-specific recognition of the viral coat protein (CP). Recent findings point to a role of Rx1 in the nucleus whereby it could directly bind host genetic material, though it remains unclear how this process eventually leads to defence. A possibility is that Rx1 recruits other host factors, for example via the CC domain, which is predicted to act as scaffolds for nuclear signalling. Here, we used the CC domains of Rx1 and the Rx1-like protein Gpa2 (mediates defence against the nematode Globodera pallida) as baits in a Co-IP/MS analysis after cell fractionation to co-purify putative interactors from Nicotiana benthamiana. Five hits (designated Rp01-Rp05) were further prioritized as candidate Rx1/Gpa2 interacting proteins. Similar pull-down experiments confirmed complex formation with the full-length immune receptors in plantae. Interestingly, co-expression of Rp05 alters the subcellular distribution of the Rx1-CC domain, hinting its role in Rx1-function. Transient overexpression experiments confirm that Rp05 could in fact potentiate defense against PVX. Interestingly, however, this occurs independently of Rx1. We substantiated this model by demonstrating that Rp05 could influence HR-responses by other NLR proteins (e.g. Gpa2, Sw5A/B and Mi-1) indicating that it may be a common downstream component in immune signaling. Currently, we focus on elucidating the detailed molecular underpinning of Rp05 function in R-gene mediated resistances using Rx1 as the principal model system.

Valérie Hoogers (Council member)

PhD student, Molecular and Cellular Life Sciences, Utrecht University
Project title: The molecular machinery involved in shoot-to-root signaling during shade avoidance

About my research
The research project aims to get a better understanding of shoot-to-root signaling during shade avoidance. Upon changes in light quality, changes in root system architecture (RSA) are induced. However, thus far it remains unknown how these above-ground conditional changes are perceived by the roots. Shoot-to-root mobile compounds, like HY5, auxin and GA, possibly play a role in this signaling and therefore will play a central role in the project. The role of these factors in changes in RSA upon neighboring shade will be examined by phenotypic analysis of HY5/auxin/GA biosynthesis and signaling mutants and by micrografting mutant shoots onto WT roots (and vice versa). Furthermore, cell-type specific translatome profiling will be performed to identify the tissues responding to light quality changes and to find candidate targets of the shoot-derived mobile factors.

Ivo Gariboldi (Council member)

PhD Student, 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.

Michelle van der Gragt (Council member)

PhD student, Plant Physiology, University of Amsterdam
Project title: Master old resistance in new tomatoes: transcriptional control of metabolite production by small RNAs

About my research
Wild tomatoes have the ability to defend themselves against pests by producing a wide variety of natural defence compounds in glandular hairs (trichomes). Centuries of breeding focussing on yield led to a loss of production of such compounds in cultivated tomato and many effective insecticides have been banned, resulting in realistic threats to vegetable production in Europe. Introduction of a terpenoid-biosynthetic pathway from a wild ancestor into cultivated tomato trichomes led to enhanced insect resistance. However, the regulatory networks that govern the production of defence compounds are essential in order to successfully incorporate ‘wild resistance’ into breeding material and it appears that classical transcription factors themselves are controlled by another important layer of regulators; miRNAs. To elucidate miRNA-based transcriptional regulation of biosynthetic pathways, we will associate various metabolites of the trichomes of 20 different tomato accessions to quantitative trichome transcriptomes via a Systems Biology approach. In addition, we will sequence small noncoding RNAs of each of the trichome libraries. Quantitative comparison of RNA databases will lead to the identification of mRNAs targets for miRNA-directed degradation. The aim is to unravel posttranscriptional regulatory networks that control metabolite biosynthesis in tomato trichomes. Candidate target genes and corresponding miRNAs will be validated experimentally for their role in trichome development, metabolite production and insect- resistance and both will be target to screen for allelic variation. This proposal will be an important contribution to a better understanding of the production of natural defence metabolites and provides tangible leads towards control over sustainable tomato production.

Hao Zhang (Council member)

PhD student, Plant-Microbe Interactions, Utrecht University
Project title: Identification and characterization of Pseudomonas spp. genes involved in plant-microbe interactions

About my research
Beneficial microbes provide plants with important services, such as enhanced mineral uptake, nitrogen fixation and biocontrol. Several beneficial Pseudomonas strains are identified as nonsymbiotic plant growth promoting rhizobacteria (PGPR) or biocontrol bacteria, e.g. P. simiae WCS417r (PGPR), P. putida WCS358r (PGPR) and P. protegen CHA0 (biocontrol bacteria). PGPR can boost plant growth and health, e.g. by facilitating nutrient uptake and stimulation of root growth, or by reducing the level of disease through biocontrol measures such as induction of systemic resistance (ISR), antibiosis or competition for nutrients. However, the genes of bacteria which are involved in plant-microbe interaction are not clear. My project aims to identify and characterize molecular components and novel functions of Pseudomonas spp. that facilitate rhizosphere colonization and positively affect plant functioning.

Ties Ausma (Council representative for Groningen)

PhD Student, 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.



Graduate School Experimental Plant Sciences