PhD Candidate, Plant Breeding, Wageningen University & Research Project Title: Molecular breeding and evolution in allopolyploids: novel and applied methodologies
About my research This research is focused on allopolyploids, organisms that harbour more than two copies of each chromosome and where each of these copies originates from a different ancestral species. Many agricultural crops have this condition, especially in the ornamental sector, and among those is Fragaria x ananassa, the garden strawberry. Applying standard analytical tools in these crops is in many cases not possible, meaning that adaptations to standard methods need to be designed an implemented.
In this project multiple technologies are being adapted to handle the anomalies of allopolyploid genetics. First, genotyping using whole-genome sequencing (WGS) data, particularly assessing the effect of sequencing depth on genotype accuracy, a special concern in allopolyploids. Secondly, linkage mapping using WGS genotypes, which is already a challenge without the added allopolyploidy. Thirdly, the study of ancestry in a wide range of strawberries, a relevant topic since the ancestors of allo-octoploid strawberry have not been fully identified yet. Lastly, quantitative-trait-locus (QTL) analysis of metabolic data in strawberries, aiming to characterize the wide aromatic variation in strawberry.
Martha van Os, secretary
PhD candidate, Plant Physiology, Swammerdam Institute of Life Sciences, University of Amsterdam Project title:Scensitive nature: Green leaf volatile perception in plants
About my research Green leaf volatiles (GLVs) are an integral part of plant defense against biotic and abiotic stresses. They are emitted within seconds of damage to photosynthetic tissues and are known for their smell of cut grass. GLVs can have a direct or indirect defensive effect by repelling herbivores or pathogens or by attracting predatory insects. They also serve as within- or between-plant signals that either induce or prime plant defenses. However, it is still unknown how plants perceive volatile compounds and how the specificity of the volatile signal is transduced in the plant.
This research focuses on the GLV Z-3-hexenal and its isomer E-2-hexenal, as they are among the most abundant and influential volatiles in the GLV cluster. I aim to elucidate receptor candidates in Arabidopsis with forward genetics screens and proteomics approaches to further study plant GLV perception and implications for plant’s self-recognition and interactions with herbivorous insects and pathogens. Additionally, (3Z):(2E)-hexenal isomerases were recently identified in both insects and plants that convert Z-3-hexenal to E-2-hexenal. This change in the Z-3-/E-2-ratio affects the behavior of insects like foraging predators and host-seeking herbivores, and is expected to also alter plant defense response. For this part of my research I use potato, a crop species that unlike Arabidopsis has high isomerase activity, to study the role of hexenal isomerase in plants’ adaptive ability interact with its environment and its effect on ecological relations between plants and insects.
About my research Seeds are the foundation of global food production. Their viability, germination and resistance to stress are key to feeding the world. Conventionally, plant breeders coat the surface of seeds with extra materials to improve their handling and vitality, a process known as coating . The ingredients in seed coatings include nutrients, herbicides, fungicides, and insecticides. Seed coating promotes the rapid and uniform germination of seeds, ensures their survival against abiotic and biotic stress factors, and ensures a high crop yield. Seed coating technology is emerging as an alternative tool to conventional farming because seed coating uses minor amounts of chemical inputs during its application (Rocha et al., 2019). Despite their effectiveness, synthetic pesticides and fertilisers can accumulate in plants, soil and water, causing toxicity to microbial populations. Thus, we need less toxic and more biodegradable coatings.
Plant beneficial microbes (PBMs) can be an alternative to the use of agrochemicals in plant production. PBMs help plants maintain or increase plant growth, unlock nutrients for the plant, and reduce crop loss caused by pathogens, insects and abiotic stress. For example, Trichoderma and Pseudomonas strains added to agricultural soils can antagonise pathogens and induce resistance in plants against bacterial, viral and fungal pathogens. In this project, the chair groups of PMI, Microbiology and NMR aim to develop sustainable seed coatings with plant-beneficial properties, based on fungal materials. We are looking at ways in which seed coating materials antagonize plant pathogens to protect emerging seeds from disease. Moreover, by using pathogen bioassays and digital plant phenotyping tools, we evaluate the contribution of our seed coatings to long-term plant health and resistance. We will also delve deeper into the modulation of the plant’s transcriptomic landscape and microbiome, when seeds interact with PBMs. This project can help us understand how fungal materials can be used in seed coating technology to support plant growth and resistance to pathogens.
Max Frencken, council member
PhD candidate, Plant Systems Physiology, Radboud University Project title: HeatGenes: toward a generic genetic framework for plant reproductive heat-tolerance.
About my research As a consequence of climate change, weather extremes, such as heat waves, are expected to become increasingly frequent. As sessile organisms, plants are affected by these events in both the vegetative and reproductive phase. Heat stress during reproductive development leads to catastrophic yield loss in many food crops, imposing pressure on future food security. In the past, studies have shown during the reproductive stage, male gamete development is the most sensitive to high temperatures. However, past studies mostly focused on short extreme high temperature effects (heat shock) and few have investigated the effects of heat wave-like long-term mild heat (LTMH).
This is the fundamental drive of the HeatGenes project, a NWO (TTS)-funded study, performed in cooperation between the Radboud University and multiple companies involved in plant breeding. We expect the genetic basis of the reproductive heat-tolerance phenotype to be well-conserved among angiosperms. By performing genome-wide association studies (GWAS) on multiple plant species (e.g. Arabidopsis thaliana, tomato, common bean, carrot, and Brassica sp.), we are identifying quantitative trait loci (QTLs) and candidate genes associated with the heat-tolerance phenotype. A study in Arabidopsis thaliana will provide insights on molecular/physiological pathways involved, while studies in various commercially valuable crop species will directly provide germplasm for heat-tolerant lines. Additionally, we will develop reproductive heat-tolerance screening assays for plant species for which none existed previously.
Gül Hatinoğlu, council member
PhD candidate, Laboratory of Molecular Biology / Plant Developmental Systems, Wageningen University & Research
About my research Plants continuously grow through their main shoot, but certain signals during this growth will lead to budding of additional, lateral shoots. In tomato, these so-called axillary shoots compete for energy with fruit production, and to increase yield they are removed manually. However, their removal adds to labor costs and might cause an infection at the sites of the wound and is time-consuming. Molecular studies revealed a number of shoot outgrowth-suppressing genes, from the model plants Arabidopsis and tomato. In my project, we aim to elucidate the underlying mechanism of axillary shoot regulation in tomato. We are investigating regulatory network of shoot branching by using techniques such as CRISPR-Cas9, yeast-one-hybrid and RNA-seq.
Zhang Jiang, council member
PhD candidate, Plant Ecophysiology / Molecular Plant Physiology, Utrecht University Project title: Physiological genomics of plant responses to multiple abiotic stresses
About my research Plants often encounter environmental stresses simultaneously or sequentially as stresses rarely occur in isolation. Responses to multiple stresses are often distinct than either stress applied in isolation. It is therefore vital to characterize the mechanisms of plant acclimation to multiple abiotic stresses. In my project we analyze two stress combinations: high ambient temperature + drought and a sequential stress: flooding followed by drought, both of which come up frequently and cause severe destruction of crops. The physiological, morphological and phenological responses to these stresses was characterized in the Arabidopsis thaliana. Based on this information, a transcriptome approach will be used to identify underlying genes and molecular processes controlling relevant traits. Finally candidate genes that potentially contribute to stress acclimation will be identified and functionally validated. Ultimately the identification of plant traits and regulatory networks mediating acclimation to multiple stresses will be very relevant towards the breeding of stress-tolerant crops with sustained yields.
Bram Kamps, council member
PhD Candidate, Entomology, Wageningen University & Research Project title: The double trouble of Insect attacks and water stress: how plants defend against insect herbivory while facing water stress.
About my research Due to global climate changes, an increasing challenge in agriculture is to cope with more severe outbreaks of insects against the backdrop of more frequent drought and heavy rain events. The problem is magnified since an excess as well as a shortage of water not only reduces yield but may also reduce the resistance of plants to insect herbivores. Although plants in nature and agriculture commonly face combinations of biotic and abiotic stresses, responses to these stresses have usually been studied in isolation.
In my project I explore how a small group of different plant species from the Rorippa genus handle a combination of water stress and insect herbivory simultaneously. These plants are differently adapted to water stress but have an overlapping insect community, making it an interesting study system. The question is how these adaptations might help them cope in a simultaneous stress environment. I study this by combining a variety of experiments ranging from fieldwork to transcriptomics.
Thalia Luden, council member
PhD candidate, Plant Developmental Genetics, Leiden University Project title:Rejuvenator: the potential of regulating plant longevity
About my research Polycarpic plants flower more than once in their lifetime, and need to resume vegetative development after flowering to continue growth and prepare for the next flowering cycle. Monocarps, on the other hand, do not resume this vegetative growth and die after flowering. Control of vegetative growth is of major agri- and horticultural interest, as it can help to improve the quality of leafy vegetables and the yield and quality of cuttings and flowers. Recently, the Arabidopsis REJUVENATOR/AHL15 transcription factor gene has been identified as a key regulator of vegetative growth. While striking phenotypes have been described in plants with altered RJV/AHL15 expression, the molecular mechanism of RJV/AHL15-induced vegetative growth remains unknown.
With this research, we aim to unravel the regulatory pathways surrounding RJV/AHL15 to gain understanding of vegetative development in plants. This will be done by studying different effects of RJV/AHL15 activity in Arabidopsis thaliana such as its effect on the transcriptome and its role in changing the epigenetic landscape of the genome, and the natural variation of RJV/AHL15 in different Arabidopsis ecotypes and other plant species. Understanding how vegetative development is regulated in plants will not only help breeding efforts in commercial crops, but also shed light on how the diversity of life history strategies has evolved in plants.
Sanne Matton, council member
PhD candidate, Plant-Environment Signaling, Utrecht University
About my research Plants are able to perceive the quality and quantity of the light in their environment using several different light receptors, which enables them to respond adequately to their light environment and optimize light harvesting for photosynthesis. Via their phytochrome photoreceptors plants are able to detect shade. As a consequence, when a shade avoiding plant like Arabidopsis thaliana perceives shade its energy investment shifts away from processes like growth of the leaf lamina, root system and fruits towards an increased elongation of the stem and upwards growth of leaves. The shade avoidance response, which is also present in many crops, thus affects yield of edible and usable parts of said crops.
The shade avoidance response has been researched thoroughly in seedlings, and already some work has been done on adult plants. In my project I focus on adult plants, further elucidating growth responses upon spatial and temporal fluctuations in light quality and quantity in Arabidopsis thaliana and Solanum lycopersicum. For example monitoring leaf growth responses when only a small part of the leaf is shaded, but also investigating the effect of fluctuations in the light quality or quantity over time. The aim of my project will be to elucidate the molecular pathways underlying local light dependent growth responses and the effect spatial and temporal fluctuations in light quality and quantity have on leaf growth and development.
Davy Meijer, council member
PhD candidate, Entomology, Wageningen University & Research Project title: LEDs make it resilient!
About my research The introduction of light emitting diode (LED) technology in horticulture has contributed greatly to improving both productivity and sustainability in greenhouse crop production. Their biggest advantage for horticulture is their ability to tightly control the spectral composition of the light. Over the past decades, our knowledge on how different wavelengths of light influence plant growth and development has increased tremendously. Using LEDs, this knowledge is now being exploited to increase the yield and quality of greenhouse crops.
The next step is to use LEDs for integrated pest management (IPM). Light quality is an important mediator of plant stress tolerance and can play an important role in plant-herbivore interactions. In this project, we will look at the effects of different wavelengths of light on the plant’s immune responses to herbivore feeding, to the attraction and efficiency of biological control agents and to the feeding behavior and reproduction of herbivore pests. We aim to find light quality-effects that boost the plant’s natural defenses, while at the same time maintaining productivity and quality.
Judit Nadal Bigas, council member
PhD candidate, 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 favorable, 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.
Milan Plasmeijer, council member
PhD candidate, Plant Physiology, University of Amsterdam and Green Biotechnology, Inholland University of Applied Sciences Project title: Biosynthesis, regulation and transport of floral volatile benzenoids and phenylpropanoids; a CRISPR-approach
About my research Many plants are dependent on insects for their reproduction and need to attract these pollinators to their reproductive organs. Flower morphology, pigmentation and scent emission all have major impact on pollinator behavior. In my research, we focus on the emission of floral volatile benzenoids and phenylpropanoids (FVBPs) in model organism Petunia hybrida, which attract nocturnal hawkmoths. Scent emission in P. hybrida is tightly controlled and strictly regulated to coincide with the activity of the hawkmoths, which are active during nightfall. Our group has identified candidate genes that are involved in the circadian regulation and biosynthesis of FVBPs, and genes that are involved in internal transport of precursors to feed in the biosynthetic pathway of FVBPs. By setting up different CRISPR-based gene editing protocols for Petunia, I will make knock-outs and knock-downs to further characterize the role of these genes in FVBP biosynthesis. In addition, I will specifically modify promoter elements of the circadian R2R3-MYB transcription factor ODO1 to understand their role in circadian emission of FVBPs. We will thus extend the current comprehensive model of FVBP biosynthesis, which may be used for several commercial purposes (eg. production of economically important metabolites, bringing back scent in crops that have lost scent during domestication, improving flower scent and longevity).
Myrthe Praat, council member
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.
About my research The root microbiome is a highly complex and dynamic system in which millions of microbes interact with each other and with the plant root. Within a natural root microbiome, it is therefore hard to tell which microbes or which interactions lead to a specific plant phenotype or a shift in microbiome composition. Another way to study microbiomes is by inoculating plants with a self-assembled collection of microbes called a Synthetic Community or SynCom. This small collection of microbes makes it easier to map the interactions between plant roots and microbes, while being a simplified version of the natural root microbiome.
In this project, we aim to map the interactions between roots and microbes of three plant species concerning rhizosphere and endosphere colonization; Lotus, Arabidopsis and barley. For each of these plants we have a collection of hundreds of microbes that we can use in SynCom inoculations. We will observe which microbes are recruited by each plant and look more closely at the functional characteristics (or genes) of these recruited microbes. The data that will be produced shall be the driving factor to select potentially relevant microbes for more SynCom inoculation experiments.
Iris Zahn, council member
PhD candidate, Laboratory of Molecular Biology / Plant Developmental Systems, Wageningen University & Research
About my research The moment at which a plant starts flowering is very important for its reproductive success and therefore tightly regulated by many genes. This has been thoroughly studied in the model species Arabidopsis. However, this network has only to a limited extent been translated to crop species, even though flowering time and inflorescence development are major determinants of yield. I focus on tomato homologs of two key regulatory genes that act on different regulatory layers of the flowering network: SUPPRESSOR OF OVEREXPRESSION OF CONSTANS1 (SOC1) and FRUITFULL (FUL). SOC1 integrates environmental and internal cues important for flowering and thereby determines the moment of floral transition. In this developmental phase, FUL acts as floral meristem identity gene. I aim to identify which factors regulate SOC1 and FUL homologs in tomato and how this influences flowering. To do so, I investigate the function of these key regulators, the regulatory motifs controlling their expression and transcription factors binding to these sequence motifs. Together, this knowledge will help to further unravel the network regulating flowering and inflorescence architecture in tomato.