RESPONSE Project Descriptions

Dusan Denic (ESR01)

Unlocking epigenetic variation to breed sustainable crops in a changing climate

Advisor: Prof. Ueli Grossniklaus, Department of Plant and Microbial Biology, University of Zurich

Partner: Marc W. Schmid, Director, MWSchmid GmbH (MWS), Zurich

Agricultural productivity needs to be significantly increased by 2050 to meet the needs for food, feed, fibre, and fuel production. The longterm goal of this project is crop improvement through unlocking the potential of epigenetic variation. Apart from genetically modified crops, the development of new cultivars has largely relied on classical breeding, which is based on genetic variation in the primary gene pool. Unfortunately, very little is known about how stable epigenetic variation, so-called epialleles, are inherited over generations, how they are influenced by genetic background, and how they respond to environmental influences. This project will investigate these aspects in the model plant Arabidopsis thaliana with a focus on
DNA-methylation, a prominent epigenetic mark that can easily be assessed. By analyzing public data from 87 accessions of A. thaliana, ~100 loci with a high anticorrelation of gene expression and DNA-methylation were identified.

The accessions clearly fell into two groups, some of which also show a correlation with an associated phenotype. We will follow the DNA-methylation status of 20–30 loci over several generations in different F1 hybrids and recurrent backcrosses in A. thaliana plants to assess the stability of epialleles across generations and their dependence on genetic background. This knowledge will help the seed and agroindustry to make decisions regarding the inclusion of epigenetic variation in breeding programs. This may influence policy decisions with regard to epigenetic modifications, and contribute to the development of more resilient, sustainable cultivars in the long term. The success of the project relies on combining various disciplines, including genetics, molecular biology, ecology, and – through the secondment – statistics and bioinformatics. A secondment of 3 months is foreseen at MWSchmid GmbH (MWS) with expertise in experimental design, statistics, bioinformatics, data analysis, and
data presentation. The unique competences of MWS are essential for optimal data analysis and exploitation of the results. It will also provide insights into small business operations. Throughout the project, MWS will participate in regular meetings to monitor and discuss progress and possible adjustments. The results of the project
will be published in open-access journals that are respected in the field and presented at international conferences. 

Katharina Jung (ESR02)

Wheat responses in changing climates studied in Asian varieties as underexploited genetic and genomic resources

Advisor: Prof. Kentaro Shimizu, Department of Evolutionary Biology and Environmental Studies, University of Zurich 

Partner: Masahiro Kishii, Senior Scientist, International Maize and Wheat Improvement Center (CIMMYT)

Bread wheat is one of the three major crops in the world, but its yield is projected to be reduced by rapid climate changes. To create sustainable food systems, the critical mission of breeding centers, including the International Maize and Wheat Improvement Center (CIMMYT), is breeding for anticipated climates. The paucity of genomic information, caused by the large genome size and allohexaploidy, has been a major obstacle in the genetic research on bread wheat, but recently the assembly and analysis of the complex genome was accomplished: the 10+ Wheat Genomes Project completed the de novo assembly of ten world-leading varieties. A recent study (Balfourier et al. (2019), Science Advances 5(5): eaav0536) reported that, despite harboring large amounts of ancient genetic variation, Asian landraces and traditional varieties are largely unexploited. 

Therefore, this project will focus on the variation of 25 representative lines composed of landraces and old cultivars from Asia established by the National Bioresource Project – Wheat of Japan. First, by applying the expertise of CIMMYT, the variation of traits that are important for climate changes, such as disease resistances or stress tolerances, will be measured within the 25 varieties. Second, novel promising traits will be mapped using the nested association mapping (NAM) lines, constructed from the crossing of the 25 core lines, combining the advantages of quantitative trait locus mapping with association mapping. The mapped chromosomal regions will be used for breeding in response to climate changes. The results will be published in open access journals and made available to the general public. Field data will be sent to breeders inside and outside CIMMYT using CIMMYT global network.

Linda Frattini (ESR03)

Developing a source-to-sink value chain for Swiss industrial carbon dioxide via a holistic approach

Advisor: Prof. Marco Mazzotti, Department of Mechanical and Process Engineering,
ETH Zurich

Partner 1: Dr. Cornelia Schmidt-Hattenberger, Senior Research Scientist, Group Leader Geological Storage, Deutsches GeoForschungsZentrum GFZ Potsdam

Partner 2: Dr. Jan-Justus Andreas, Policy Manager Industry, Bellona Europa (Brussels, Belgium)

The scientific community recognizes the key role that carbon dioxide (CO2) capture and storage (CCS) systems will play as part of the efforts to mitigate climate change, either to mitigate emissions today or to enable negative emissions in the future. CCS is available and feasible from a technological point of view. Nevertheless, the public acceptance, the political support and the regulatory feasibility of CCS are very limited in many countries, particularly in Europe, including Germany and Switzerland. In this context, my project aims at tackling this question: Is the vision of a source-to-sink value chain for Swiss industrial CO2 feasible, what are the hurdles to make this vision real, from a technical, economic, regulatory, political, social perspective,
and how can these be tackled? The key challenge in this project is indeed its interdisciplinary nature, whereby technical and scientific knowledge and social sciences expertise have to be integrated. The way we intend to address this is by exploiting the main PI’s network of collaborations at ETH Zurich, as well the Energy Science Centre network in order to cover the different scientific domains effectively. Furthermore, Linda will take two secondments at the GeoForschungsZentrum Potsdam, Germany and at Bellona Europa, Belgium – two of the most active and prestigious foundations working on different aspects of the CO2 value chain. Interacting with such a pool of experts, Linda will design a source-to-sink value chain for Swiss industrial CO2.

Indeed, the project will deliver: (i) a blueprint of a CCS value chain for Swiss waste-to-energy operators, and for other sectors such as cement or gas-fired power generation; (ii) a cost-benefit analysis of the same, with the identification of possible business models; (iii) an understanding of societal perception about CCS, and a new narrative on how to communicate about CCS; (iv) an assessment of political and regulatory interventions necessary to enable the whole CCS value chain above. The outcome will consist of 1–2 scientific publications, material for the public, workshops with stakeholders, panel discussions
involving students, lectures at ETH Zurich and in high schools. Moreover, we will formulate policy-recommendations (e.g. policy brief, blog article, etc.) based on stakeholder meetings.

Bessie Noll (ESR04)

Energy transition and the transport sector – assessing the impact of European and national policies on future drive technology mixes, energy use and emission pathways

Advisor: Ass. Prof. Tobias Schmidt, Department of Humanities, Social and Political
Sciences – Energy Politics Groups, ETH Zurich

Partner: Nils Epprecht, General Manager, Schweizerische Energiestiftung (SES), Zurich

The transport sector is one of the largest energy consumers and plays a crucial role in mitigating climate change. With recent cost reductions for battery electric vehicles, a fundamental transformation of the predominant drive technologies towards low-carbon technologies seems possible. However, there is great uncertainty about the speed and outcome of the transition, since a variety of drive technologies still compete for low-carbon road mobility and transport and with increasing modal shifts towards rail. To address this challenge, we will develop a novel model for global projections of technology mixes for mobility and transport until 2040. Embedding a probabilistic discrete choice model within a system-dynamic model architecture, we will consider feedbacks between technology deployment, cost improvement and further factors, and thus contribute to policy advice. Specifically, this project will address uncertainty in freight transport decarbonization. As evidenced by increasing global demand for goods and services, the freight sector represents a critical analysis point for emissions reduction and an anticipated option for electrification given the likely definitive trend towards total electrification in the passenger transport sector. Entry barriers for alternative fuel freight vehicles in the market, however, include high cost of infrastructure and high capital investment as the technologies required to
power long-range road transport, for instance, are not yet cost effective. 

The developed model will therefore address the positive economic feedback effects of technological development and deployment but perhaps more importantly, identify policy intervention points that would effectively assist a shift from conventional to alternative fuel drive-train technologies. In collaborating with the Swiss Energy
Foundation (SES), avenues and best practices for policy intervention will be readily experienced and discussed first-hand by Bessie during the secondment and can thus be incorporated in the model architecture and assessment. Finally, upon completion, quantitative results as well as the model itself will be open sourced for future researchers to build upon and for other relevant industry stakeholders to reference.

Linda Brodnicke (ESR05)

Engineering the Policy-Enabled Transition to Sustainable Multi-Energy Sytems

Advisor: Prof Giovanni Sansavini and Matthias Gysler, Department of Mechanical and Process Engineering - Reliability and Risk Engineering lab, ETH Zurich

Partner: Swiss Federal Office of Energy (BFE / SFOE)

Multi-energy microgrids are projected to play a key role towards the transition to the sustainable energy system. Their benefits in terms of carbon emission reduction, cost effectiveness and reliability are increasingly confirmed by researchers, as well as public and private organizations. Multi-energy microgrids are mainly investigated using techno-economic optimization approaches, which provide their target design for a variety of external conditions. However, this target design can only emerge as a collective result of the independent decision-making of the agents that plan, live in, use and operate the current energy distribution systems. Thus, a transition to distributed multi-energy systems can only be enabled by supporting informed decisions by the aforementioned user groups, i.e. customers and system operators.

The project aims to identify energy policies which facilitate this transition by bridging the gap between techno-economic design and policymaking. This will be done by leveraging and combining the technical expertise on multi-energy systems within the Reliability and Risk Engineering group at ETH and the policy-related expertise of the project partner, the Swiss Federal Office of Energy (BFE). The results of this project will be published in relevant scientific journals and the policy recommendations emerging will be used to inform updates to the Swiss Energy Strategy 2050.

The research question will be targeted with a combination of two modelling approaches: The first stage includes a sensitivity analysis aiming to identify challenges and favorable conditions for the deployment of multi-energy systems. The analysis will build on existing models and will focus on policy instruments such as carbon taxes and caps. In the second stage, the behavior of different user groups will be modeled using agent-based modeling. Calibrating the model using data from the BFE will allow to identify promising policy instruments for enabling the transition to multi-energy systems.

Danli Fei (ESR06)

Chromatin-based controls in the reproductive lineage

Advisor: PD Dr. Célia Baroux, Department of Plant and Microbial Biology, University of Zurich

Partner: Dr. Peter Majer, Bitplane AG, Zurich

The nucleus is more than a genetic container. This organelle is the chief orchestra of cellular processes by controlling and fine-tuning gene expression in response to developmental and environmental cues. The combination of DNA and histone proteins that make up the nuclear content is often referred to as chromatin. The function of chromatin is packaging long DNA molecules into more compact, denser structures. Linker histones bind the nucleosome at the entry and exit sites of the DNA. The modification of this structural proteins in chromatin alters local chromatin structure and therefore gene expression.

In this project, we aim to elucidate chromatin dynamics principles underlying cellular reprogramming during developmental or physio- logical transitions. My project focuses on the somatic-to-reproductive cell fate transition which leads to germline differentiation and then seed formation. Our group has shown that in the model plant Arabi- dopsis, the differentiation of both male and female spore mother cells (SMC) is accompanied by large-scale chromatin reprogramming including the loss of linker histones (H1), chromatin decondensation, and large-scale epigenetic changes (She et al., 2013, 2015). Specif- ically, the goal of this project is to address the role and mechanisms of H1 dynamics during female sporogenesis in Arabidopsis, focusing on ubiquitinylation and the proteasome-degradation pathway. The purpose of this research is to contribute knowledge on the molecular and epigenetic mechanisms controlling plant reproduction, in turn influencing seed yield.

Planned outcomes of this project are the elucidation of the role of ubiquitination in H1 dynamics controlling in turn plant reproduction, as well as the higher visibility of image processing-based analyses to diversify research approaches in plant sciences. To strengthen my professional network, a three-month secondment is foreseen at Bitplane AG, focusing on the documentation of plant science case studies using Imaris as a resource for plant scientists to promote innovation. The role of Bitplane AG is to provide a training in science application communication. The result will be published on the Imaris Learning Centre webpage

Dabwiso Sakala (ESR07)

The role of biodiversity in sustainable energy transitions for charcoal

Advisor: Prof. Maria Joao Ferreira dos Santos, Department of Geography, University of Zurich

Partner: Clovis Grinand, Researcher / Project Manager, Nitidae France

Global demand for charcoal is increasing mainly due to urban population in developing countries. More than half the global population now lives in cities, and urban-dwellers are restricted to charcoal use because of easiness of production, access, transport, and tradition. Growing demand for charcoal, however, may lead to increasing impacts on forests, food, and water resources, and may even create additional pressures on the climate system. The project will for the first-time link trait-based approaches and ecosystem models to the case of charcoal production in the tropics. Its findings will contribute to the fields of functional diversity (within ecology), social ecological systems, complexity science and energy science. Specifically, this project will build on an existing project in the lab looking into the livelihood impacts and drivers of charcoal production in Tanzania. We will build on this expertise to integrate the role of biodiversity in sustainable energy transitions for charcoal, namely through integration with societal drivers of charcoal use, which are dependent to some extent on traits for charcoal production but determine trait evolution as well. The project will review and embed the social, economic and cultural components of the history and evolution of charcoal use with trait evolution to determine their contribution to carbon cycling.

The secondment partner Nitidae will hereby provide connection to local conditions and advancement of capacity in the project areas. This integration is fundamental and will enhance the relevance of the project beyond earth system and natural sciences, towards other disciplines. This project is highly relevant for society because a large fraction of urban populations in sub-Saharan Africa already depend on charcoal for their energy and cooking needs, and this is projected to grow. The demand from these urban populations is extremely linked to rural population livelihoods, biodiversity loss, and carbon cycling and accounting. One of the outcomes will be a White paper (e.g. policy recommendations for biodiversity and livelihood enabling charcoal sector or best practices for nature-based solutions for the charcoal sector). The results from the project will benefit societal groups in the target countries by providing results on the carbon and livelihood effects of charcoal production, fundamental to inform carbon and biodiversity policies, indicator reporting at national and subnational scales, as well as sustainable development objectives and goals that meet both poverty alleviation and biodiversity and climate change goals.

Reah Gonzales (ESR08)

Strategies for improving forage productivity under future climates

Advisor: Prof. Bruno Studer, Institute of Agricultural Sciences, ETH Zurich

Partner: Stephane Charrier, Station Manager / Breeder, Royal Barenbrug Group, France

Climate change increases the occurrences of unpredictable weather conditions, intense drought events, and has detrimental effects on food production and security. Drought stress significantly limits crop yields. In previous studies, quantitative trait loci (QTLs) regulating transpiration rate and leaf elongation had strong positive effects in association with drought tolerance in wheat. Furthermore, extensive research in maize revealed that the efficiency of photosynthesis is hampered under drought stress. The physiological and genetic mechanisms involved in the response of forage grasses to drought stress are not well understood, indicating the need for precise modulation of growth under drought stress. In this project, we aim to unravel the physiological and genetic mechanisms involved in the response of forage grasses to drought stress. To achieve this aim, in co-operation with Royal Barenbrug Group (Mas-grenier, France), we will screen populations of Lolium perenne and Festuca arundinacea for drought responses on a high throughput phenotyping platform as well as under field conditions. The phenotyping platform is a novel precise method of determining the points at which the drought stress slows and arrests leaf elongation,
a physiological measure of genotype-specific adaptability to drought stress. A diverse panel of individuals with contrasting responses to drought will form the basis for the development of a segregating F2 population. The F2's will be screened for drought responsive traits on the high throughput phenotyping platform as well as under field conditions. The same plants will be genotyped-by-sequencing and QTL analyses will be conducted to identify regions in the genome associated with drought tolerance. Identified QTLs will form the basis for the development of Kompetitive allele specific PCR (KASP) markers for use in marker-assisted breeding for drought tolerant forage grasses, ensuring sustainable production under future climates.

Fei Wu (ESR09)

ROSE: Role of bioenergy in sustainable energy systems

Advisor: Prof. Anthony Patt and Dr. Stefan Pfenninger, Department of Environmental Systems Science – Climate Policy, ETH Zurich

Partner: Dr. Adrian Müller, Research Institute of Organic Agriculture (FiBL), Frick

Bioenergy is currently a major source of renewable energy in Europe, but its role in a 100% renewable Europe towards 2050 is uncertain. It may be able to help balance fluctuating wind and solar power. However, there are doubts about its sustainability and conflicts with other forms of land use, including for food production. Hence, this project will take a step back to investigate possible roles of bioenergy in a fully renewable and largely electrified European energy system from an interdisciplinary perspective.

Specifically, this project aims at answering three interconnected questions: (1) What different roles can bioenergy provide for power system flexibility or non-electrified energy demand in a 100% renew- able Europe by 2050 – and to what extent are these two roles syner- gistic? (2) Can biomass supply for such roles be produced within Europe in a sustainable way with respect to fertilizer input and land use? How might a shift towards more plant-based and land demanding diets affect this endeavor? (3) What is the impact of the EU’s 2030 targets and current bioenergy support policies on likely bioenergy deployment pathways, and do they help or hinder the achievement of the roles identified in (1) and (2) by 2050?

This first question will be answered by Euro-Calliope (a European energy system model developed in Anthony Patt’s lab). The second one will be explored through the global mass-flow food system model SOLm, in collaboration with the Research Institute of Organic Agri- culture, FiBL. The final step is to provide feedback to the first two questions through the combination of Euro-Calliope and SOLm as well as interviews with stakeholders. Besides scientific publications and open-sourced models, the project will also provide a policy brief to inform policymakers on flexible, sustainable, and cost-effective pathways highlighting the role of bioenergy in achieving a fully renew- able European energy system by 2050.

This fellowship is hosted by the Energy Science Center.

Manuel Belanche Guadas (ESR10)

Quality-enhanced power semiconductor devices for reliable energy conversion (QEPSREC)

Advisor: Prof. Ulrike Grossner, Department of Information Technology and Electrical Engineering, Advanced Power Semiconductor Laboratory, ETH Zurich

Partner: Florian Krippendorf, mi2-factory GmbH, Jena, Germany

Power semiconductor devices are a fundamental part of the power electronics that compose all electrical energy systems required in society. From renewable energy generation to electric vehicles and power supplies markets, power semiconductor devices can strongly contribute to the reduction of global energy loss and improvement in power management. Along with the emergence during the last two decades of such markets, a remarkable amount of R&D was conducted in the field of power electronics providing solutions for the increasing semiconductor devices requirements.

However, with increasing demands on performance and efficiency, traditional Si-based devices have reached their performance limits. Consequently, a migration to more robust semiconductor materials is necessary. Wide-bandgap semiconductors, e.g., Silicon Carbide (SiC), are emergent viable alternative given their superior electrical properties. However, SiC-based semiconductor technology is rather young and hence comprehensive understanding of its electrical behavior and an improvement in device quality and reliability is needed.

The aim of the project is the development of a novel ion-implan- tation technology to realize SiC-based super junction devices, desig- nated to outperform the existing wide-bandgap semiconductor devices. In collaboration with mi2-factory GmbH, given their state- of-the-art energy filters technology, the focus will be on the ion implantation process as a key process for the fabrication of efficient and reliable high-voltage devices. The modelling of super junction device structures, in addition to the development of adequate fabri- cation technologies, will eventually allow the prototyping of high quality and reliable super junction structures based on Silicon Carbide.

This fellowship is hosted by the Energy Science Center.

Laurent Giguère (ESR11)

Developing climate-ready apple production systems in Switzerland

Advisor: Prof. Rachael Garrett, Institute for Environmental Decisions, ETH Zurich

Partner: Schweizer Obstverband / Fruit-Union Suisse

In the context of a rapidly changing climate, the research project Developing climate-ready apple production systems in Switzerland pursues the goal of increasing the climatic resilience of the Swiss apple sector to make sure it can continue to maintain its enviable position as the country’s leading fruit sector and as one that significantly contributes to Swiss food self-sufficiency.

The project’s first step investigates how climate change has affected apple growing in Switzerland until now, and how it is likely to affect it in the decades to come. Concretely speaking, an agro-climatic model linking production data from Switzerland and other important European apple-producing regions to climatic data representative of those areas is built, with the intent of estimating the region-wide impact of extreme weather phenomena like drought, heat waves and late frost on apple yields. The estimates derived from this model are then used to forecast how apple yields are likely to evolve across the different Swiss apple-growing areas in the future, based on the most recent climate change scenarios available for the country. In parallel to this statistical work are a series of semi-structured interviews carried out with apple growers whose orchards are spread out across Switzerland. By aiming to capture how the impacts of climate change translate into changes in apple growers’ lives, these interviews fill the need to gather inputs on how producers adapt to new climatic realities, what are the biggest hurdles currently slowing down their adaptation, as well as, which tools they think they lack to make their orchards more resilient.

Drawing on the outputs of both the agro-climatic model and the field interviews, the project will head into its final phase, where in-depth assessments of the most promising solutions for the development of more resilient production systems, such as the introduction of cultivars robust to specific abiotic stress factors, the expansion of irrigation systems and changes in growing areas, will be made. As a final step, and in partnership with the Schweizer Obstverband/Fruit-Union Suisse, the project’s conclusions will be summarized in the form of a policy paper addressed to Swiss apple producers, in an effort to help the latter transit towards more climate-resilient apple-growing systems in the future.

Yutang Chen (ESR12)

Exploitation of genomic resources to advance forage breeding programs

Advisor: Prof. Bruno Studer, Department of Environmental Systems Science, ETH Zurich
Partner: Dr. Ingo Lenk, DLF Seeds & Science, Denmark

As the world population continues to grow, food security is a serious topic for plant scientists and breeders. Thanks to the great efforts made in improving the yield of main staple crops such as rice, wheat, and maize, more and more people in our world could escape from hunger. However, eating only enough staple food cannot provide complete and balanced nutrition for a human being since staple food may be low in other essential nutritional elements such as protein. Fortunately, protein can be supplied by other sources, for example, eggs, meat and milk, and in order to produce these animal products, high-quality forage is very important. This is exactly the rationale of our project: developing genomic resources to improve the breeding of high-quality forage grasses, which are at the base of sustainable livestock production.

Festuca pratensis Huds., commonly known as meadow fescue, is an important forage grass from the Festuca-Lolium species complex. Breeding improved varieties of F. pratensis using traditional methods requires many years. However, with state-of-the-art genomic selection approaches, the time-consuming process of selecting superior plants phenotypically could be largely reduced. Genomic selection in F. pratensis can benefit from a high-quality reference genome assembly; it can not only accelerate the identification of genes underlying agronomically important traits but also provide plenty of useful genetic markers for trait selection. With the dramatic decrease in cost for whole-genome sequencing and the rapid development of bioinformatic tools in genomics, it has now become feasible to conduct such an ambitious genome sequencing project in F. pratensis. Beyond paving the way to genomic selection, this project will also contribute to the establishment of best practices for high-quality assembly and annotation of multiple genomes from the Festuca-Lolium species complex using the latest technologies.

The whole project can be broken down into the following four tasks: 1) constructing a phased, chromosome-scale, diploid genome assembly of F. pratensis, 2) interpreting the biological meaning of the genome sequence by annotating its genic regions, 3) performing pan-genome analysis with other F. pratensis genotypes or genomes of other grass species to detect common core genes as well as individually unique genome elements and 4) applying the results from 1) - 3) to dissect the genetic basis of agronomically important traits of F. pratensis and identify QTL and genetic markers, which can be used to aid selection in forage grass breeding programs.

Yuanyuan Liang (ESR13)

Towards improved crop resilience – discovering essential factors that control chloroplast development

Advisor: Prof. Samuel C. Zeeman and Dr. Barbara Pfister, Department of Biology, Institute of Molecular Plant Biology, ETH Zurich

Partner: Dr. Klára Panzarová, PSI (Photon Systems Instruments), spol. s r.o., Drasov, Czech Republic

Understanding the mechanisms by which chloroplasts develop and maintain their function under adverse conditions is of unparalleled global significance. As they house photosynthesis, even small alter- ations in chloroplast function imposed by environmental stresses can result in drastic yield losses. Maintaining crop yields in the face of increasingly unfavorable environmental conditions requires innova- tions that allow improvements in the plastid’s housekeeping metab- olism and hence the stress resistance of these crucial organelles.

In this project, we aim to identify factors involved in the funda- mental processes of chloroplast homeostasis. Our recent data suggests that an Arabidopsis protein which was predicted to be involved in carbohydrate metabolism is actually associated with components of the plastid gene expression machinery and is essen- tial for plastid development. We will apply molecular biology approaches to understand how this protein and related factors enable the development and homeostasis of chloroplasts, thereby identifying novel targets to increase the resilience of these essential organelles in crops. In collaboration with Photon Systems Instruments (PSI) in the Czech Republic, we will explore fast and non-destructive in situ scanning methods for characterizing the photosynthetic efficiency of plants. These will not only provide valuable data for this research project but also lay the groundwork for improved technologies to capture changes in the function of individual chloroplasts in real-time.The methodological and scientific outcomes of this project will be presented at science or agricultural fairs and stakeholder meetings and published open access in international peer-reviewed journals and bioinformatic datasets, which will provide novel knowledge for breeding strategies.

Alberto Linares (ESR14)

ChromoBreed: From chromatin to plant breeding

Advisor: Prof. Sylvain Bischof, Department of Plant and Microbial Biology, Epigenetics and Chromatin Biology, University of Zurich

Partner: Dr. Etienne Bucher, epibreed AG, Basel

The ability to engineer genetically modified crop species has promise to revolutionize plant breeding, through targeted modifications of specific plant traits. However, widespread use of this technology is currently hampered by ethical and legal barriers. A potentially exciting alternative that avoids some of the concerns in standard bioengineering is to remodel the epigenome to improve plant traits. Importantly, this approach may be subjected to less strict regulation because it does not permanently modify the DNA base sequence and may thus be more likely to gain public support.

In this project, we will characterize the epigenetic mechanisms underlying a novel breeding technology that is based on the mobility of endogenous transposable elements (TEs). In recent years, TEs have been used as a promising tool to alter plant traits. TEs are DNA sequences that can multiply and move to different genomic locations. Because they are potentially deleterious for the genome, TEs are targeted by repressive epigenetic mechanisms that silence their expression and thus prevent their ability to transpose to unwanted regions of the genome. However, certain stimuli or environmental conditions can favor the reactivation of TEs. For example, exposure to heat leads to the transcriptional upregulation of the retrotrans- poson ONSEN and its transposition throughout the genome. This heat-inducible transposition system has been used to screen for new ONSEN insertions resulting in expression changes of nearby genes that control plant traits. Despite its successful application in Arabi- dopsis and rice, the molecular mechanisms controlling TE reactivation for this breeding strategy remains to be elucidated.

The proposed project aims at elucidating the epigenetic pathways that regulate the activity of TEs and apply the obtained knowledge to improve transposition-mediated plant breeding. Together with the partner organization, epibreed AG, this emerging technology will be applied to improve plant traits. The obtained results will be published open access in international peer-reviewed journals and presented at international conferences. New molecular pathways leading to improved transposition-mediated breeding will be patented.

Fabian Hess (ESR15)

Unlocking genetic resources of buckwheat to diversify Swiss agricultural and food systems

Advisor: Prof. Bruno Studer, Department of Environmental Systems Science, ETH
Partner: Philipp Holzherr, ProSpecieRara, Switzerland

The excellent nutritional quality of buckwheat (Fagopyrum esculentum) as well as its high ecological value makes it an extremely valuable crop for the future of agriculture. However, the lack of efforts to genetically improve buckwheat – combined with the tremendous progress achieved in breeding programs of other staple crops – led to the nearly complete disappearance of buckwheat cultivation in Switzerland. Consequently, most of the domestic genetic resources of buckwheat were lost over the last centuries.

This project aims at reviving a large and diverse buckwheat collection with over 150 accessions of worldwide origin. The material will be multiplied to produce the seeds needed for conducting the planned trials and analyses. Field trials will be conducted over multiple locations and years to accurately describe the phenotypic diversity of the accessions and to identify agronomically and nutritionally interesting traits. In addition, the genetic diversity within and between the accessions will be characterized by means of genome-wide allele frequency fingerprints (GWAFFs) derived from genotyping by sequencing (GBS). Combining the phenotypic and genotypic information in genome-wide association studies (GWAS) will allow to link plant traits to genomic markers.

To ensure that the buckwheat varieties meet the consumers’ taste and find their way into farmer’s fields, this project is carried out in collaboration with ProSpecieRara – a Swiss Foundation dedicated to the conservation and utilization of cultivated plants and farm animals. In the setting of this collaboration stakeholder workshops will be organized to identify the needs of different actors in the buckwheat value chain and to actively involve them in the selection of suitable accessions.

With this project we anticipate identifying buckwheat varieties adapted to Swiss production conditions and to the market’s needs. Furthermore, we aim to prepare the ground for buckwheat improvement through breeding by establishing genomic tools which will facilitate the process of combining beneficial traits of multiple accessions. The buckwheat varieties will be made available through the Swiss National Gene Bank (PGREL/RPGAA) and the outcomes of the project will be shared through stakeholder meetings and scientific publications.

Paul Donadieu de Lavi (ESR16)

Towards more resilient and sustainable regional food systems

Advisor: Prof. Johan Six and Dr. Dominique Barjolle, Department of Environmental Systems Science, ETH Zurich
Partner: Charles Raphaël, FiBL

Climate change is causing a slow and profound transformation in food systems, leading to a weakening of their production. In developed countries, agriculture is a major contributor to global warming. Therefore, it is essential that it reduces its carbon footprint by moving towards more sustainable practices. Furthermore, the increase in the frequency of extreme climatic events, as well as the pandemic of COVID-19, reveal the vulnerability of our food system. Hence, it is essential to increase their resilience.

In developed countries, public authorities, through agricultural and land use policies, play an essential role in building a sustainable and resilient agriculture. The territorial level is the most relevant to support the transformation of these food systems because its inhabitants and producers are the best witnesses and experts about the strengths and weaknesses of their regions. Several countries have already recognized this. For example, France has set up successful Territorial Food Projects (PAT) and Switzerland is testing Regional Agricultural Strategies.

The final objective of this PhD is to create an approach to facilitate the implementation of regional agri-food strategies that improve the sustainability and resilience of regional food systems. This approach, designed for public authorities, is intended to be used in Switzerland as well as in all developed countries interested in the decentralization of agricultural and land-use policies.

To achieve this goal, we will work in close collaboration with Swiss public authorities, farmers, and regional value chains in two regions of Switzerland.

More precisely, we will start by (1) defining the dimensions and characteristics of the appropriate area for the implementation of a regional agri-food strategy. We will then seek to (2) understand the relationships that link the actors of the regional food system and their impacts on the sustainability and resilience of the system. Finally, we will apply this knowledge to (3) build an approach for the Swiss regional authorities for the implementation of a regional agri-food policy.

Sudesh Dahal (ESR17)

Sustainable storage hydropower for a resilient future energy system

Advisor: Prof. Robert Boes, Laboratory of Hydraulics, Hydrology and Glaciology VAW, ETH Zurich
Partner: Dr. Christian Dupraz, Swiss Federal Office of Energy BFE

For decades, hydropower has been an important pillar of the electric power system in Alpine regions, providing both generation of electric energy and storage of energy by high-altitude impoundments of water; and it is still today.
Simultaneously to the future deployment of new renewables including solar and wind as part of the energy transition, hydropower facilities will require a transformation to maintain their role as the backbone of an increasingly volatile and extended electric power system. In 2019, the Swiss Federal Office of Energy published an updated edition of its hydropower potential study, stating that considerable efforts are necessary to maintain and extend today’s hydropower capacities to meet the requirements set out in the Swiss Energy Strategy 2050. Among other factors, the study specifies reservoir sedimentation as a negative impact on hydropower storage capacities in Switzerland. An estimated loss of 7% of the seasonal storage capacity in Swiss reservoirs is anticipated until 2050. In many reservoirs, the sedimentation rate is much more acute, creating operational and dam safety problems. The project aims at reducing the uncertainties related to the assessment of long-term reservoir sedimentation under the effect of climate change. This will lead to better information of the future availability of Swiss hydropower’s storage capacities. Incorporated in upcoming editions of the hydropower potential study, these results may directly influence policy decisions shaping the development of prospective Swiss energy systems.
Therefore, the hydropower section of the Swiss Federal Office of Energy is involved as a partner organization. Numerical modelling will be applied to simulate the effects of different sediment management strategies. Besides engineering challenges, environmental and consequently also societal issues arise by the questions to be dealt with.
This fellowship is hosted by the Energy Science Center.

Monika Golarczyk (ESR18)

Monitoring the effect of deforestation and reforestation on vertebrate diversity using river environmental DNA (eDNA)

Advisor: Prof. Loïc Pellissier, Department of Environmental Systems Science, ETH Zurich
Partner: Arnaud Lyet, WWF US and Dr. Tony Dejean, SPYGEN (France)

Forest loss and degradation jeopardizes the provisioning of essential ecosystem services to society. Restoration projects, which often involve a mix of planting native vegetation and assisted natural regrowth, aim to bring these ecosystems back to the reference condition of old-growth forests. To ensure their success, one of the crucial
aspects of forest restoration is to enable recovery of faunal communities. Unfortunately, this task is often undermined by the limited empirical evidence on species responses to forest loss and regeneration, making it difficult to adopt effective management and restoration strategies.

To address this knowledge gap, we will use a novel approach of quantifying biodiversity through environmental DNA (eDNA) to compare vertebrate diversity between forests at different stages of succession: from old-growth tropical forest through degraded pasture to recently restored forest. Coupled with environmental data, information on catchment-level biodiversity will help improve understanding of the mechanism of habitat selection by forest-dwelling communities in the context of forest loss and restoration.

Beyond understanding of the drivers of biodiversity loss and recovery, in order to adapt effective management and restoration strategies, policymakers need tools for rapid biodiversity assessment and long-term monitoring. Several studies confirm that the analysis of eDNA for terrestrial biodiversity assessments is more time- and cost-effective than traditional methods (such as, e.g., camera traps
and mist netting). However, the application of eDNA in biodiversity monitoring, especially in terrestrial ecosystems, remains largely unexplored. To this end, one of the overarching aims of this project is to apply a range of laboratory and computational techniques to contribute to the standardization of eDNA-based methods in monitoring of terrestrial biodiversity.
The secondment partner organization, World Wildlife Fund for Nature (WWF), has a long history of working towards the conservation of threatened wildlife and ecosystems. With their expert help, we aim to use the knowledge gathered in this project to advance the existing indicators of biodiversity. Improved tools for monitoring changes in biodiversity will facilitate the implementation of restoration and conservation projects in line with the global strategic efforts for restoring nature.

Simon Landauer (ESR19)

Land use diversity effects on the functioning of anthropogenically-dominated landscapes

Advisor: Prof. Dr. Pascal A. Niklaus, Departement of Evolutionary Biology and Environmental Studies, University of Zurich
Partner: Dr. Eva Spehn, Swiss Biodiversity Forum, Swiss Academy of Sciences (SCNAT)

World-wide, accelerated structural change alters diversity, composition, and spatial configuration of land use patterns, with unknown consequences for landscape functioning. Recent research suggests that landscape functioning can be promoted by novel types of diversity effects that arise in mosaics of different land uses but not in the smaller, relatively uniform plots of biodiversity-ecosystem functioning experiments. However, the ubiquity of such landscape-level diversity effects and the specific mechanisms that underpin these remain unknown.
My PhD research project addresses this knowledge gap by investigating remotely-sensed landscape productivity in different biomes at large spatio-temporal scales and under a wide range of environmental conditions. Adopting study designs and concepts from experimental community ecology, we test whether effects comparable to the well-established species-diversity effects in small plots also occur when larger units such as entire ecosystems interact at the landscape scale. To investigate this hypothesis, we analyze the association of landscape diversity and landscape-level functioning using multispectral satellite images and land-cover information. The underlying mechanisms are investigated with statistical effect partitioning techniques, with trait-based approaches, and with semi-mechanistic, process-based models.
Should such landscape-level effects be important, as is expected, this would call for inclusion of these additional scales in the analysis and modeling of diversity-functioning relationships. A sound understanding of interactions among ecosystems within a landscape would open opportunities in management and conservation. To explore their potential, historic land use changes will be evaluated in connection
with the consequences for landscape functioning they might have had in the past.
The project’s vision is a science-informed land management approach that leverages landscape-scale mechanisms to enhance and stabilize landscape-wide functioning, similar to the way species diversity is nowadays managed to protect local ecosystem functions and services.

Matthew Cooper (ESR20)

Legacy effects of land-use on tropical soils as constraints on the restoration success and service provision of tropical forests in Uganda 

Advisor: Prof. Sebastian Dötterl, Department of Environmental Systems Science, ETH Zurich
Partner: Wouter van Goor, Face the Future (Netherlands, Uganda)

Project description (available soon)

Xeniya Kim (ESR21)

Application of plant peptides for the sustainable improvement of crop resistance to biotic and abiotic stresses (‘PEPSTRESS’)

Advisor: Prof. Cyril Zipfel, Department of Plant and Microbial Biology, University of Zurich
Partner: Dirk Balmer and Katrin Hermann Syngenta Crop Protection AG - Biological Science, Switzerland

Massive crop losses occur annually due to diseases and abiotic factors. Attempts to reduce the impact of biotic and abiotic stresses traditionally involve breeding and the extensive use of chemicals. Development and use of agrochemicals require an urgent rethink, due to novel regulations surrounding their development and use. Currently, many chemicals are being increasingly banned, and the EU is aiming for a ‘zero-residue’ agriculture. The new sustainability and intensification challenges that agriculture is currently facing call for a careful evidence-based evaluation of the solutions that could be implemented to sustain food and feed production. There is therefore a regained interest in ‘natural’ plant-derived products, as these would be aligned with an increasingly restrictive registration legislation, and could be utilized by both conventional and organic agriculture. While the importance of plant peptides in all aspects of plant biology - including responses to environmental stresses - is increasingly becoming important, their potential use has not been yet fully
evaluated. PEPSTRESS directly aims at filling this gap, and capitalizes on the complementary expertise of our group in peptide-based signaling and of Syngenta in crop protection. The project is built on our recent identification of novel families of stress-responsive plant peptides.
In my PhD project, I aim to decipher the mode-of-action of these peptides in activating stress responses, study the regulation and evolution of such peptides, and test the efficacy of peptide treatments on crops’ stress resistance. Since it was reported that some peptides inhibit the growth of some plant pathogens, the direct antimicrobial/
antifungal activity of the whole peptide family will be assessed.
This project will fill (1) a societal need for more sustainable crop management products, (2) a regulatory need for products with negligible impact on the environment and proven human safety, and (3) an industrial need for efficient complementary or alternative technologies to current controversial chemical or genetic solutions. As such, PEPSTRESS will inform academia, industry and policymakers of the potential use of peptides as novel natural crop improvement treatments, and will also lead to potential development of commercial products by the industrial partner.

Nathalia Perez Cardenas (ESR22)

Inferring legacy of human activities on tropical forest plant diversity with spatial genetics and remote sensing

Advisor: Prof. Maria J. Santos, Department of Geography, University of Zurich and Prof. Dr. Meredith Schuman, Departments of Geography and Chemistry, University of Zurich
Partner: Dr. Mikey O’Brien, South East Asia Rainforest Research Partnership - SEARRP

Humans have transformed tropical forests dramatically through the acquisition and changes of resources dynamics and modification of conditions, bringing about change in Earth’s surface, both in current and early times of human occupation. Recent research points out that long term human modification explains some present-day
patterns of biodiversity because human activities, past plant management and agricultural practices could have a lasting effect on plant diversity in tropical forests. Yet, a lack of integrated studies that connect past land systems with modern vegetation has left unanswered questions about the legacy of long-term land use on the current plant composition and diversity in rainforests. However, how long human-driven effects on forest plant species and traits persist, and what kind of patterns emerge in genetic diversity, remain unknown.
My PhD project aims to unveil patterns and effects of the legacy of human presence on plant species, traits, and genetic diversity in Borneo tropical forests. We hypothesize that with long-term and increasing human presence and intensity, species richness increases until an inflection point is reached, after which a decrease in species richness (along with functional and genetic diversity) is expected. We predict that such effects occur along a gradient of distance to human settlement. I use a novel combination of remote sensing with field data and genetic analyses, expecting to detect persistent effects of long-term human presence on species and functional diversity, even if dampened by natural restoration and forest resilience. Recognizing the long-term human shaping of global biodiversity is key to understanding contemporary and future ecosystems and their restoration.