PlantHUB Project Descriptions

Mercedes Thieme

Exploiting genetic variation in barley for crop quality improvement

Advisor: Prof. Samuel Zeeman, ETH Zurich

Barley (Hordeum vulgare L.) is one of the major world crops and is used not only for feed purposes but also as a raw material for brewing beer. In particular, storage starch from barley seeds functions as a carbohydrate source for the yeast to produce alcohol. Starch is stored in discrete, semi-crystalline, water-insoluble granules, which differ in shape and size depending on the botanical origin. Barley shows a bimodal distribution of starch granules, where small, spherical shaped granules (ø 1 – 8 µm) account for 80 – 90% of the total starch granule number, but for only 10 – 15% of the starch weight. Accordingly, the large, lenticular granules (ø 8 – 25 µm) account just for a small amount of the total starch granule count but contribute most to the total starch weight. While comprehensive knowledge about the chemical composition of starch and the enzymes involved in its synthesis already exists, we are still lacking the explanation of how granule initiation occurs, how the ratio of differently shaped and sized granules is determined, and how their semi-crystalline order is established. Using genetics, I am looking for a connection between phenotypes with altered granule properties and the underlying genotype. Genome-wide association studies will enable me to identify molecular markers associated with specific starch granule characteristics in field-grown material from different seasons. Further, I will search for novel lines with improved starch granule characteristics in chemically induced mutant populations. This project will provide fundamental insights into the factors controlling starch granule size, shape and properties - knowledge that can be used to improve crop quality. My industrial partner, Carlsberg Research Laboratory, provides facilities and expertise in barley breeding and trait development. Here the aim will be to introduce new traits to improve commercial barley cultivars.

Industry Partner:

Dr. Ilka Braumann, expert in trait development and pre-breeding related to improving plant stability, climate tolerance and starch quality in barley.

Dr. Cuesta-Seijo, expert in activity measurements of starch biosynthetic enzymes, structure analysis of storage carbohydrate

The Carlsberg Laboratory in Copenhagen (Denmark) was created in 1875 and is owned by the Danish Carlsberg brewery. The founding father of the Carlsberg brewery and laboratory - J.C. Jacobsen – supported science in chemistry and physiology, especially relating to brewing. In the past, it featured a Department of Chemistry and a Department of Physiology. Nowadays, the laboratory has four research platform focusing on “Raw Materials” like barley, “Yeast and Fermentation”, “New Ingredients” and “Brewing Science and Technology”. Research results in raw materials platform are applied through Carlsberg’s own breeding efforts.

Anton Hochmuth

Using advanced imaging and profiling technologies to map starch biosynthesis in barley endosperm

Advisor:  Prof. Samuel Zeemann, ETH Zurich

Starch is the most important source of carbohydrates in human diet and a major component of livestock feed. Additionally, there are many applications for starch in industrial processes like brewing and papermaking. As a consequence, the demand for suitable starch is constantly increasing. Starch it is extracted from many different plants and tissues, like tubers (e.g. potato) or seeds (e.g. cereals). This so called storage starch takes the form of insoluble, semi-crystalline granules which differ in shape, size distribution and functional properties between plant species. Even though the chemical composition of starch granules and the enzymes involved in their biosynthesis are known, we still lack the explanation of how granules are initiated and grow to yield the diversity of shapes found in nature. My research project focuses on starch biogenesis in barley endosperm. Barley has two types of starch granules – small (ø 1-8µm) and large ones (ø 8-25µm). Their bimodal distribution and spherical (small) to lenticular (large) shape is well characterised, but the underlying mechanism explaining how the two types of granules form has not yet been resolved. With X-ray microtomography, I expect to see the initiation time points for small and large granules in different parts or the endosperm across developmental stages. This will allow us to reconstruct a 3D model of the barley endosperm. That knowledge will guide me in other methods to display the spatio-temporal gene network and proteome profiles in regions of interest at different developmental stages. This project provides fundamental knowledge and is linked to the great interest of my industrial partner Carlsberg Research Laboratory to improve starch quality and quantity in a staple crop. Their facilities and expertise in breeding and trait development – practically applied to the knowledge I gain about starch granule development – may result in new, improved commercial barley cultivars

Industry Partner: 

Dr. Ilka Braumann, expert in trait development and pre-breeding related to improving plant stability, climate tolerance and starch quality in barley.

Dr. Cuesta-Seijo, expert in activity measurements of starch biosynthetic enzymes, structure analysis of storage carbohydrate

The Carlsberg Laboratory in Copenhagen (Denmark) was created in 1875 and is owned by the Danish Carlsberg brewery. The founding father of the Carlsberg brewery and laboratory - J.C. Jacobsen – supported science in chemistry and physiology, especially relating to brewing. In the past, it featured a Department of Chemistry and a Department of Physiology. Nowadays, the laboratory has four research platform focusing on “Raw Materials” like barley, “Yeast and Fermentation”, “New Ingredients” and “Brewing Science and Technology”. Research results in raw materials platform are applied through Carlsberg’s own breeding efforts.

Claudio Cropano

Self-fertility for powerful grass hybrids

Advisors: Prof. Bruno Studer, Dr. Chloe Manzanares, ETH Zurich

Forages provide to a high percentage the feed energy consumed by ruminants and are important resources for sustainable energy and biomass production. Among forage crops, the obligate allogamous grass Lolium perenne, also known as perennial ryegrass, is one of the world´s most economically valuable grass species. In addition, L. perenne represents, as turf grass, an essential component of perennial grasslands used for landscape architecture, sport fields and soil protection. The outcrossing nature of perennial ryegrass is caused by self-incompatibility (SI) an evolutionary mechanism preventing self-pollination, shared by more than half of the angiosperms and by other forage grass species. In breeding programs, SI can be used as a tool to promote crosspollination and genetic diversity but it also represents a constraint for the creation of inbred lines for hybrid breeding. Although highly effective in preventing inbreeding, SI can be overcome, either by exploitation of non-functional alleles at genes determining the initial pollen-stigma self-recognition or mutations on the downstream cascade leading to self-fertility (SF). Indeed, SF has been found in several self-incompatible forage grass species, such as L. perenne, but its genetic and molecular basis remain to be characterized. My project aims at unravelling the genetics behind SF in L. perenne and the evaluation of hybrids of this grass for breeding. A more detailed knowledge on the mechanism underlying SF will facilitate its introgression into advanced breeding germplasm and allow the development of inbred parental lines to create powerful grass hybrids.

Deutsche Saatveredelung AG actively contributes to the project by providing breeding material that allows genetic characterization of novel SF sources. In addition, DSV plays a crucial role for the design and the evaluation of a hybrid breeding strategy that exploits the introgression of SF sources in breeding germplasm.

Industry Partner:

Nic Boerboom, Junior Breeder Forage Crops

Deutsche Saatveredelung AG (DSV) is an international plant breeding company with headquarters in Germany. For over 90 years, DSV has focused on the breeding and the production of forage and turf grasses, oilseeds, clovers, cover crops, cereals and maize. Every year, DSV sells 51,000 tons of top-quality seeds to farmers all around the world. DSV has a 600-strong workforce, and thanks to its subsidiaries in Denmark, Great Britain, France, the Netherlands, Poland, Ukraine and through its shareholdings, marketing organizations and partners worldwide, maintains a global presence and a solid position in the market.

Maximilian Vogt

Exploiting reproductive traits for hybrid breeding in grasses

Advisors:  Prof. Bruno Studer, Dr. Timothy Sykes, ETH Zurich

Perennial ryegrass (Lolium perenne L.) is widely used for forage production in both permanent and temporary grassland systems. To increase yields in perennial ryegrass by fixation of heterotic patterns, an effective and reliable hybrid breeding strategy is needed. Cytoplasmic male sterility (CMS) is a widely applied mechanism to control pollination for commercial hybrid seed production. In breeding programs, CMS is a valuable tool to control pollination direction, but it can also be a constraint as maintaining the trait in breeding populations can be difficult. The identification of the genetic control as well as the underlying molecular mechanisms involved would enable better control of the CMS trait in breeding programs. In cooperation with Deutsche Saatveredelung and its affiliated entity Norddeutsche-Pflanzenzucht, a segregating population of perennial ryegrass will be screened in order to identify molecular markers linked to restorer of fertility (Rf) genes. In addition, interspecies crosses will be conducted for the introgression of nonfunctional restorer genes (maintainers) to maintain CMS in L. perenne and L. multiflorum (Italian ryegrass). To further investigate the mechanisms underlying the restoration of fertility in CMS affected plants, a  population of perennial ryegrass will be generated, which compiles all features for molecular genetic research. Molecular and cytogenetic approaches in combination with in silico computing of sequence information will be used to decipher restoration on a cytogenetic level. The main accomplishments for this project will be the identification of gene(s) or loci responsible for restoration of fertility, as well as the design of a multi-parent breeding population to characterize heterotic patterns for improved breeding.

Industry Partner:

Michael Koch DSV

Deutsche Saatveredelung AG (DSV) is an international plant breeding company with headquarters in Germany. For over 90 years, DSV has focused on the breeding and the production of forage and turf grasses, oilseeds, clovers, cover crops, cereals and maize. Every year, DSV sells 51,000 tons of top-quality seeds to farmers all around the world. DSV has a 600-strong workforce, and thanks to its subsidiaries in Denmark, Great Britain, France, the Netherlands, Poland, Ukraine and through its shareholdings, marketing organizations and partners worldwide, maintains a global presence and a solid position in the market.

Giacomo Potente

Efficient capturing and third-generation sequencing of complex genomic regions

Advisors: Prof. Elena Conti, Dr. Péter Szövényi, University of Zurich

One of the most intriguing breeding systems that flowering plants have evolved is heterostyly. Heterostyly is a floral syndrome consisting of two main characteristics: (a) reciprocal herkogamy, i.e. the presence, within the same species, of two (distyly) or three (tristyly) floral morphs in which stigmas and anthers are reciprocally positioned, and (b) a self- and intra-morph incompatibility system. Altogether, these two features favor inter-morph crosses, thus promoting outcrossing and so limiting inbreeding. Since Darwin, the genus Primula has been a model for the study of distyly and, since the early 20th century, it has been known that this floral syndrome is controlled by few genes tightly linked together to form a supergene (the so-called S-locus). However, recent studies based on high-throughput DNA sequencing have challenged the dominant hypothesis on how the S-locus controls the different morphs, showing the importance of genomic studies for understanding how heterostyly is controlled by the S-locus. Nevertheless, genomic resources for heterostylous species are scarce. The aim of my PhD is to gain a better understanding of how heterostyly is controlled, from a genetic point of view, by the S-locus, using Primula veris, a distylous species, as a model. The first step to achieve this goal will be to get a high-quality genome assembly for P. veris. This will be achieved by using a combination of third-generation sequencing technologies, physical mapping (Hi-C and/or optical mapping) and linkage mapping. Subsequently, I will focus my attention on developing a method for efficiently capturing and sequencing long DNA fragments, with the purpose of applying this technique to target the S-locus of other Primulaceae species. Finally, I will perform functional genetics experiments to disentangle how heterostyly is genetically controlled by the S-locus.

I will spend half of my PhD at the University of Zurich and half in Leiden (Netherlands), at BaseClear BV., a company that offers DNA and RNA sequencing services, as well as downstream data analysis and interpretation. There, I will have the chance to use cutting-edge sequencing technologies, such as the Oxford Nanopore Technologies GridION, and to be supported by experts in the fields of molecular biology and bioinformatics, both during the sequencing of the Primula veris genome and while developing a method for targeted sequencing of long DNA regions. Moreover, during the three years of my PhD I will spend six months at the University of Potsdam (Germany), in Prof. Michael Lenhard’s lab, whose main research field is the molecular basis of organ-size control in plants. In Prof. Lenhard’s lab I will perform some functional genetics studies aimed at better understanding how the different genes in the S-locus control the development of the floral organs in the two morphs.

Industry Partner:

Dr. Danny Duijsings, Head of research and development

BaseClear BV. is an independent service laboratory for DNA-based research. Since it’s foundation in 1993 BaseClear BV. offers high quality DNA and RNA sequencing and bioinformatic solutions. BaseClear BV., with its team of more than 50 specialists, has extensive experience in Next Generation Sequencing having state-of-the-art sequencing platforms from Illumina and PacBio at its disposal and exploring more recent technologies such as Oxford Nanopore.  Furthermore, BaseClear BV. has a dedicated R&D department involved in various research projects including eDNA research, microbial metagenomics and plant genomics.

Secondment Partner:

Prof. Michael Lenhard, University of Potsdam

Seydina Issa Diop

Large-scale isolation and sequencing of full chromosomes

Advisors: Prof. Elena Conti, Dr. Péter Szövényi, University of Zurich

Although techniques for the separation of complete chromosomes exist it is time consuming, expensive and is not generally applicable for a wide range of organisms. Nevertheless, diseases or important phenotypic traits are linked to special chromosomes which separation and sequencing would be highly beneficial. We propose to establish a technology to specifically sequence the chromosomes of interest by conducting targeted capturing and/or sequencing of sex chromosomes. Genome sequencing will be done by using PacBio`s long-reads technology and Oxford Nanopore`s single molecule sequencing. The proposed workflow is yet not available for either of the sequencing technologies and is full of technical challenges that must be solved. As a model system we will use the liverwort, Marchantia polymorpha, which offers many benefits and enable us to investigate various questions related to the sex chromosome evolution in a haploid-dominant system. The sex chromosomes of M. polymorpha can be easily isolated because sex is expressed in the dominant haploid phase, and males and females bear either a Y or an X chromosome. The objectives of my research project are (1) to establish a methodology to specifically capture and/or sequence large fragments of specific chromosomes, (2) to sequence selected regions by synthesis and by single molecule sequencing, and (3) to obtain a full resolution of the complex sequence of plant sex chromosomes in a haploid-dominant plant system and reveal their mode of evolution.

Expected Results:

  • Establish a methodology to specifically target selected regions of sex chromosomes
  • Functional analysis of sex chromosome linked genes and their evolutionary trajectories
  • Isolation of specific chromosomes of complex genomes will allow direct sequencing of the selected regions by synthesis and by single molecule sequencing – the work flow will be offered by BaseClear BV. as a service

Full resolution of the complex sequence of plant sex chromosomes in a haploid-dominant plant system

Industry Partner:

Dr. Danny Duijsings, Head of research and development

BaseClear BV. is an independent service laboratory for DNA-based research. Since it’s foundation in 1993 BaseClear BV. offers high quality DNA and RNA sequencing and bioinformatic solutions. BaseClear BV., with its team of more than 50 specialists, has extensive experience in Next Generation Sequencing having state-of-the-art sequencing platforms from Illumina and PacBio at its disposal and exploring more recent technologies such as Oxford Nanopore.  Furthermore, BaseClear BV. has a dedicated R&D department involved in various research projects including eDNA research, microbial metagenomics and plant genomics.  

Secondment Partner:

Prof. Michael Lenhard, University of Potsdam

Aya Yokota

Integrating hyperspectral imaging into phenomic applications for plant stress assays

Advisor: PD Dr. Diana Santelia, University of Zurich

As the climate change threat grows, the interest in plant responses to the fluctuating environmental conditions increases. Plants are subjected to various abiotic stresses where drought is one of our major concerns. Water is essential for any biological activity and its scarcity is one major limitation for plant productivity. At cellular level, water scarcity causes efflux of water from the cytosol leading to the loss of turgor and impaired plant growth. Recent studies have provided new insights into the mechanisms of plant drought stress tolerance. This mechanism is mediated by starch degradation, in a abscisic acid (ABA)-dependent manner. Starch degradation leads to the accumulation of “osmolites” in the leaves which can be transported to the root. There they will lower the internal osmotic potential and facilitate water uptake from the soil. Starch is an insoluble granule well known for its nutritive values contained in many staple crops. As a carbohydrate source for plants, starch is also present in the leaf in a transitory form. It is accumulating during the day and degraded during the night to sustain heterotrophic metabolism when the photosynthesis doesn’t occur. It is now known that starch can be also metabolized during the day to mediate drought stress tolerance. In agriculture production, the demands on high-yield crops especially under stressed conditions are increasing. Using tomato (S. lycopersicum) as an economically valuable plant, in my project we will explore the conservation of drought stress tolerance mediated by starch metabolism. For an efficient identification of relevant crop traits, phenotyping systems are required. One emerging and promising phenotyping method is based on optical and non-invasive sensors. Using hyperspectral imaging it is possible to follow the whole life cycle of a single plant and estimate its content in different plant molecular structures, such as water or starch. My project aims 1) to validate key components for starch degradation regulation in response drought stress 2) to integrate phenotyping systems for an efficient identification of high-yield crops suitable to future climate and 3) to deliver optimized hyperspectral imaging system and appropriate image processing in collaboration with the company LemnaTec.

Industry Partner: 

Dr. Marcus Jansen, Chief Scientist, Biologist

For 20 years, LemnaTec GmbH has been specialized in developing plant phenotyping methods, which includes hard- and software together with application solutions for plant phenotyping. This non-invasive approach allows the measurement of phenotypic plant properties.

Franco Conci

Plant phenotyping to understand mechanisms of salinity tolerance

Advisor: PD Dr. Diana Santelia, University of Zurich

Soil salinization is one of the most concerning forms of soil degradation, affecting increasing portions of Europe’s irrigated lands. Natural soil weathering, climate change and farming policies are predicted to spread the occurrence of saline soils worldwide. High salinity affects normal plant growth by increasing transpiration and decreasing water use efficiency. The study of plant salinity tolerance has been hindered in the past by the lack of reliable known traits. In this project, I will investigate the possibility of using thermal imaging quantification of plant transpiration for salt stress detection. The amount of transpiration in plants is regulated by stomatal aperture. Stomata are able to open and close in response to external stimuli by accumulating or releasing osmotically active molecules, such as inorganic and organic ions and sugars, as osmolytes in the vacuoles of guard cells. The morphology of guard cells changes in response to the variation in vacuole turgor, enabling stomatal movement. One of the first responses to salt stress in plants is stomatal closure to prevent water loss through transpiration. A better understanding of the stomatal regulation in plants under salt stress may provide insight on the mechanism of salinity tolerance. During this project, I will investigate the role of sugars as osmolytes in salinity tolerance through molecular characterization and thermal imaging phenotyping of Arabidopsis thaliana. The focus is set on monosaccharide fluxes across the plasma and vacuolar membranes, involving several transporters as well as sugar hydrolyzing enzymes. The contribution of each candidate will be assessed and quantified at the molecular level. A crucial step for identification of suitable candidate genes will be the correlation of gene expression patterns with stomatal response to salt stress. Gas exchange variations will be quantified in single- and multiple knock-out (K.O.) mutants using infra-red gas analyzers. Thermal imaging protocols for salt stress detection and quantification will be developed in collaboration with the company LemnaTec GmbH. Contribution of the candidate genes to the mechanism of salinity tolerance will be assessed and quantified through thermal imaging of single- and multiple K.O. mutants, and supported by complementary molecular experiments.

Industry Partner:

Dr. Marcus Jansen, Chief Scientist, Biologist

For 20 years, LemnaTec GmbH has been specialized in developing plant phenotyping methods, which includes hard- and software together with application solutions for plant phenotyping. This non-invasive approach allows the measurement of phenotypic plant properties.

Secondment Partner: 

Prof. Ulrich Schaffrath, RWTH Aachen

Camilo Chiang

Dynamic control system for multi-channel LED illumination systems to enable near-natural plant growth

Advisor: PD Dr. Günter Hoch, University of Basel

Since horticultural LED technology evolves rapidly and becomes more and more economical, an increasing number of growth facilities are installing LED grow light as replacement for HPS lamps. Current LED light systems cannot reproduce the full sun spectrum effect, in sufficient radiative strength. The large choice in LED systems and the option to dim individual channels in a multi-channel system results in an immense variety of different spectra to be used. If LED lightning systems are used in research growth facility, this difference in spectral composition poses a significant challenge for the comparability of observations in plants grown in different LED indoor chambers. This is especially true since an universally agreed-on standard spectrum for LED plant growth chambers is currently missing. Within this project we aim to develop optimized setups for different LED systems (differing in number and quality of single spectra LEDs) to enable near-natural plant growth in LED-lit growth facilities. This will be achieved by comparing growth and functional traits in different plant species grown in the field with the same set of species exposed to exactly the same climate in computer controlled LED-lit growth chambers. By changing the LED light spectra within the growth chambers, LED setups that reveal the most natural plant performance can be identified.

Based on the findings from these experiments will expect the following final results:

  • A common protocol for reporting light conditions of LED-systems in research growth facilities to enable a better comparability of light conditions among different LED-based growth chambers.
  • A LED light controller or software tool to calculate and report the optimal mixture of individual wavelength-channels (within the limitation of the specific lamp type) to enable a growth chamber illumination for natural-like plant growth and development.
  • A marketable lightning system that integrates this software.

Industry Partner: 

Daniel Bankestad, R&D Project leader

Johan Lindqvist, R&D Engineer

Heliospectra AB (publ – listed on Nasdaq OMX First North; headquarter in Gothenburg, Sweden) was founded in 2006 and specializes in intelligent lighting technology for plant research, greenhouse cultivation and controlled environment agriculture. The company produce several models of LED lamps with different levels of functionality. For example, the research model has up to 9 individually controlled types of diodes. Software and hardware for precise control of the lighting is also part of the product portfolio. Further on, smart control based on sensor feedback is being developed. Saving energy and improving crop quality are the main objectives behind the Heliospectra lighting systems.

Florian Cueni

Dynamic isotope model to trace the geographical origin of agricultural products

Advisor: Prof. Ansgar Kahmen, University of Basel

Consumers are paying increasing attention to the geographic origin of agricultural products. Analytical tools that allow to independently verify the geographical origin of a product are thus in high demand for food quality control. Stable oxygen and hydrogen isotopes in plants change with longitude and latitude and show an annual variability. Several tools using stable isotopes for origin analysis already exist and are used in private or government-operated food quality control laboratories. Most of these tools are based on agricultural reference materials with known geographic origin, compromising their precision and universal applicability. By employing mechanistic meteorological and plant physiological models the general applicability should be improved. The objective of my research project is to develop a new web-based interface that allows probability estimates of the geographic origin of plant derived organic material with increased precision and improved general applicability. This new tool will be based on dynamic seasonal and inter-annual variability in the oxygen and hydrogen isotope composition of precipitation,and species specific and climate (temperature and relative humidity) depended modifications that apply when the oxygen and hydrogen isotope signal of precipitation is imprinted into plant organic material.

Expected Results:

  • A better mechanistic understanding on what drives the stable oxygen and hydrogen isotope composition in agricultural plants.
  • A new spatial model that accounts for seasonal and inter-annual variability in weather and species-specific isotope effects and will allow the simulation of the oxygen and hydrogen isotope composition of plant materials with increased precision.

Together with Agroisolab GmbH a web-based interface will be developed, based on simulations with the new dynamic isotope model and probability density functions, the likelihood of geographic origin of a given sample can be estimated with much improved accuracy - serving the needs of consumers and industry to validate the origin of agricultural products.

Industry Partner: 

Dr. Markus Boner, Managing Majority Partner, Food Chemist

The Agroisolab GmbH is one of the leading laboratories for isotope analytics in Europe. They have an outstanding field of competence in the area of declaration and origin testing, source monitoring organic material of any kind, in particular applying to food products and agricultural raw materials. Services include application-focused services, products, research and development around the stable isotope analytics tailored especially to our customer's needs. They offer comprehensive information and competent service concerning all application possibilities in the field of isotope analytics.