EMPHASIS Partner Countries
Plant Phenotyping in Austria
The Austrian plant phenotyping landscape covers areas of fundamental and applied plant research. From Arabidopsis to trees – from subcellular phenotyping to shoots and roots. The high-throughput plant phenotyping platform at the VBCF PlantS facility is designed for RGB screening of Arabidopsis and is fully integrated in a state-of-the-art phytotron allowing complex environmental simulations. This system is complemented by deep expertise of GMI in phenotypic data analysis and genome-wide association studies (GWAS). At the BOKU several platforms for manual destructive and non-destructive root phenotyping are established. One of those rhizobox type setups is located in a plant growth cabinet equipped with LED illumination and incorporates a hyperspectral camera. The Core Facility Cell Imaging and -Ultrastructure Research and the Mass Spectrometry LAB of the Dept. of Ecogenomics and Systems Biology (University of Vienna) enable organelle stoichiometric analyses. The department also facilitates several modern plant physiology techniques for instance concerningthe measurement of so-called “SPAC” [Soil-Plant-Atmosphere-Continuum] including “SRI” [Soil Root Interface]. The University of Innsbruck has facilities for imaging chlorophyll fluorescence fromwhole plants to sub-cellular level, which is used in projects associated with mapping stresses in plants, lichens and alga.
The Austrian Plant Phenotyping Network (APPN), established in 2017, is an Austrian network of biologists, breeders, technology developers, imaging experts, statisticians and bioinformaticians working in the field of plant phenotyping.
The APPN aims to unite the Austrian plant phenotyping community in order to facilitate research collaborations, development of plant phenotyping infrastructure and methodologies, staff training, staff exchange and networking activities. The goal is to increase the visibility and impact of plant phenotyping and to facilitate communication between stakeholders in academia, industry, government, and the general public. The APPN is also very well connected with the Czech and Slovak cross-border plant phenotyping community. The initiative intends to support the EMPHASIS project and to reach a legal status by the end of 2017.
Austrian Plant Phenotyping Network (APPN): www.appn.at
For a small European country as Belgium, it has a lot of plant phenotyping research, scientists and facilities. The plant phenotyping installations in Belgium are very diverse. Some are focused on in-field crop phenotyping using remote sensing technology, like drones, or use ground-based crop phenotyping installations. Others have fully automated high-throughput shoot analysis platforms in controlled conditions, or focusing on root phenotyping with hydroponics and rhizotrones. There are research groups that preform low throughput/deep phenotyping on cellular level and groups that investigate pre-& postharvesting of plant organs, like fruits and vegies. But also automated systems to test plant response to pathogens and modelling virtual experiments, crop performance, rootmodelling and ideotyping we can add to the list of plant phenotyping activities in Belgium.
The BPPN aims to increase visibility and impact of plant phenotyping in Belgium, function as a channel for sharing information, provide support for collaborative projects, organize networking activities, facilitate plant phenotyping training and last but not least link the BPPN to Plant Phenotyping community in Europe though EMPHASIS.
With the mindset of "two heads are better than One" Belgian scientists of academia and industry involved in plant phenotyping came together to discuss the formation of a Belgian Plant Phenotyping Network (BPPN) in the first official BPPN meeting on the 12th of October. Plant researchers from University of Gent, Antwerp, Leuven, Louvain-La-Neuve, Liege, Brussels but also plant scientist of Belgian institutes as VIB, ILVO, CRA-W, PCFruit and VITO expressed their interest in such kind of network. Together they decided to form an all-inclusive network where all whom is involved in plant phenotyping in general, in Belgium, can be a member. Thereby they forming a multidisciplinary network of plant biologists, imaging experts, breeders, modellers and technology developers.
Next steps? The BPPN would like to be more formalized and are now in the process of writing a Memorandum of Understanding (i.e representing a ‘written handshake’), want to set up a website and will organize more networking activities in the future. The BPPN actively supports the EMPHASIS-prep project and has the intention to function as a national node for EMPHASIS in the future.
Agricultural Research Institut
Plant Phenotyping in Cyprus
Cyprus is a country-island in the south-east Mediterranean, located in a climate-change hotspot, as identified by a number of respected international climate models. Upon the foundation of the Republic of Cyprus in the early 60s, emphasis was given by the new Government and its International advisors (FAO, USAID, etc.) to the development of the agricultural sector. Consequently, the Agricultural Research Institute (ARI) was founded in 1962 as the first Research Institute in the country according to the best international standards. Since then, ARI plays a key role in developing and applying cutting-edge agricultural technologies and is a global pioneer in the development of novel field phenotyping methods and techniques since the early 2000’s. Specifically, it has been focusing on accurate whole-plant (whole-genome) field phenotyping using novel experimental designs (known as the honeycomb selection designs) at distances excluding interplant competition and minimizing the coefficient of variation of the measured traits. The research focus on field phenotyping has been gradually expanding to encompass the associated soil microbial populations as well, incorporating technologies such as genomics, precision field robotics, sensors, and UAVs.
The Agricultural Research Institute is the main driver of Field Phenotyping research in the country and the sole Institution that directly connects field phenotyping with applied Plant Breeding activities under the drought-prone and climate-challenging Cyprus environment. In addition, ARI stimulates and coordinates relevant research efforts among other research Institutions and Universities in Cyprus, founded at a later stage.
Plant Phenotyping in Czech Republic
Plant phenotyping using non-invasive methods is dynamically developing field of research in the Czech Republic. It represents multidisciplinary approach to assess developmental, growth, physiological and pathological traits of (especially) crop species. It aims to enhance significantly the speed and accuracy of selection processes in plant breeding, agro-chemistry and biotechnology to make plant research more effective. In parallel it offers valuable benefits to academic and applied research in fields of plant physiology, plant stress biology, phytopathology, biotechnology and precise agriculture. Besides the high-throughput screening, it provides also detailed and precise analysis of plant physiological responses in field or controlled conditions.
Centre of the Region Haná for Biotechnological and Agricultural Research, Palacký University in Olomouc (www.cr-hana.eu)
- Development and testing of new plant growth regulators
- Development and implementation of protocols for HTS and large-scale bioassaying
- Field trials and field phenotyping
CEITEC, Masaryk University in Brno (www.ceitec.eu)
- Generating basic knowledge on the molecular mechanisms allowing integration of various signaling pathways
- Development and implementation of technologies to improve plant stress tolerance
- Phenotyping on cellular and tissue level
Photosystems Instruments, s.r.o. (Drásov; www.psi.cz)
- Optics, electronics and software engineering to develop scientific instruments for research in biological and agricultural sciences
- Manufacturing instrumentation for advanced imaging and non-imaging of optical signals in plants and algae
- Development and manufacturing innovative technology for cultivation of plants and for non-invasive complex analysis of various plant traits in fully automated manner
Please describe if possible national networks within your country (structure, governance, )
Czech plant phenotyping network (CzPPN; www.czppn.com) was established in 2017 by two academical institutions (Palacký University in Olomouc and Masaryk University in Brno) and a private company Photosystems Instruments, s.r.o. (Drásov, CZ). CzPPN aims to interconnect particular research infrastructures and their potential users. CzPPN would like to mediate access to these infrastructures for external users with their own research projects. CzPPN enhances formation of wide community of specialists and users of plant phenotyping coming from academia as well as from industry. This way it wants to contribute to implementation and standardization of advanced methods not only in basic, but also in applied and agronomical research in Czech Republic.
University College Dublin
Plant phenotyping in Ireland
Agriculture and the production of food, fodder and timber is a key contribution to the Irish economy. Therefore research directed towards improving grass/fodder, forest, cereal and horticultural crops yields for the dairy, meat, timber, food and brewing industry is a key focus. Due to the unique Irish climate several research groups focus on mitigating plant pathogens and diseases.
SFI is one of our national funders and was very cooperative in helping set up our National Plant Phenotyping Network (PPN-Ireland). They have recently funded several large phenotyping infrastructures, One such example is PICS - Physiology infrastructure for crop stress. €1.2M to UCD (Angela Feechan and Saoirse Tracy) will consist of a high resolution X-ray CT scanner, harvester with NIR analyser, humidity chamber, NO analyser and hyperspectral drone with LIDAR capabilities. PICS will enable biotic and abiotic stresses to be measured simultaneously in the lab and the in the field. A second funded project was Phenomics and future experimental platform, which was funded in 2016. €1.3 M (Jennifer McElwain and Saoirse Tracy). This will consist of state of the art climate controlled growth chambers and a large X-ray CT scanner which is already in place at UCD. UCD is a member of IPPN, so these facilities are available for access to any group globally.
Teagasc the state agriculture and food development authority has a series of research centers distributed across the country. A wide range of crops including; forage, horticultural, combinable, root and forestry are phenotyped across these centers and on commercial farms in controlled environment, glasshouse and field environments. State of the art molecular biology facilities and bioinformatics resources allow the phenotype information to incorporated into breeding programmes using a range of techniques such as marker assisted or genomic selection. The information and resources are utilized either in in-house potato, perennial ryegrass and clover breeding programmes or through collaboration with external breeding programmes.
National Phenotyping Networks
Our National Phenotyping Network is PPN-Ireland. Our committee is made up of members from across the Island of Ireland. We were formally established in June 2016.
Plant Phenotyping in Italy
Plant phenotyping is emerging as a major area of research in plant biology and agriculture in Italy. Among the many research carried out by Italian institutions, the following are highlighted.
A first research area matches genotype selection and breeding with analysis of phenotypic performances, especially under stress conditions. These studies are carried out: i) at the University Alma Mater of Bologna to map and clone QTLs for drought resistance in maize and wheat; ii) at the Marche Polytechnic University to study phenotyping pipelines for the linkage mapping of domestication traits, specifically addressing fruit breeding; iii) at the University of Basilicata and CNR-Agrobios for early identification of stress response (water and nutrients) through application and validation of image analysis for aboveground and root architecture, respectively; iv) at the University Sant’Anna di Pisa and the Institute for Advanced Studies of Lucca, where a new platform for phenotyping rosette-shaped plants (Phenotiki) was developed.
At the Cereal and Industrial Crop Research Centre of the Council for Agriculture (CREA-CI, Foggia), phenotyping for early vigour, a trait useful for Mediterranean type environments (characterized by early winter rainfalls) was carried out on two experimental field trials with bread and durum wheat cultivars. Using Unmanned aerial vehicles (UAVs) strictly higher-resolution images were captured weekly throughout the vegetative phase of wheat, from emergence to stem elongation stage. The soil cover rate of the crop was estimated by a proprietary software developed in house.
At the Foundation Edmund Mach of San Michele all’Adige and at CNR-Institute for Sustainable Plant Protection, the Volatile Compound Facilities allowed direct high-throughput and high-sensitive analysis of volatomes, automatically and non-invasively phenotyping the volatile compound emission (including also semi-volatiles and some plant hormones) of more than 200 plants per day. Research on phenotyping is characterizing activities of several other CNR Institutes.
The X-ray microCT laboratory of the CNR-Institute for agricultural and forest systems in the Mediterranean is carrying out “high resolution” phenotyping of protein-rich seeds, within the Horizon2020 project "Protein2Food" (http://www.protein2food.eu/research-activities/crop-production/). That laboratory is also performing phenotyping of seeds, leaves and stem of hemp plants under the project for the Campania region rural district "Bio-district of Canapa Irpina” (http://www.isafom.cnr.it/index.php/44-news/376-plant-phenotyping-activity-at-x-ray-microct-laboratory-of-cnr-isafom).
The CNR-Institute of Agricultural Biology and Biotechnology has recently been funded a research (Regione Lombardia, project SPHERA, in collaboration with the regional technology park, PTP) to field phenotype cultivars of durum wheat and soybean for useful traits and resistance to abiotic and biotic stresses. Wheat research undertaken by this same CNR Institute also focuses on single seed descent from 150 landraces, stored at the Institute of Biosciences and Bioresources Seed Bank. This material is phenotyped within the flagship project INTEROMICS using the scanalyzer 3-D System (LemnaTec) phenomic platform at Metapontum-AgroBios Research Centre of ALSIA-Basilicata. This same facility, which is used as a hub for most of the phenotyping activities in Italy, including greenhouses, conveyor belts and image chambers allowing observations from various angles; optional filter/sensor in non-visible spectrum (NIR and Fluorescence); and plant weight combined to an accurate water dosage. The facility also provides end-users analysis of nutrients and biostimulants effects, screening of mutants lines and crosses for new phenotypes, and impact of root biomass, root distribution and water uptake (index of plant activity) in water stress resistance.
The Joint Research Unit (JRU) denominated Italian Plant Phenotyping Network (PHEN-ITALY) was established in 2016. The JRU is coordinated by CNR and gathers people and research facilities actively working on plant phenotyping. The main infrastructure is centered on the high throughput phenotyping platform of ALSIA-Metapontum Agrobios and associated CNR Research Unit. Eleven universities and research organizations are members of the JRU, which represents the national node of the preparatory action for the development of the European Infrastructure for Multi-scale Plant Phenotyping And Simulation for Food and Security in Changing Climate (EMPHASIS-PREP).
ALSIA - Agency For Development And Innovation In Agriculture of the Region Basilicata (Metapontum Agrobios)
CNR – National Research Council
CREA -Council for Agricultural Research and Analysis of Agricultural Economics
UNITUS -Tuscia University
UNIVPM -Marche Polytechnic University
UNIBO - ALMA MATER STUDIORUM – University of Bologna
UNIBAS -University of Basilicata
SSUP - Sant'Anna - School of Advanced Studies
IAM-CIHEAM - Mediterranean Agronomic Institute of Bari
UNIBA - University of Bari Aldo Moro
UNIPD - University of Padova
FEM – Foundation Edmund Mach
Prof. Dr. Bogdan Wolko
Plant Phenotyping in Poland
Plant phenotyping in Poland is done at universities and at research institutes belonging to the Polish Academy of Sciences or to the Ministry of Agriculture and Rural Development; large experiments are also performed by breeding and seed companies and by the Research Center for Cultivar Testing (COBORU). A recent survey has shown that phenotyping is carried out mostly by conventional methods. However, Polish plant scientists have successfully participated in EPPN calls for access to image phenotyping platforms, which resulted in a number of high-throughput experiments. Phenotyping is mostly done in projects studying genetic diversity, agrotechnical factors, and plant reactions to biotic or abiotic stresses, and is financed by national and international projects. More than half of survey respondents declared carrying out molecular-level quantitative measurements (of proteins, metabolites etc.) in addition to classical phenotyping with respect to morphological or phenological traits. All respondents expressed the opinion that the level of phenotyping techniques could be improved by international collaboration in this area. There is no formal plant phenotyping network in Poland yet. However, R&D projects involving large-scale phenotyping experiments have been conducted by consortia composed of several tightly collaborating scientific and commercial partners.
Plant Phenotyping in Portugal
The phenotyping technologies used by the PT community are mainly low-throughput methods as there is no automated platform available in Portugal. The access to high-throughput methodologies is essential and has been possible through international collaborative projects. However, several crops/trees relevant for Portuguese agriculture/forestry require specific approaches and/or require the local use of resources, e.g. field robots and remote sensing platforms should be available in our crop fields and orchards. All over the country, Research Centres, Universities and Polytechnic Institutes are active in plant phenotyping, showing the strong engagement of the Portuguese community. The Portuguese scientists present at the meeting reassured their support to the EMPHASIS initiative and aims to get organized in order to actively contribute for EMPHASIS-PREP.
Biological Research Center Jibou
Plant Phenotyping in Romania
In Romania there is a real potential for future growth of phenotyping studies, as many research entities are interested in plant research topics:
Universities: 13 (12 public, 1 private), National Institutes for Research and Development: 9, Research Centers & Stations: 5, Research Groups within commercial sector: 2
However, modern phenotyping is only rarely used in Romania and most of the studies are performed on the frame of international collaborations!
In present phenotypic studies are being conducted at: Biological Research Center Jibou (Interactive effects of drought and salt stress on plant development in potentially salt resistant landraces of tomatoes); Babes-Bolyai University Cluj-Napoca (The research group of Prof. Rackosy Elena is interested in obtaining resistant forms of potatoes using somatic hybridisation); Alexandru Ioan Cuza University, Iasi (The research group is focused on ecotoxicologic evaluation, bio monitoring and bioremediation of quality of environmental factors).
At Biological Research Center Jibou there are the following facilities for phenotyping studies:
- Monitoring PAM Fluorometer for Long-term Monitoring of Photosynthesis
- Open FluorCam System for combined multispectral and kinetic fluorescence imaging
- PAM 2500 High-performance Field and Laboratory Fluorometer
- Fluorometer FL 3500, Sensitive head, P 700 module
- Flow-through WATER-PAMChlorophyll Fluorometer
- LAI-2200C Plant Canopy Analyzer
- ULM 500 Universal Light Meter
- Light Meter VLX – 3W, for PAR measurements
- UVA, UVB meter SpectroSense
- FytoScope FS 130 Growth Chambers
- LI-3000C Portable Leaf Area Meter
The main issues that hinders the development of phenotypic studies in Romania are the lack of predictability in time and amount of the financial support from governmental or private entities.
Future perspectives for development of plant phenotyping in our country could be:
- Raising awareness of the importance of the field among interested ministries (research, education, agriculture and environment)
- Establishment of research clusters around existing poles of knowledge
- Introduction of these techniques on student curriculum
- Facilitation of Romanian researchers access to existing infrastructure abroad
The plant phenotyping landscape in Sweden
In general, high-quality plant growth facilities are available in Sweden, but high-throughput phenotyping equipment is mostly lacking. Several new facilities for plant cultivation and phenotyping have been established in Sweden lately and during the last 2-3 years the universities in Stockholm and the SLU in Alnarp. Others have updated their facilities, especially with LED lights and more advanced cameras and sensors for phenotyping. There is also a recent trend with adaptions to larger plants such as crops and trees in custom-made facilities, whereas, off-the-shelf cabinets for the model plant Arabidopsis have been installed as part of the facility services in many places. As an example of new, advanced climate chambers, the recently inaugurated Biotron at SLU Alnarp (http://www.slu.se/en/faculties/ltv/resurser1/biotron/) lacks high-throughput phenotyping but offers very precise climate and light conditions also for large plants and with some chambers equipped with wavelength adjustable LED lights.
An automated phenotyping platform for GM poplar trees is currently under construction at the Umeå Plant Science Centre (UPSC) and will be ready by 2018. The facility will have space for 280 trees that circulate on a conveyor belt and are fully monitored regularly (growth, leaf area, possibly equipped with IR camera and fluorescence and/or multispectral scanner).
Several efforts are ongoing to improve field phenotyping efforts in Sweden including manipulations in field. For example, the nationally coordinated infrastructure SITES (www.fieldsites.se) is currently investing in new drones and imaging equipment for their field stations. In field studies, remote sensing with UAVs and satellite images are becoming increasingly popular for use in agriculture due to reduced costs of obtaining the data and availability of software for analysis. Low cost commercial drones can be mounted with various cameras such as RGB, NDVI or multispectral sensors. The RGB cameras are the most affordable option albeit with some limitations compared to other sensors. The images from drones can be processed in the open source software opendronemap (www.opendronemap.org) or other commercial software. Using satellite images from Sweden (or other countries), CropSAT (www.cropsat.se) quantifies the variation in the biomass for a given area. This data can be freely downloaded from the website to the on-farm equipment for variable spraying of fertilizer in the field. Thus, low cost phenotyping both in the controlled conditions and in the field is a promising resource for effective analysis of agronomic traits in crops grown in Sweden or elsewhere.
Sweden participates also in relevant networks such as the Nordic Plant Phenotyping Network (NPPN), which facilitates collaboration between academy and industry (technology providers, breeding companies) within plant phenotyping. In addition, Sweden participates in the NOVA network grant for PhD training, ”Phenotyping technologies in plant-environment interactions”.
Plant Phenotyping in Switzerland
The focus of Agroscope’s plant phenotyping activities is the functional characterization of germplasm of the main crops cultivated in Switzerland. Our research aims at the identification of genotypes which are adapted to our soil and our climate, are resistant to disease and support an environmentally sound production of high-quality plant products for human consumption or for feed for livestock. It also seeks to meet the numerous quality criteria required by the market, the development of an increasingly healthier diet, and to increase the efficiency of food chains and the sustainability of agricultural systems.
At the moment our phenotyping activities rely on the conventional assessments that Agroscope has been doing for several decades and also UAVs equipped with RGB, multispectral (red, green, near IR), and thermal infrared (7.5-13.5 µm) cameras. We recently got funds for a hyperspectral camera (475-875 nm) that we already ordered and we expect to start using it during the advanced growth stages of summer crops and for the 2017-2018 season of winter crops. We also started the construction of a small portable cart to carry sensors for proximal sensing. The sensors used with the cart include the same sensors that we use with the UAVs and also thermometers, and cameras for 3D reconstructions (time of flight and stereo technologies).
Our plant phenotyping activities during the next two years will be conducted in the frame of the following main projects:
- Evaluations of varieties and production techniques: https://www.agroscope.admin.ch/agroscope/de/home/themen/pflanzenbau/ackerbau/forschungsprojekte/sorten-anbautechnik.html
- Evaluation of performance and quality of genotypes and field crops with tools of the digital economy (Internal strategic project of Agroscope).
- SOLACE: Horizon 2020 EU project from 2018 to 2022.
Currently there is no national plant phenotyping network. The most similar to a national network are the experimental networks of Agroscope that cover the entire Swiss territory.