EMPHASIS Partner Countries


 EMPHASIS-PREP Policy Manifesto

The EMPHASIS infrastructure is based on previously established national infrastructures in Germany, France, the United Kingdom and Belgium.

 Since its inclusion in the ESFRI Roadmap 2016, EMPHASIS has supported

  • the financing of plant phenotyping infrastructures through national/regional funding mechanisms,
  • applications for inclusion in the national infrastructure roadmap,
  • several initiatives that have been formed to establish plant phenotyping at national level.

In addition, several countries are in the process of initiating their national activities and are integrated into the EMPHASIS Council.

 

 


Contact: Jakub Jez
Vienna Biocenter Core Facilities GmbH (VBCF)
jakub.jez@vbcf.ac.at
(+43) 1 7962324 7090

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.

National networks

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

Key institutions

VBCF

Gregor Mendel Institute of Molecular Plant Biology

University of Vienna, Ecogenomics and Systems Biology

Department of Crop Sciences (BOKU)

Department of Forest- and Soil Sciences (BOKU)

University of Innsbruck, Institute of Botany

Austrian Agency for Health and Food Safety (AGES)

 

 

Contact person

Country profile

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.

Dora Chimonidou
Agricultural Research Institut

dari@ari.gov.cy

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.

Key institutions

Agriculture Research Institute

The Cypris Institute

University of Cyprus

Cyprus University of Technology

 

Contact person:

Lukáš Spíchal
Centre of the Region Haná for Biotechnological and Agricultural Research, Palacký University in Olomouc

lukas.spichal@upol.cz

 

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.

Key institutions

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.

 

Svend Christensen
University of Copenhagen
svc@plen.ku.dk
(+45) 51 48 94 21

Carl-Otto Ottosen
Aarhus Univrsity

coo@food.au.dk(+45) 22903105

Country profile

The research activities in Dept of Food Science, Aarhus University in phenotyping is focussed on deep physiological phenotyping using state of art photosynthesis and chlorophyll fluorescence most in relation to heat stress or combinations of stresses and elevated CO2 on several field crops. We are are part of the EPPN2020 with the facility DynaPheno providing access to combinations of high tech greenhouses, drought spotters for water and nutrient management and a temporary non functional Planteye for 3D analysis. By November 2019 we move to a new location near Aarhus with state of art greenhouses and climate chambers.

 

 

 Kristiina Himanen
University of Helsinki
kristiina.himanen@helsinki.fi
(+358) 294157944

 Country profile

 Contact person:

Francois Tardieu

INRA

tardieu@supagro.inra.fr

Plant Phenotyping in France

Author: Francois Tardieu

https://www.phenome-fppn.fr/phenome_eng/

Phenome-EMPHASIS develops a versatile, high-throughput infrastructure and a suite of methods for characterising hundreds of genotypes of different species under environmental scenarios of climate changes (e.g. drought, high CO2, high temperatures). The infrastructure consists of (1) four installations in controlled conditions (capacity of >1000 plants each) for in-depth analysis of leaf or root system under ranges of water deficits, CO2 concentration, temperature or biotic interactions (in Montpellier, Dijon, Toulouse and Angers); (2) two field platforms with semi-controlled environments, in particular large rainout-shelters and one free-air carbon enrichment (FACE) system (capacity 800 plots each, in Clermont Ferrand and Blois); (3) three field platforms with higher throughputs (capacity 2000 plots each, in Dijon, Toulouse and Montpellier) for evaluation in normal field conditions. All installations can manipulate and/or control environmental conditions in order to identify well-characterised scenarios. Platforms are equipped with a consistent set of 3D functional imaging techniques, namely detailed imaging of roots and shoots in controlled conditions, canopy imaging with an autonomous 'phenomobile' that captures functional and 3D images of each plot, and drones that image hundreds of plots jointly. Two supporting platforms centralise metabolomic and structural measurements for phenotyping experiments.

Fig. 1. Typical installations and equipment. (i) Rainout shelters near Blois (Arvalis). (ii) Phenomobile equipped with multispectral cameras and LiDARS (Toulouse), (iii) controlled condition platform for measuring architecture, radiation use efficiency and stomatal conductance (Montpellier) (iv) Root imaging (1000s plants, Dijon). (v) Early detection of disease symptoms via fluorescence (Angers)

Phenome-EMPHASIS offers four categories of services at national level (i) A centralized web access, which describes each installation and provides templates for access, (ii) a common information system, progressively deployed in all nodes, which organises phenotypic data for open, joint analyses across installations (FAIR requirements). (iii) Common vectors (e.g. phenomobiles, drones), common imaging device and pipe lines of analysis, for both controlled and field conditions, (iv) Statistical applications for handling large phenomic datasets. These methods and techniques are transferred towards a wide plant community, academic and industrial.

Fig. 2. Methods developed at infrastructure level (i) 3D imaging of a wheat microplot, (ii) virtual canopy made of 3D plants for calculating light interception, (iii) information system for field and platform data, (iv) On line application for outlier identification

Phenome-EMPHASIS involves INRA, Arvalis and Terres Inovia. It is funded till 2023, and is listed on the French roadmap for strategic infrastructures. It is managed by an executive committee, has an institutional board, a scientific advisory board and an industrial advisory board. It organises meetings for a wide community of stakeholders in addition to consortium meetings.

 Contact person:

Uli Schurr
Forschungszentrum Jülich

u.schurr@fz-juelich.de

Phenotyping in Germany

Progress in plant and agricultural research is a prerequisite for solving some grand challenges on the global scale in particular to guarantee higher crop yields and plants that are optimized for higher resistance and to cope with environmental stresses. In recent years progress had been made in all relevant scientific topics in plants and plant breeding, leaving plant phenotyping as the major bottleneck. In particular better systematic measurements and high throughput measurements of relevant plant-phenotypes under defined environmental conditions covering from lab to field is a key requirement to bridge the gap between genome an phenome.

Therefore, the federal government sponsored the initiation of the German Plant-Phenotyping Network in 2013 with a significant funding of approx. 36 Mio. Euros. In this network the most relevant key players merged their efforts in order to develop user-oriented and demand driven developments for modern plant phenotyping (technologies and facilities) in a constant dialogue with users from academia and industry. The three partners of this network are the Research Center Jülich (coordination), the Leibnitz Institute of Plant Genetics and Crop Plant Research (IPK) Gatersleben and Helmholtz Center Munich (HMGU) – all bringing in a unique but complementary expertise in both: plant phenotyping science and methodological and technological competences. The wide range of competences of Jülich in developing and operation of phenotyping technologies including in Eco-Physiology and screening is supplemented by the unique competences of Gatersleben (plant gene banking and genetics) and Munich (plant pathology). All sites provide outstanding competences in bioinformatics and data management.

The target of the DPPN project is the development of phenotyping infrastructures and concepts in a dialogue with potential academic and industrial users including technology developers. The scientific validation of the methods and technologies developed in DPPN is via access to those facilities in projects (in particular national, European or global projects). Currently access is provided by the participating centers of DPPN upon user inquiry directly at the respective DPPN sites. After the end of the project phase in 2019 DPPN will be sustained as a non-profit association (DPPN e.V.). So the DPPN-partners will also will stay under one roof in order to foster German plant phenotyping a concerted manner. In general, DPPN was initiated to be open for other relevant German institutions to join in, since there are more competences in plant phenotyping in Germany (in particular the Julius Kühn Institutes, but also at several universities, like e.g. Hochschule Osnabrück, University Hohenheim and University Bonn). However, these other potential players in Germany have not been integrated into the DPPN project but will be able to join an extended German network that will be implemented during the preparatory phase of EMPHASIS.

DPPN (German Phenotyping Network)

The Partners of DPPN are  FZJ (Forschungszentrum Jülich, Plant Sciences IBG-2), IPK (Leibniz Institute of Plant Genetics and Crop Plant Research),  and HMGU (Helmholtzzentrum München, German Research Center for Environmental Health).

 

 

Contact person:

Dr. Panagiotis Kalaitzis

panagiot@maich.gr

 

Sónia Negrão

University College Dublin

sonia.negrao@ucd.ie

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.

Contact person

Moshelion Menachem
E-mail: menachem.moshelion@mail.huji.ac.il

Country profile

 

Contact person

Plant Phenotyping in Italy

Website: http://www.phen-italy.it/

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.

National networks

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).

 Key institutions

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

Primary contact:

 Rick van de Zedde, Wageningen University & Research, rick.vandezedde@wur.nl, +31 31 317 480156

Country profile:

 Key partners:

  1. Wageningen University (WU) / Wageningen Research (WR) (www.phenomics.nl)
  2. University Utrecht ( https://www.uu.nl/en/organisation/department-of-biology)
  3. NIOO-KNAW (https://nioo.knaw.nl/en)
  4. Nijmegen ( http://www.ru.nl/plantecology)
  5. UvA (http://sils.uva.nl)

 Plant Phenotyping in The Netherlands

Phenomics NLResearch groups at the key partners are currently studying the behaviour of plants at different levels: from model and individual plants to the growth of crops in climate rooms, greenhouses and on the field. Combining all knowledge, expertise and facilities on plant phenomics into one single national platform, named PhenomicsNL - the Dutch Plant Phenotyping Network - will speed up developments. A targeted Scopus analysis in the period 2011-2016 on key words ‘plant*’ and ‘phenotyp*’ shows that WU has a leading position with 262 publications in The Netherlands, 4th in the EU and 6th world-wide. 

 

   The partners have established several public-private partnerships and has been a partner in notable European initiatives such as SPICY,

Phenomen-ALL and the European Plant Phenotyping Network (EPPN). And also in new programmes/ on-going initiatives, WR is partner in this ESFRI project EMPHASIS-PREP, member in the International Plant Phenotyping Network (IPPN) and in the on-going EPPN2020 in which WU offers transnational access to its existing climate-room based plant phenotyping facility ‘Phenovator’.

On the other hand is WR involved in several public-private partnership projects in which phenotyping technology is developed/ exploited:

Disease detection module                     

Left: Disease detection module, with 3D TOF and hyperspectral imaging cameras, designed to be placed in front of a tractor for field phenotyping, designed specifically to detect potato plants on field infected with diseases.

Mid: An Unmanned Aerial Vehicle (UAV) with an advanced 3D LIDAR sensor underneath. Research access for external partners to this drone is offered through Shared Research Facilities @ WUR.  

Right: An automated robotic system to collect leaf samples of seedlings in the breeding process for further processing by sequencers to determine the DNA profile of new varieties.

 National roadmap

National roadmap for infrastructure

In The Netherlands ‘plant phenotyping’ has been accepted on the Dutch NWO Roadmap for Large-Scale Scientific Infrastructure with the Netherlands Plant Eco-phenotyping Centre (NPEC), selected based on the compatibility with strategic priorities, such as the Dutch National Research Agenda, the top sectors and the European roadmap for large-scale research facilities (ESFRI).

NPEC is a partnership between Utrecht University and Wageningen University & Research, and also includes affiliated groups from Leiden University, NIOO-KNAW and the University of Amsterdam. This future facility will provide scientists with next generation growth platforms to enable research designed to unravel to the  interactions between plants, their microbiomes and the environment. These interactions determine the growth, the health and traits – the phenotype – of plants. More info: www.wur.eu/npec






The plant phenotyping community in Norway has formed a consortium that includes the major plant science universities and research institutes in the country, with the aim to establish a national plant phenotyping platform that can serve as a Norwegian node in EMPHASIS.

Here you can read about the current facilities and relevant research activities at the partner universities and research institutes. The plans for the establishment of the Norwegian Plant Phenotyping Platform (PheNo) is presented in a separate section at the end.

The Norwegian University of Life Sciences (NMBU) located at Ås, about 30 km south of Oslo has a long tradition in agricultural plant research and hosts excellent growth facilities for both controlled climate and field-based plant phenotyping. These facilities are operated by the Centre for Plant Research in Controlled Climate (SKP) (https://www.nmbu.no/tjenester/sentre/skp), which is a national research infrastructure centre owned by NMBU and the Norwegian Institute of Bioeconomy (NIBIO). SKP operates more than 200 small and large controlled climate units (phytotrons, growth chambers, green houses etc), including GMO certified growth rooms, and 45 ha of land for field experiments with accompanying service facilities.

The plant research at NMBU covers both basic plant biology and applied crop genetics and plant breeding. The university also has strong research groups in robotics and engineering as well as image analysis.

Figure 1. Vollebekk field research station at NMBU. 

 

Current field phenotyping activities at NMBU take place at Vollebekk research station (Figure 1) are centered around the use of UAV-based multispectral imaging for monitoring plant growth and prediction of grain yield in plant breeding nurseries and high-resolution close-up imaging using the Thorvald robotic platform developed at NMBU (Figure 2).

Figure 2. Thorvald field phenotyping robot. 

 

To learn more about the field phenotyping activities at NMBU, you could have a look at the virtual field day videos and presentations from June 2020:

https://nordicphenotyping.org/activities/annual-nppn-field-day-2020/

Contact persons:

Prof. Morten Lillemo (morten.lillemo@nmbu.no)

Prof. Odd Arne Rognli (odd-arne.rognli@nmbu.no)

Jan Roger Torp Sørby (jan.sorby@nmbu.no)

 

University of Oslo (UiO)

Plant research at UiO focuses on basic plant molecular genetics, epigenetics and genomics and evolutionary aspects of plant development and reproduction. The research environment focuses on a mechanism-based understanding of plant biology by genomics and in-depth phenotyping methods. For a guided video tour to some of UiO plant activities see this educational video (https://youtu.be/9QYOSdg4ULw).

The UiO:PlantLab (Figure 3) is the central facility for controlled climate plant growth at UiO, and offers controlled simulated environmental settings (including additive gases (CO2, O3), daylight/ metal-halide / LED variable spectrum light sources, ) in 30 GMO S3 or non-GMO full phytotron chambers. Services also include vernalization and stratification rooms, germination chambers, Insect-plant interaction rooms, light- and fluorescent microscopy and image analysis facility and DNA/RNA/Protein isolation facilities. Quality control is maintained by continuous growth parameter logging /online interface and plant health control and workshop service by permanent staff.

For more information see UiO:PlantLab pages (http://www.uio.plantresearch.no).

Contact person:

Prof. Paul Grini (paul.grini@ibv.uio.no)

 

Figure 3. Plant research activities at the UiO:PlantLab

 

Climate Laboratory Holt

The Climate Laboratory Holt just outside Tromsø (Figure 4) is jointly maintained by UiT The Arctic University of Norway (UiT) and the Norwegian Institute of Bioeconomy Research (NIBIO). This is the northernmost phytotron in the world and provides unique opportunities for plant phenotyping under arctic light conditions. There are no sites at comparable latitudes worldwide with the same opportunities for plant phenotyping.

 

Figure 4. Climate Laboratory Holt outside Tromsø. 

 

The Climate Laboratory contains 6 daylight (6 to 27°C) and 4x2 dark phytotrons (0.5 to 27°C) and also controlled S3 growth rooms. It also has additional greenhouse rooms as well as facilities for sample preparation, storage and basic equipment for analytical and molecular biological laboratory work. The controlled growth facilities have recently been upgraded with significant investments by UiT and features growth chambers of high technical standard. The research at the climate laboratory vary from more basic scientific projects focusing for instance on bioenergy production and molecular interactions of parasitic plants, to projects with more directly applicable focus. Climate laboratory is located in in close vicinity to field trial facilities. The field trial research is concentrated on pre-breeding on fodder grasses (Graminor trials), potatoes and different berry species in addition to studies on plant adaptations and interactions to northern/arctic climate conditions. A combination of field trials and controlled experiments in the phytotron provide vital knowledge on plant physiology, production and quality under northern growing conditions, including combination of 24 h daylength and special light qualities during the growing season in addition to extreme weather conditions during all seasons.

 

Contact persons

Prof. Laura Jaakola, UiT (laura.jaakola@uit.no)

Dr. Inger Martinussen, NIBIO (inger.martinussen@nibio.no)

  

NIBIO Center for Precision Agriculture (CPA)

The NIBIO Center for Precision Agriculture (CPA) is situated at Apelsvoll in inland Norway. While Apelsvoll has served as an agricultural research station for more than 100 years, research on precision agriculture started in 2001. This research led up to the establishment of the CPA in 2016. The purpose of the CPA is to contribute to a resource-efficient and sustainable agriculture by shortening the time-span for farmers to adopt new agricultural technology.

 CPA has various remote and in-situ sensing systems, including a wide range of UAV and ground vehicle platforms. The primary focus is on state-of-the-art spectrometers and hyperspectral cameras to obtain reflectance and fluorescence information, from which a multitude of plant properties are inferred. In addition, thermal cameras are utilized for plant stress detection, and sensors for mapping soil variation are used along with conventional sensors for weather data acquisition.   

 

Figure 5: Left: NIBIO Apelsvoll Research Station. Right (top): Research UAV with hyperspectral camera. Right (bottom): Electrical tractor and autonomous tractor, in this case the autonomous tractor is set up to be a slave of the electric tractor.

 

For more information regarding the CPA, projects and published research: https://precisionag.no/

Contact person:

Kjersti Balke Hveem (kjersti.balke.hveem@nibio.no)

 

The Norwegian University of Science and Technology (NTNU)

The Norwegian Colour and Visual Computing Lab (ColourLab) based in Gjøvik is an internationally leading laboratory in the field of color imaging science, image- and video processing, color management, image analysis and computer vision. Two of the main research focus areas are multi-/hyper-spectral imaging and Artificial Intelligence (AI) for image processing and analysis in applications such as precision agriculture. The research group consists of 46 members in total including 17 PhD students.

The ColourLab has over 200 m2 of equipped lab space with a wide range of imaging devices including RGB, Multispectral, hyperspectral, IR, NIR, ToF still and video cameras in addition to various illumination sources and light measurement instruments including state-of-the-art spectrometers and calibration charts. Furthermore, it has several powerful workstations used for developing and training deep learning models for large image collection processing and analysis. ColourLab participates in several H2020 projects with spectral imaging and AI at their core.

The Wireless Sensors Networks Lab (WSN) at NTNU has various types of wireless sensors measuring soil moisture content, soil electrical conductivity, pH, temperature, wind speed and other environmental qualities used to characterise an agricultural field. All those sensors can be connected to one another forming a WSN communicating through cellular IoT gateways to deliver the data directly to the cloud.

 

Contact person:

Prof. Faouzi Alaya Cheikh (faouzi.cheikh@ntnu.no)

 

 

Plans for the National Plant Phenotyping Platform (PheNo)

A national infrastructure proposal was submitted to the Research Council of Norway in November 2020, with the aim to establish a national plant phenotyping platform to become a Norwegian node in EMPHASIS.

The investment plan includes a total budget of 96.1 mill NOK, of which 42.7 mill NOK is for equipment. A strong commitment from the partners is reflected in an own contribution of 29.0 mill NOK while 67.2 mill NOK is requested in national infrastructure grants from the Research Council of Norway.

PheNo will be a distributed national infrastructure (Figure 1) equipped with reliable and well-proven phenotyping platforms that can serve the needs of both basic and applied plant science research and industrial applications in plant cultivation and plant breeding. Realizing that both research and industry need reliable and affordable phenotyping solutions, the focus has been on selecting technology that is easy to operate, update and with reasonable running costs that can be afforded by the targeted user groups.

 

Figure 6. Distribution of PheNo nodes with phenotyping installations indicated by solid lines. Dashed lines indicate partner locations that will benefit from the services.

 

The Norwegian Plant Phenotyping Platform (PheNo) will be able to provide the following access services at affordable costs to the identified target groups:

Access to state-of-the-art phenotyping facilities

Location

Main target users

  1. Controlled conditions phenotyping

 

 

 

  1. Semi-automated multispectral laser scanning of plants

NMBU, UiO, UiT, NIBIO

Plant scientists, students, producers and industry

 

  1. High-resolution robotized phenotyping of small plants

UiO

Plant scientists, plant breeders, technology developers

 

  1. Hyperspectral imaging of plants

NMBU, UiT, NIBIO Holt

Plant scientists, industry

 

  1. Automated high sensitivity in vivobioluminescence imaging

UiO

Plant scientists, students

  1. Field phenotyping

 

 

 

  1. Lean UAV-based field phenotyping with RGB, multispectral and hyperspectral imaging

NMBU, NIBIO CPA

Plant scientists, plant breeders, agronomists, technology developers

 

  1. Intensive field phenotyping using field robot

NMBU, NIBIO CPA

Plant scientists, plant breeders, industry, technology developers

 

  1. Intensive phenotyping in polytunnels for fruits and berries

NIBIO CPA

Plant scientists, plant breeders, technology developers, producers and industry

 

  1. Intensive phenotyping under semi-controlled field conditions using polytunnels

NMBU

Plant scientists, plant breeders, producers and industry

 

  1. Root studies using mini-rhizotron under semi-controlled field conditions

NMBU

Plant scientists, plant breeders, agronomists

  1. Seed phenotyping

 

 

 

  1. Image-based batch phenotyping of seed samples

NMBU

Plant scientists, plant breeders, analytical testing industry

 

  1. Automated seed sorting based on 3D imaging and NIR spectroscopy

NMBU

Plant scientists, plant breeders, analytical testing industry

 

  1. Hyperspectral imaging of seed samples

NMBU

Plant scientists, technology developers, analytical testing industry

 

  1. Robotized phenotyping of individual seeds and precision sorting for growth experiments

UiO

Plant scientists analytical testing industry

 

  1. High-resolution digital measure of seedgermination and seedling emergence

UiO

 

Plant scientists, plant breeders

Data analysis services of phenotyping data

All

(NTNU lead)

Plant scientists, plant breeders, agronomists, students

Training and education

 

 

 

  1. Training courses on specific topics in plant phenotyping (based on user demand)

All

(NMBU lead)

All target groups

 

  1. Lectures and hands-on training in plant phenotyping as part of teaching activities

NMBU, UiO, UiT, NTNU

University students

 

Controlled environment phenotyping

Low-cost semi-automated platforms for high-resolution plant phenotyping under controlled conditions will be established at NMBU, UiO and UiT based on the PhenospexTraitFindersystem.PlantEye F500 multispectral 3D scanners in dual mode will enable automated measurements of plant morphological, growth and physiological traits (Figure 7). The sensors will be mounted on push carts that can be conveniently moved between greenhouse compartments and serve the phenotyping needs of multiple experiments over the same time periods. The integrated software for data management and visualization will ease the integration of sensor metadata into the data analysis making it a highly useful phenotyping platform for non-specialized users. At the UiO:PlantLab, the system will be established for phenotyping small to medium size plants while the setup at NMBU will focus on studying medium to large sized crop plants under controlled conditions. At UiT and NIBIO Holt it will be installed in the unique northern daylight phytotron, which will attract international interest as there are no sites at comparable latitudes worldwide with the same phenotyping opportunities. Thesame infrastructure setup at the different locations maximizes exchange of experience and allows experiments to be performed at different scales and conditions using identical multispectral technology. It will also be used in teaching activities at the three universities.

Figure 7. Source: Phenospex

 

In addition, a multipurpose PhenoAIXpert (LemnaTec) high sensitivity bioluminescence imaging station and a high-end automated PlantScreen™ Phenotyping System (Photon Systems Instruments) will be installed at the UiO:PlantLab: i) The PhenoAIxpert ESoffers top-view imaging and a phenotyping for small plants, seedlings, plant organs, petri dish root growth and other samples. The system provides luminescence imaging combined with multispectral phenotyping used for genetic reporters for gene activity or molecular interactions, and luminescence-labelled probes such as metabolites or microbes. It is suitable for testing of experimental setups (before entering a large-scale automated setup) and for small-scale dedicated experiments. It will be configured to handle setups on demand, e.g., cell culture analysis or pollen tube germination analysis. ii) The PlantScreen™ robotized system will be installed in a growth chamber for climate and developmental studies, with options for plant pathogen studies, and fully programmable environmental settings (humidity, temperature, day-length and LED based light intensity and spectrum) allowing mimicking of extreme, or rapidly changing environments and to replicate historical or live meteorological data. The system allows high-throughput and high-precision digital plant phenotyping for small to mid- scale plants grown in soil or in vitro using a robotic XYZ system with a number of sensors for image-based analysis of growth dynamics and physiological performance including hyperspectral imaging. The PlantScreenTM system thus represents a highly versatile system for physiological, developmental and ecological high-throughput analysis.

 

Field phenotyping

The upgraded field stations at NMBU and NIBIO CPA will be able to offer flexible and inexpensive field phenotyping solutions that can produce high-quality phenotyping data at an affordable cost for the users. Field trial operations at NMBU, which are currently manual and low throughput, will be automated and digitalized under the concept of “digital farm” with GPS-controlled field trial operations (planting, spraying, irrigation, harvesting etc.) and barcoding of samples. This includes a new tractor suitable for field trial research, two tractor-mounted planting machines (for yield trial plots and for single rows/hillplots), field trial sprayer with section control, irrigation system and fertilizer spreaders, all fully compatible with GPS and precision farming operations. This will save labor costs and increase the precision in planting and management of field trials, which will increase the value of the high-throughput field phenotyping services.

With UAV-based field phenotyping, large areas can be covered in a short period of time, which makes it possible to compare the performance of hundreds or thousands of field trial plots at multiple time points during the season at a reasonable cost. As flexible platforms for remote sensing, both light-weight UAVs with integrated cameras and larger UAVs with exchangeable cameras and sensors will be acquired. The CPA at Apelsvoll is already well equipped with UAVs and UAV mounted phenotyping sensors. At Vollebekk, DJI Phantom 4 drones with integrated multispectral camera will be acquired as standard equipment for UAV phenotyping, together with a larger multi-rotor UAV platform (e.g. BFD 1400-SE8-D heavy lift endurance platform) with exchangeable VIS/NIR and SWIR hyperspectral cameras (e.g. HySpex Mjolnir VS-620).

mproved field phenotyping robots based on the Thorvald platform (Grimstad and From 2017) will be used as vehicles for proximal data acquisition. Our existing phenotyping robot (Figure 8), which has already been in operation at Vollebekk since 2017 will be improved with adjustability for different fields and crops. Moreover, the robot will be upgraded to capture data and navigate autonomously. A dedicated software will aid the operator in monitoring the robots’ actions in real time. Similar robots will be acquired at both stations. To serve the needs for fruit and berry research in polytunnels, a tailored phenotyping robot for polytunnels will also be available at NIBIO CPA.The use of an interchangeable portfolio of RGB, multispectral and hyperspectral cameras on the UAV and field robot platforms will allow for highly flexible field phenotyping solutions. This maximises the use of available resources, increases the flexibility of experimental designs and enables phenotyping solutions to address the wide range of research questions regarding climate adaptation, sustainability and productivity from the users.

 Figure 8. Thorvald field phenotyping robot at NMBU. 

 

At NIBIO CPA, several instruments for manual crop physiology measurements will be acquired for calibrating remote sensing data: i) a leaf area index meter to provide accurate, quick and robust measurements of leaf area, length and width used to predict photosynthesis production, evapotranspiration and plant growth; ii) a photosynthesis system for measuring gas exchange and fluorometer for measuring chlorophyll-a fluorescence including a portable porometer suitable for a quick screening of plant respiration related to water stress; iii) a high-resolution spectrometer for measuring sun-induced chlorophyll fluorescence; iv) a spectrophotometer-based chemistry analyser system for measuring specific analytes in the plant samples, including enzyme activity or organic acids content. Moreover, the new infrastructure will include a powerful workstation enabling efficient processing and analysis of the remotely sensed and reference data.

At NMBU, the construction of two permanent polytunnels (each 12 m wide, 40 m long) will enable manipulation of temperature, humidity and rainfall in field trials. Their design will allow growing the plants in the soil on site. Temperature and rainfall will be modulated according to experimental needs by opening or closing the roof and the side walls. Such construction will also allow access for tractors, combine harvesters, phenotyping robot and other equipment. These polytunnels can be used to address many questions related to temperature and rainfall effects on plant growth development and yield. Modern horticultural production is moving from the field to semi-controlled conditions, and these polytunnels can also give valuable input for developing new production systems of berries and vegetables.

A mini-rhizotron facility will be established in conjunction with the polytunnels to enable studies of root growth in field experiments. Established methodology (Black et al. 2017) will be used to shoot transparent acrylic tubes into the ground at a 30° angle from the vertical of the soil surface. Multispectral cameras will be able to slide down the transparent tubes and take pictures at repeated times down to depths of 100-150 cm. This will allow monitoring of root growth over time and trace single roots during their development. Coupled with soil sensors, this facility will enable us to study both above ground plant canopy development and below ground root development under different climate scenarios, which is unique in a Norwegian context.  

IoT environmental sensors will enable on-line tracking of environmental parameters in field trials to be coupled with the captured phenotypes. Soil moisture profiles, temperature, humidity, wind speed and direction, atmospheric pressure, rainfall and lighting conditions will be measured using variant sensor density (e.g. a dense network of soil sensors is advised due to possible gradients whereas atmospheric pressure sensors can be fewer). We will develop flexible sensor systems based on commercial, simple or high-end sensors integrated into a custom network operated by Arduino microcontrollers. Data transferred over IoT networks will be relayed to the SQL database through an edge computing unit and a gateway. Such architecture gives enormous flexibility as sensors can be swapped according to needs and programmed to interface with the microcontroller. The database will be made accessible through a web interface for real-time status view, which allows early detection of malfunctions, giving control over the experiments and ensuring minimal data loss.

Seed phenotyping

A robotized 3D seed phenotyping systems (Phenoseeder) (Jahnke et al. 2016) will be installed at UiO:Plant­Lab, tooffer solutions for automated 3D-imaging and weighing of individual seeds combined with precision sorting or planting of seeds for downstream plant growth experiments or further hyperspectral- or molecular phenotyping. Using a robotic arm, each seed is automatically and individually imaged using a 3D imaging unit for instant seed volume determination. The seed is sequentially weighed on high-precision balances before being sorted into batches according to the phenotypic analysis. A semi-automated seed germination system (SeedAIXpert, LemnaTec) will be installed at UiO:PlantLab. The system allowsfor measuring seed metrics, germination and seedling emergence quality. The system is compatible with most seed types and operates with filterpaper-, germination trays-, microtiter plates- and Petri-dish based germination assays. The imaging software is fitted with an analysis package using machine learning models to determine parameters such as germination rate (in case of time series), germination percentage and root length determination.

At NMBU, three different phenotyping solutions will be established to serve specific needs related to the field trial research:: i) The MARVIN ProLine seed analyser (MARViTECH GmbH), an image-based solution for fast and reliable measurements of individual seed traits such as grain weight, seed length, width, diameter etc. from batch seed samples within less than seconds. ii) For high resolution data and sorting of individual seeds based on 3D imaging and NIR spectroscopy, the Qsorter Explorer (QualySense AG, Switzerland) will be installed. It provides accurate phenotyping of up to 30 seeds per second and will be highly useful for seed sorting purposes and obtaining individual seed distributions of more complex seed traits such as seed composition (protein content, oil content etc.), disease infestation (e.g. Fusarium infection), pre-harvest sprouting (e.g. sprouted vs non-sprouted grains), etc. based on validated calibration models. iii) an experimental setup with hyperspectral camera (VNIR and SWIR) for gathering high-resolution images from seed samples. This will be highly suitable for the training of deep learning models and developing calibrations to automatically detect seed features associated with disease infection and sprouted grains in the high-throughput platforms.

 

 

 

Prof. Dr. Bogdan Wolko
bwol@igr.pozan.pl

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. 

Contact person

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.

 

Geographical distribution of EMPHASIS expressions of interest in Portugal (updated July 2019).

Geographical distribution of EMPHASIS expressions of interest in Portugal (updated July 2019).

Cosmin Sigora
Biological Research Center Jibou
cosmin.sicora@gmail.com

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:

  1.  Monitoring PAM Fluorometer for Long-term Monitoring of Photosynthesis
  2.  Open FluorCam  System for combined multispectral and kinetic fluorescence imaging
  3.  PAM 2500 High-performance Field and Laboratory Fluorometer
  4.  Fluorometer FL 3500, Sensitive head, P 700 module
  5.  Flow-through WATER-PAMChlorophyll Fluorometer
  6.  LAI-2200C Plant Canopy Analyzer
  7.  ULM 500 Universal Light Meter
  8.  Light Meter VLX – 3W, for PAR measurements
  9.  UVA, UVB meter SpectroSense
  10.  FytoScope FS 130 Growth Chambers
  11.  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

Dr. Ankica Kondic-Spika 
Institute of Field and Vegetable Crops

kondicspika@gmail.com

Country profile coming soon

 Marian Brestic
Slovak University of Agriculture in Nitra
marian.brestic@gmail.com
(+421) 37 61 44448

 Country profile coming soon

Jóse Luis Araus
Universitat de Barcelona
jaraus@ub.edu

Marta da Silva Lopes 
IRTA
marta.dasilva@irta.cat

Manuel Jamilena Quesada
Universidad de Almería
mjamille@ual.es

 

Country profile

At IRTA, research areas of application of phenotyping technologies focus on improving crop adaptation to climate change under Mediterranean conditions and enhancing crop efficiency in the use of resources. High-throughput field phenotyping tools, based on the capture of images at different spectrum ranges, are used to decipher phenotype-genotype relationships and identifying genomic regions related to stress tolerance, resilience and input efficiency. New methods for quantifying water balances, determining crop physiological status as well as other relevant plant traits are being developed.

The team of crop ecophysiology at the Faculty of Biology of the University of Barcelona is working in the development of new avenues for phenotyping, with special emphasis in field phenotyping and low cost approaches. Special emphasis has been given to the use of RGB images and ground as well as aerial platforms, not just to assess crop growth and senescence but also for other purposes such as early ground covering or ear counting. Besides that, thermal and multispectral imaging are the main categories of sensors deployed. In addition the signatures of different stable isotopes are regularly analyzed to assess different objectives (grain yield, water status, ear photosynthesis, root functioning).

Key Institutions:

IRTA, Institute for Food and Agricultural Research and Technology), (www.irta.cat).

Universitat de Barcelona, Crop Ecophysiology Group Section of Plant Physiology, Faculty of Biology, University of Barcelona. https://www.researchgate.net/.../Integrative-Crop-Ecophysiology-... -

National Network:

In spite not a specific network for Plant Phenotyping has been created, many research networks exist in areas related to plant phenotyping where advances in the topic may be discussed, like ‘Sociedad Española de Genética’, ‘Sociedad Española de Fisiología Vegetal’, the FiRCMe network (Yield Physiology and Quality for cereal breeding), as well as a strong tradition of collaborative research.

General opinion about the specific-country needs (prepared by J.L.Araus)

What is considered strategic is the need to developing flexible, high throughput platforms for field phenotyping. Specific needs to phenotype quality traits and the evaluation of biotic stresses may need the implementation of special platforms and even indoor facilities. However, the general perception is that there is no need at the country level of a high throughput indoor facility. Specific needs may be covered with ongoing collaborations with already existing platforms abroad. 

Erik Alexanderson, Erik.Alexandersson@slu.se
Swedish University of Agricultural Sciences (SLU)
Alnarp, Sweden

Aakash Chawade, aakash.chawade@slu.se
Swedish University of Agricultural Sciences (SLU)
Alnarp, Sweden

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 5 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 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.

National and Nordic Networks

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”. In 2018 the NordForsk-funded university hub NordPlant started. NordPlant focuses on plant phenomics and climate modelling for future crops and trees in the Nordic countries (www.nordplant.org).

Contact person:
Juan Herrera
Agroscope
juan.herrera@agroscope.admin.ch

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:

 National networks

 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.

Key institutions

Agroscope

University of Bern

University of Zürich

ETH

University of Lausanne

University of Geneve

Contact person ( University of Nottingham )

Malcom Bennett

Tony Pridmore

Darren Wells

 Plant Phenotyping in the UK

 Phenotyping in the United Kingdom spans a range of environments, organs and scales. Both root and shoot phenotyping tools are in everyday use, and vary from custom built laboratory and glasshouse facilities to large scale, commercially sourced, glasshouse and field systems. Together, these are capable of recovering traits across a wide range of species and growth stages, from individual Arabidopsis seedlings to field plots of mature wheat.

 Specific phenotyping facilities include:

  • large scale glasshouse phenotyping (Lemnatec, PSI, Phenospex) at the National Plant Phenotyping Centre, Aberystwyth
  • crop phenotyping via a boom system, lean sensor network and mobile platform at the John Innes Centre, Norwich
  • 2D and 3D root phenotyping, including X-ray analysis of roots grown in soil, at the Hounsfield Facility, University of Nottingham
  • gantry-based field phenotyping incorporating a variety of 2D and 3D imaging modalities at Rothamsted Research
  • chlorophyll fluorescence and multispectral imaging of shoots and electrical impedance tomography of roots at the Wolfson Centre for Disease Phenomics, Sheffield
  • a managed drought facility, glasshouse ground and aircraft-based phenotyping at NIAB, Cambridge
  • a new phenotyping glasshouse with Lemnatec sensor gantry, and new sensor development and Agri-informatics lab, both linked to soil research facilities at Cranfield University.

 A strong technology development community experienced in the production and distribution of phenotyping hardware and software backs up the UK’s physical resources. Of particular interest are image and data analysis software tools, novel sensors and sensor integration, agricultural robotics and lean imaging hardware.

 The UK phenotyping community is linked via a recently announced network: PhenomUK. PhenomUK is jointly funded by the UK Research Councils’ Technology Touching Life programme and aims to bring researchers from the engineering, physical and life sciences together to further develop phenotyping technologies and prepare the UK to play a full role in EMPHASIS.

Key institutions

o   http://p3.sheffield.ac.uk

o   http://www.earlham.ac.uk/ji-zhou

o   https://www.nottingham.ac.uk/microct/

o   https://www.nottingham.ac.uk/research/groups/cvl/projects/plant-phenotyping/plant-phenotyping.aspx

o   http://www.niab.com

o   https://www.plant-phenomics.ac.uk

o   https://www.agri-epicentre.com

o   https://www.rothamsted.ac.uk/field-scanalyzer