Austria: New high-throughput phenotyping platform at Vienna BioCenter Core Facilities (VBCF)
Within the planned infrastructure, plants are transported on conveyor belts from the growth area to the imaging cabinets equipped with state-of-the-art sensors. The imaging units are physically separated from the growth area (two individually controlled phytotrons) facilitating the parallelization of measurements via a sample loop and thus improving the throughput, flexibility and sensor utilization.
The PHENOPlant project evolved out of the Austrian Plant Phenotyping Network (APPN.at) initiative, was funded by the Austrian Research Promotion Agency (FFG) and built by PSI (Photon System Instruments).
The infrastructure is operated by the Plant Sciences Facility of the Vienna BioCenter Core Facilities GmbH and available in a fee4service mode to national and international user from academia and industry.
Specifications:
Environment:
- Temperature: 0°C-40°C
- Humidity: 40-80% rel.hum.
- Light: adjustable LED light spectrum, up to 1000 µmol m-2 s-1
- CO2: ambient – 2000 ppm
- Highly controlled environments & dynamic simulations
Capacity:
Designed for crop plants up to 100cm height (incl. pot), 50cm width and for Arabidopsis
- 200 x 5L pots or
- 400 x 3L pots or
- 800 x 2L pots or
- 4000 x 250mL pots (Arabidopsis).
Sensors:
- RGB (top- & side-view)
- 3D laser scan
- PAM chlorophyll fluorescence
- LWIR thermal imaging
- Hyperspectral imaging (VNIR and SVIR)
- Automatedweighing & watering stations (two tanks each).
- Mobile weather stations for live dynamic environmental simulation
Contact:
Jakub Jez
Head, Plant Sciences Facility
Vienna BioCenter Core Facilities Gmbh (VBCF)
Dr. Bohr Gasse 3
1030 Vienna, Austria
https://www.viennabiocenter.org/vbcf/plant-sciences/phenoplant/
https://twitter.com/VBCF_PlantS
https://www.linkedin.com/in/jezjakub/
https://www.plant-phenotyping.org/db_infrastructure#/tool/156/
Sweden: A virtual tour of the Biotron at SLU Alnarp
The tour was held over zoom by Ramesh Vetukuri, who is the Biotron Development leader and Julia Nilsson who is a Horticultural Engineer at the Cultivation Unit. They guided the approximately 35 participants through the facility and showed the various growth chambers. After the presentation there was a lively session of questions and answers. The whole presentation was recorded and can be seen here.
Italy: Successful first Phen-Italy call for access to plant phenotyping infrastructures
Participation to the call has demonstrated once more the great interest plant phenotyping covers in Italy and the raising needs to invest in this emerging field for sustaining plant productivity and efficient use of resources in agriculture and forestry.
Greece: Lab-in-the-field, multi-spectral imaging technology for early warning of plant stress and pathologies
Chania, 26/03/2021
The project takes full advantage of the unique capabilities of QCELL’s PhenoCheck camera, a battery operated, wearable/handheld macro-imaging system to monitor crops in situ. The PhenoCheck camera collects spectral information from leaves, stems, fruits, etc. and can display, in real time, a vegetation index and spectral maps in reflectance and fluorescence imaging modes. The camera integrates a specially adapted dome illumination module for isolating ambient light and providing consistently calibrated illumination and reliable measurements.
The project partners are focusing on tomato, pepper, aubergine and other plants under biotic and abiotic stresses. At any selected spot, the PhenoCheck handheld camera instantly provides information about changes in the spectral phenotype and helps to monitor and control treatment options. For example, the device might provide early warning for fungal infections (e.g. Botrytis cinerea) before the effects become visible. In addition, the effects of salinity stress might be identified at an early stage and reliably quantified to guide intervention. Another important application of the PhenoCheck camera might be the fruit ripening assessment to predict the optimal harvest date. By offering spectral information in the Near Infrared (NIR) spectral range, internal quality attributes are obtained. These data, together with the measured spectra in the visible part of the spectrum, offer a better prediction of fruit ripeness.
This technology could become a powerful tool in the hands of agricultural scientists and individual growers, with software modules that address a large array of applications for the smart farm. Accelerating the Agri-tech revolution, the SpectraPlant project team collects carefully curated spectral data and provides laboratory-based analyses of the specimens. The data are analysed with sophisticated mathematical models and artificial intelligence methods to improve the analytical power of the platform and expand its reach in various conditions that affect the plant phenotype. By integrating all these unique features, the PhenoCheck camera comprises a valuable tool for controlling and optimizing farming by enabling reduced use of fertilizers, pesticides and water.
New tools for data sharing in plant research
The tools have been developed by a team from EMPHASIS in collaboration with ISBE and ELIXIR within the EOSC-Life demonstrator project Plant A+. The objectives of Plant A+ are to cross data from different domains – phenomics, genetics and environmental data – and to improve standardisation to enable integration and re-use of existing data in plant science.
Italy: Phen-Italy launches first call for access to national phenotyping infrastructures
Access to research infrastructures is granted on the basis of a research project proposal aiming at answering a clear scientific question and addressing a technological challenge in the field of plant phenotyping.
The application can be submitted by a single user or a research group. In the latter case, the application must be submitted by the group leader.
Each individual user (or research group) can submit only one application for access to the research infrastructures.
Infrastructures participating in the call:
- ALSIA FieldNet
- ALSIA PhenoLab
- CREA-CI Field Phenotyping Platform
- Nitrogen forest experiment
- PIANTA
- Root-DISTAL-UNIBO
Deadline for submission: 23 April 2021
EOSC-Life publishes midterm Achievements Brochure
Within the EOSC-Life project, 13 ESFRI projects from the Health & Food sector including EMPHASIS are developing a digital platform for cooperation across disciplinary boundaries in order to make data available and usable in accordance with FAIR principles.
The 12-page brochure features an updated design and offers a brief overview of the project, followed by achievements in the following areas:
- Populating the EOSC with data
- Packaging tools and workflows for use in the cloud
- Cloud deployment and cloud resources
- Providing access
- Connecting users
- Informing & training users
Browse through the brochure and find out how you can benefit from work we’re doing within the project!
RI-VIS publishes three white papers on international cooperation between research infrastructures
International cooperation on the level of research infrastructures is key to addressing major global challenges including climate change, infectious disease, food security and natural disasters. The EU-funded RI-VIS project, a consortium of 13 partners from European research infrastructures, aims to increase the visibility of European research infrastructures and raise awareness in new communities beyond Europe. As part of this goal, RI-VIS has just published three white papers providing region-specific recommendations to funders, policy makers and research infrastructure managers on how to increase international collaboration among research infrastructures. Each white paper focuses on specific regions: (1) African-European, (2) Latin American-European and (3) Australian-European cooperation, respectively.
The papers collate the insights of a total of 21 experts from research infrastructures, policy-makers and relevant governmental institutions from different regions collected through in-depth interviews. Each paper is structured into sections that cover examples of successful collaboration, lessons learned and possible challenges as well as a summary of key recommendations.
Even though many of the recommendations given are specific to the respective regions, some prominent themes emerge in all three white papers. These include issues such as funding, the importance of aligning scientific priorities and mutual benefits. Other key recommendations cover collaboration frameworks, global challenges, access, personal relationships, staff recognition and communication platforms.
Belgium: VIB and ILVO jointly obtain regional funding to establish the ‘EMPHASIS-Belgium’ consortium as national node of EMPHASIS
Continued improvements in crop performance are needed to cope with climate change and to keep pace with population growth. To tackle these global challenges, novel approaches are required to identify superior crop varieties and to explain the genetics of agriculturally important traits. Synergies between (Belgian) phenotyping installations, coordination of phenotyping initiatives and training, and access to state-of-the-art phenotyping platforms and data are needed to drive world-leading plant and agricultural sciences.
The EMPHASIS-Belgium consortium has received funding of Research Foundation Flanders (FWO) within the International Research Infrastructure (IRI) programme, a high-level funding programme for large-scale international investments and linked with the Flanders Department of Economy, Science and Innovation (EWI). This will enable EMPHASIS-Belgium to play a pivotal role to facilitate multiple services such as access to its state-of-the-art controlled condition and highly equipped field phenotyping facilities, data and modelling tools and innovation, to the benefit the Flemish, Belgian and European plant phenotyping community (i.e. plant phenotyping institutes and companies). The national node will (i) coordinate the consortium and further development of EMPHASIS-Belgium and integrate the Belgian phenotyping community – Belgian Plant Phenotyping Network (BPPN) – in international initiatives of EMPHASIS; (ii) ensure communication and interaction between project partners; (iii) facilitate services of the national node, including networking; (iv) ensure access to specific platforms and data of field (ILVO) and controlled condition phenomics (VIB).
Within the consortium, VIB Center for Plant System Biology (PSB), will take the lead. VIB is one of the world’s best performing plant research centres and has extensive expertise in plant phenotyping. The centre owns multiple state-of-the-art, automated and high-throughput, controlled conditions plant phenotyping installations, and heavily invested in the development of data management software for phenotyping infrastructure called PIPPA (PSB Interface for Plant Phenotype Analysis). PIPPA is a central user interface and database for experimental setups in plant phenotyping installations and (meta)data analysis, and will be linked to the EMPHASIS data layer, ones established, to enable open access to its data. Within EMPHASIS-Belgium, VIB will provide access to multiple platforms for controlled environment phenotyping, including an exchangeable sensor portfolio that will provide high levels of flexibility to meet the scientific requirements for a broad range of users.
The ILVO-Plant Sciences (ILVO, ilvo.vlaanderen.be) performs research from agricultural soil to product. ILVO focusses on sustainable plant production with special focus on soil management while reducing nutrient losses and increasing soil organic carbon, and the yield and quality of the primary product. ILVO has more than 80 years of proven records in plant breeding, with extensive expertise on biotic and abiotic stress research and has built significant experience related to field phenotyping in the context of breeding and crop management. ILVO develops tools for close remote sensing using different sensors mounted on UAVs for a broad range of crops, and has experience in gathering and analysing phenotypic data in high spatio-temporal resolution of large trials. Up till now, phenotyping activities under field conditions focused on above-ground plant parts, but in this consortium ILVO will develop a fully operational field-scale automated phenotyping infrastructure enabling the monitoring of root function and entire canopy behaviour at high spatio-temporal resolution, coupled with abilities to impose drought. Combining below- and aboveground sensing techniques will allow the establishment of a ‘systems approach’ to the dynamics of plant adaptation to the future climate under (real) field conditions.
For further information: Merlijn Morisse (merlijn.morisse@psb.vib-ugent.be)
Plant Phenotyping for a Sustainable Future
Edited by Roland Pieruschka and Michela Janni
The invited papers in this special issue – published in association with the Society of Experimental Biology virtual conference (SEB2021), the International Plant Phenotyping Network, the EU project EPPN2020, and the plant phenotyping research infrastructure EMPHASIS – focus on plant phenotyping as the key tool for understanding plant-environment interactions. The collected reviews will explore how this understanding translates into improving plant and crop productivity, quality, and tolerance to biotic and abiotic stress, including cross links to molecular biology, plant breeding, genetics and genomics, and bioinformatics.
Darwin Review
Bettina Berger, Patompong Saengwilai, Michael Selvaraj, Carolyn Lowrenze Dill, Alexander Buksch The state of global community
Reviews
Eva Rosenqvist, Carl-Otto Ottosen Phenotyping using photosynthetic processes
Kioumars Ghamkhar, Robert Koller, Uli Schurr Phenomics for genebank material and seeds
Ankica Kondić-Špika Plant phenotyping as a tool in creating climate resilient crops in Pannonian region
Mahlein A-K, Schaaf G, Lobet G, Vanderborght J, Bauckhage C, Kersting K, Gall J Identification and interpretation of crop features from phenomic data by machine learning
Katja Herzog, Anna Kicherer, Reinhard Töpfer Phenotyping in Grapevine – Perspectives for perennials
Patrick Langan, Villő Bernard, Joey Henchy, Nadia Al-Tamimi, Sónia Negrão Phenotyping for waterlogging tolerance: current trends and future prospects
Gordon Wellman, Christian Zörb, Sandra M. Schmöckel Phenotyping of Traits Related to Salinity Tolerance
Lukáš Spíchal, Nuria De Diego Phenotyping approaches in biostimulant research and development
Boris Rewald, Gernot Bodner Phenotype this! Established and emerging root phenotyping techniques from shovelomics to hyperspectral imaging, root counting to mechanistic modelling
Erik Alexandersson, Thomas Roitsch, Kristiina Himanen Functional phenomics to understand and improve crop resilience in the Nordic countries within climate change scenarios
Invitation to submit
We welcome contributions to this special issue. If you would like to submit a paper (either research or review), please email a title and brief outline for the consideration of the editors. All papers are peer reviewed to the usual standards and must fit within the scope of the journal. The deadline for submissions is 31 October 2021
Contact
JXB Editorial Office, c/o North Campus Academic Porters, County College, Lancaster University, LA1 4YE, United Kingdom • +44 (0)1524 592715 • j.exp.bot@lancaster.ac.uk • @JXBot • academic.oup.com/jxb
Images courtesy of Marina Tikhonova, Andreas Eckert, Luiz M. Santos (Pexels), Sudip Maiti, Ralf-Uwe Limbach (FZJ), Ulrike Beukert, Michiel Huybrechts, Giovanni Rallo (EMPHASIS Photo Competition 2020).