Project deliverable Open Access
Morisse, Merlijn; Wells, Darren; Alary, Pierre-Etienne; Janni, Michela; Fahrner, Sven; Hollebecq, Jean-Eudes; Saint Cast, Clement; Dhondt, Stijn
The objective of EMPHASIS-PREP is to develop a long term, distributed, pan-European infrastructure for state-of-the-art plant phenotyping experimental installations, which aims to improve crop performance to cope with climate changes and to keep pace with population growth. To tackle these global challenges, novel approaches to identify improved plant phenotypes and explain the genetic basis of agriculturally important traits are required. The new and existing plant phenotyping platforms use non-destructive, image-analysis based determination of the phenotype of plants and allow for a characterization of plant traits.
Plant researchers require to test the improvement of plant and crop performance by using all categories of plant phenotyping infrastructure (as described in the deliverable D2.1. criteria list for plant phenotyping infrastructure) which can and should be combined together in a multiscale plant phenotyping approach, ideally, within a coordinated infrastructure, linked with an integrated data management system for storing and analysing (meta)data, and with modelling platforms associated with the phenotyping platforms.
To be able to form this distributed plant phenotyping infrastructure and understand the comparability and/or differences between installations, it is essential to map the capacity, throughput, focus of plant phenotyping, species used in the installations, use of data management systems, and many more details about the installations. A key objective of EMPHASIS-PREP is to map the existing and upcoming infrastructures for controlled conditions to enable multi-scale phenotyping with open access to installations. Moreover, to test crop performance in a changing climate, setting up large experiments in different natural environments is needed, and mapping the field phenotyping facilities in Europe to form networks of fields is highly recommended.
The mapping exercise has been done by EMPHASIS-PREP partners in extensive collaborations and discussions with the national plant phenotyping community in Europe. Extracting detailed information of the existing and upcoming infrastructures was done through surveys and workshops. Four regional workshops have been organized in different regions of Europe. Plant scientists of these regions were asked to present their plant phenotyping infrastructures and activities. Moreover, during these workshops networking moments and breakout sessions were allowing discussion on the demand of the plant phenotyping community and the criteria of EMPHASIS plant phenotyping infrastructure. Starting with this information the pillars of EMPHASIS could be confirmed in the criteria list, deliverable 2.1.
Furthermore, work package 2 (WP2), together with WP3 and WP4, developed multiple surveys to extract more details of these infrastructure. By this, an EMPHASIS database could be generated that contains information about the installation name, detail of the phenotyping installations set-up and experimental design, contact information, access models of the local infrastructure and meta-data details. Based on this database it was possible to develop a map which visualizes the different installations per region.
With the mapping efforts 182 plant phenotyping installations of controlled conditions, intensive fields and networks of fields have been mapped and stored in the EMPHASIS-PREP database.
Phenotyping under controlled conditions (i.e., in glasshouses and controlled environment chambers) represented the largest number of installations (112), the majority of which are automated. Most installations focus on shoot and canopy phenotyping and on species of agronomic importance, dominated by cereal crops; while a smaller number addresses root properties.
Phenotyping in field has been identified in 70 installations, with:
Virtual platforms as modelling and data management systems, have been mapped. A total of 116 plant models have been mapped. Many of these models are developed in France, Germany, Netherland and United Kingdom. The plant models are developed by different groups and for different aims, leading to a considerable diversity of species studied (e.g. legume species, crop species, perennial species…) and model predictions (e.g. prediction of root or shoot characteristics at plant or regional scales). An overview of the models is available under: https://emphasis.plant-phenotyping.eu/modelling
The data management is (partly/ in some sites) shifting from homemade solutions to some global e-infrastructures compliant with FAIR criteria and EPPN2020 requirements defining i) environmental and plant measurements ii) statistical analysis of phenotyping experiments, iii) information systems. These e-infrastructures are based on web services. These services facilitate the interactions between different installations and aim at linking EMPHASIS information within the so-called EMPHASIS-layer that will provide a unified models allowing single entry point queries in different information systems.
Finally, the broader European research infrastructure landscape has been analysed in order to identify potential synergies.
EMPHASIS-PREP_D2.3_Mapping of upcoming and existing infrastructures.pdf