Project deliverable Open Access
Morisse, Merlijn; Wells, Darren; Alary, Pierre-Etienne; Hollebecq, Jean-Eudes; Saint Cast, Clement; Pieruschka, Roland; Dhondt, Stijn
The objective of EMPHASIS is to develop a long term, distributed, pan-European infrastructure equipped with state-of-the-art plant phenotyping experimental installations, which provide access to user community and enable excellent science that aims to improve crop performance and address future grand challenges. There is an increasing demand for use of phenotyping infrastructure which requires different infrastructure categories as described in the deliverable D2.1. Criteria list for plant phenotyping infrastructure. Access to phenotyping facilities and services requires 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 provide services related to plant phenotyping infrastructure considering the comparability and/or differences between installations, it is essential to map the new and existing plant phenotyping facilities that use non-destructive, image-analysis based determination of the phenotype of plants and allow for a characterization of plant traits. This mapping has been performed and the results are summarized in the EMPHASIS-PREP deliverable D2.3: mapping of existing and upcoming infrastructures.
This deliverable, D2.4, will extensively evaluate the gaps and limitations based on the mapping activities. Moreover, where possible, the gaps will be strategically addressed by presenting in what perspective EMPHASIS could tackle these gaps and enable services to the benefit of excellent plant phenotyping science in Europe.
Both the mapping and the analysis of gaps has been done by EMPHASIS-PREP partners in extensive collaborations and discussions with the plant phenotyping community in Europe driven by four regional and three topical workshops, two surveys, and workshops during the annual support group meetings. During the workshops, breakout sessions were organised to extensively discuss about the gaps of plant phenotyping in Europe and how to address these limitations. Furthermore, EMPHASIS-PREP developed two surveys, which had the purpose to assess the phenotyping landscape, and included and dedicated questions on how the participants see the future of phenotyping, what gaps there identify and how to tackle these gaps. The development of a virtual map in the scope of the mapping deliverable was very effective to find regional gaps for specific plant phenotyping infrastructure in Europe.
1. Gaps in the mapping data extraction
We mapped the plant phenotyping infrastructures in Europe in details (Deliverable 2.3) and were able to identify limitations that need to be addressed in the future. The mapping involved the plant phenotyping community from academia and industry at large but the results may be biased for installations from academia. Additional efforts to evaluate plant phenotyping within the industry sector may be required.
Moreover, countries with a well-established national networks have a higher number of installations in the database. It could be assumed that well-connected national communities can be easier addressed and provide feedback on their installations in contrast to facilities that are in the process of establishing national communities. Thus further and continuous evaluation of the dynamic phenotyping landscape will be required and an important tool for service provision by EMPHASIS.
2. Gaps in harmonizing and innovating plant phenotyping infrastructure
The need for a collective harmonisation of protocols and experimental design strategies to ensure reproductive and interoperable data was clearly expressed. Moreover, innovation through knowledge and technology transfer is very much needed to ensure qualitative sustainable phenotyping. To address these limitations a harmonisation and innovation pilots were initiated and are under development (Deliverable 6.3).
3. Gaps in plant phenotyping categories
Controlled condition plant phenotyping
The survey indicated that there are gaps in geographical location of installations under controlled conditions. There are further limitation of required throughput rates to address mapping populations potentially driven by limited automation and the use of more advanced sensor technologies. The capacity for root phenotyping is less-developed than for shoot and canopy studies.
Geographical gaps have also been identified for intensive fields. There was a limited response with respect to intensive field and further identification and characterisation of intensive field sites is required.
Networks of lean field phenotyping
Networks of fields are very difficult to map. Some institutes own land for field experiments, while others have annual renting opportunities with local land owners. The latter causes the overall total of fields in the database to be substantially underestimated. Although minimal equipment, like UAVs for imaging analysis in lean field phenotyping is more commonly used, there appears to be a limitation with respect to the analysis of these imaging data. Multi-climatic trials across Europe are essential to breed for new crop varieties, needed to cope with the changing climate. Access procedure to networks field sites is rather challenging needs to be developed, a field pilot that is under development (Deliverable 6.3) will support this development.
The plant model database populated through the review of the literature indicated that there are gaps in the plant models inventoried (e.g. models developed by industry are not published) and the plant model availability (i.e. not directly available). Moreover, the diversity observed between the plant models will constitute challenges to improve the interoperability between the phenomics data and the plant models through a unique portal. EMPHASIS, through the next modelling pilot that is under development (Deliverable 6.3), will encourage the modelling community to adopt and develop harmonized standards for interfacing models with phenomics data sources.
Data management systems
The survey revealed that a high number of local infrastructures are not using data management system that will allow interoperability of data. Thus, FAIR principles are not applied yet in many information systems. Several steps are required before these principles can be effective, enabling interoperability. The data pilot (Deliverable 6.3) that is under development will provide users some tools and standards to enable interoperability.