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Report

Teaser, summary, work performed and final results

Periodic Reporting for period 1 - EPPN2020 (European Plant Phenotyping Network 2020)

Teaser

Summary

Major improvements in crop yield are needed to keep pace with population growth and climate change. Whilst plant breeding has greatly benefited from advances in genomics, phenomics remains a major bottleneck. EPPN2020 aims at providing European public and private plant scientists with access to a wide range of state-of-the-art plant phenotyping facilities, techniques and methods. It aids the community in progressing towards excellence across the whole phenotyping pipeline, involving sensors and imaging techniques, data analysis in relation to environmental conditions, data organization and storage, data interpretation in a biological context and meta-analyses of experiments.
EPPN2020 objectives are
- To provide European researchers with access to key European phenotyping facilities in controlled conditions, which examine different plant organs and ranging from metabolic phenotyping to whole-plant and canopy performance, with a focus on throughputs from 100s to 1000s of plants, allowing genetic analyses. This involves (i) precise imaging of the growth, architecture and function of root systems, leaves and reproductive organs (ii) well-characterized environmental conditions, with control/manipulation of temperature, soil water status and CO2 concentration and novel methods able to measure temperature and light conditions for each individual plant in installations, (iii) measurement, with the same throughput, of metabolites, ion concentrations and fluxes of water or nutrients sufficient to assemble a physiological phenotype. We have included two pioneering, highly equipped field platforms able to manipulate both the concentration of CO2 in air (Free Air Controlled Environment, FACE) and rain received by plants (rainout shelters), with throughputs that are uncommon for this type of equipment.
- To perform Joint research activities (JRAs) to address the major challenges facing phenomics in the coming decades. After that a large number of platforms has been built, the priority is to design methods for adequate data collection and for the analysis of heterogeneous datasets involving thousands/millions of data points, contrasting environmental conditions and tens/hundreds of measured traits. EPPN2020 also aims at organizing these datasets in such a way that joint analyses can be performed across platforms, in an open data environment. Three interdependent JRAs are implemented at consortium level, with close links between them and strong interaction with each installation of EPPN2020
- To perform networking activities aiming at establishing intensive cooperation and increasing integration between facilities involved in EPPN2020 and outside, as well as user groups and technology innovation communities by (i) creating a web portal for organizing internal (collaborative work) and external communication (providing a unique entry point to all infrastructures and â€˜one-stop shopâ€™ for phenotyping publication news); (ii) implementing a series of workshops for diffusion of the methods developed in JRAs, and organizing symposia open to the phenotyping community, including industrial partners. Users of transnational accesses are encouraged to become EPPN2020 ambassadors, a role that involves them actively engaging with colleagues in their respective countries to promote the use and development of plant phenotyping tools, expertise and facilities amongst their scientific community.

Work performed

During its first 18 months, EPPN2020 involved:
- 42 accesses to 31 installations in 15 infrastructures were made available to Plant Scientists who are not member of the consortium, from 23 countries including 4 non-European countries. A procedure with a smooth access has been designed based on a web portal that includes information on all available installations, and on a fair and open selection process with two calls per year.
- A Joint Research Activity on sensorics develops novel techniques and methods for environmental and plant measurements. (i) Assessing the temporal and spatial variabilities of environmental conditions in installations. (ii) Ensuring adequate procedures for reproducible calibration of sensors and cameras. (iii) Developing novel pipe lines of image analysis. (iv) Favouring common practices in the Plant Science community via common experiments and via formalized exchanges with the Plant communities for genomics and modelling.
- A Joint Research Activity on data analysis that develops tools for progressing towards standardized statistical analyses and facilitating the combined analysis of data coming from multiple installations and measurement scales. (i) Outlier identification and quality control of phenomic datasets, (ii) statistical design and analysis of phenomic experiments, (iii) Data integration between platform and field datasets.
- A Joint Research Activity about data management (WP3), in particular via the development of a European Information System compliant with the FAIR (Findable, Accessible, Interoperable and Reusable) specifications for (i) data interoperability in Plant Science, (ii) developing distributed information systems able to be deployed in the European Phenomic community,.
- Networking Activities (WP5, NA2) involved (i) workshops addressing 700 participants from academia and industry, while nearly 8000 scientists were addressed by EPPN2020 dissemination activities such as presentations at meetings and conferences by EPPN2020 partners (ii) the website reached over 5500 recurring visitors, and >60.000 visitors, about 60% of visitors were from Europe, 30% from the USA, 10% others. Hence, EPPN2020 plays an important role as a nucleus to utilize synergies and competences with other national and international projects and initiative, to link diverse stakeholders.

Final results

Experiments in EPPN2020 installations allowed important scientific discoveries, which will be published within three years after the end of experiment. Importantly, accesses have been the first contact of many plant scientists with Phenomics, thereby extending the standards for data acquisition, analysis and organization well beyond the phenomics community.
The three Joint Research Activities provide the Plant Research community with the necessary methods for progressing in the assessment of plant responses to a changing climate, which require that many genotypes and many environmental conditions are explored in common multi-site, multi-scale experiments.
Because plant breeding is entering in a â€˜big dataâ€™ era, the methods designed and diffused by EPPN2020 will allow the public and private communities to stay in the world competition. This has large consequences for employment in SMEs that design and distribute technologies, and in European breeding companies that may delocalize part of their activities in countries with cheaper manpower if a considerable effort is not performed for automatized procedures.