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European Plant Phenotyping Network 2020

Periodic Reporting for period 3 - EPPN2020 (European Plant Phenotyping Network 2020)

Reporting period: 2020-05-01 to 2021-10-31

A reliable evaluation of varieties and agronomic practices is essential to secure European agricultural production (food security), lower pesticides usage (agro-ecology) and increased resilience of management practices (climate change). This requires assessing the ability of hundreds of varieties to cope with a range of environmental conditions representing current and future scenarios of climate or crop management. Indeed, two plants sharing the same genotype can display markedly different plant structures, functions and metabolisms when placed in contrasting environmental conditions. Phenomic experiments of EPPN2020 aimed to provide, in controlled conditions (indoor and field), the necessary elements for understanding and exploiting the genotype x environment interaction observed in genetic and agronomic field studies. EPPN2020 focused on (i) well-characterized environmental conditions, with control/manipulation of temperature, soil water status and CO2 concentration, (ii) precise imaging of the growth, architecture and function of root systems, leaves and reproductive organs for 100s to 1000s of plants, allowing genetic analyses (iii) measurement, with the same throughput, of metabolites and fluxes of water or nutrients to assemble a physiological phenotype.

This was in a context of 'big data' in which several experiments need to be analysed jointly, even by scientists who did not participate to them. EPPN2020 focused on (i) tracing environmental conditions and phenotypic information with necessary metadata, (ii) providing the community with appropriate statistical tools and experimental designs, (iii) organising datasets in a FAIR way (findable, accessible, interoperable, reusable), making use of the rapid progress of internet of things and of web semantic.

EPPN2020 provided the European Plant Science community (public and private) with access to phenomic installations chosen for excellence, with a capacity of hundreds of genotypes and dedicated to innovative non-invasive measurement of traits at different levels of plant organization. It provided this community with methods and software tools for organization, storage and joint analysis of experiments at different scales (organ to canopy), time resolutions (minutes to days), for contrasting environmental conditions (current or future). EPPN2020 coordinated its activities with the ESFRI infrastructure EMPHASIS, with the communities of modelling and genomics and with national programs.
Over its whole life cycle, EPPN2020 involved:

144 accesses to 31 installations, granted to scientists of 40 countries including 19 non-European countries. They addressed a large diversity of scientific questions, mostly the genetic diversity of responses to environmental cues, but also symbiosis with micro-organisms. 45% of the users were female. 70% of users had no previous cooperation with access providers. 30% of accesses in controlled conditions were based on datasets previously collected in field experiments.

Joint Research Activities (JRAs) which defined and facilitated the good practices in phenomics, via the mapping of current practices, training sessions and the design, test and dissemination of methods and software tools.
- A JRA on sensorics favoured the integration of datasets, via (i) common environmental characterization with up-to-date methods with wiki documentation, (ii) adequate procedures for reproducible and traceable calibration of sensors and cameras. All installations providing transnational accesses reached a 'level 1' that ensures standardized environmental characterization and an efficient calibration of sensors and cameras. A 'Level 2' was reached by most installations for mapping conditions in the platform and performing a common calibration only requiring transmission of digital material.
- A JRA on data analysis provided the community with methods, software tools and tutorials: (i) a generator of experimental designs for the diversity of installations in controlled conditions, (i) an integrated tool, available in R, for identification of outlier points in growth curves, outlier plants in panels of genotypes and calculation of genotypic means taking into account spatial variations, (iii) methods for the integration of datasets between several experiments in platforms or field.
- A JRA on data management, from organ to field. Training tools are available for progressing towards FAIR-compatible datasets (level 1): all objects (plants, sensors, vectors) are identified with Unified Resource Identifiers URI) and all measured variables have reproducible names with the "quadruplet" trait entity/trait characteristic/method/unit. Level 2 involved installation of local information systems in each node which collect, organize and store information from phenotyping experiments and automatically generate machine-readable variable names connected with public ontologies and URIs. Information systems were implemented in 19 local infrastructures throughout Europe.

A trans-platform trans-JRA experiments involved 13 platforms for testing all methods designed in JRAs, for addressing methodological issues in phenomics and for exchanges with other communities (e.g. genomics or modelling).

Networking Activities linked stakeholder communities (i) a web portal reached over 31.000 recurring visitors, and >85.000 visitors, about 55% of visitors were from Europe, 35% from the USA, 10% others (ii) a series of workshops for diffusion of the methods addressed 1100 participants from academia and industry, while nearly 10 000 scientists were aware of EPPN2020 activities via presentations at meetings and conferences (iii) users of transnational accesses were 'EPPN2020 fellows' with facilitated access to information and training courses
Experiments in EPPN2020 installations allowed important scientific discoveries, made available to the scientific community via academic journals and datasets in public repositories. This contributed to the design of varieties able to cope with climate change and the transition to agroecology.

The three Joint Research Activities provided the Plant Research community with the necessary methods for progressing in the assessment of the genetic variability of plant responses to environmental conditions, which require that many genotypes and many environmental conditions are explored in common multi-site, multi-scale experiments.

The methods designed and diffused by EPPN2020 allow the public and private plant 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 automated procedures.

All methods and software tools, but also the know-how and the working groups will continue existing and will be further developed via the ESFRI infrastructure EMPHASIS.
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