Report

Teaser, summary, work performed and final results

Periodic Reporting for period 1 - EMPHASIS-PREP (Preparation for EMPHASIS: European Infrastructure for multi-scale Plant Phenomics and Simulation for food security in a changing climate)

Teaser

Food security and increasing plant biomass availability in a sustainable manner for human nutrition and bio-industries is a key challenge for the coming decades. It requires integrated solutions and new technologies to improve plant production specifically through breeding...

Summary

Food security and increasing plant biomass availability in a sustainable manner for human nutrition and bio-industries is a key challenge for the coming decades. It requires integrated solutions and new technologies to improve plant production specifically through breeding. Today´s breeding approaches typically produce about 1% yield increase per year for key crops, which is below the improvement required to meet increasing global demand. In the past decades, genetic improvement has been a major source of yield increase, together with improved cropping systems. While genotyping efficiency is increasingly rapid and costs decline due to industrialized sequencing pipelines, the analysis of crop performance with respect to structure, function, quality and interaction with the environment – phenotyping - has become the bottleneck for the exploitation of crop genetic diversity. This requires substantial and concerted action for accelerating development and availability of phenotyping infrastructures.

The European Strategic Forum for Research Infrastructure (ESFRI) has identified plant phenotyping as a strategic priority for Europe and listed EMPHASIS on the ESFRI ROADMAP in March 2016. In the Preparatory Phase of EMPHASIS, the project EMPHASIS-PREP will develop a pan-European infrastructure through the integration of existing national infrastructure and foster the generation and integration of additional complementary facilities based on the user demand. The specific objectives of the preparatory phase project EMPHASIS-PREP are the development and implementation of a business plans for a long-term operation of EMPHASIS, including:
● establishment and further development of state-of the-art plant phenotyping community and infrastructure in Europe
● provision of services that address the demand of diverse users to exploiting scientific and innovation potential of the infrastructure
● establishment of the data management and e-infrastructure that enables access and reuse of high-quality data according to the FAIR (Findable, Available, Identifiable, Reusable) principles
● development of a sound governance structure that allows open and transparent processes involving all stakeholders.

Work performed

EMPHASIS-PREP has implemented all relevant coordination and support structures and processes, resulting in an effective project management bringing together all eight partners from six countries in Europe.

Within the first phase of the project EMPHASIS-PREP has started a mapping of the current plant phenotyping landscape and user demand in Europe, including e-infrastructures and data management. The mapping included a series of regional conferences: i) Portugal, March 2017 , ii) Vienna, April 2017, iii) Gothenburg, July 2017, iv) Tartu, November 2017. The meetings were complemented by dedicated surveys, workshops to inform about EMPHASIS and learn about the requirements of specific research areas such as: i) viticulture, ii) model plant research, iii) root phenotyping, iv) deep learning and machine learning, v) horticulture, vi) data management, vii) modelling. Further workshops related to i) field phenotyping, ii) phenotyping technology are in preparation. Based on these mapping, EMPHASIS-PREP has started developing pilots to evaluate future services related to i) access to field facilities, ii) innovation, iii) standardization, iv) modelling.

Important steps were also initiated for the development of the European information system. There is a need for the access to phenotypic and environmental information, and to all necessary metadata for either re-analysis of any dataset produced by an EMPHASIS node or meta-analysis of several datasets, thereby following the FAIR requirements. EMPHASIS-PREP in cooperation with EPPN2020 are designing an approach that allows connecting of local information systems and interoperability of datasets, a prototype is currently under development. Data policy has been developed as a Data Management Plan within the EPPN2020 project for data from Transnational Access experiments, which may be adapted for EMPHASIS.

EMPHASIS-PREP is also developing a stakeholder engagement strategy beyond the dedicated meeting with a major goal to establish national plant phenotyping communities with their representatives involved in shaping the EMPHASIS business plan. In addition to the existing national infrastructures (Germany, France, UK, Belgium) several national infrastructures were funded via national / regional funding schemes (Finland, Netherlands), proposals for national infrastructure roadmaps were submitted (Estonia and Poland), the establishment of national initiatives was initiated (Ireland, Italy, Austria, Czech Republic, Cyprus) national plant phenotyping initiatives are being initiated (Bulgaria, Denmark, Greece, Israel, Norway, Portugal, Romania, Serbia, Slovakia, Spain, Sweden, Switzerland). Representatives of all these countries are involves in the EMPHASIS Support Group involved in shaping EMPHASIS.

Along the community engagement and development of services, the legal models were analysed and each type of legal entity has been assessed in consideration of the EMPHASIS infrastructure characteristics. Additionally the development of a formal governance framework for the Implementation Phase to ensure continuation of EMPHASIS after the Preparatory Phase project is in progress.

During the Preparatory Phase, EMPHASIS-PREP established a close cooperation with other ESFRI projects in cluster projects such as CORBEL or ENVRIPlus. Additionally a close interaction was established with the project AnaEE (Roy et al. Nature Plants 2017) and with ELIXIR where common data management will be defined in a Cooperation Strategy document. Additionally, there is a strong link to the I3 project EPPN2020 providing Transnational Access to the user community providing a best-case example for access to phenotyping installations. Finally, EMPHASIS-PREP members started building management competences by the participation of members of the coordination office in the Executive Master in Management of Research Infrastructure programme, supported by the EC.

Final results

EMPHASIS aims to start the operation phase in 2021 based on the results of EMPHASIS-PREP and provide a set of services to the user community defined on their demand. In order to enable an efficient and effective transition from the Preparatory Phase project to the long-term operation, an intermediary governance will be established in the second half of the EMPHASIS-PREP project to foster the i) development of the operational phase, ii) implementation of services, iii) development of the required competences.

In summary, EMPHASIS will create a portfolio of benefits for a range of stakeholders:
● access to state-of-the-art infrastructures in Europe for a wide range of scientists (biologists, plant scientists, etc) and technology developers
● advancement in basic and applied plant sciences based on the in depth understanding of plant environment interaction and the use of new technologies
● application of future and emerging technologies at plant phenotyping infrastructures, e.g. artificial intelligence, robotics, machine learning
● transfer of new technologies, respective competences and phenotyping data to the scientific community and to the market beyond plant phenotyping
● Increase in competences in the operation of infrastructures
● Societal progress towards a sustainable bio economy

Website & more info

More info: https://emphasis.plant-phenotyping.eu/.