Periodic Reporting for period 2 - PRO-GRACE (Promoting a Plant Genetic Resource Community for Europe)
Periodo di rendicontazione: 2024-01-01 al 2025-10-31
Plants underpin food production, agriculture, and the transition towards a sustainable bio-based economy. Plant Genetic Resources (PGR) are essential to food security, climate resilience, and agricultural innovation. More than two million plant accessions, representing only a portion of the material conserved ex situ by around 400 European genebanks and institutions, are documented in the European search catalogue EURISCO, and even more diversity exists in situ across farmlands and wild habitats. However, information on these resources is fragmented or missing, and many collections are at risk due to climate change, habitat loss, biological invasions, and limitations in infrastructure and management capacity.
The ESFRI Roadmap identified a structural gap in the European research landscape: the absence of a dedicated Research Infrastructure addressing the conservation, characterisation, and sustainable use of PGR. PRO-GRACE addresses this gap by developing the concept for a future European Research Infrastructure on Plant Genetic Resources (GRACE-RI). The project aims to define the scientific, technical, organisational, and regulatory foundations required to move from a fragmented system of genebanks and data repositories to a coordinated, service-oriented, and quality-assured infrastructure.
PRO-GRACE pursues this goal through nine interlinked objectives, covering quality management and certification of genebanks, integration of ex situ and in situ PGR information into EURISCO, development of standards and protocols for PGR management and phenotyping, definition of scientific services, analysis of ethical and regulatory frameworks, identification of users and stakeholders, and dissemination, training, and governance planning.
The ESFRI Roadmap identified a structural gap in the European research landscape: the absence of a dedicated Research Infrastructure addressing the conservation, characterisation, and sustainable use of PGR. PRO-GRACE addresses this gap by developing the concept for a future European Research Infrastructure on Plant Genetic Resources (GRACE-RI). The project aims to define the scientific, technical, organisational, and regulatory foundations required to move from a fragmented system of genebanks and data repositories to a coordinated, service-oriented, and quality-assured infrastructure.
PRO-GRACE pursues this goal through nine interlinked objectives, covering quality management and certification of genebanks, integration of ex situ and in situ PGR information into EURISCO, development of standards and protocols for PGR management and phenotyping, definition of scientific services, analysis of ethical and regulatory frameworks, identification of users and stakeholders, and dissemination, training, and governance planning.
During the first year of the project, considerable progress was made towards the achievement of the main project objectives.
- A project public website was set up (www.grace-ri.eu)
- An inventory of the state of quality management and the use of standards in European ex situ genebanks has been compiled, based on the data of 60 contributing genebanks. Based on the results of the inventory, and on discussions with various partners and other stakeholders, a complete overview of the available standards for genebank operations could be produced, including their level of adoption in European genebanks, the need for new standards and ways of formulating those.
- A complete overview of the available standards for collecting and displaying genetic and phenotypic data and images was produced, setting the stage for generating a unified standards system for incorporating missing information into EURISCO.
- A list of the possible scientific services, stakeholders, promoters, and utilizers of the proposed RI and a list of genomic, metabolomic, bioinformatic and phytosanitary methodologies on which these services will be based was produced.
- A compilation of existing standards, protocols and descriptors for the evaluation of the phenotypes and agronomic characteristics of PGR was produced, setting the stage for the generation of a unified, crop-specific system incorporating the ECPGR, MIAPPE, Crop Ontology, EMPHASIS and final user recommendations and methodologies.
During the second reporting period, the project progressed from preparatory and mapping activities to the consolidation, validation and demonstration of its technical and scientific outputs:
- Frameworks and standards for the documentation, management and sharing of PGR data were finalised, including minimum information requirements, harmonised descriptors and modular approaches enabling progressive adoption by genebanks and related institutions with different capacities.
- Targeted cross-work-package alignment and validation activities were undertaken to ensure consistency between data standards, quality management frameworks, information system architectures and the envisaged scientific service portfolio, strengthening the internal coherence of project outputs and their readiness for implementation within a distributed European Research Infrastructure.
- Significant advances were achieved in the development and testing of crop-specific methodologies for the characterisation and evaluation of PGR, including unified recommendations, protocols and metadata templates explicitly addressing interoperability, data reuse and FAIR principles.
- Proof-of-concept interconnections between external phenotypic databases and EURISCO demonstrated the technical feasibility of a federated data architecture based on standardised interfaces and persistent unique identifiers.
- A comprehensive framework for the integration of in situ conserved PGR into existing ex situ-oriented infrastructures was developed, operationalising the principle of complementary conservation and defining concrete mechanisms for linking in situ and ex situ data and access pathways through EURISCO.
- The definition of the scientific service portfolio envisaged for GRACE-RI was completed, identifying priority service areas, potential providers and user communities, and complemented by the development of governance models and a preliminary financial plan, laying the foundation for the transition of GRACE-RI from concept to future implementation.
- A project public website was set up (www.grace-ri.eu)
- An inventory of the state of quality management and the use of standards in European ex situ genebanks has been compiled, based on the data of 60 contributing genebanks. Based on the results of the inventory, and on discussions with various partners and other stakeholders, a complete overview of the available standards for genebank operations could be produced, including their level of adoption in European genebanks, the need for new standards and ways of formulating those.
- A complete overview of the available standards for collecting and displaying genetic and phenotypic data and images was produced, setting the stage for generating a unified standards system for incorporating missing information into EURISCO.
- A list of the possible scientific services, stakeholders, promoters, and utilizers of the proposed RI and a list of genomic, metabolomic, bioinformatic and phytosanitary methodologies on which these services will be based was produced.
- A compilation of existing standards, protocols and descriptors for the evaluation of the phenotypes and agronomic characteristics of PGR was produced, setting the stage for the generation of a unified, crop-specific system incorporating the ECPGR, MIAPPE, Crop Ontology, EMPHASIS and final user recommendations and methodologies.
During the second reporting period, the project progressed from preparatory and mapping activities to the consolidation, validation and demonstration of its technical and scientific outputs:
- Frameworks and standards for the documentation, management and sharing of PGR data were finalised, including minimum information requirements, harmonised descriptors and modular approaches enabling progressive adoption by genebanks and related institutions with different capacities.
- Targeted cross-work-package alignment and validation activities were undertaken to ensure consistency between data standards, quality management frameworks, information system architectures and the envisaged scientific service portfolio, strengthening the internal coherence of project outputs and their readiness for implementation within a distributed European Research Infrastructure.
- Significant advances were achieved in the development and testing of crop-specific methodologies for the characterisation and evaluation of PGR, including unified recommendations, protocols and metadata templates explicitly addressing interoperability, data reuse and FAIR principles.
- Proof-of-concept interconnections between external phenotypic databases and EURISCO demonstrated the technical feasibility of a federated data architecture based on standardised interfaces and persistent unique identifiers.
- A comprehensive framework for the integration of in situ conserved PGR into existing ex situ-oriented infrastructures was developed, operationalising the principle of complementary conservation and defining concrete mechanisms for linking in situ and ex situ data and access pathways through EURISCO.
- The definition of the scientific service portfolio envisaged for GRACE-RI was completed, identifying priority service areas, potential providers and user communities, and complemented by the development of governance models and a preliminary financial plan, laying the foundation for the transition of GRACE-RI from concept to future implementation.
Besides project's main achievements, some high profile results enhance our knowledge of PGRs beyond the present state of the art:
- Chromosome-level assemblies of N. benthamiana (widely used as a model system and biofactory plant) and of C. arabica (the most highly prized and widely consumed coffee tree) comprising analyses reconstructing their polyploidization and diversification histories (10.1038/s41477-023-01489-8 10.1101/2023.09.06.556570)
- The reconstruction of the domestication and differentiation history of a large worldwide collection of eggplant, highlighting two probable centers of domestication in India and South-East Asia and several post-domestication migration routes irradiating from such domestication centers (10.1111/tpj.16455)
- A multi-environment association study highlighting candidate genes for robust agronomic quantitative trait loci in a worldwide Capsicum core collection (10.1111/tpj.16425)
- The genealogical tracing of Olea europaea using chloroplast and nuclear markers (10.1186/s12870-023-04440-3)
- The mapping of loci related to kernel quality and/or to to stem rust resistance in cultivated/wild wheats (10.1002/tpg2.20413 10.3389/fpls.2023.1253385)
- Chromosome-level assemblies of N. benthamiana (widely used as a model system and biofactory plant) and of C. arabica (the most highly prized and widely consumed coffee tree) comprising analyses reconstructing their polyploidization and diversification histories (10.1038/s41477-023-01489-8 10.1101/2023.09.06.556570)
- The reconstruction of the domestication and differentiation history of a large worldwide collection of eggplant, highlighting two probable centers of domestication in India and South-East Asia and several post-domestication migration routes irradiating from such domestication centers (10.1111/tpj.16455)
- A multi-environment association study highlighting candidate genes for robust agronomic quantitative trait loci in a worldwide Capsicum core collection (10.1111/tpj.16425)
- The genealogical tracing of Olea europaea using chloroplast and nuclear markers (10.1186/s12870-023-04440-3)
- The mapping of loci related to kernel quality and/or to to stem rust resistance in cultivated/wild wheats (10.1002/tpg2.20413 10.3389/fpls.2023.1253385)