Periodic Reporting for period 1 - PRO-GRACE (Promoting a Plant Genetic Resource Community for Europe)
Reporting period: 2023-01-01 to 2023-12-31
Plants are the basis of all food, feed and renewable bioenergy production and are essential for the transition from a fossil-based to a bio-based economy. Plant Genetic Resources (PGR) play a key role in ensuring this transition, as well as food security and climate mitigation. More than 2 million plant accessions are preserved “ex situ” in 410 institutes in Europe and associated countries and listed in the EURISCO database; even more diversity is found “in situ” in European farmlands and wild habitats, where it contributes significantly to agricultural resilience and climate mitigation. Detailed information on “ex situ” accessions is, at best, fragmentary, while for “in situ” accessions it is almost non-existent. A considerable part of these resources could be lost over the coming decade due to limitations in the “ex-situ” infrastructure and management, climate change, habitat loss, and invasive/alien species. The roadmap 2016 of the European Strategy Forum on Research Infrastructures (ESFRI) identifies a clear gap in the sector “Plant facilities – unlocking green power”, i.e. the lack of a European Research Infrastructure (RI) specifically dedicated to PGRs. PRO-GRACE will undertake the first step to fill this this gap, by developing the concept of a novel (RI) dedicated to the conservation and study of PGRs. The concept will describe the proposed distributed structure, governance, economic plan and scientific services of the proposed RI, and will be the basis for a full proposal at the next ESFRI call. If implemented, this new RI will aim to catalog, describe, preserve and enhance European plant agrobiodiversity, and translate the results into conservation practices and agricultural innovation, and will collaborate with global organizations dedicated to Plant Genetic Resources and with other established ESFRI RIs working on complementary fields. (eg ELIXIR, EMPHASYS, DISSCO, LIFEWATCH, MIRRI).
This general aim will be articulated into a series of specific objectives:
• Ensure proper conservation of, and access to PGR, by developing a certification system for ex situ genebanks, and creating mechanisms for conservation, monitoring and access to in situ PGR.
• Develop and test strategies and software for integrating into EURISCO the still missing information from European genebanks and in situ conservation sites as well as that developed by different European projects on PGR, with the goal of constructing an integrated European PGR information system.
• Develop and test standards and protocols for the quality-assured ex situ and in situ management of PGR, which are particularly important in the second case, in which changing environmental conditions and novel pests/invasive species can rapidly erode genetic diversity.
• Develop and test a list of scientific services that the GRACE-RI will provide to the scientific community, and the potential providers of such services.
• Develop and test unified strategies, procedures and standards for evaluating phenotypic traits of PGR stored both in situ and ex situ and providing the information to end-users (breeders, farmers).
• Analyse the ethical, social and regulatory context that enables the transition of European genebanks to become more complex research infrastructures, including the policies, laws and challenges that presently hamper an open exchange of PGR and their genetic information (for instance, Digital Sequence Information, DSI), and the equitable sharing of benefits arising from their use.
• Propose a concept, governance model, and preliminary financial plan for the future GRACE-RI.
• Identify the “customers” of the future RI, review their needs, disseminate and communicate the project’s findings, and train perspective user groups in the use and conservation of PGR.
This general aim will be articulated into a series of specific objectives:
• Ensure proper conservation of, and access to PGR, by developing a certification system for ex situ genebanks, and creating mechanisms for conservation, monitoring and access to in situ PGR.
• Develop and test strategies and software for integrating into EURISCO the still missing information from European genebanks and in situ conservation sites as well as that developed by different European projects on PGR, with the goal of constructing an integrated European PGR information system.
• Develop and test standards and protocols for the quality-assured ex situ and in situ management of PGR, which are particularly important in the second case, in which changing environmental conditions and novel pests/invasive species can rapidly erode genetic diversity.
• Develop and test a list of scientific services that the GRACE-RI will provide to the scientific community, and the potential providers of such services.
• Develop and test unified strategies, procedures and standards for evaluating phenotypic traits of PGR stored both in situ and ex situ and providing the information to end-users (breeders, farmers).
• Analyse the ethical, social and regulatory context that enables the transition of European genebanks to become more complex research infrastructures, including the policies, laws and challenges that presently hamper an open exchange of PGR and their genetic information (for instance, Digital Sequence Information, DSI), and the equitable sharing of benefits arising from their use.
• Propose a concept, governance model, and preliminary financial plan for the future GRACE-RI.
• Identify the “customers” of the future RI, review their needs, disseminate and communicate the project’s findings, and train perspective user groups in the use and conservation of PGR.
During the 1st year of the project, considerable progress has been made towards the achievement of the main project objectives:
A project public website was set up (www.grace-ri.eu) with the aim of serving as an information hub for the community working towards the construction of the future GRACE-RI.
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 into EURISCO the still missing information.
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.
Finally, the organization of the 1st International workshop and training school on Plant Genetic Resources has provided a forum for discussing the above issues with >200 stakeholders of the future GRACE-RI from 47 European and extra-European countries, mostly public researchers working on PGRs, with existing research infrastructures, as well as with EU-funded projects on PGRs, and providing training on PGR management to the above stakeholders.
A project public website was set up (www.grace-ri.eu) with the aim of serving as an information hub for the community working towards the construction of the future GRACE-RI.
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 into EURISCO the still missing information.
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.
Finally, the organization of the 1st International workshop and training school on Plant Genetic Resources has provided a forum for discussing the above issues with >200 stakeholders of the future GRACE-RI from 47 European and extra-European countries, mostly public researchers working on PGRs, with existing research infrastructures, as well as with EU-funded projects on PGRs, and providing training on PGR management to the above stakeholders.
Besides the above-mentioned progress towards project objectives, a series of high profile publications advanced our knowledge of PGRs beyond the present state of the art:
The publication of 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 (https://doi.org/10.1038/s41477-023-01489-8(opens in new window); https://doi.org/10.1101/2023.09.06.556570(opens in new window))
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 (https://doi.org/10.1111/tpj.16455(opens in new window))
A multi-environment association study highlighting candidate genes for robust agronomic quantitative trait loci in a worldwide Capsicum core collection (https://doi.org/10.1111/tpj.16425(opens in new window))
The genealogical tracing of Olea europaea using chloroplast and nuclear markers (https://doi.org/10.1186/s12870-023-04440-3(opens in new window))
The mapping of loci related to kernel quality and/or to to stem rust resistance in cultivated/wild wheats (https://doi.org/10.1002/tpg2.20413(opens in new window); https://doi.org/10.3389/fpls.2023.1253385(opens in new window))
The publication of 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 (https://doi.org/10.1038/s41477-023-01489-8(opens in new window); https://doi.org/10.1101/2023.09.06.556570(opens in new window))
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 (https://doi.org/10.1111/tpj.16455(opens in new window))
A multi-environment association study highlighting candidate genes for robust agronomic quantitative trait loci in a worldwide Capsicum core collection (https://doi.org/10.1111/tpj.16425(opens in new window))
The genealogical tracing of Olea europaea using chloroplast and nuclear markers (https://doi.org/10.1186/s12870-023-04440-3(opens in new window))
The mapping of loci related to kernel quality and/or to to stem rust resistance in cultivated/wild wheats (https://doi.org/10.1002/tpg2.20413(opens in new window); https://doi.org/10.3389/fpls.2023.1253385(opens in new window))