Standards for collecting and displaying genetic data

Plant genetic resources (PGR) are crucial for sustainable crop production and for ensuring food and nutrition security. To support efficient conservation and accessibility, the integration of genetic data has become essential through practices known as 'next-generation genebanking'. 

The European Search Catalogue for Plant Genetic Resources (EURISCO) is a centralized repository for passport and phenotypic data on PGR conserved in European collections. However, it currently lacks representation of genetic data, which has seen significant advancements over the last two decades through EU-funded projects.  Such valuable genetic information remains scattered across literature, specific websites, and databases from different projects, highlighting the pressing need for its integration into EURISCO.

Harmonizing and making genetic data FAIR (findable, accessible, interoperable, and reusable) requires Permanent Unique Identifiers, standardized metadata, and open-source protocols. Integrating this data with EURISCO will enhance decision-making and sustainable use of PGR, contributing to global food security. Two models for data FAIRification exist: create new standards or exploit (rather than replace) existing resources and promote their use.

In Deliverable 1.2, we comprehensively reviewed existing standards and public repositories for nucleotide sequence, genetic polymorphisms, makers and, variants to identify currently implemented standards, requirements, and features related to the management and sharing of genetic data and its metadata.

We assessed their strengths and weaknesses to evaluate their suitability for linking genetic data with EURISCO. Additionally, we propose a set of recommendations that the PRO-GRACE community can follow in pursuing this objective.

To foster universal adoption of the recommended standards and their future implementation, we propose the following steps:

  • Develop detailed guides and tutorials
  • Store them at the EURISCO central hub for direct download, along with comprehensive guides and tutorials
  • Host them on GitHub for collaborative editing and versioning
  • Include them in RDMKit and Fairsharing collections to achieve wider dissemination
  • Conduct training courses in collaboration with WP1 partners to educate and encourage the PGR research community to embrace reporting standards from the outset of their research
  • Advocate for journal adherence to PGR reporting standards to ensure consistency in published datasets

Deliverable 1.2 was led by CSIC in collaboration with CREA, UNITO, ENEA, INIAV, MAICH, NASC, CNR, NORDGEN, UEB.

For more information, download the Deliverable report

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