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Information Standards for Plant Genebanks

Explore the context of plant genebanks, genetic erosion, and conservation approaches, including data structures, management, and standards for documentation. Discuss future steps for information exchange and data format standardization.

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Information Standards for Plant Genebanks

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  1. Information Standards for Plant Genebanks Theo van Hintum Centre for Genetic Resources, The Netherlands

  2. Information Standards for Plant Genebanks • the context and big issues • basis of further discussion in other sessions • plant genebanks in historical context • the resulting documentation landscape • data structures in use in genebanks • standardisation in plant genebank documentation

  3. Information Standards for Plant Genebanks • plant genebanks in historical context • farmers have been domesticating crops since c. 10,000 years • selection adapted phenotypes from wild populations • in ‘centers of origin’ • result: landraces

  4. Information Standards for Plant Genebanks • Vaviliov’s centres of origin

  5. Information Standards for Plant Genebanks • plant genebanks in historical context • since c. 1850 crop genetic diversity disappears due to monocultures and habitat destruction • scientific plant breeding based on Mendel and de Vries • urbanization, desertification, climate change • result: genetic erosion

  6. Information Standards for Plant Genebanks • plant genebanks in historical context • to keep the diversity available it needs to be conserved • ex situ: collections under controlled conditions (genebanks) • in situ: protection wild species in nature • on-farm: use and development of diversity in ‘traditional’ farming systems • genebanks are the ex situ component in the range of conservation approaches • evolved from research and breeding collections • estimated 500 in Europe

  7. Information Standards for Plant Genebanks • plant genebanks in historical context • living collections

  8. Information Standards for Plant Genebanks • DB management in the documentation landscape • local documentation systems of genebanks • paper • spreadsheets • proper databases

  9. MCPD MCPD ex situ exchange format ex situ exchange format National Inventory National National Inventory Inventory ex situ PGR ex situ PGR ex situ PGR ex situ PGR ex situ PGR ex situ PGR ex situ PGR ex situ PGR ex situ PGR holding institute holding institute holding institute holding institute holding institute holding institute holding institute holding institute holding institute ECCDB ECCDB ECCDB Information Standards for Plant Genebanks • the landscape is complex

  10. Information Standards for Plant Genebanks • data categories in plant genebanks • genebank management data • internal use only (data models vary) • passport data • broad external use (institute, national, European, incl. breeders) • fairly standardized (Multi-Crop Passport Descriptor (MCPD) list) • characterization & evaluation data • broad external use (breeders, researchers, others incl. institutes) • limited availability • range of models varying level of detail • data about distribution and use of germplasm • institute (internal), national, international administration (e.g. Treaty)

  11. Information Standards for Plant Genebanks • format or coding systems for plant genebanks • passport data • MCPD widely accepted descriptor list for data exchange • simple • incomplete and not expandable • MCPD contains or refers to coding systems for a/o countries, origin types, population types • institute codes remains a problem – attempt of World Information and Early Warning System on Plant Genetic Resources (WIEWS) • no systems for taxonomy, or other descriptors (user type, coordinate type, etc.)

  12. Information Standards for Plant Genebanks • format or coding systems for plant genebanks • characterization and evaluation data • no accepted data structure for C&E exchange • level of detail important due to GxE interaction • some proposals have been developed now • trait names not standardized • several standards are available (Bioversity, UPOV) with rather low acceptance, incomplete crop coverage and not expandable • ontologies are being developed

  13. Information Standards for Plant Genebanks • next steps facilitation information exchange • change of MCPD • to become more flexible • to accommodate new (ITPGRFA and AEGIS) requirements • development better standards for • institutions • taxonomy • development C&E exchange format • introduction and use of life science identifiers (LSID) • allow exchange with data outside the plant genebank community • compliance to Access to Biological Collection Data (ABCD 2.06)

  14. Information Standards for Plant Genebanks • summarizing remarks • plant genebank documentation developed locally • local solutions no standardization • passport data were exchanged • need further standardization • C&E data are the next major step • format for data exchange needed • ontologies needed • part of TDWG community

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