Information Standards for Plant Genebanks

Centre for Genetic Resources, the Netherlands

Information Standards for Plant Genebanks

Theo van HintumCentre for Genetic Resources, The Netherlands


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



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



Genebanks Vaviliov’s centres of origin



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



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



Genebanks plant genebanks in historical context living collections



Genebanks DB management in the documentation landscape local documentation systems of genebanks

• paper

• spreadsheets

• proper databases



Genebanks the landscape is complex

holding institute

ex situ

PGR holding institute

ex situ


ex situ


ex situ


ex situ


ex situ


ex situ


ex situ


ex situ

PGR

Inventory

National Inventory

National Inventory

National

MCPD ex situ exchange format ex situ exchange format MCPD

ECCDB

ECCDB

ECCDB



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)



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.)



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



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)



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

Information Standards for Plant Genebanks

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