genebanking in the sequencing era - nordgen€¦ · introduction of quality management system ......
TRANSCRIPT
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Centre for Genetic Resources, The Netherlands (CGN) Centre for Genetic Resources, The Netherlands (CGN)
Genebanking in the sequencing era
EUCARPIA Genetic Resources meeting 2013
Rob van Treuren & Theo van Hintum
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Centre for Genetic Resources, The Netherlands (CGN) Centre for Genetic Resources, The Netherlands (CGN)
The sequencing era
.............. increasing data output
decreasing costs ..............
Introduction of Next-Generation Sequencing (NGS) technologies
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Centre for Genetic Resources, The Netherlands (CGN) Centre for Genetic Resources, The Netherlands (CGN)
Expected impact of NGS technologies
§ Boost to genomics research & crop improvement ● Whole-genome sequencing
● Identification of genomic variation
● Linking genomic and phenotypic data
● Marker-assisted selection
● Introgression of novel variation
§ Modified genebanking ● Collection management
● User-oriented operations
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Centre for Genetic Resources, The Netherlands (CGN) Centre for Genetic Resources, The Netherlands (CGN)
Expectations realistic for all genebanks?
§ CGIAR research centers ● Single or few staple crops
● Availability of facilities and expertise
● Conservation and research strongly integrated
§ National genebanks ● Variety of crops
● Access to facilities and expertise often limited
● Conservation and research usually not integrated
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Centre for Genetic Resources, The Netherlands (CGN) Centre for Genetic Resources, The Netherlands (CGN)
Impact on collection management?
§ Management areas involved ● Acquisition
● Characterization
● Maintenance
§ Traditional molecular markers ● Similar range of applications
● Similar expectations
● No routine use by genebanks ● Expertise
● Costs
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Centre for Genetic Resources, The Netherlands (CGN) Centre for Genetic Resources, The Netherlands (CGN)
Genebanking in the sequencing era?
§ Conservative approach ● NGS applications considered the domain of user community
● User community facilitated by strengthening core business
● Improvement quality management procedures
● Access to a wider diversity of a crop’s gene pool
§ Innovative approach ● NGS applications considered drive for genebank innovation
● User community facilitated by developing new services
● Novel collection types
● Novel information services
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Centre for Genetic Resources, The Netherlands (CGN) Centre for Genetic Resources, The Netherlands (CGN)
Quality management procedures
§ Present status for many genebanks ● Poor access to material
● Poor quality ● Seed viability
● Documentation
§ Developments for improvement ● Introduction of quality management system
● Documented procedures
● Monitoring system
● Improvement of procedures
● Operational standards ● Based on community consensus (FAO guidelines / AEGIS)
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Centre for Genetic Resources, The Netherlands (CGN) Centre for Genetic Resources, The Netherlands (CGN)
Quality management procedures
● Examples ● Individual genebanks (CGN, IPK)
● Global Crop Diversity Trust coordinated CGIAR genebanks
● AEGIS-AQUAS
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Centre for Genetic Resources, the Netherlands
CGN: certified genebank
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Centre for Genetic Resources, The Netherlands (CGN) Centre for Genetic Resources, The Netherlands (CGN)
Access to a wider diversity § Present status for many crops
● Unbalanced collection composition
● General under-representation of crop wild relatives
§ Developments for improvement ● Inventory of gene pools
● Species composition
● Inter-fertility with crop species
● Gap analysis ● Under-represented species in genebanks
● Under-represented distribution areas
● Directed acquistition ● Targeted collecting expeditions
● Novel varieties with new characteristics
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Centre for Genetic Resources, the Netherlands
Gap analysis Daucus carota maximus
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Centre for Genetic Resources, The Netherlands (CGN) Centre for Genetic Resources, The Netherlands (CGN)
Novel collection types
§ Present status ● Single collection for conservation and use
● Accessions may be unsuitable to serve both purposes
§ Innovation: introduction of multiple collection types ● Conservation collection
● Primary goal: long-term conservation
● Secondary goal: use
● User-oriented collections ● Mapping populations (‘special sets’)
● Genetically purified lines (‘allele collections’)
● Populations of unthreatened wild relatives
● Other types .........
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Centre for Genetic Resources, The Netherlands (CGN) Centre for Genetic Resources, The Netherlands (CGN)
Different collections: different management
§ Conservation collection ● Standard management procedures
● Less defined user community
● Distribution according to ITPGRFA
§ User-oriented collections ● Custom-made management procedures
● Participation by user community
● Specific user groups
● Distribution conditions ● No sMTA
● Cost recovery
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Centre for Genetic Resources, The Netherlands (CGN) Centre for Genetic Resources, The Netherlands (CGN)
Novel information services
§ Present status ● Poor quality of documentation
● Poor access to phenotypic and genotypic data
● Limited on-line search and ordering facilities
● Services offered from a provider’s point of view
§ Innovation: introduction of user-oriented PGR portals ● Entry points for specific user groups
● Example: crop portals
● Access to genebank data ● Collections, user-oriented collections, phenotypic data, sequencing data
● Information about obtaining material
● Interactive platform
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Centre for Genetic Resources, The Netherlands (CGN) Centre for Genetic Resources, The Netherlands (CGN)
Agenda forthcoming years
§ Genebanks ● Implementation proper protocols
● Creation of transparancy / quality management
● Expertise development (genomics)
§ Genebank community ● Operational standards
● Crop strategies (formulation and implementation)
● Data repositories and PGR portals
● Capacity building
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Centre for Genetic Resources, The Netherlands (CGN) Centre for Genetic Resources, The Netherlands (CGN)
Agenda forthcoming years
§ Cooperation with user community ● Support to genebank operations
● Providing material and data
● Input to PGR portals