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
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
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
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
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
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
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)
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
Centre for Genetic Resources, the Netherlands
CGN: certified genebank
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
Centre for Genetic Resources, the Netherlands
Gap analysis Daucus carota maximus
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 .........
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
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
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
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
