Genebanking in the sequencing era - Nordgen€¦ · Introduction of quality management system ......

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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

The sequencing era

.............. increasing data output

decreasing costs ..............

Introduction of Next-Generation Sequencing (NGS) technologies

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

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

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

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

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)

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

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

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 .........

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

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

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

Agenda forthcoming years

§ Cooperation with user community ●  Support to genebank operations

●  Providing material and data

●  Input to PGR portals

Genebanking in the sequencing era - Nordgen€¦ · Introduction of quality management system ......

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