Product Line 1.1. Ex situ conservation and dissemination of rice germplasm
The rice gene pool encompasses a huge wealth of potentially valuable genes to support sustainable development and to improve livelihoods by addressing the problems of climate change, evolving pests and pathogens, problem soils, better nutrition, novel agricultural technologies, and improved yield potential. The gene pool is represented in the genebanks of the CGIAR by more than 130,000 accessions. Outside the CGIAR, the BRIC countries hold another 170,000 accessions, mostly in India and China, including many accessions not duplicated in the CGIAR. Four other countries (Japan, Korea, Thailand, and the U.S.) hold well-secured national collections with more than 20,000 accessions each. Together, these comprise some 80% of the known world holdings of rice. An additional 120,000 accessions are scattered among around 40 genebanks worldwide with varying degrees of security. The extent of duplication of accessions among genebanks is largely unknown.
This product line addresses the first step toward realizing the potential value of this diversity: keeping it securely, effectively, and efficiently maintained and readily available for distribution to users as required to meet user-defined targets. It ensures the sustainability of developments in rice agriculture by conserving the full range of rice diversity, including genes with unknown function and genes that may serve unknown development targets as well as current priorities. It includes the basic operations involved in maintaining and disseminating germplasm conserved in the CGIAR collections. It also includes activities required to improve the efficiency and effectiveness of conservation, at the level of individual genebanks and globally, and to fill global gaps in the conserved gene pool.
All aspects of germplasm conservation and dissemination are critically dependent on high-quality integrated data management. Workflow management systems that ensure adherence to best practices are essential for quality control and quality assurance in the laboratory. Appropriate data validation procedures are essential to ensure accurate data. Integration of data from different stakeholders involved in germplasm management is essential for rational joint management decisions in a global system. This includes cross-referencing of accessions from different genebanks, and linking genebank accessions to the research and breeding programs that use them. Through the International Crop Information System (ICIS), IRRI has developed the world’s first information management system with the capacity to provide all this functionality in one integrated system, setting the scene for raising efficiency and effectiveness of conservation and use to unprecedented levels. Essential developments in the system are included within the product line.
At the most basic level (product 1.1.1), the genebanks of the CGIAR must be maintained and coordinated. Currently, each CGIAR center has a mandate to conserve and manage its own germplasm collection. The GRC is recognized as a flagship crop genebank. It operates a continuous program of registering, duplication, characterization, testing, regeneration, documentation, and distribution of its germplasm, and must be maintained to serve the needs of rice researchers. Similarly, the AfricaRice Genebank must maintain and distribute its rice germplasm. CIAT needs to upgrade its seed processing and storage facilities for maintaining its working collections. These collections will be duplicated for conservation in the GRC and fully documented in the International Rice Information System (IRIS) Genetic Resources Information Management System (GRIMS). The basic operations of the three CGIAR genebanks will be critically analyzed to identify and cost the operations that could benefit from coordination or centralization (such as long-term conservation), and those that must remain separate within each institute (such as distribution to local users). Based on this analysis, a plan will be developed and implemented for efficient conservation and use of accessions held within the CGIAR.
Second (product 1.1.2), since the CGIAR holds only a small proportion of the total gene pool of rice, action is required to improve conservation of the global rice gene pool. This will be achieved by developing a rational, efficient, and effective global system for the conservation of rice diversity, in partnership with other rice genebanks and the Global Crop Diversity Trust. A key target will be to improve coordination among genebanks, thus avoiding unnecessary duplication of efforts and sharing responsibilities when appropriate. This in turn will require a mechanism to facilitate joint decisions, based on a global database of rice accessions cross-referenced to show the correspondence between accessions in different genebanks. Through a concerted program coordinated by the Trust, unique accessions will be rescued in genebanks where secure conservation is threatened by inadequate capacity. Investment in identifying and filling gaps in collections will be undertaken only in the context of the global strategy.
Third (product 1.1.3), in response to the growing evidence that current best practices for germplasm conservation are not optimal, conservation research will be undertaken. There is an urgent need to conduct novel research on the consequences of applying different regeneration, postharvest, and management procedures on the genetic integrity of conserved germplasm and on the physiological quality of conserved seed. The research results will be used to devise and test improved procedures for germplasm tracking and for handling plots and seeds to improve the quality of conservation.
Finally (product 1.1.4), an integrated rice germplasm documentation and sourcing system will be deployed, initially covering the genebanks of the key GRiSP institutions. We have adapted the germplasm documentation facilities of ICIS by augmenting its schema and engineering specialized data entry and validation tools to create the GRIMS. Its development is well advanced but still requires further development of tools for sample tracking, data quality assurance, and intellectual property rights for seed distribution under the Standard Material Transfer Agreement (SMTA) of the International Treaty on Plant Genetic Resources for Food and Agriculture (ITPGRFA). GRIMS will be improved to accommodate the needs of other GRiSP partners, to be linked to the GCP Integrated Breeding Platform being developed in theme 2 that includes GCDT, GRIN-Global, and GENESYS collaborations.
1.1.1. Sustained and enhanced management of the rice collections of the CGIAR
1.1.2. Enhanced conservation of the global rice gene pool
1.1.3. Improved conservation of rice in genebanks
1.1.4. Data management for quality assurance
For the overall management and operation of the rice genebanks at IRRI, AfricaRice, and CIAT, our primary partners are the Global Crop Diversity Trust (GCDT), Inter-Center Working Group on Genetic Resources (ICWG-GR), FAO-Commission for Genetic Resources for Food and Agriculture (CGRFA), Central Advisory Service for Intellectual Property (CAS-IP), ITPGRFA, and Svalbard Global Seed Vault. The ICWG-GR plays the role of setting up the operational basis and mechanisms for coordination among the genebanks of the CGIAR. For enhancing and improving conservation of the global rice gene pool, our primary partners are curators of genebanks of national programs. The list of research partners includes those currently active in activities under the global system for rice conservation. Participation is dynamic and is expected to increase.
For data management, our partners are the ICWG-GR, ITPGRFA, Generation Challenge Program, United States Department of Agriculture, and Bioversity International. A large majority of local adapters/users are within GRiSP. This reflects the fact that this product line provides the starting point for all germplasm-related research in GRiSP, and emphasizes the need for close coordination with other product lines to ensure effective progression along the value chain to achieve impact.
This product line provides the starting point for addressing all development objectives based on using and improving rice germplasm, in all themes of GRiSP and in all other rice research and development projects even outside the formal GRiSP partnership. To solve a substantial share of these problems, it is necessary that relevant germplasm be made readily available to any and all projects; and that the relevant germplasm for each project be readily identified. It is assumed that each project has the competence to exploit germplasm provided under this product line.
The immediate users are GRiSP researchers and the global community that use rice genetic resources. These include advanced research institutes, the private sector, NARES, NGOs, and farmers. All organizations and individuals are accepted and encouraged as users. There is only one restriction: users must comply with the terms of the Standard Material Transfer Agreement, a contract that encourages the fair use of genetic resources for research, breeding, and training for food and agriculture, while preventing their misappropriation and misuse.
Effective delivery of the right germplasm to the right user requires close interaction between this product line and users. As new knowledge is generated through other research in GRiSP, the knowledge fed back will enable this product line to target more effective use of germplasm for specific development objectives. Sequence information will be an increasingly important component of the genebank database and is expected to grow dramatically over the next 5 years. Theme 2 research will provide trait evaluation data from breeding lines and theme 4 research on quality and specialty rice varieties. Theme 3 research will provide information on the match required between a variety and the farming system used for its production.
The final users—farmers—will adopt improved rice germplasm and provide important feedback to breeders through participatory varietal selection work in theme 2. Diffusion on a large scale will be achieved through linkages with development and private-sector partners (theme 6).
It is assumed that the basic operating costs of the CGIAR genebanks (product 1.1.1) will be financed through a system-wide genebank maintenance window coordinated by the Consortium and the Global Crop Diversity Trust. Product 1.1.1 is included within the scientific and operational framework of GRiSP to ensure effective delivery, but its costs are excluded from GRiSP budget calculations.
The GCDT has played a key role in the development of the global system of rice conservation (product 1.1.2). The framework for the global system has been established with financial support from a grant from the GCDT, but practical mechanisms need to be established for its continued operation, especially to facilitate the participation of stakeholders that will not receive GCDT grants. This is beyond the current budget and will require additional resources.
A conservation research laboratory (product 1.1.3) has been set up at IRRI. Additional sources of funding will need to be identified to undertake the research identified as necessary to achieve the proposed milestones.
Basic capacity has been established for data management, both for high-quality curation and for the development of required new software applications. However, the team is significantly underresourced and can make only slow progress relative to the magnitude of the task at hand. Additional programmers and data curators are required at all three CGIAR centers to complete the world-leading system envisioned.