Activated GEnebank NeTwork (AGENT)

Plant Genetic Resources (GenRes) hold the key for adapting crops to a changing climate. The actual use of GenRes in crop improvement, however, is limited and in stark contrast to their potential and promise. In order to promote a more systematic effort to exploit GenRes, major international initiatives (DivSeek1, The Global Plant Council2) advocate for generating extensive genotypic and phenotypic data for GenRes stored in genebanks (GB) in order to facilitate their educated selection and utilization in breeding and agriculture. Already in 1967, Krull and Borlaug stated “the problem […] is less a lack of genetic variation but rather of efficiency in identifying and incorporating it”3. Now 50 years later, a total of approx. 7.4 million accessions are stored in more than 1,750 GB around the world but the unanswered questions about their use remain the same: (i) How many independent accessions are needed to represent the global genomic diversity of a crop species? (ii) How many duplicates do we maintain in GB? (iii) How good are we in tracking the identity of GB accessions and how do we maintain their genetic integrity? (iv) How to select most efficiently the accessions best suited for different purposes? (v) What is the most systematic approach to maximize the value and use of GenRes? (vi) Which bioinformatic and database infrastructure is needed to facilitate data mining of global GenRes collections in the context of other information (reference genome sequences, re-sequencing datasets, phenotyping data, reference transcript datasets, etc.)? (vii) Is climate change dependent (dis-)appearance of diversity already captured in the GB? Until recently, answering these questions in a concerted and coordinated manner was impossible, because the technology was not widely available, approaches were too costly, or no funding frameworks were in place to support internationally harmonized strategies and processes. Furthermore, data management (data storage, analysis, access) infrastructure with established standards and agreed ontologies is still missing. 1 McCouch et al. (2013) Nature 499:23-24. 2 Gruissem et al. (2012) J Plant Biol 55:343-348. 3 FAO. The second report on the state of the world's plant genetic resources for food and agriculture, (FAO, 2010).

- Establish an actively cooperating genebanks (GB) network, working on agreed standards and protocols on the (i) activation of hitherto passively stored Genetic Resources (GenRes) information and (ii) the accumulation of new GenRes data; - Implement the FAIR (Findable / Accessible / Interoperable / Reusable) principles for the accumulation and management of new and already existing GenRes data to maximise their impact in breeding and conservation; - Generate exemplary new genotypic information for European barley and wheat collections in order to establish a roadmap and process towards a complete global wheat/barley GenRes biodiversity atlas; - Use this extensive genotypic information to assess the level of quality and redundancy of existing GenRes collections as a basis to implement new ways of quality control and management; - Use the genotypic information as the foundation of coordinated GenRes training populations for sustained and defined phenotyping of independent GenRes collections as the base for pan-European level genome-wide prediction across GenRes collections; - Mine the new and historic genotypic and phenotypic information to drive gene/trait/knowledge discovery and future GenRes collection missions; - Extend the established GenRes phenotyping and training population activity with the establishment of a coordinated evaluation network of stakeholders (e.g. breeders, farmers, NGOs) that collaborates on the phenotypic evaluation of AGENT GenRes, thereby increasing data density on collections and helping to disseminate the societal impacts of GenRes; - Provide the community with a new database and novel data-mining tools and opportunities to facilitate the better-informed selection of GenRes for a diverse set of purposes; - Use and complement existing flagship information resources for wheat and barley and the improved data standards and infrastructure to translate knowledge into improved management of GenRes for other crop species across European GB, thereby maximising the impact of the project.

The dissemination of AGENT results will contribute to agrobiodiversity, better-documented archiving, and informed selection of genetic resources which, in turn, will enable future breeding of crops more durable to changing climates and environmental conditions. Resilient crops will support the stability of farmer incomes and help sustain sufficient food supplies, particularly as project concepts are transferred to GenRes collections and stakeholders at international scale. In addition, AGENT will establish high-quality, standards, harmonized for the global management of genetic resources, by activating a network of genebanks that generate added-value information for specific and general collections.

The dissemination of AGENT results will contribute to agrobiodiversity, better-documented archiving, and informed selection of genetic resources which, in turn, will enable future breeding of crops more durable to changing climates and environmental conditions. Resilient crops will support the stability of farmer incomes and help sustain sufficient food supplies, particularly as project concepts are transferred to GenRes collections and stakeholders at international scale. In addition, AGENT will establish high-quality, standards, harmonized for the global management of genetic resources, by activating a network of genebanks that generate added-value information for specific and general collections.

AGENT will increase the quantity and quality of data in established information systems for crop genetic resources by accumulating de novo high-density genotypic and phenotypic data for 15,000 accessions of wheat and barley. This information will be combined with pre-existing genotypic/phenotypic data for more than 50,000 and 20,000 wheat and barley accessions, respectively, to develop a comprehensive diversity of atlas European wheat and barley genetic resources. AGENT promotes innovative ways of sharing resources and services between genebanks/in-situ conservation sites in Europe, and beyond. It avoids the cumbersome physical exchange of resources by instead increasing the value of individual collections through a shared information resources and databases.

UPDATES

Launched in 2020, AGENT standardizes and pools phenotype information from global genebank networks within a single database and revolutionizes plant genetic resource information sharing. Our Genetic Resources Team is also accelerating research digitalization through tools such as the CGIAR Breeding Program Assessment Tool, which aids design and analysis, and helps the breeding management system centralize breeding data.

In 2021, ICARDA scientists helped devise more straightforward tools and procedures for genomic work, and through AGENT, are working with partners to collect and standardize phenotype information from global genebank networks within a single database.

In 2022, ICARDA multiplied a precision collection, single seed descent derived from its genebank accessions. This collection was tested for disease and, in parallel with other project partners, standard global checks were field- and disease-tested at the seedling stage. In addition, ICARDA has contributed to sharing genebank historical data and developing accessible and easy tools to analyze those data.