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Activated GEnebank NeTwork

Periodic Reporting for period 1 - AGENT (Activated GEnebank NeTwork)

Reporting period: 2020-05-01 to 2021-10-31

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. 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”. Now 50 years later, a total of ~7.4 million seed accessions are stored in more than 1,750 genebanks (GB) around the world but the unanswered question about their efficient use remains the same. Until recently, the technology was not widely available, approaches were too costly, or no funding frameworks were in place to support internationally harmonized strategies and processes towards systematic unlocking of genetic resources for crop improvement. Furthermore, a data management (data storage, analysis, access) infrastructure with established standards and agreed ontologies to support such effort was missing.
The AGENT project will address the above question by establishing an actively cooperating network of European (and international) GB and converting these from passive seed repositories into active bio-digital resource centres. Part of their material will be purified and complemented with dense genotypic information (‘precision collections’, ‘bridging collections’) and by an approach of systematic, coordinated, standardized and sustainable accumulation of phenotype information. The objectives of the project will be exemplified using barley and wheat, two of the most important crops both in Europe and at an international level. Concepts and protocols established for these species can be easily transferred to datasets existing for other crop GenRes collections, thus generating impact for holdings of many crop species far beyond the project boundaries.
The central theme of the AGENT project is to establish an actively collaborating network of European GB. In a concerted effort the unique and redundantly shared proportion of genetic diversity of the European wheat and barley GenRes collections will be identified. Each AGENT partner GB is selecting a ‘precision collection’ of 500 wheat and/or 500 barley accessions, which, on the basis of existing passport information, are potentially unique. This will reveal the unique crop diversity at the GB level. Furthermore, ‘bridging collections’ of up to 150 wheat and/or 150 barley accessions shared between GB of the same eco-geographic and climatic mega-environments of Europe will be selected to allow integration of GB GenRes data on the basis of historical phenotype records. The third set of material (‘general checks’) is composed of recent wheat and barley cultivars (50 winter, 50 spring-type) that are distributed to all AGENT GB and are repeatedly grown throughout the duration of the project (and possibly beyond) to determine the climate effect at each AGENT partner GB site. Biotic and/or abiotic stress phenotype information will be collected for the ‘precision collections’ and based on genotypes this will enable cross GB-collection genomic prediction to support future informed GenRes selection. Genotyping of the ‘precision’ and ‘bridging collections’ is already accomplished by about two thirds. Phenotyping of the material will start in the second reporting period. ‘General checks’ were already phenotyped at all partners for one season. Plant material exchange to breeder’s networks for the purpose of phenotypic evaluation has been established. A data management and integration platform was partially implemented for FAIR data accumulation, storage and exchange among AGENT partners. Programming of data import into EURISCO as well as of web-applications to support data-mining and visualization has been initiated.
AGENT aims to deliver a concept for the systematic and sustainable accumulation of a genomic and phenomic diversity atlas, exemplarily for barley and wheat, by establishing an actively interacting network of GB. AGENT will establish an efficient, transparent, reliable and innovative conservation system in Europe, based on sharing resources, expertise and reciprocal support. At the same time, AGENT will trigger systematic utilization of the material conserved, extending beyond the timeframe of this project. These expected achievements will allow a leap forward in the level of efficiency and services offered by European GBs, consolidating interaction between conservation and use. The latter has been a long-standing (but to date, largely unaccomplished) goal of the European GenRes community. The AGENT project has an ambition in mitigation of negative impacts imposed by climate change by providing the plant breeding community with tools for facilitated information about desired genes in GenRes over the most of Europe and thus underpin an improved breeding process.
Based on AGENT’s achievements, stakeholders will become able in the future to select GenRes on the basis of a new quality of information provided by AGENT GB. First, the composition (level of uniqueness / redundancy) of individual European GenRes collections will be determined using dense accession-specific genotype information. Furthermore, the collaborative accumulation of phenological but also biotic and abiotic stress related phenotype information for the genotyped material of AGENT partner GB is establishing a novel data foundation to perform genomic predictions across the AGENT GB network – in other words: future selection of GenRes will take into consideration the complementary (but also redundant) diversity held by AGENT partner GB. This will be facilitated through new functionalities of the database EURISCO and newly developed associated web-tools, thus allowing to select GenRes specifically for multiple purposes. This will shorten the time to application in pre-breeding, and as such contributing to meet the rising global need for plant-based food, feed and other products.
Activities of the AGENT project are in line with Sustainable Development Goals (SDG) of the United Nations (UN), specifically SDG15 (life on land: ‘halt biodiversity loss’), since dissemination of AGENT results will contribute to increased agrobiodiversity. In the long term, we also impact on SDG1 (‘no poverty’) and SDG2 (‘zero hunger’) as better documented archiving and better-informed selection of GenRes will enable the future breeding of crops more durable under changing climate and environmental conditions. This will support the stability of income to farmers and help sustain sufficient food supplies, especially as concepts proven in AGENT are transferred to a broader network of GenRes collections and stakeholders at the international scale.
AGENT Experimental Field at partner institution CREA-CI
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