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IMAGE Report Summary

Project ID: 677353
Funded under: H2020-EU.3.2.

Periodic Reporting for period 1 - IMAGE (Innovative Management of Genetic Resources)

Reporting period: 2016-03-01 to 2017-08-31

Summary of the context and overall objectives of the project

The Global Plan of Action for Animal Genetic Resources (AnGR) is a reference document to set up the strategy safeguarding animal genetic diversity and promoting its sustainable use. Gene banks collections constitute a backup and are currently poorly used. Breeding and conservation programmes are complex by nature, since multiple targets (conservation of diversity, improvement of productivity, maintenance of fertility and fitness) are aimed at simultaneously. The overall objective of IMAGE is to develop genomic methodologies, enhance reproductive biotechnologies, and sustain an integrated bioinformatics approach for a better knowledge and exploitation of animal genetic resources. The ultimate goal of the project is to demonstrate the benefits brought by gene banks to the development of more sustainable livestock farming systems. To achieve this goal, IMAGE is organised in 6 research and innovation Work Packages (WP), one Outreach WP (WP7) and the coordination WP.

The aim of WP1 is to include stakeholders in the decision process and to test the adoption of solutions proposed by other WPs of the project through demonstration and technology transfer.
WP2 will map the characteristics of gene bank collections throughout Europe, review the relevant regulations and enable detailed technical and socio-economic analysis, up to the rationalization of collections. WP3 is addressing the efficiency of the conservation methodologies applied to germ cells/tissues across species. It will focus on the most difficult cases, here the chicken (semen, gonads, germ cells) and the pig (embryo), and favour the less invasive possible methods. WP4 aims at developing and using innovative means of genetic characterisation combining the latest genotyping and sequencing techniques, with the development of new strategies for analysis. WP5 will set up a conceptual model for the integration of the four classes of data (collections, genomics, georeferences and phenotypes) into one database as the basis for across-classes and across-Europe data analysis. The IMAGE data portal will feature a diversity browser and an interactive web interface to guide the use of genetic material. WP6 will develop methods to make the best use of the improved knowledge on breeding populations and gene bank collections, in order to support informed conservation decisions and design better targeted programmes. Current approaches will be upgraded with functional information. WP7 will enhance the effective use of research results through converting them into a suitable format to a broad public of stakeholders and will involve third countries, with the help of FAO. Guidelines will be developed for a judicious adoption of new tools to enhance management of animal gene banks. A training strategy will be set up to strengthen human resources for AnGR conservation programs.

Work performed from the beginning of the project to the end of the period covered by the report and main results achieved so far

The IMAGE Dialogue Forum met first at EAAP2016 conference and identified general opinions from a broad spectrum of stakeholders. The second event (at EAAP2017) discussed the impact of sanitary regulations with a consensus to support the creation of specific measures for gene banks and initiate a dialogue with the European Commission. A sociological online-survey was implemented to determine stakeholder attitudes toward genetic innovation. A specific ABS survey was prepared.
WP2 implemented a Europe-wide survey on germplasm and genomic collections and aggregated a draft survey report. A diagnostic tool for the quality management was developed and implemented through in-depth interviews. A costs survey was performed in order to analyse gene bank operations from an economic point of view. Case studies were identified to contribute to the rationalization of gene bank strategies.
All the tasks of WP3 have been initiated. The main results so far include improvements in the semen cryopreservation process and progress in the knowledge about biological factors of semen quality. The quality of vitrified pig embryo is under study. The chicken embryo cannot be preserved, so that improved treatments are being developed to preserve and use primordial germ cells (PGCs) or gonadic tissues.
WP4 has identified and integrated the genomic data sources for the whole project. Focussed sequencing efforts are currently underway to generate new data for gene bank collections of chicken, pig, and ruminants. Results so far show the potential of using genomic information to discover deleterious variation (a potential basis for inbreeding depression) and to predict functional variation that has been positively selected in a breed.
WP5 has defined a data-flow plan: gene bank data from the main sources (Cryoweb, well organized National DBs, and others) are transferred to the EMBL-EBI's BioSamples database through an injection tool. Storage and long-term sustainability are ensured by BioSamples. The common data pool (CDP), a local database, will be routinely updated by downloads from BioSamples, ENA and EVA in order to have a database directly linked to the portal.
WP6 has created the R-package “RekomBre”, to optimise a large variety of breeding schemes based on deterministic formulas and stochastic simulation approaches. A demonstration project aiming at the introgression of a known mutation into a high-performing layer line has been designed and started. The optimum contribution selection methods have been analysed and areas requiring methodological developments have been identified. The limitations of describing the complex inter-locus segregation variances and covariances in modelling the development of IBD across the genome have been overcome through the use of covariance functions.
IMAGE partners participated in National and International scientific meetings, which allowed a broad dissemination of the project in the scientific community. Communication with the general public was established through a website, project flyer, newsletter and social media. Partners organised face-to-face meetings with national stakeholders. Training needs and opportunities were identified and a global training plan was developed.
The kick-off meeting took place in Paris, May 19-20, 2016. The data management plan and the risk management plan were discussed at the first annual meeting in Goettingen, March 21-23, 2017, which featured plenary sessions with WP progress reports, two invited talks from other EU projects, a PhD session, and the feedback from the IMAGE Scientific Advisory Board. Three parallel sessions were organised for single- and joint WP meetings.

Progress beyond the state of the art and expected potential impact (including the socio-economic impact and the wider societal implications of the project so far)

At this stage, progress beyond the state is observed at the following levels:
- a growing involvement of stakeholders with a major concern regarding the impact of sanitary regulations and ABS regulations on exchanges of animal genetic resources,
- a better knowledge of the gene bank collections in Europe,
- a growing motivation towards quality management system for animal gene banks,
- the development of new approaches to enhance reproductive biotechnologies,
- an inventory of molecular data on gene bank collections showing the fragmented access to data because of different SNP chips or different access rules,
- an innovative data model for the IMAGE portal in order to centralize access to various sources of information on gene bank collections,
- the “RekomBre” package as a new simulation software to model and optimize conservation schemes,
- the full involvement of third countries participants in the training activities.

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