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Innovative Management of Genetic Resources

Periodic Reporting for period 2 - IMAGE (Innovative Management of Genetic Resources)

Reporting period: 2017-09-01 to 2019-02-28

Gene banks collections constitute a backup for animal genetic resources. 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.

WP1 will include stakeholders in the decision process and collect opinions on challenges and solutions proposed by other WPs.
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 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. 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-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. 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.
The IMAGE Dialogue Forum has taken place each year. The discussion initiated in 2017 had an impact on the preparation of the delegate act of the new EU Animal Health law, which now includes the possibility to set up specific measures for gene banks by national authorities. In addition to a sociological online-survey and an ABS survey, IMAGE implemented an ethical survey regarding the choice of breeds for cryoconservation.
WP2 implemented a Europe-wide survey on germplasm and genomic collections. A diagnostic tool for the quality management was developed and implemented through in-depth interviews. Results from economic optimization showed that cooperation between European gene banks could decrease the overall cost of gene banking for a given number of breeds. Several case studies (18) were identified to contribute to the rationalization of gene bank strategies.
All the tasks of WP3 are progressing with very encouraging results. Improvements in the semen cryopreservation process have been validated and biological predictors of semen quality have been identified. Modelling the vitrification process has proven to be an efficient approach to improve quality of vitrified pig embryo. Significant progress with primordial germ cells (PGCs) and transfer of gonadic tissues has been made in chickens.
WP4 has identified and integrated the genomic data sources for the whole project. New data on gene bank collections have been produced for chickens, pigs, and ruminants. Results so far show the potential of using genomic information to discover deleterious variation and to identify genes determining morphological variation among local breeds. The design of a multi-species SNP chip is now initiated to propose a cheap and convenient tool to assess diversity in gene banks.
WP5 has defined a data-flow plan from the main sources (Cryoweb, well organized National DBs, and others) 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. The injection tool is now being tested on national data sets.
WP6 has finalized a publicly available R-package “MoBPS”, to optimise a large variety of breeding schemes including scenarios for using gene bank material. The demonstration project aiming at the introgression of a known mutation into a high-performing layer line has reached the third generation. Selection signatures in a Spanish cattle breed have been identified with a new generic Hidden Markov Model which analyses allele frequency trajectories by comparing old to recent molecular data produced in WP4.
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. Several training sessions were organized in third countries (Argentina, Colombia) and in Europe (PhD training in Wageningen).
The Annual Meeting of IMAGE successively took place in Goettingen, Vienna and Brescia. Each of them featured plenary sessions with WP progress reports and parallel sessions for single- and joint WP meetings. The program always included two invited talks from other EU projects, a PhD session, and the feedback from the IMAGE Scientific Advisory Board.
At this stage, progress beyond the state is observed at the following levels:
- recognition of the need for specific measures for local breeds in the delegate act for germplasm exchanges of the EU Animal Health law
- participation of a range of stakeholders in the ethical survey regarding the choice of breeds for cryoconservation
- a better knowledge of the gene bank collections in Europe,
- a growing motivation towards quality management system for animal gene banks,
- an economic optimization model to minimise cost of preservation for a given number of breeds in Europe
- the development of new approaches to enhance reproductive biotechnologies,
- an inventory of molecular data on gene bank collections
- the production of sequencing data on gene bank collections
- the preparation of a multi-species SNP chip to facilitate the assessment of genetic diversity stored in gene banks
- an innovative data model for the IMAGE portal in order to centralize access to various sources of information on gene bank collections,
- the “MoPBS” package as a new simulation software to model and optimize conservation schemes,
- the full involvement of third countries participants in the training activities.
IMAGE side-event at FAO : coordinator, WR and FAO partners with a member of the SAB
IMAGE WorkPackages and interdependencies
IMAGE Kick-Off meeting, Group Photo