Periodic Reporting for period 3 - IMAGE (Innovative Management of Genetic Resources)
Reporting period: 2019-03-01 to 2020-02-29
Gene banks collections constitute a backup for animal genetic resources and make an integral part of breeding and conservation programmes. 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 is to demonstrate the benefits brought by gene banks to the development of more sustainable livestock farming systems.
IMAGE was presented to stakeholders from the livestock sector in four dialogue fora to raise awareness about the value of gene banks. The large survey on ethical perceptions of gene banking revealed the main drivers for acceptance or rejection of the use of new technologies, like embryo grafting or cloning, in the context of conservation of livestock populations. A framework has been produced to support rationalization of collections considering for the first time the cost-effectiveness of gene banking at European or national scale. A gap analysis showed the need to strengthen cryoconservation of germplasm towards local breeds before they became endangered and too much inbred. The usefulness of a quality management system was underlined to sustain gene bank operations. New methods have been tested and validated for germplasm preservation, particularly in birds with improved procedure for semen and new developments on primordial germ cells which will accelerate recovery of lost genotypes.
Analysis of new molecular data combined with pre-existing data sets led to identify genomic regions associated to environmental variation in sheep; a case study in cattle has shown the interest of keeping ancient samples to study the dynamics of selection response. A low-cost genotyping tool has been developed for several species and will be made publicly available in order to help characterize the diversity in gene banks across countries and to compare it with the on-farm diversity. A new web portal is open to connect gene bank samples with all associated data. A new software, MoBPS, is now publicly available to guide the introduction of gene bank material into breeding programmes.
All innovations have been disseminated in Conferences and training sessions held in Europe, Argentina, Colombia, Egypt and Morocco. IMAGE achievements will be used to update FAO guidelines for cryoconservation of animal genetic resources.
IMAGE was presented to stakeholders from the livestock sector in four dialogue fora to raise awareness about the value of gene banks. The large survey on ethical perceptions of gene banking revealed the main drivers for acceptance or rejection of the use of new technologies, like embryo grafting or cloning, in the context of conservation of livestock populations. A framework has been produced to support rationalization of collections considering for the first time the cost-effectiveness of gene banking at European or national scale. A gap analysis showed the need to strengthen cryoconservation of germplasm towards local breeds before they became endangered and too much inbred. The usefulness of a quality management system was underlined to sustain gene bank operations. New methods have been tested and validated for germplasm preservation, particularly in birds with improved procedure for semen and new developments on primordial germ cells which will accelerate recovery of lost genotypes.
Analysis of new molecular data combined with pre-existing data sets led to identify genomic regions associated to environmental variation in sheep; a case study in cattle has shown the interest of keeping ancient samples to study the dynamics of selection response. A low-cost genotyping tool has been developed for several species and will be made publicly available in order to help characterize the diversity in gene banks across countries and to compare it with the on-farm diversity. A new web portal is open to connect gene bank samples with all associated data. A new software, MoBPS, is now publicly available to guide the introduction of gene bank material into breeding programmes.
All innovations have been disseminated in Conferences and training sessions held in Europe, Argentina, Colombia, Egypt and Morocco. IMAGE achievements will be used to update FAO guidelines for cryoconservation of animal genetic resources.
Each year, the IMAGE Dialogue Forum has gathered representatives of policy makers, NGOs and academics. One outcome was a contribution to the delegate act on ‘Germinal products’ of the new EU Animal Health regulation, in order to allow for national derogations for gene banks. A review on Access and Benefit Sharing provided a guideline on how to interpret the Nagoya Protocol for gene banks. An ethical survey provided insight on acceptance of new technologies and supported the complementarity between in situ and ex-situ conservation of livestock populations.
A framework has been proposed for rationalization of gene bank collections, the main criterion being to maximise cost-effectiveness for current and future users. A gene bank should define its strategy in cooperation with its stakeholders. National case studies were used to illustrate rationalisation aspects. Gap analysis revealed an insufficient conservation efforts for local breeds. Economic optimization showed that enhanced cooperation between European gene banks could decrease the overall cost of gene banking for a given number of breeds.
New protocols for reproductive biotechnologies were validated: improvements in the semen cryopreservation process; biological predictors of semen quality based upon new proteic or proteomic markers or upon integrity assessment of nucleic acids. New marker genes were highlighted to assess embryo quality in pigs. Significant progress with primordial germ cells (PGCs) and transfer of gonadic tissues was achieved in chickens with application to the preservation of local breeds in Hungary and France.
The molecular variation detected by genotyping and sequencing led to new knowledge: (i) detection of genes important for adaptation to environmental variation with landscape genomics (ii) identification of functionally relevant polymorphisms and causal mutations for morphological traits in chickens (iii) distinction between old and recent selection signatures in cattle (iv) monitoring of inbreeding in local breeds under a conservation programme. A multi species SNP array incorporating neutral, functional and ancestral markers was developed in order to map genetic diversity.
The IMAGE web portal integrates data from gene banks and collections with genomics data, geographical information systems data, and other information generated by IMAGE. The diversity browser is a stand-alone tool, computing principal component analysis (PCA) of a reference dataset and a batch of samples of interest. An interactive web interface is provided to guide the use of genetic material.
A generic geneflow concept has been developed to feature any breeding or conservation program. The simulation software MoBPS (Modular Breeding Program Simulator) is publicly available as an R-package with a graphical user interface. It was successfully applied to the introgression of a new trait (blue egg shell color) taken from a local breed into a high-performing layer line, and to the optimization of the conservation of a Colombian cattle breed. A new method for a time-series analysis showed the usefulness of long term gene bank collections for the detection of selection signatures.
The major outcomes were presented at the final scientific conference of IMAGE and were assembled to propose an update of the FAO guidelines for cryoconservation. Training sessions took place in third countries and in Europe: eight courses were organized overall, with 239 trainees from 36 countries.
IMAGE organized two sessions at the EAAP conference, one was devoted to synergies with other H2020 projects from the same Common Dissemination Booster, Fitter Livestock Farms. The usefulness of gene banks was presented at the Animal Task Force meeting on adaptation of livestock to climate change. IMAGE published its policy brief at the end of 2019.
A framework has been proposed for rationalization of gene bank collections, the main criterion being to maximise cost-effectiveness for current and future users. A gene bank should define its strategy in cooperation with its stakeholders. National case studies were used to illustrate rationalisation aspects. Gap analysis revealed an insufficient conservation efforts for local breeds. Economic optimization showed that enhanced cooperation between European gene banks could decrease the overall cost of gene banking for a given number of breeds.
New protocols for reproductive biotechnologies were validated: improvements in the semen cryopreservation process; biological predictors of semen quality based upon new proteic or proteomic markers or upon integrity assessment of nucleic acids. New marker genes were highlighted to assess embryo quality in pigs. Significant progress with primordial germ cells (PGCs) and transfer of gonadic tissues was achieved in chickens with application to the preservation of local breeds in Hungary and France.
The molecular variation detected by genotyping and sequencing led to new knowledge: (i) detection of genes important for adaptation to environmental variation with landscape genomics (ii) identification of functionally relevant polymorphisms and causal mutations for morphological traits in chickens (iii) distinction between old and recent selection signatures in cattle (iv) monitoring of inbreeding in local breeds under a conservation programme. A multi species SNP array incorporating neutral, functional and ancestral markers was developed in order to map genetic diversity.
The IMAGE web portal integrates data from gene banks and collections with genomics data, geographical information systems data, and other information generated by IMAGE. The diversity browser is a stand-alone tool, computing principal component analysis (PCA) of a reference dataset and a batch of samples of interest. An interactive web interface is provided to guide the use of genetic material.
A generic geneflow concept has been developed to feature any breeding or conservation program. The simulation software MoBPS (Modular Breeding Program Simulator) is publicly available as an R-package with a graphical user interface. It was successfully applied to the introgression of a new trait (blue egg shell color) taken from a local breed into a high-performing layer line, and to the optimization of the conservation of a Colombian cattle breed. A new method for a time-series analysis showed the usefulness of long term gene bank collections for the detection of selection signatures.
The major outcomes were presented at the final scientific conference of IMAGE and were assembled to propose an update of the FAO guidelines for cryoconservation. Training sessions took place in third countries and in Europe: eight courses were organized overall, with 239 trainees from 36 countries.
IMAGE organized two sessions at the EAAP conference, one was devoted to synergies with other H2020 projects from the same Common Dissemination Booster, Fitter Livestock Farms. The usefulness of gene banks was presented at the Animal Task Force meeting on adaptation of livestock to climate change. IMAGE published its policy brief at the end of 2019.
- a better knowledge of the gene bank collections in Europe,
- a comprehensive rationalization framework for the rationalization of collections
- a growing motivation towards quality management system for animal gene banks,
- specific measures for gene banks in the delegate act for Germinal Products of the new EU Animal Health law
- a large scale ethical survey regarding the choice of breeds for cryoconservation
- an economic optimization model to minimise cost of preservation for a given number of breeds in Europe or within a country
- new protocols enhancing the success and reliability of reproductive biotechnologies,
- new molecular data on gene bank collections
- a new multi-species genotyping tool 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 optimize breeding and conservation programmes
- a strong involvement of third countries participants in the training activities
- a proposed update of the FAO guidelines for cryoconservation of animal genetic resources
- a comprehensive rationalization framework for the rationalization of collections
- a growing motivation towards quality management system for animal gene banks,
- specific measures for gene banks in the delegate act for Germinal Products of the new EU Animal Health law
- a large scale ethical survey regarding the choice of breeds for cryoconservation
- an economic optimization model to minimise cost of preservation for a given number of breeds in Europe or within a country
- new protocols enhancing the success and reliability of reproductive biotechnologies,
- new molecular data on gene bank collections
- a new multi-species genotyping tool 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 optimize breeding and conservation programmes
- a strong involvement of third countries participants in the training activities
- a proposed update of the FAO guidelines for cryoconservation of animal genetic resources