Final Report Summary - EADGENE_S (Strengthening the implementation of durable integration of EADGENE)
Executive Summary:
By integrating the key European teams in genomics, bioinformatics, animal health and animal models, EADGENE gathered a critical mass of scientists and a unique access to complementary resources across host and pathogen models. It boosted the development of innovative functional genomics as a powerful tool in veterinary molecular medicine; which contributed to a better understanding of host-pathogen interactions, for the improvement of animal health and food safety.
Building on these achievements, EADGENE_S ensured the longer term integration of European resources in animal disease genomics, grouping together the leading institutions. It strengthened the creation of a sustainable core group of European research centres of excellence, highly committed to integrating their resources and national facilities.
Common research tools and platforms for joint research are being shared and upgraded; the partners are implementing common research methods, standards and protocols; and the project consolidated the skills and expertise throughout the partnership with a programme of workshops, training courses, short-term missions, internships and studentships. EADGENE_S also promoted efficient technology transfer to industry to ensure timely commercialisation of new methods and technologies.
Project Context and Objectives:
Project context and objectives
Animal health issues are of critical importance to European citizens, affecting their health, well-being and lifestyle choices in many ways. Disease control has traditionally relied on interventions. However, animal health is now faced with new challenges and new opportunities. By integrating the key European teams in genomics, bioinformatics, animal health and animal models, the NoE EADGENE had enabled the gathering of a critical mass of scientists and a unique access of complementary resources across host and pathogen models and the development of innovative functional genomics. Building from these benefits, EADGENE_S will ensure a long-term integration of the European resources in animal disease genomics grouping together the leading institutions. It will strengthen durably the creation of a core group of European research centres of excellence highly committed to integrating their resources and national facilities. To achieve this, EADGENE_S will:
1) Expend, share and upgrade common research tools and platforms for joint research projects
2) Further develop common research methods, standards and protocols
3) Maintain, consolidate and further develop high quality common research projects on animal genomics and genetics in Europe
4) Support strategies for durable integration, particularly by providing opportunities for further funding
5) Consolidate the skills and expertise throughout the partnership with a programme of workshops, training courses, short-term missions, internships and studentships
6) Provide platforms for the development, management and dissemination of knowledge
7) Ensure efficient technology transfer to the industry.
Work performed and main results
Joint coordination of research activities: The joint coordination of research activities in EADGENE_S followed the line of successful collaborations initiated during EADGENE, but with the major difference that the current collaborations needed to rely mainly on in-kind contributions, which necessarily limited their scale. Notwithstanding this difference, partners have been coordinating successfully their activities reflected by extensive on-going collaborations, both formal and informal, between the partner Institutes. Further, major proposed consortia for last Framework VII calls and future Horizon 2020 calls are based around EADGENE partners. Research priorities have been identified through the activities of the established working groups.
Development and sharing of common research tools and platforms: Particular attention was paid to High Throughput Sequencing (HST) technologies and methods to analyse genome-wide data. This included structural and functional genomics, the bioinformatic and analytical tools necessary to interrogate the obtained data, and the experimental facilities necessary to generate e.g. the animal phenotypes and the genomic data. This was achieved through three contrasting tasks, which addressed the issue at three levels: resources and facilities, bioinformatics tools and approaches, and analytical tools and techniques.
Joint research training, workshops and mobility: Several dedicated workshops have been organized (Gene Network Analysis, Visualization of genomic data, and systems biology, Advances in genomic selection, Next generation sequencing data processing, miRNA technology). Also, an international conference on Mastitis resistance was co-organized. Mobility grants have been successfully selected (13 grants for exchanges between EADGENE_S partners and non EADGENE_S partners). Common fund for exchange of genomic resources was used.
Communication and technology exchange: The EADGENE_S website has been continuously updated. It ensured also that the public was informed about the results of both EADGENE and EADGENE_S, their tools and resources and on training & career opportunities and relevant events. The EADGENE_S Industry Day presenting research with potential applications for breeding was organized with industry representatives from the animal breeding sector in Europe, as well as visits of EADGENE_S scientists to Industries. Final conference “Healthy livestock and people” was organized gathering scientists, industry and stakeholders. Films, brochures and flyers were disseminated, with emphasis on potential applications of animal disease genomics research for breeding.
Expected results and impacts
The expected results are more efficient research efforts by means of coordination and integration achieved by the scientists, able to integrate their resources and facilities, leading to a sustainable integration of the research. The related expected long-term impact is an ongoing structuring impact on the research in the field of animal disease genomics and increased applications of animal disease genomics research for breeding.
Project Results:
a) WP1: Joint coordination of research activities
Objective
• To coordinate research programme implementation among the EADGENE_S partners in order to enable a stronger integration between key European animal genomics and health research organisations to efficiently cope with new research needs.
• To implement multidisciplinary projects in the Animal Genomics & Animal Health area and attract funding for the financial viability of EADGENE ERG by - Identifying existing and future needs. - Prioritising recommendations and coordinating EADGENE_S members planning for animal genomics and infectious disease, particularly on host-pathogen interactions, according to society and industry needs. - Maintaining, consolidating and further developing high quality common research projects on animal genomics and health in Europe. - Providing for sustainable funding for the EADGENE ERG.
Approach
Research agenda coordination
• Establishing priorities for future actions and a detailed road map to implement optimal joint research activities.
• Identifying research priorities, knowledge gaps, tools and method necessary to deal with the identified research challenges in each of the research thematic priorities within their field of expertise
Joint execution of research projects
• EADGENE_S common research agenda implemented through the collaborative work of the Working Groups.
• EADGENE_S common research agenda implemented with the support from a range of sources, including in-kind contributions from each EADGENE_S partners, industry funding and third-party private finance, the Framework Programme, other sources of European funding and national research programmes.
• Implementing projects through - Labelling projects resulting from the WG initiatives to promote the project in existing calls at a regional, national, trans-national and European level ; Setting up specific calls; Implementing common or coordinated plans to facilitate the sharing or management of data, tools & resources (see WP2); Setting up of research proposals submitted to national, European and international funding bodies
Financial viability of EADGENE
• Self-financing through the institute’s own resources to support their participation in research
• Annual membership fee used to fund additional tasks in addition to the efforts brought as in-kind
• Additional funding sources (collaboration with industry, collaboration with non-profit-making private foundations, successful proposal submissions at regional, national, European and international calls)
Achievements
The joint coordination of research activities in EADGENE_S followed the line of successful collaborations initiated during EADGENE, but with the major difference that the current collaborations needed to rely mainly on in-kind contributions, which necessarily limits their scale. Notwithstanding this difference, partners have been coordinating successfully their activities in running projects and joint efforts in organising answers to new calls. Identification of research priorities was completed through the activities of the established working groups.
Task 1.1: Research agenda coordination
Prior identification of research thematic priorities:
When preparing the project, three research thematic priorities had been identified, based on the research projects and identified gaps during the EADGENE NoE period:
1. Studying the genome - environment interactions and the resulting physiological processes that underlie health traits and that are significantly modulated by environmental factors, in particular pathogens
2. The identification of molecular variation (genes, DNA markers) and molecular “signatures” (transcriptomic, proteomic, metabolic profiles) associated with disease susceptibility traits using high throughput genomics technologies
3. The development of tools and strategies to modulate biological processes underlying health traits by using the knowledge generated within 1) and 2)
Around these three priorities, three interactive Working Groups (WG) have been organized at the beginning of the project. During the Kick-off meeting, two leaders per WG were chosen, experts in their WG field and covering different partner institutes. One to four scientists per WG per partner were identified, forming a core group of experts covering the three research thematic.
In order to identify research priorities, knowledge gaps, tools and methods necessary to deal with the identified research challenges in the three research thematics, a questionnaire has been elaborated in the first period. In order to gather common and specific priorities, a unique questionnaire for the three WGs was designed, divided in four parts, a first general part common to all WGs and three following parts addressing specific issues for each WG. Answers (detailed answers given in Annex of periodic report Year 1) to the questionnaire were collected by the WG leaders and a first feedback was conducted. Two conference calls were organized within respondents of WG2 & WG3. As the main conclusion from the feedback and conferences was the need and wish to share data, it was decided to organize a two day joint meeting of WG2 & WG3 (22nd and 23rd of October 2012 in Brussels). The meeting included:
1. Presentations from invited speakers on data integration, visualization and analysis
2. Presentation on dataset to be shared from WG2 and WG3 participants
3. Presentation on new methods developed by WG2 and WG3 participants
4. A general Discussion and 1 to1 meetings.
The outcome of this interactive workshop was a strengthened common interest for further sharing experimental data and exchanging on methodological developments. Request for using common resources to acquire new data was expressed. Proposals for using the allocated EADGENE_S fund for exchange of genomic resources were presented. A selection and validation of the proposals was further made by the Management Team (see task 3.3 Fund for exchange of genomic resources).
In the same line, clear gap in appropriate analytical tools to analyse and interprete gene expression data was identified and again highlighted during the final miRNA workshop. Decision for producing a common large set of expression data was decided (see WP2 task 2.3).
“EADGENE_S Roadmap”: Research priorities, resources and needs
An updated review of the feedback questionnaire was performed to establish the road map of EADGENE_S by updating on research priorities, resources and gaps (see Annex 1).
Highlights are presented:
Main areas of EADGENE_S research:
• Characterization and genetic analysis of immune responses / immunocompetence, immune development, immunomodulation, immune gene variation and the impact on disease susceptibility, (all species)
• Genetics of infectious diseases, disease resistance and breeding for disease resistance (all species)
Main issues of EADGENE_S research:
• Preventive animal health
• Breeding for disease resistances
• Vaccination strategies
• Antimicrobial resistance, alternatives to antibiotics
• Nutritional health (Microbiota)
• Environmental footprint
• Animal health management
Contribution to the aims/objectives of EADGENE_S:
• Expertise, experimental work, production of (large-scale) data and development of genomic and proteomic, and statistical methodologies, which can be all shared and contributing to a better understanding of animal health related mechanism and genetic control.
• Sharing knowledge, upgrading, developing common research tools, competences and methods in order to develop joint research projects, especially using high throughput post-genomics approaches (integrative biology)
Main research questions/strategies for EADGENE_S to address:
• EADGENE should continue to be the European reference in research related to animal food health and quality, the main lines of research in EADGENE being: animal breeding for disease resistance, nutrition and animal health and looking for alternatives to the use of the antibiotics
• Optimization of resources between EADGENE_S partners.
• Definition of new phenotypes and measures for disease surveillance and for disease resistance
• Sharing and developing methods to integrate genomic, transcriptomic and proteomic data from different biological levels and platforms
• Providing integrated data in an accessible format to researchers and industrial collaborators.
• Filling up the bridge between academia and industry
Prospects through multidisciplinary research within EADGENE_S “follow up”
Done already but could be better shared or enriched:
• To be better exchanged: methodologies, joint data gathering (from experimental and field data) facilitating large scale health data scoring and analysis (workshops, Meta analysis)
• To be better shared: expertise/experience in in vivo and in vitro challenge experiments. High-throughput sequencing, bioinformatics
• To be better developed: models combining epidemiology, economics and genetics
• To be better agreed: definition and methods to estimate resistance/tolerance
• To be better accessed: both performance, parasite burden, measure of immune response
Not been done adequately and needs to be further developed through collaboration
• Improve the mechanisms for communication and collaboration between groups inside EADGENE_S (to sustain virtual laboratory of reference in the field of animal genomics )
• Common controls for phenotype analysis between partners and development of new phenotypes
• Stronger interactions between biologists and statisticians
• Uniform analytical approaches
• Development of visualisation tools
• Animal disease trait ontology
• Metagenomic studies
• Systems biology approaches
• Evaluation of the effects of genomic discoveries on resistance/tolerance at the long term
Done but need to be addressed at a different scale
• Changing scale from animal to herd/population definition of resistance to allow implementation in animal breeding & improving dialogue with breeding companies
• Possibility to have validation populations for large scale studies and validate results in other breeds and in different environments
• Linking genome variation to large scale recordings of animal health traits and (Re) defining health traits.
• Evaluating the impact of individual resistance/tolerance at the population levels in short and long terms, in economic environments, on both hosts and parasites.
Techniques still missing looked for
• All techniques that allow the use of rapid and cheap methods for large scale (deep) phenotyping (at the population level) for complex traits such as disease resistance.
• All developments around Gene network inference from RNASeq data, as well as methods to jointly analyze heterogeneous genomic data (transcriptome, proteome, etc.)
Beyond the EU contract period of EADGENE_S, partners wish that EADGENE would continue to be the European reference in research related to animal health and food safety.
EADGENE_S partners have in common a core of diverse and complementary research activities reflecting a strong potential for a joint coordination of research, addressing common social and environmental issues. These research activities are developed around the dissection of complex health traits, covering a complementary range of diseases and immune responses, and using an up-to-date and original panel of genomic tools and novel methodologies, which are quite unique (see full list Annex 1, answer 4.d.).
The main added value of EADGENE_S remains the capacity of sharing and optimizing resources, developing innovative strategies, for a better use in generating new knowledge and applications via technology transfer to industry.
Emerging research fields to be further developed in the future are metagenomics and system biology (see details in Annex 1, WG1).
Main gaps to address still include integration of data from different sources and large scale recording of health traits that the scientific community wishes to best exploit by i.e. meta-analysis. Ultimate goal is to identify easy to measure health biomarkers.
Needs for tools or methods continue to evolve (like the development of visualization tools which has been adequately dealt with during the project) and new needs will arise. Once identified, best and successful ways to address new needs remain dedicated workshops to allow joint learning and facilitate further collaborations.
Task 1.2: Joint execution of research projects
Success in Integrating Activities in EADGENE and subsequently in EADGENE_S is reflected by extensive on-going collaborations, both formal and informal, between the partner Institutes.
Implementation of the research agenda through the collaborative work of the Working Groups
Partners in EADGENE_S have been carrying on some of their collaborations initiated during EADGENE on their own support in the different working groups. Lists of projects or research thematic relevant to the different WG are listed in Annex 1. Some of these projects were presented during the WG2&3 meeting, favouring exchange of data and methodologies. Implementing common or coordinated plans has been acilitating the sharing or management of data, tools and resources (see WP2);
All these joint elaboration and execution of various research projects have been greatly facilitated by the mutual knowledge of each other resources and expertise, acquired during the previous EADGENE then EADGENE_S periods.
Implementation of the research agenda with the support from external sources
Most of the informal or formal collaborations have been taken place, using support from a range of sources, including in-kind contributions from each EADGENE_S partners, contributions raised through national funding.
Mechanisms to label projects to promote the project in existing calls at a regional, national, or trans-national level were used. Several successful examples of its kind are - a German research network on mastitis build beyond the EADGENE(_S) partnership including industry, which was greatly facilitated. – several French projects applied to a large thematic program on the “sustainable management of animal health” aiming at promoting interdisciplinary research at the institute level which were facilitated by running EADGENE(_S) projects.
Significant collaborations from subgroups of EADGENE_S partners have been occurring thanks to joint participation to running European projects, like “3SR”, “PoRRSCon”. Joint proposals have been submitted and succeeded to the European infrastructure project “NADIR”, to have jointly access to disease challenge facilities. Also, several EADGENE_S partners are collaborating through the training Erasmus EGS-ABG, an European Graduate School in Animal Breeding and Genetics, through jointly PhD projects, together with an industrial partner in most cases, illustrating a successful third-party private financing mechanisms.
Implementation of the research agenda through strategic coordination and relationships
EADGENE_S partners have been setting up research proposals submitted to national, European and international funding bodies. Notably, mutual knowledge has been also greatly favouring the participation of a major part of the current EADGENE_S consortium to the preparation of two proposals at the last FP7 call, as well as to the ANIHWA Era-Net calls. And major consortia preparing the future Horizon 2020 calls are also based around EADGENE_S partners. Implementation of the research agenda, indentifying main gaps and issues relevant for future prospects have been well coordinated with larger organisations like the FABRE-TP platforms, several EADGENE_S partners having also active members in the platform. Coordination and lobbying has been also very efficient with the ATF (Animal Task Force), illustrated by the final co-organized conference “Healthy Livestock and People�.
Strategic relationships have been also encouraged between EADGENE_S partner institutes thanks to the mutual knowledge and trust gained during both EADGENE(_S) projects. These were for example illustrated by increasing requests of EADGENE scientists to act as experts or reviewers in each other institutes. These strategic relationships are paving the way for sustainable construction of the ERA in the field of animal disease genomics.
Task 1.3 Financial viability of EADGENE
Projects conducted in EADGENE_S have been made possible because these are fitting the strategic orientation of most partner institutes, as detailed in Annex 1 (question 6). But the execution of joint research projects has been relying mostly on the self financing through the institute’s own resources. These were in-kind participation of scientists, use of fund raised through internal or national call, access to partner facilities to organize workshops, access to data, or also very valuable access to research infrastructures and animal resources. Additional funding sources from joint international call have been limited (ex “NADIR”) but preparation for such next infrastructure calls or large collaborative projects are now in process. Finally, request to partner institutes for an annual membership fee hasn’t been a possible option, given the limited financial flexibility of most EADGENE_S partners at the moment. Partner institutes that could participate are already sustaining complementary bodies like Technology Platforms (ex. FABRE-TP) or projects (ex. Discontools), with which we have to join forces in the most efficient way.
b) WP2: Development and sharing of common research tools and platforms
Objective
• To develop, harmonise and update the virtual and physical resources, tools and platforms needed to conduct future research in the field of animal genomics and animal health. This may include databases, biological resources, facilities, analytical tools, common research methods and common analytical methods.
• To apply particular attention to High Throughput Sequencing (HTS) technologies and methods to analyse genome-wide data. This includes: structural and functional genomics, the bioinformatics and analytical tools.
• To update existing resources and approaches will to meet the needs of a future transnational research projects on animal genomics and animal health, accounting for the rapid rate of change in current state-of-the-art and technologies.
Approach
Integrating Biological Resources and Facilities
• Identify requirements for new shared resources
• Promote sharing and coordination between partners (to avoid unnecessary duplicated efforts)
• Facilitate access and optimise the use of expensive high throughput analysis equipment
• Establish good laboratory practices and protocols for production of high quality comparable results from different laboratories
• Provide (or update) a legal framework for sharing to protect intellectual property rights
Integrating Bioinformatics Tools and Approaches
• Exchange best practice in the development of Bioinformatics tools
• Identify strategic requirements in Bioinformatics
• Advance the annotation of newly sequenced genomes
• Provide know-how and expertise to curate and interpret HTS data
Integrating Analytical Tools and Techniques
• Identify appropriate discovery pipelines and experimental designs in animal genomics and health
• Identify key requirements and gaps in analytical tools and approaches
• Encourage best practice in genomic data analysis by hosting workshops or specific training
Achievements
Task 2.1: Integrating Biological Resources and Facilities
Shared resources:
All partners were contacted for ideas for new resources they would like to see established (MS5). This resulted in two final suggestions for new common resources (Deliverable D2.2). Both of these comprised requested sequence information on available biological samples:
A) Analysis of microRNA (miRNA) in the udder of E. coli infected cows (involving two partners)
B) Genomic sequencing of bovine S. aureus strains (involving four partners)
The two sequencing projects have now been performed and EADGENE_S funding was allocated from Task 3.3 "Fund for exchange of genomic resources". The resulting data are being submitted to publicly available databanks (such as GenBank). These sequence data constitute important common resources for future research on host-pathogen interactions related to an animal disease (mastitis) which results in large economic losses for the European livestock industry. These data are also of general relevance for understanding of the mechanisms deployed by host mammals to combat infectious disease. The sequenced S. aureus strains will be available for further experimental analysis, including challenge studies, through collaboration.
Updates on legal issues, resources and facilities:
During the previous EADGENE network several resources designed to facilitate collaborative research were established. These included databases of available resources and facilities, a model Material Transfer Agreement to regulate IPR issues, and a list of elements to consider for contracts between a visitor and a hosting facility. It was also important to agree on common sets of rules regarding experimental procedures such as Good Laboratory Practices (GLP), Standard Operating Procedures (SOP) and Quality Assurance/Quality Control (QA/QC).
During the EADGENE_S project partners have been asked to update the databases. This has resulted in updated files listing the present available Biological resources and the Technological facilities and tools (Deliverables D2.2 and D2.3). The updated information will enable partners to share resources and facilities, and to reduce or avoid duplication of effort.
Technologies to analyse genomics, transcriptomics and other responses related to host-pathogen interactions have moved rapidly forward towards ever more high-throughput sequencing since the EADGENE_S work description was produced. Many laboratories now choose to buy such services from commercial companies instead of running own facilities. Consequently organising meeting on advanced "omics" laboratory facilities and technologies was not essential for most partners any more. Hence, formalised meetings of key scientists and lab managers were not specifically organised. Instead, partner scientists engaged in informal discussions on experimental strategies, sample preparation etc., during the other EADGENE_S meetings and workshops which were organised.
The model Material Transfer Agreement and the list of elements to consider for contracts between a visitor and a hosting facility have been updated (Deliverable D2.6). Only slight adjustments to bring the text up to date in accordance with the EADGENE_S contract were necessary. The established legal documents are model contracts that need to be adjusted for each specific case of sharing resources or facilities. Consequently they will continue to be useful for the partners, as well as others, in the future.
Task 2.2: Integrating Bioinformatic Tools and Approaches
Best practice and strategic requirements in bioinformatics tools and approaches:
Outputs from these activities were covered in detail in Deliverable D2.5. A summary of six key areas for consideration is given here in order to give an overview of the topic, provide information on software and provide information and training. These areas are: 1. Data acquisition and quality control, 2. Genome and transcriptome assembly, 3. Sequence alignment, 4. Sequence processing environments, 5. Data storage and transmission, and 6. Training in bioinformatics. Specific software details can be found in Deliverable D2.5.
1. Data acquisition and quality control
Since the beginning of NGS (next generation sequencing), several platforms have been put to market by different manufacturers (Roche 454 GS-FLX Junior, Illumina GAIIx / HiSeq / MiSeq, ABI Solid, Ion torrent PGM, Pacific Bioscience). Information about the costs of a run can be found at: http://www.molecularecologist.com/next-gen-table-2b/.
These platforms use different technologies to sequence bases on light or electricity emission during the nucleotide incorporation. The same platform can also have different generations, different sequencing kits, etc. So, whenever a biologist gets a data set, he or she has to check its quality. One of the main ideas underlying this quality checking phase is the random selection of the sequencing process. The quality checking software packages will give figures on one hand from a random selection process and, on the other hand, from real data. This will permit to check whether or not the sequencing has been done as a random selection. Figures such as the number of reads and the number of nucleotides are also to be considered when you get a dataset. Quality control of the data is one of the first task biologists have to perform when they get the datasets, as described next.
2. Genome and transcriptome assembly
Most farm animal genomes have been sequenced, but for those that are not it is still challenging to sequence and assemble a large genome. The quantity of nucleotides produced per run has increased considerably, but the length of the sequences is still very short. Therefore, it is still difficult to produce large contigs in genome assemblies. In order to create longer reads, some strategies include overlapping both sequenced ends of the same fragment. Others involve breaking down the assembly problem in smaller pieces. Using a whole-genome shotgun approach for large genomes results in having to disentangle all repeats simultaneously. Different groups are working on protocols, such as RADSeq mate pair (http://www.plosone.org/article/info:doi/10.1371/journal.pone.0018561) or Moleculo (http://moleculo.com/) to tag reads coming from the same initial long fragment in order to perform local assemblies. Downsizing can also start with chromosome sorting using FACS (fluorescence activated cell sorter); usually used for very large genomes (http://www.sciencemag.org/content/322/5898/101.full).
New tools are available to bridge contigs and form scaffolds using multiple mate-pair libraries produced by NGS (http://www.ncbi.nlm.nih.gov/pubmed/21149342). PacBio reads can help fill the blocks of undetermined sequences between the contig (http://www.plosone.org/article/info%3Adoi%2F10.1371%2Fjournal.pone.0047768). The scaffolds are ordered in pseudo molecules using optical mapping (http://www.ncbi.nlm.nih.gov/pubmed/17868451) or genetic maps based on RADSeq.
Assembling a large genome is still a challenge but solutions are improving. The bioinformatics community is putting a great effort, e.g. http://www.assemblathon.org into confronting the different assemblers in order to find the best one for each data combination. Certainly, one or more plant genomes should be part of the next test set. New solutions such as minia (http://link.springer.com/chapter/10.1007%2F978-3-642-33122-0_19) enable the assembly of large data sets on a desktop computer thanks to a low memory footprint. But the first draft genome sequence is not the end of the story, and multiple reference genomes will be needed to show all possible structural variations.
3. Sequence alignment
Most of NGS analyses include an alignment of the reads versus a reference. The reference is more often than not the genome of interest but can also be a set of contigs representing the transcriptome of the studied species. Different algorithms have been developed to align short reads. Burrow Wheeler has been one of the most successful in the past years. Many software packages are available to globally align (genomic reads on a genome) or splice align reads (transcript reads on a genome). The community gathered by the 1000 human genome project has set up a standard alignment format called SAM (Sequence Alignment Map). This standard is now widely adopted. Manipulation of the SAM files to sort, merge and index them is done using samtools or an equivalent package.
4. Sequence processing environments
Most bioinformatic software packages are developed implementing a simple command-line interface. Using such packages requires that the user is familiar with a Unix environment, which is not the case for most biologists. The main idea of bioinformatic web processing environments is to mask the complexity of the command line, and the use of HPC clusters, through a simple web interface. These environments are also meant to be a lab books for the users, they store all the process which are launched and as well as the parameters. Many bioinformatic platforms have implemented their local tools and organised training session on these tools.
5. Data storage and transmission
The large data volumes produced by the sequencers induce storage and transfer difficulties. These bottlenecks have to be addressed in order to be able to analyse the datasets. The storage architecture has to be designed in order to permit multiple CPUs (processors) to access the data, at the same time using specialized file systems. Backing up such large volumes is not feasible on traditional tape system. Disk replication is now commonly used in this type of architecture. To optimize the usage of the network, protocols using UDP instead of TCP as transport layer can be used. The Aspera solution set up by NCBI (http://www.ncbi.nlm.nih.gov/ and EBI-EMBL (http://www.ebi.ac.uk/ena/) speeds the transfer more than ten-fold.
6. Training in bioinformatics
The new sequencing technologies are now adopted by a wide range of users, some of which scarcely used the previous generation. These technologies democratize the monitoring of new features of the cells such as transcription factor binding, regulation through small RNAs and methylation. The converging of these two trends results in the need to quickly enlarge the community of people able to process the data. Biologists have to be trained on data quality control and first analysis steps. Many bioinformatic platforms have set up training catalogues covering these topics. For more advanced analysis, such as assembly, the biologists should team up with a group of bioinformaticians.
Advance the annotation of newly sequenced genomes:
Considerable effort has been ongoing amongst EADGENE_S partners, both formally and informally, to enhance the annotation of the sequenced livestock genomes. Deliverable D2.7 describes the formal effects to deliver (to the scientific community) detailed annotation files for current chicken, bovine and pig microarrays, along with the appropriate documentation and user guides to interpret and use this information.
The detailed microarray annotation files may be found at: www.sigenae.org/index.php?id=128. Specifically the latest files are found under the header: Description and Annotation Version 8, Ensembl 69 and RefSeq: December 2012. These files contain annotation for the following microarray chip designs: Chicken 20k, Bovine 24k and Pig 25k. Documentation for these files and also for other resources held on the Sigen@e platform resource may be found at http://www.sigenae.org/index.php?id=9.
We believe that these files will of great value to the wider scientific community for as long as the microarrays remain in use. In principle, detailed and accurate annotation of genes, sequences and features is critical to any study which explores the function of livestock genomes.
Provide know-how and expertise to curate and interpret HTS data:
The expertise and know-how to curate, analyse and interpret HTS data has been provided through (i) the report on report on strategic requirements in bioinformatics (Deliverable D2.5) where an extensive list of training courses is given along with general information on bioinformatics, (ii) the exchange of scientists within EADGENE_S and accompanying informal training, and (iii) a specific 5-day course dedicated to the analysis of genome sequence data (described in Deliverable D2.4).
Task 2.3: Integrating Analytical Tools and Techniques
Identify key requirements and gaps in analytical tools and approaches:
Analytical tools and techniques move beyond the bioinformatic treatment of genomics data, insofar as they provide formalised, usually probabilistic, methods for interpreting data, drawing inferences and providing tools for practical implementation of results. Examples may include the detection of SNPs associated with performance traits or health outcomes, inference of networks and pathways from extensive gene expression data, or analysis of SNP chip data to provide whole-genome estimates of genotypes for traits of importance in the field of animal health.
An extensive summary of requirements and knowledge gaps in this field was provided in Deliverable D2.1. This Deliverable was drawn up after person to person consultation with experts in the field within EADGENE_S. It is important to point out that part of the Task comprised a survey and request to EADGENE_S WP2 members for suggestions to fill unmet needs. The survey failed to elicit concrete suggestions, possibly reflecting the vast and confusing array of analytical tools freely available. We emphasise that this wide choice presents a confusing picture for researchers new to the field, making a summary of requirements and knowledge gaps all the more important.
The tools presented and described in D2.1 fall into three major categories: 1. analysis of genetic marker data, 2. analysis of genome sequence data, and 3. analysis and interpretation of gene expression data. Full details can be found in D2.1 however some pertinent points are as follows.
Analysis of genetic marker data
Analyses of genetic marker data can be statistically and computationally demanding, and it is a huge advantage for any scientist embarking in the field to be R-literate.
Linkage studies are less common now with the availability of high density SNP arrays, however they still have a role to play in some circumstances, particularly in species where limited recombination is seen in one sex as this can enable efficient initial genome scans (e.g. reduced recombination in male salmonids). GridQTL (www.gridqtl.org.uk/) and QTLmap (accessed via https://qgp.jouy.inra.fr/) remain freely available packages of choice for this task. It should be noted that these packages are produced by EADGENE_S partners, UEDIN and INRA, respectively.
Association studies, assuming population-wide linkage disequilibrium between markers and causative mutations, have become feasible with the availability of dense SNP arrays. The platform of choice for animal geneticists wishing to perform association analyses on individual markers, i.e. treating markers as fixed effects, is GenABEL (www.genabel.org/). This suite of packages gives a wide range of options for mixed model association analyses, fully accounting for population structure and genetic relationships amongst animals. Alternatively, mixed model association analyses are readily programmed into generic platforms such a R, where appropriate libraries are available, or performed using general mixed model packages such as ASREML, with appropriate scripting to perform multiple analyses.
Treating markers as random effects (i.e. estimating variance components for markers) is an alternative approach to performing association studies, and it provides a convenient framework for genomic prediction. A well-publicised software suitable for many situations is GCTA. However, “Advanced Complex Trait Analysis (ACTA)” is a modified version of GCTA with dramatically improved computational performance, produced by UEDIN. It is accessible at http://www.epcc.ed.ac.uk/software-products/acta.
Analysis of genome sequence data
Reference genome sequences are now available for most economically important livestock species and individual researchers are now often faced with re-sequence data from individual animals. The challenges are to efficiently align these data against the reference sequence and extract summary data and genome features of interest. Features may include SNPs, indels, methylation patterns, RNAseq quantification, etc.
A huge array of software is available for these sequencing-related tasks, and with high throughput genomics the techniques and requirements have converged across species. A comprehensive list of available software, including the language, licence agreements, required operating system, useful summary and direct link to the software can be found at http://seqanswers.com/wiki/Software/list.
Analysis and interpretation of gene expression data
Software packages for the analysis and interpretation of gene expression and related data are more diverse than for sequence and marker data, possibly reflecting the greater diversity of data sources and research objectives in the analysis. One common objective is gene network analysis, and an important component of network analysis is the visualization and analysis of network graphs. BioLayout Express3D (www.biolayout.org) has been specifically designed at UEDIN for visualization, clustering, exploration and analysis of very large network graphs in two- and three-dimensional space, derived from biological data. This has proven useful for the interpretation of gene expression data in a wide variety of circumstances. It has also been the focus of one of the successful EADGENE_S workshops. Other commonly used packages and repositories are given in D2.1.
Moving forward, we wish draw attention to two identified gaps. Firstly, moving towards post-analysis and interpretation of gene expression data, including regulatory network reconstruction, there is as yet no central repository, just tools available at individual websites. There is an identified need for harmonisation and unification of techniques in this field. Secondly, a desired endpoint of many functional studies is to combine genetic marker and gene expression data. However, methods combining genotype and gene expression data into networks tend still to be in the development stage and require direct contact with researchers in the field. Again, a clear gap in appropriate analytical tools exists.
This gap in appropriate analytical tools to analyse and interprete gene expression data was highlighted during the final miRNA workshop, where all the EADGENE_S participants concluded that there was a big lack of large “real” expression RNAseq data. Further exchanges between EADGENE_S partners, especially on developing methodologies would be possible if there was a common large data set produced, which hasn’t been afforded yet by individual partners. Decision for producing a common large set of expression data was thus decided.
Encourage best practice in genomic data analysis by hosting workshops or specific training:
This task was addressed through the provision of training workshops (i.e. courses aimed particularly at PhD students and young post-docs), one in each of the three areas identified above when identifying requirements and gaps in analytical tools. These areas were: 1. analysis of genetic marker data (focussing on genome-wide selection), 2. analysis of genome sequence data, and 3. analysis and interpretation of gene expression data (utilising and exploiting the software BioLayout Express3D). Details are provided in Deliverable D2.4.
These courses have enabled training for many young scientists within EADGENE_S, as well as providing a welcoming arm to promising young scientists who are currently outside the EADGENE_S network but aim to be centrally involved in the topic. By running these courses, EADGENE_S has facilitated the communication of best practice in these topics and assisted in the training of the next generation of scientists.
c) WP3: Joint research training, workshops and mobility
Objective
• Train researchers and other key staff to be conversant with the theoretical and experimental approaches for the range of disciplines represented in the Network
• Increase the critical mass of skilled scientists and technicians in the area of genomics, and host-pathogen interactions and in the underpinning technologies.
• Establish a higher level of standardisation of methodologies related to the EADGENE_S areas of interest and to define best practices for research approaches and methods for analysis.
• Implement a programme for the exchange and dissemination of resources, materials and information between EADGENE_S members and between academic laboratories and commercial companies to achieve transfer and exploitation of this technology in the commercial sector.
Approach
• The organisation of dedicated training courses, especially for young scientists, on topics relevant to functional genomics and host-pathogen interactions, such as; gene network analysis, visualisation of genomic data, systems biology approaches, disease resistance in farm animals, and functional genomics and breeding in aquaculture (duration 1-3 days per training course).
• The organisation of workshops to increase the critical mass of skilled scientists and technicians in the area of functional genomics, host-pathogen interactions and the underpinning technologies, to define best practises, and to compare experimental approaches and analysis methodologies (together with Tasks 2.2 and 2.3).
• The organisation of workshops in specific areas (for example Salmonella infections in chickens, mastitis in cattle, etc.) to exchange and discuss research outcomes, to define remaining knowledge gaps, and to discuss strategies for developing complementary approaches or joint research projects.
• Facilitating short to medium term exchanges of staff between members of the consortium and between academic laboratories and stakeholders (governmental bodies, commercial companies) to achieve transfer and exploitation of relevant knowledge and technology in the animal sector. In addition, the exchange of genomic resources will be facilitated.
Achievements
Task 3.1: Thematic group training and standardisation of methodologies in functional genomics and host-pathogen interactions (M1-M24)
This task includes the organization of five workshops (WS):
The EADGENE_S network sought to provide training for younger scientists in the diverse disciples contributing to up-to-date research in Farm Animal Biology. Therefore a series of divers workshops was organized under the umbrella of its Workpackage 3 “Joint research training, workshops and mobility” to enhance mutual understanding among biologists, veterinarians and bioinformaticians, for example.
1. International conference on the physiology and genomics of mastitis (Tutzing, October 31st-November 2nd, 2011).
Infection and inflammation of the udder (mastitis) is not only a key disease for dairy animals but also presents a highly relevant model of host pathogen-interaction for infection biology in general. The conference “Physiology and Genomics of Mastitis” was held in Tutzing (Germany) from 31st of October to November 2nd to summarize key results from interdisciplinary experimental work on mastitis, as it has been conducted in several national and trans-national European networks during 2004 - 2011. The program can be found at http://mastitissymposium2011.fbn-dummerstorf.de/. Overarching goal of that conference was to juxtapose state-of-the-art research on the pathogen-specific physiology of mastitis with very recent advances having been made in firmly establishing genetic foundations of the respective susceptibility of the host. Experts in the field updated in key note lectures on the current knowledge about the pathogen-species dependent mastitis physiology, signal transduction in relevant host cells, pathogen perception and mastitis causing bacteria. Progress on genetic aspects of mastitis susceptibility were outlined at hand of data from the EU sponsored SABRE and Quantomics programs. Most of the participants contributed specific results from those research consortia with EADGENE being among them. Bringing together the diverse expertise of veterinary science, molecular immunology and microbiology with that of biochemistry and quantitative genetics provided a unique forum to learn about the different angles to viewing the same trait. This has helped to make the participants conversant and widen their horizon and also to building up new scientific relations. Sixty seven delegates from eleven countries attended that symposium. It was co-sponsored by the Deutsche Forschungsgemeinschaft (DFG), by EADGENE_S and industry.
2. Gene Network Analysis, Visualization of genomic data, and systems biology (Ljubljana, June 5th-7th 2012).
Global transcriptome profiling studies during host pathogen interaction generate a wealth of data, given that for each time point during the experiment mRNA concentrations from more than 20.000 genes are being recorded. Hence, it is key challenge for understanding the underlying principles of the host reaction to filter out and separate the relevant information from the irrelevant background “noise”. This requires bioinformatics expertise and application of biostatistical procedures to ultimately visualize the relevant information. Demonstration and training was provided in that workshop. It was held from June 5th-7th in Ljubljana, Slovenia. Scientific leader was Prof. Tom Freeman from University of Edinburgh / Roslin Institute. Twelve delegates from seven countries participated in this very fruitful course. A short report on the workshop was published in the EADGENE_S newsletter. This training course focussed on suitable experimental approaches to generate suitable data to study co-regulation of genes and to identify key regulators (transcription factors) of regulatory gene networks (nodes) and effector genes (edges). Various open-source and commercial software products were used as well as bioinformatical software tools for biological interpretations. Training was also offered for visualising gene networks and to introduce the principles of systems biology.
3. Next generation sequencing data processing (Wageningen, December 10th-14th 2012).
The Next Generation sequencing technology is not only technically demanding but is also producing so much more data than the –meanwhile “old”- microarray based global transcriptome profiling that in depth training in the downstream data processing is absolute necessity. This was provided in the Sequence Data Analysis Training School, in Wageningen (NL), during December 10th-14th, 2012. The program can be found at http://www.basgen.nl/sdac/. The workshop was co-sponsored by the EADGENE_S program. Forty five delegates from different European countries, but also from Ghana, Iran, Israel and the USA attended this work shop. It was designed mainly for PhD students and postdoctoral fellows working with high volume next generation sequence data. The workshop introduced into the latest developments in this field. It focussed on learning to analyse sequence data by applying the state of the art methods to real datasets. Data analysis exercises had been carried out by participants in a virtual server environment (i.e. Cloud Computing, provided and also sponsored by Amazon). Throughout the course useful approaches and strategies for analysing data were learned. Important algorithms and their software implementations were introduced, and the participants were familiarized with the usage of scripting language(s) to connect different available software tools and how to construct a data analysis pipeline. Some examples of downstream analyses making use of such data pipelines have been demonstrated. A combination of lectures and exercises made this a very vivid training course.
4. Workshop on Principles of Whole Genome Selection (Dummerstorf, April 21st-23rd, 2013)
The introduction of the Whole Genome SNP typing has revolutionized the basis for efficient selection in breeding programs. These global SNP typing approaches yield 60.000 or 600.000 genomic criteria rather than several hundred of the previously known genetic markers. Once again, special training is required to familiarize the researchers with the new opportunities provided by this new technology, but also the requirements for its successful application. Thus that workshop was organized by the Leibniz Institute for Farm Animal Biology (Dummerstorf, Germany), from April 21st – 23rd. Seventeen delegates from six countries participated in this workshop. The scientific program was designed by Norbert Reinsch (Institute for Genetics and Biometry, FBN). It started with a demonstration of what it takes to generating the raw data in the wet-lab using the Illumina technique for Whole Genome SNP-typing. This was followed by lectures and exercises on the mathematical and biostatistical backgrounds to for applying such data into selection schemes. The workshop was concluded by a presentation from breeding industry (Fritz Reinhardt, vit, Verden, Germany [www.vit.de]) demonstrating at hand of the German Holstein breeding population that implantation of Whole Genome Selection virtually doubled selection efficacy during the last three years. A short report on that workshop was published in the EADGENE_S News Flash.
5. MicroRNA Workshop “MicroRNA Technology, Relevance and Application” (Brussels, May 15th, 2013).
MicroRNAs are very short, non-coding RNA molecules. Their function is to post-transcriptionally down regulate gene expression through targeted mRNA destruction. The significance of this gene regulatory mechanism for Farm Animal physiology is only now becoming appreciated. Handling and analysis of such small RNA moieties requires the application of sophisticated techniques. Therefore the EADGENE_S partners PTP and Pribright Institute have organized that work shop. It was held on May 15th, 2013 in Brussels as a satellite meeting to the last EADGENE_S event “Healthy livestock and people”. Speakers from Italy, Spain and France introduced the twenty five participants into the topic. Their lectures covered the biology of miRNAs and their significance for Farm Animals in development and in specific organs but also during host-pathogen interaction. The horizon of the delegates was widened by listening to examples from human cancer biology and plant physiology where miRNAs have been identified as relevant factors for controlling gene expression.
Task 3.2: Mobility grants for individual training activities (M1-M24)
Activities of this task facilitate the exchange of (young) researchers between European laboratories, in order to facilitate technology transfer and dissemination of expertise and information between members of the consortium and between academic laboratories and stakeholders to achieve transfer and exploitation of this technology in the animal sector.
We have opened different calls, starting the first on December 15, 2011 and continuing to December 15, 2012. We have developed a flyer that was distributed among all EADGENE_S partners (Annex 2). We have employed the EADGENE_S web page to announce the different calls and the conditions for applications (http://www.eadgene.info/AboutEADGENE_SERG/ShortTermStaygrants/tabid/424/Default.aspx).
The different applications have been evaluated by Executive Committee formed by Dr. Alice Pedrotti (INRA), Dr. Bjørn Høyheim (NSVS), Dr. Marjolein Neuteboom (EFFAB), Dr. Hans-Martin Seyfert (FBN), and Dr. Diego Llanes (UCO). Evaluation forms and criteria are included in Annex 3 and 4. After the mobility period activity reports and financial statements are due by the trainees.
We believe that the activities of this task have facilitated the exchanges between European laboratories, to bring about technology transfer and dissemination of expertise and information among members of the consortium and between academic laboratories and stakeholders to achieve transfer and exploitation of this technology in the animal sector.
In the following tables a summary is given of the researchers selected for the different STS projects. In total we have granted thirteen students from different countries. Twelve were Europeans and one from Saudi Arabia.
Four of the twelve students elected Roslin Institute as the visiting laboratory and two elected an INRA laboratory. Others selected laboratories from different countries such as Wageningen University, University of Córdoba, London or Milano and research centres CIMA and INIA in Spain.
• DECEMBER 15, 2011
Name Laboratory origin Visit laboratory
Debby Lipschutz-Powell The Roslin Institute. UK. INIA Spain
Nicholas Sanderson * Institute for Animal Health. UK. The Roslin Institute. UK
Pouneh Maraghechi * Animal Biotechnology Dept. Hungary INRA, Jouy en Josas – France
• MARCH 15, 2012.
Name Laboratory origin Visit laboratory
Juan M. Herrero. Murcia University. Spain. Wageningen University.
Carmen Aguilar * Genetic depart. Córdoba Spain CIMA. Spain
Agnes Wiedemann * INRA Tours-Nouzilly France University, London
Mahmoud Mohamed Ahmed * King Faisal University. The Roslin Institute
• JUNE 15, 2012.
NameLaboratory originVisit laboratory
Endre Barta Agricultural Biotechnology CenterHungary. INRA. Jouy en josas
Marjorie Bardiau Université of Liège. Universita' degli Studi di Milano
• DECEMBER 15, 2012.
Name Laboratory originVisit laboratory
Guillaume Sallé.INRA Nouzilly. Institute Roslin, Edinburgh
Maria Saura* INIA. Madrid Institute Roslin, Edinburgh
Sonia Martinez *University of León. University of Córdoba
* Reports included.
A summary of the reports presented up to now by the different applicants are included in the Annex 5.
Task 3.3: Fund for exchange of genomic resources (M1-M24)
Numerous biological and molecular resources exist in different European laboratories which could contribute in a cost effective way to ongoing European and national projects. For the establishment and maintenance of common resources an inventory has been organized in order to identify specific needs of the partners and ask them for opinions on what would be useful, and who might be in the position to provide such resources. A budget was earmarked in order to cover costs of generating resources. During the joint WG2 and WG3 meeting in Brussels 22 - 23 October 2012 a request on potential common resources needed was presented and the matter was discussed extensively and the discussion was continued by email. This resulted in two final suggestions for new common resources. Both of these represent sequence information on available biological samples:
* Analysis of microRNA (miRNA) in the udder of E. coli or S. aureus infected cows (Partners FBN, Germany and AU, Denmark). Analysis of miRNA in various udder samples of cows infected with either E. coli or S. aureus (the experiments were performed by the Mastitis working group during the EADGENE project) will provide important knowledge on the regulation of gene expression during infection with the two different bacterial species and concomitantly provide a source (miRNA sequences) for further analysis of the host immune reactions during infections.
* Genomic sequencing of bovine S. aureus strains (Partners ULG, Belgium, FBN, Germany, PTP, Italy and NSVS, Norway). S. aureus is recognized worldwide as a pathogen causing many serious diseases in humans and animals, including mastitis in ruminants such as cattle, sheep and goat. During the last decades a shift in S. aureus mastitis from acute and clinical cases to more chronic and subclinical cases (the bacteria seems to survive within the cells of the host) has been observed. So far no study of isolates has succeeded in identifying the actual properties at the basis of the “new” virulence trait of intracellular survival. The genomic sequence of a selection of characterized S. aureus mastitis strains with different pathogenicity and from different geographical regions of Europe (Belgium, Germany, Italy and Norway) will together with the bacterial strains provide important resources for further analysis and understanding of the mechanisms behind ruminant mastitis.
Both suggestions were accepted by the management team. These two sequencing projects are now (June 2013) in progress. The resulting data will be submitted to publicly available databanks (such as GenBank + link on the EADGENE_S website). These sequence data constitutes important common resources for future research on host pathogen interaction related to an animal disease (mastitis) resulting in large economic losses for the European livestock industry. It may also be of general relevance for understanding of the mechanisms of infectious diseases in mammals. The sequenced S. aureus strains will be available for further experimental analysis including challenge studies through collaboration.
The cost (EUR 14 000) for establishment of these resources is covered by the earmarked budget for generation of new resources:
Analysis of microRNA (miRNA) in the udder of E. coli or S. aureus infected cows. Total cost EUR 6000, - transferred from NSVS to FBN. This covers preparation of libraries for sequencing of miRNA from E. coli and 5. aureus infected bovine udders (EUR 5000,-) and sequencing of the libraries (EUR 1000,-). Analysis of raw data is covered by the partners.
Genomic sequencing of bovine S. aureus strains. Total cost EUR 8000, - transferred from NSVS to ULG, Belgium. This covers library construction, sequencing and assembly of the genome of 16 S. aureus strains. Cost for DNA extraction is covered by the partners.
Potential Impact:
d) WP4: Communication and technology exchange:
Objectives:
• Ensure the take up of EDAGENE findings by the industry, the research community, and policy makers, to improve innovation and knowledge transfer throughout Europe.
• Obtain feedback from industry, policy makers and society to improve the research planning direction towards a competitive balanced sustainable industry in animal genetics genomics and animal health.
• Increase awareness of host-pathogen interactions and disseminate knowledge to relevant end-users (animal breeding and production industry, policy makers, consumers, scientific community).
Achievements:
Task 4.1: Material, Knowledge and Technology Transfer
This task focused on dissemination to the industry, research community and policy makers.
Transferable material, knowledge and technologies
• Disseminating EADGENE_S activities and relevant animal genomics and health news is one of the main objectives of WP 4. In order to transfer the information, approximately once every three months the relevant news items have been gathered and spread within an EADGENE_S newsflash to a broad audience containing science, policy, industry and other potential stakeholders. Besides relevant animal genomics and health news items, the EADGENE_S newsflashes also informed partners and stakeholders about coming training activities and events, but also about new developed tools, funding opportunities and calls for short term grants.
• Besides the EADGENE_S newsflashes, email alerts have been spread when necessary, for example to announce an event or to spread an important news item. These newsflashes are also used to announce the EADGENE Days and Industry events.
• In addition to the EADGENE_S newsflashes and email alerts, the EADGENE_S website contains useful information for the network. For example, EADGENE_S meetings are announced and news about EADGENE_S achievements is available. Relevant meetings for the Network have also been announced on the partners’ webpages, such as the EFFAB website.
• The dissemination of EADGENE_S activities and relevant animal genomics and animal health news is an ongoing activity. Within the Network, built within EADGENE and continued within the EADGENE_S Research Group, information is disseminated by word of mouth all the time. Besides this, regular email alerts and email newsflashes draw the attention of the Network members to relevant events and news items. This in its turn creates the opportunity to maintain and even strengthen the network of the EADGENE_S European Research Group.
• The phenotypic database created during the EADGENE project is still available, and has been updated within the EADGENE_S project. On the website of the EADGENE_S project people can find whether the information they need is available. This information can be data, samples or animals for sampling. The phenotypic database has been shared with relevant industrial partners.
Ethical guidelines poster and brochure
Within the EADGENE project, identification of ethical challenges relevant to research in the field of animal disease genomics has been an important task. In order to do this, several workshops involving Network participants were organised in the EADGENE project by using the ethical matrix – a conceptual tool for supporting discussions on ethics and technology. One of the outcomes of the workshops was the need for best practices for research, to enhance the relationship between science and the rest of society. That resulted in the development of ethics and welfare guidelines and a checklist for projects involving live animals.
To disseminate the developed guidelines and checklist to the EADGENE network, the flyer ‘Ethics in animal genomics research: How to deal with ethical issues in your organisation?’ has been send to all the EADGENE_S stakeholders. The flyer explains how research and industry organisations can identify and deal with the ethical challenges within their company by using practical evaluation tools that were developed in the EADGENE project: 1. ethical matrix workshop, 2. ethics and welfare guidelines and 3. checklist. To give a more detailed description of these tools, a brochure was developed in which organisations can find more information on how they can use the tools, and especially how they can organise an ethical matrix within their organisation. Also the brochure has been sent to all stakeholders within the EADGENE network.
Task 4.2: EADGENE_S website
The project uses the website as a main means of presenting information to users that are external to the project. The website:
1. Presents EADGENE_S, its partners and objectives
2. Provides public information on the relevant issues
3. Publicizes events where the results of the project will be disseminated
4. Provides latest news and information and contact details for the participants
5. Allows interested parties to register their interest in the project
The EADGENE website (http://www.eadgene.info/) had a public side for the public, industry and scientists which was regularly updated during the EADGENE project with research progress, news, events, training courses, career opportunities and other information relevant to the EADGENE project, and a secure partner area of the EADGENE website (Intranet). This design has remained the same for the duration of the EADGENE_S project.
The EADGENE website has been updated to EADGENE_S. Information on EADGENE_S was added. Besides this, all relevant information is kept to ensure the public is informed about the results of both EADGENE and EADGENE_S, their tools and resources and on training & career opportunities and relevant events.
Entering the website, it still maintains the same layout as the EADGENE website, only now it is integrated with the news, events etc. of the EADGENE_S project as well. In the menu bar above it is possible to click on both ‘About EADGENE’ and ‘About EADGENE_S’.
Task 4.3: EADGENE Days and Industry events
EADGENE_S Industry Day April 20 2012, Edinburgh, UK
On April 20 2012, the EADGENE_S Industry Day took place at the Roslin Institute, Edinburgh, UK. The meeting was held as a satellite to the Annual General Meeting of EFFAB, which meant that there were many industry representatives present from the animal breeding sector in Europe. The event kicked off with a dinner and the following day there were several presentations:
• Marker-assisted selection for the production of IPN-resistant salmon eggs by Aqua Gen - Thomas Moen, AquaGen
• Can we control PRRS using genetics? - Steve Bishop, The Roslin Institute & R(D)SVS, University of Edinburgh
• Exploring genetic variation in resistance to coccidiosis in poultry: towards realistic possibilities for breeding? - Marie-Hélène Pinard van der Laan, INRA
• Practical tools to breed for healthier milk from more robust cows - Eileen Wall, SAC (EU-RobustMilk)
After each presentation there was time for discussion, on either the contents of the presentation or a more general discussion. The most interesting issue raised during the discussion was the question whether there IS such a thing as pre-competitive research. There was a difference in view not only between the researchers present and the industry representatives, but also differences between the different breeding organisations.
During the EADGENE_S Day presentations and discussion, two main critical issues emerged:
• The fact has been underlined that despite the enormous potential of genetic and genomic technologies to help improve and stabilize animal production, comparable animal health data across Europe are missing and the uptake within the Animal Genomics & Animal Health sector is still in its infancy. By continuing the cooperation with industries, using proven road mapping and brain-pooling techniques with a wide range of companies, the project will identify the main constraints restricting widespread adoption of genomic technology in animal production. Thus, this project will determine the actions needed to effectively transfer knowledge to this domain.
• Recent developments in animal production are related to questions such as breeding strategies, resistance to disease and stress, and optimization of nutrition. The EADGENE_S project aims to contribute to the development of a sustainable animal sector through disease prevention.
Final EADGENE_S event May 2013, Brussels
In collaboration with the Animal Task Force, the final EADGENE_S event was held in Brussels on the 14th of May 2013. During this event, a seminar was organised bringing together science, industry and policy to map the needs of the industry and researchers and to raise awareness about animal genomics and health. This seminar was the final activity of the EADGENE_S project, with the main aim to find integrated approaches for securing animal health and sustainability in Europe. The seminar started with an overview of the project results of EADGENE and EADGENE_S, followed by the research priorities for the coming years. Subsequently, several presentations were given by science, industry and policy, giving an overview of the current policy, best practices and available technology, and necessary actions to improve animal health security for the future.
During the seminar it was stressed that further improving animal health will remain an important issue for ensuring a sustainable livestock sector in Europe, and integrated and innovative approaches are needed to realize improved animal health. In addition, it was specifically mentioned that policy, research and industry should join efforts to improve the animal health potential for Europe. Animal health should be given priority on the policy agenda, and policy, industry and science play a role in agenda setting and opinion leadership. Researchers should share their knowledge clearly and understandable and frequently with policy-makers, politicians and the public, by using the platforms available.
As a satellite to the seminar, two industry sessions were held with the aim of describing the projects on animal genomics and health that are currently running, demonstrating which technologies and tools have been developed and determining the research priorities are for the future. During the morning satellite meeting, several FP7 projects focused on animal health and genomics presented their goals and results to science, policy and industry. As a consequence, science, policy and industry could find out which projects are running, what the aims are, and discuss the needs for future research in animal health and genomics.
Task 4.4: Visits to animal breeding and products companies
In order to demonstrate and discuss the available technologies that were developed in the EADGENE and EADGENE_S projects, different company visits have been done together with a mixed audience from science and industry.
Visit Landcatch salmon breeding company
The first visit was organised to Landcatch, a Hendrix Genetics owned salmon breeding and genetic services company in the UK. Landcatch is well known for scientific innovation, having been a world leader in the implementation of many genetic and genomic techniques. Consequently, it served as an excellent first contact point for an EADGENE_S organised “Seeing-is-Believing” visit. The remit of the visit was to enable region-specific problems and solutions to be addressed, bringing together the industry and academics that are involved in commercial application of Animal Genomics & Animal Health. The visit was designed to demonstrate possibilities and opportunities and to discuss future areas of development in the context of business, ethical, legal and social issues. Detailed discussions centered on the biology of salmon production, the application of genetic and genomic technologies to salmon breeding, the role of salmon aquaculture in the rural communities of Scotland, salmon breeding as a commercial enterprise and future research and technology requirements. New research requirements were identified, as discussed below.
The discussions were followed by the “seeing” part of the trip, in which the University delegates had the opportunity to see around the premises see salmon breeding and husbandry in practice, observe the animal health and vaccination procedures, and discuss issues directly with staff responsible for the fish husbandry. This provided an excellent opportunity to benchmark the discussions, and to appreciate the on-the-ground difficulties of putting science into practice in a challenging environment.
The visit served multiple purposes. It gave University academics and students the opportunity to appreciate the realities of breeding in practice, it allowed practitioners with day-to-day responsibilities at the breeding unit an opportunity to meet with researchers, and it allowed cross-fertilisation of ideas. Particularly important was the research opportunity highlighted during the visit, and the potential funding sources that were identified to facilitate this research. Specifically, the protozoan disease amoebic gill disease (AGD) was identified as the current major limitation on farmed salmon production, and the researchers were able to come to an appreciation of the outcomes of the disease and the obvious distress that it causes to the fish. Further, a genetic strategy to approaching resistance to this disease was drawn up, based on previous success with diseases such as infectious pancreatic necrosis. Finally, a funding opportunity likely to arise during 2013 was identified, and agreement was reached to work collaboratively towards solving this problem.
Visit Leibniz Institute for Farm Animal Biology (FBN)
A second visit was organised to the Leibniz Institute for Farm Animal Biology, at Dummerstorf in Germany. FBN is a member of the Leibniz Science Association and conducts basic and applied research into the biology of farm animals. FBN studies the functional biodiversity of livestock as a basis for domestication and as a key component of both sustainable agriculture and the food supply. Cooperation with science and industry at national and international levels is a key component of the research performed at the FBN. The institute is currently involved in 146 collaborations, with partners at 319 institutes in 45 countries. The FBN lays great store in training young scientists. Some 26 FBN researchers also have teaching responsibilities and hold visiting professorships and lectureships at six different universities. Because FBN has several unique facilities (laboratories, experimental farms, respiration and climate chambers, surgery facilities), FBN was an excellent place for an EADGENE_S visit to get a demonstration of the newest techniques in animal health genomics.
The visit was organised as a satellite to the EFFAB annual meeting, which resulted in a diverse audience from both science and industry that joined the visit. At the beginning of the visit, the director of FBN Professor Dr. Manfred Schwerin gave a presentation about the history of FBN and the different running research projects. After the presentation, the participants were guided through the different facilities on the FBN campus. The first facility at FBN that was visited was the Pig Experimental Station, containing 405 animal places for reproduction, 374 animal places for experimental animal keeping, laboratories, bioacoustics, tread mill, etc. The animal housings could be seen through windows above the stable. The experimental station was a nice example of modern housing, in which experiments can be done on animal health and welfare, reproduction, feed efficiency, physiology, etc.
Newest techniques for DNA sequencing
Experimental pig farm at FBN
The next facility that was visited was the genome biology building, in which the newest techniques on prosequencing, chip hybridization, DNA sequencing and proteomics were demonstrated in the laboratory. These modern techniques at FBN make it possible to do many different genetic and genomic studies, for example to identify genes that are related to immune response or modeling of genetic variation regarding animal health. Other facilities that were visited were the nutritional physiology building with techniques as mass spectrometry, deuterium analyser and AA analyser, and the Animal Service Station where facilities for metabolism and reproduction research were demonstrated. The Animal Service Station showed some impressive facilities: respiration chambers, climate chambers, surgery facilities and laboratories, all suitable for large farm animals. Very unique were the facilities to perform animal welfare measurements. FBN has specific techniques to measure animal welfare, for example by using vocalisation to detect fear, pain and stress, but it can also be used to detect estrus and lameness.
The visit showed that FBN has very unique facilities which are very suitable for current and future research in animal production. The participants were impressed by the modern techniques that FBN has, and resulted in a lively discussion about possibilities for collaboration between FBN and research institutes and industry. Currently, research priorities will focus more and more on sustainability and efficiency in animal production, and the systemic and integral approach of FBN seems to match this focus well.
EADGENE_S movies: implementation of developed technologies in animal genetics
Complementary to the seeing-is-believing visits, demonstration of developed technologies within EADGENE and EADGENE_S was also done by making two movies, which were shown to a broad audience at the industry dinner session ‘from theory to practice’ at the final EADGENE_S event in Brussels. The two movies show the implementation of two examples of research and technology that has been developed within EADGENE and EADGENE_S.
Movie 1
• AquaGen, Atlantic salmon breeding company
• Problem: viral disease Infectieus Pancreatic Necrosis (IPN) in Atlantic salmon
• Developed technology: DNA marker tool to identify the animals that are resistant to IPN
• Interview with CEO of AquaGen Odd Mage Rodseth and director R&D Nina Santi
Movie 2
• Cobb Europe, Broiler breeding company
• Problem: parasitic disease avian coccidiosis in chicken
• Research: investigate the possibility to select for increased resistance to coccidiosis in chicken
• Interview with director of R&D of Cobb Europe Gosse Veninga
The two movies were shown at the evening session, in between the courses of the dinner. The movies explained the diseases IPN and coccidiosis, what the problem of these diseases are in terms of animal health and welfare, costs for the industry and consequences for the environment and human health, and in which way genetic technology can be used to reduce or solve the problem. After each movie, there was time for questions from the audience. That resulted in a lively discussion about how to improve the developed techniques and data gathering, further implementation of the techniques into breeding programmes and future needs for research. The movies are published on the EADGENE website.
Task 4.5: Individual technology transfer discussions
Meetings
During the final EADGENE_S event in Brussels May 14, specific attention was given to inform industrial stakeholders about running projects in animal health genomics, and to find out their interests and needs for future research. In the satellite meeting ‘overview of FP7 projects on animal health and genomics’, industry could find out which running research projects were of interest for them, and in what way the project results can be implemented within their company to improve animal health. During the session, both scientists and industry got the opportunity to discuss their needs for future research.
During the satellite dinner session ’from theory to practice’, two specific examples of developed research within EADGENE(_S) were demonstrated to industrial stakeholders. In that way, the practical implementation of developed techniques in genetics and genomics to improve animal health could be shown. After the demonstration of the two examples, industrial stakeholders had the opportunity to ask questions to the involved scientists about the techniques and in which way these techniques could be put into practice.
Flyers
Excellent examples of Technology Transfer are found in the three examples for which flyers were made:
1. DNA marker tool to reduce IPN in Atlantic salmon
2. Towards breeding for increased resistance to coccidiosis in chicken
3. Breed for increased PRRS resistance in pigs
Specifically, for the salmon disease IPN, there has been successful Technology Transfer with both AquaGen in Norway and Landcatch Natural Selection in the UK. For cocciodiosis, Technology Transfer is ongoing with both INRA and the University of Edinburgh (UEDIN) with major breeding companies, most notably Cobb, and additional funding has recently been secured to strengthen the funding links of UEDIN with Cobb. Lastly, the PRRS example shows ongoing interaction and Technology Transfer between various EADGENE_S partners, led by UEDIN, with Genus plc – the world’s major pig breeding company.
The flyers were distributed to the stakeholders within the EADGENE_S network, and to the members of the AGRI and ENVI committee of the European Parliament. For the members of the European Parliament, the flyers were a nice example to see how animal breeding can be used to improve animal (and human) health in the future. The flyers were also published on the EADGENE website and send around by email to the EADGENE club of interest.
List of Websites:
Contact details
• Project’s coordinator:
Dr Marie-Hélène Pinard-van der Laan
Institut de la Recherche Agronomique (INRA)
Tel: +33 (0)1 34 65 21 84 email: marie-helene.pinard@jouy.inra.fr
• Project website address: http://www.eadgene.info