14TSB_ATC_IR Genome biobanking for the optimisation of valuable broiler genetic stocks

This project will develop novel technology to safeguard and harness existing poultry genetic resources by i) biobanking genetic resources for broiler lines using PGCs (the chicken functional equivalent of the mammalian stem cell) to preserve genotypes and therefore have the potential to re-introduce genotypes as needed into poultry production systems. Recent developments using PGCs provide a business opportunity to exploit a novel technology to safeguard and manage unique genetic pedigree breeding flocks. Currently there is no way to reconstitute pedigree stocks if lost to disease or natural disaster. Valuable lines that could contain useful alleles for developing markets are either maintained as living flocks or are culled from the production process. A proven biobanking procedure, coupled with complete genotyping of the biobanked material, will permit the storage of PGCs which can be returned to production as needed. Unlike mammalian agricultural species, the broiler industry is hindered by the limited semen cryopreservation program and semen storage technologies that are only reliable for hours, not days, months, or years. The use of chicken PGCs (stem cells) as a cryopreservation system has recently developed (van de Lavoir, 2006) and has not yet been developed by any of the large commercial poultry breeders. We intend to preserve the Vantress heritage line of chickens, a/the founder line for the current Cobb pedigree broiler lines that we have kept extant for the last fifty years. It thus represents an ancestral pool of genes from which the genomes of the modern lines have been selected. It will therefore include potentially useful alleles that have already been lost from the modern lines, or may be lost in the future with further selection. Cryopreserving genetic material is only one part of an integrated program to access and preserve genetic diversity required for the development of new products for emerging and transforming market segments. A careful assessment of the available genetic variation, along with an understanding of which alleles are critical for driving key performance traits is necessary to exploit the existing genetic diversity in commercial and non-commercial genetic stocks. Recent advances in sequencing technologies and efforts have provided a valuable assembly of a reference chicken genome. As the product of a publically and privately funded consortium, the effort focused on the ancestor of the modern chicken, the red jungle fowl. However, to effectively utilize genomic selection strategies in the commercial industry, a comprehensive understanding of the alleles and associated phenotypic traits of commercial purelines must be completed. To this end, this project will undertake ii) further DNA sequencing and annotation of the genomic sequence of a broiler line to produce a GeneAtlas; model for better understanding genetic variation in modern broiler lines. Currently, our ability to understand variability within and between lines of chickens is hampered by the incomplete state of the current chicken genome build and the distant relationship between modern broiler lines and the red jungle fowl. A broiler GeneAtlas will allow the exploitation of broiler genetic variability for the introgression of biobanked genetic material into new pureline populations. This broiler Atlas will be specific for Cobb commercial purelines and ancestral Cobb broiler lines. This will be a unique resource that will enable Cobb to select traits from within their various production flocks for specific markets.

This project will develop novel technology to safeguard and harness existing poultry genetic resources by i) biobanking genetic resources for broiler lines using PGCs (the chicken functional equivalent of the mammalian stem cell) to preserve genotypes and therefore have the potential to re-introduce genotypes as needed into poultry production systems. Recent developments using PGCs provide a business opportunity to exploit a novel technology to safeguard and manage unique genetic pedigree breeding flocks. Currently there is no way to reconstitute pedigree stocks if lost to disease or natural disaster. The use of chicken PGCs (stem cells) as a cryopreservation system has recently developed. We intend to preserve the Vantress heritage line of chickens, a founder line for the current Cobb pedigree broiler lines that we have kept extant for the last fifty years. It thus represents an ancestral pool of genes from which the genomes of the modern lines have been selected. A careful assessment of the available genetic variation through genetic sequencing, along with an understanding of which alleles are critical for driving key performance traits is necessary to exploit the existing genetic diversity in commercial and non-commercial genetic stocks. However, to effectively utilize genomic selection strategies in the commercial industry, a comprehensive understanding of the alleles and associated phenotypic traits of commercial purelines must be completed. To this end, this project will undertake ii) further DNA sequencing and annotation of the genomic sequence of a broiler line to produce a GeneAtlas; model for better understanding genetic variation in modern broiler lines. This project will help enable Cobb to select traits from within their various production flocks for specific markets.

The Agri-tech catalyst project is designed to have a positive effect on the sustainability of the commericial partner, Cobb Europe. The project will directly promote the sustainability, competitiveness, and the biosecurity of the poultry industry in the UK and worldwide through Cobb Europe. The novel technologies developed in this proposal will also be of benefit the academic sector, the wider conservation community both in the UK and globally, and the general public through increased sustainability and food security in the UK and abroad.

As a BBSRC institute, The Roslin Institute has a very good record of commercialisation and knowledge transfer to its stakeholders, and as part of the University of Edinburgh it aims to maintain and improve this record. To achieve this it works very closely with Edinburgh Research and Innovation (ERI) and Biosciences KTN, formerly Genesis Faraday. ERI is a non-profit subsidiary company of the University of Edinburgh, owned entirely by the University. ERI provides a complete range of pre-award research and commercialisation services for researchers, inventors, and entrepreneurs within the University of Edinburgh. ERI will expedite exploitation of the intellectual property which is expected to be concerned with novel cell culture conditions for avian germplasm. Biosciences KTN as a Knowledge Transfer Network has a mission to improve the interaction between the research community, intermediate organisations and the animal health and animal breeding industries to ensure that these industries are competitively placed to exploit the opportunities that arise from the 'biological revolution'.

Beyond the commercial breeding company, Cobb Europe, there are many conservation organisations and governmental research institutes that will benefit from the research. This research project will also directly impact efforts to produce a functional poultry biobank at the National Avian Research Facility (NARF) at the Roslin Institute. Scientific researchers from INRA, France, NARIC Agricultural Biotechnology Institute, Hungary, and the National Institute of Livestock and Grassland Science, Japan have been encouraged to visit The Roslin Institute to be trained in the germ cell culture techniques; some of these techniques are being further developed in this proposal. The technologies developed in this agri-tech proposal will be transmitted to this developing network of scientists working to establish national avian biobanks in their home countries.

Contacts have already been made with the National Standing Committee on Farm Animal Genetic Resources (NSC), which involves representatives from all stakeholders in the UK, and who have written a letter of support for the project. Prof Woolliams (RI) will keep the NSC informed of progress as he is a member of the NSC. The Roslin Institute also works closely with the Animal Production group in FAO who are the focal point for managing the Global Plan of Action on Farm Animal Genetic Resources that accompanied the Interlaken Declaration. Success will be communicated to the Biotechnology Network of FAO run by technical experts to inform all interested parties about biotechnology developments and their possible impacts.

Deliverables and milestones:
1. Presentation of project and initial results at two general public events; such as The Edinburgh Science Festival and Doors Open day at the Roslin Institute (year two and three).
2. Presentation of scientific results at three international science conferences (year two and three).
3. Publish the scientific results from study in two high ranking journals (year two and three).
4. Develop and exploit the IP generated in the project in collaboration with Cobb Europe (year three).