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

Lead Research Organisation: University of Edinburgh
Department Name: The Roslin Institute

Abstract

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.

Technical Summary

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.

Planned Impact

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).

Publications

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Woodcock ME (2017) Gene editing in birds takes flight. in Mammalian genome : official journal of the International Mammalian Genome Society

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Taylor L (2017) Efficient TALEN-mediated gene targeting of chicken primordial germ cells. in Development (Cambridge, England)

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Woodcock ME (2019) Reviving rare chicken breeds using genetically engineered sterility in surrogate host birds. in Proceedings of the National Academy of Sciences of the United States of America

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Ballantyne M (2021) Avian Primordial Germ Cells Are Bipotent for Male or Female Gametogenesis. in Frontiers in cell and developmental biology

 
Description The Agri-tech catalyst project was designed to have a positive effect on the sustainability of the commericial partner, Cobb Europe. First, we developed a genome atlas for broiler chickens that will allow the commercial partner to exploit the existing genetic diversity in their chicken flocks to select traits that will be useful for tropical environments and countries likely to be affected by climate change. The goal of this is to increase the sustainability of poultry production. Secondly, we have successfully developed amethodology to cryopreseve and reconstitute a broiler breed of chicken from frozen material. We discovered the best culture medium to propagate the reproductive stem cells from broiler chickens. This technology will allow us freeze flocks of broiler chickens. Thirdly, using genome editing technology, we have produced a new type of 'surrogate host' chicken. This 'surrogate host' chicken is sterile and does not lay eggs but can be used as a host for the reproductive cells from any breed of chicken. If frozen reproductive cells are transferred to this host hen, it will lay eggs from the other breed of chickens. Once this new host is tested, this technology will allow us to bring back any breed of chicken; commercial, rare breed, or indigenous breed of chicken, from frozen material. This has potential applications in both commercial poultry production through sustainability and protection of commercial poultry flocks and for conservation of indigenous chicken breeds.We have now published in a high impact journal that we can re-establish a broiler breed of chicken using sterile surrogate host with accompanying press coverage. We have also used the 'surrogate host' generated in this project to produce genome edited offspring and have published that work in 2021.
Exploitation Route The project will directly promote the sustainability, competitiveness, and the biosecurity of the poultry industry in the UK and worldwide through Cobb Europe through increased biosecurity of their poultry flocks and new genetic tools to be able to select the best birds for breeding. The novel technologies developed in this grant will also 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.This is a commercially funded project but our results/IP is being licensed by other companies and will be used by non-commercial entities. We are currently pursuing a patent application for the IP developed in this project and we are contracting this technology to a commercial partner, Roslin Technologies, which is offering a commercial biobanking service. The novel technology to biobank poultry that was developed in this project currently under review in a scientific journal which will help in the communication of our results to both academic and commercial audiences. We are also working with NGOs to use our cryopreservation technologies to preserve local chicken breeds in LMIC countries. Success is being communicated to the Biotechnology Network of FAO to inform all interested parties about our biotechnology developments and also through the Centre for Tropical Livestock Genetics in Health through which we intend to communicate/translate this technology to researchers in African countries for the cryopreservation of local African chicken breeds.
Sectors Agriculture, Food and Drink,Environment

URL http://roslintech.com/avian-germline-cryopreservation/
 
Description In this project we developed a 'Broiler' Gene Atlas, in which we mapped the genetic variation present in the broiler genome. This atlas will allow our commercial partner to better exploit the naturally occurring genetic variation present in their chicken flocks. The goal is to be able to identify useful genetic variation present in their chickens that can be used for increasing sustainable production; healthier birds that grow well with less feed. A second part of the project was to develop new technology needed for implementation of a chicken cryopreservation programme into the commercial partner's poultry breeding programme to increase flock biosecurity. A cryopreservation programme will safeguard production in case of outbreaks of viral epidemics such as avail influenza thus assuring food security for poultry production in the UK. This technology has already been implemented by a commercial company, Roslin Technologies, which is commercialising the results obtained from this project. A patent application has also been filed to protect the IP generated in this project for further commercial exploitation. The patent application is proceeding to the country filing stages. We have published the results from this grant in several journals and have several press articles in poultry journals/magazines describing our freezing platform. The transgenic chicken produced in this project is now being used in many subsequently awarded grants.
First Year Of Impact 2017
Sector Agriculture, Food and Drink
Impact Types Economic

 
Description Agri-tech Catalyst
Amount £850,000 (GBP)
Organisation Innovate UK 
Sector Public
Country United Kingdom
Start 01/2015 
End 01/2018
 
Description Research Grant - Mike McGrew - Initial validation of the CH1 Surrogate Host
Amount £31,005 (GBP)
Organisation Biotechnology and Biological Sciences Research Council (BBSRC) 
Sector Public
Country United Kingdom
Start 02/2018 
End 08/2018
 
Description Responsive Mode - Mike McGrew - Investigating the role of ANP32A in the replication of avain influenza virus
Amount £520,795 (GBP)
Funding ID BB/S006796/1 
Organisation Biotechnology and Biological Sciences Research Council (BBSRC) 
Sector Public
Country United Kingdom
Start 01/2019 
End 12/2021
 
Title A sterile surrogate host chicken that can be used to revive cryopreserved chicken breeds 
Description We have developed a genetically modified chicken that can be used to revive cryopreserved chicken breeds. We used precision gene editing tools to produce a chicken with a mutation in the gene DDX4. When bred to homozygosity, the chicken does not produce any eggs. This sterile chicken can be used as a host recipient for the transplantation of oocytes from other breeds of chicken. When stem cells from a rare chicken breed are transplanted into embryos from this chicken, the offspring produced will be from the rare breed of chicken. 
Type Of Material Model of mechanisms or symptoms - non-mammalian in vivo 
Year Produced 2017 
Provided To Others? Yes  
Impact This research has led to a publication in a major scientific journal. Many press articles reported this discovery and reported the positive uses of gene editing technology for preserving rare breeds of chicken. We have communicated these results to our Japanese partner of our Japan Partner Award. This chicken is currently being used tested in an Innovate UK project to develop and resurrect a rare breed of chicken. 
URL https://www.theguardian.com/science/2017/feb/17/sterile-genetically-modified-chickens-protect-rare-b...
 
Title Culturing of chicken stem cells for the cryopreservation of chicken breeds 
Description We have developed serum free culture conditions for propagating the stem cells that make sperm or eggs in chicken. These stem cells are taken from a chicken embryo and cultured in vitro to increase their numbers. These cells can then be cryopreserved safely and indefinitely. At a later time, the cells are introduced into a surrogate host embryo and the offspring from this host bird will come from the introduced cells. Our culture methods allows us to propagate these cells from any breed of chicken. These cells can be stored in liquid nitrogen and used to establish a frozen biobank for poultry breeds. 
Type Of Material Cell line 
Year Produced 2015 
Provided To Others? Yes  
Impact We have communicated this cell culture technology to many research laboratories with the goal that they would be able to replicate our findings and begin to biobank breeds of chicken using cultured stem cells. These laboratories are in Japan, Israel, UAE, Iran, France, Hungary, USA, Germany. We have worked closely through our Japan Partner Award with Dr Tagami's laboratory in Tsukuba so that his researchers could implement our cell culture methodology. 
URL https://www.ncbi.nlm.nih.gov/pmc/articles/PMC4682126/
 
Description Collaboration with industrial partner: Cobb Europe 
Organisation Cobb Europe
Country United Kingdom 
Sector Private 
PI Contribution This Innovate UK project allowed us to build a collaboration with Cobb Europe. The researchers (PI and postdoctorate researcher) working on the Innovate project communicated monthly with Cobb Europe management. We
Collaborator Contribution We have ongoing conference calls and steering committee meetings to govern the interactions between myself, Cobb Europe, and other researchers and management at the Roslin Institute.
Impact In the first instance, the outputs form this collaboration will be listed under the Innovate grant. Future outputs occurring from our continuing collaboration will be listed here.
Start Year 2015
 
Company Name ROSLIN TECHNOLOGIES LIMITED 
Description Roslin Technologies is an agriculture biotechnology company that has been established as the commercialisation arm of the world renowned Roslin Institute and University of Edinburgh's Royal (Dick) School of Veterinary Studies. As well as developing a range of new products, we offer a strong platform for industry engagement through a range of services, licencing and collaboration opportunities. Located at the University's Easter Bush Campus which is part of the Midlothian Science Zone, Roslin Technologies is well placed to play a leading role in delivering strong industry impacts from new developments in Agri-tech. Although still rapidly developing, the Zone is already one of the largest animal science innovation hubs in the world, being home also to a number of organisations with animal science expertise and an international reputation for conducting world class research and teaching. Roslin Technologies is a joint venture that builds upon a strong and novel partnership between the world leading research, knowledge and expertise that is contained within the University of Edinburgh, and two investment and business development partners with a strong global network and reach. 
Year Established 2016 
Impact Roslin Technology (commercial partner of Roslin Institute) is currently offering a commercial biobanking service to the poultry industry to biobank commercial chicken flocks using the technology partially developed in this grant. The commercial partner of this grant, Cobb Vantress, Inc, has granted Roslin Technology the right to commercially exploit the non-patentable IP from this project and has made use of this commercial biobanking service offered by Roslin Technology. I, Mike McGrew, am a consultant for the commercial biobanking service.
Website http://roslintech.com/avian-germline-cryopreservation/
 
Description Brainstorming session for Dept of Biotechnology, Bangalore, India 
Form Of Engagement Activity A formal working group, expert panel or dialogue
Part Of Official Scheme? No
Geographic Reach International
Primary Audience Professional Practitioners
Results and Impact Invited to influence future transgenic research projects in India.
Year(s) Of Engagement Activity 2016
 
Description Edinburgh Science Festival 2015 
Form Of Engagement Activity A talk or presentation
Part Of Official Scheme? No
Geographic Reach National
Primary Audience Public/other audiences
Results and Impact Speaking about cutting edge science to the general public
Year(s) Of Engagement Activity 2015
URL http://www.summerhall.co.uk/wp-content/uploads/2015/07/Summerhall-Science-Festival-2015.pdf
 
Description Interview for international news article 
Form Of Engagement Activity A press release, press conference or response to a media enquiry/interview
Part Of Official Scheme? No
Geographic Reach International
Primary Audience Professional Practitioners
Results and Impact An article in Poultry World on GMO for poultry breeding. Influenced poultry farmers and consumers.
Year(s) Of Engagement Activity 2017
URL https://www.poultryworld.net/Genetics/Articles/2017/7/Gene-editing-has-potential-for-future-poultry-...
 
Description Interview for international news_The Atlantic 
Form Of Engagement Activity A press release, press conference or response to a media enquiry/interview
Part Of Official Scheme? No
Geographic Reach International
Primary Audience Public/other audiences
Results and Impact A press interview on a recent publication that was printed in the online magazine, The Atlantic. The reach of this journal is international and substantial
Year(s) Of Engagement Activity 2019
URL https://www.theatlantic.com/science/archive/2019/10/frozen-aviary/600271/
 
Description Published article received press coverage 
Form Of Engagement Activity A magazine, newsletter or online publication
Part Of Official Scheme? No
Geographic Reach International
Primary Audience Public/other audiences
Results and Impact Published article discussed in public online forum
Year(s) Of Engagement Activity 2017
URL http://www.bbc.co.uk/news/uk-scotland-edinburgh-east-fife-39006713
 
Description Published article receiving press coverage 
Form Of Engagement Activity A magazine, newsletter or online publication
Part Of Official Scheme? No
Geographic Reach International
Primary Audience Public/other audiences
Results and Impact Press article in the Telegraph describing biobanking of chicken breeds using GM chicken hosts in a positive light
Year(s) Of Engagement Activity 2017
URL http://www.telegraph.co.uk/news/2017/02/17/rarechickensbrought-back-brink-extinction-edinburgh-unive...
 
Description Published article receiving press coverage 
Form Of Engagement Activity A magazine, newsletter or online publication
Part Of Official Scheme? No
Geographic Reach International
Primary Audience Public/other audiences
Results and Impact Press article on gene targeted chicken used to study germ cell development and to develop surrogate host chickens for rare breed conservation
Year(s) Of Engagement Activity 2017
URL https://www.ft.com/content/10000b26-f52c-11e6-8758-6876151821a6