Genome editing for quantitative traits in livestock

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

Abstract

This project will develop new laboratory techniques and new breeding methods to enhance livestock breeding programmes by genome editing. Genome editing is used to increase the numbers of animals in the breeding herd that carry beneficial genome variants. This makes it possible to conserve valuable genome variants that would otherwise be lost because they tend to be inherited together with harmful variants that must be bred out.

Although the traits that animal breeders seek to improve are each controlled by thousands of genome variants, we have shown that it is theoretically possible to produce a 33% improvement in genetic gain in a livestock breeding programme by editing as few as 5 variants.

The aim of this project is to make this theoretical possibility a practical reality by developing the techniques to do multiple edits on the same individual and the breeding methods to decide on the best edits, the best animals to edit and how best to manage the breeding programme.

The project consists of two strands of work, one will develop the genome editing methods, the other will develop the breeding methods.

The editing methods will be developed in three stages.
1. We will develop the tools to make multiple edits that do not change the function of the genome in any way. It will be much easier to test the safety and efficacy of the tools if the edits do not alter genetic function.
2. When we can make multiple edits we will configure the tools to produce edits that should improve breeding and test them on cells in culture.
3. When the tools work on cells in culture, we will use them to edit single-cell embryos and produce live, edited pigs.

We need the breeding methods to design the most useful set of edits and to deploy them most effectively in a breeding programme. The methods will be developed in the form of computer programmes that support the following three operations.
1. Analysis of a huge dataset, containing the genome sequences of 325000 pigs together with information about their pedigrees and their breeding traits, in order to decide on the most effective edits and the most useful individuals to edit.
2. A strategy for selecting which pigs to breed from that will prevent the loss of valuable genes by inbreeding.
3. A strategy for managing the breeding programme so that it generates the data needed to test the effectiveness of current edits and identify the best potential future edits.

Our industrial partner, PIC, has a breeding programme that generates the genetics in over 100 million slaughter pigs every year. This project will help make those pigs healthier and make them produce better meat with lower inputs and lower environmental impact. The breeding methods and software will be made available to other companies breeding pigs and other livestock species. The results will also be useful for understanding the genetic basis of quantitative traits, like height and health, in humans.

Technical Summary

The project aims to develop the molecular techniques and breeding methods for the use of genome editing to enhance quantitative traits in livestock.
Genome editing can retain beneficial alleles that would otherwise be lost, either because they are rare or because they are linked to deleterious alleles that must be bred out. Individual quantitative traits are influenced by many genome loci, so we need two developments:-
- Molecular techniques to produce pigs with multiplexed genome edits.
- Breeding methods to design the most useful set of edits and to deploy them most effectively in a breeding programme.

We will produce pigs with multiplexed genome edits in 3 steps:-
1. We will use CRISPR/Cas9 to produce multiplexed synonymous single nucleotide substitutions in pig zygotes.
2. We will develop the tools to produce multiplexed edits of strategic nucleotide substitutions in porcine embryo fibroblasts.
3. We will deploy the tools to produce strategic edits in pig zygotes and re-implant the zygotes to produce live pigs.

We will develop breeding methods and implement them in the form of software packages that can be deployed to analyse data, carry out simulations and support decisions in research projects and breeding programs. The software will support the following three operations:-
1. A method to prioritise quantitative trait nucleotides (QTN) for editing by accounting for effect size, current allele frequency, the degree of linkage disequilibrium with other QTN that affect the trait and by using an existing dataset of phenotypes and sequences (ours consists of 325000 individuals) to exclude QTN that are subject to epistasis.
2. A selection strategy to minimise the rates of inbreeding when genome editing resources are not sufficient to enable their even distribution across all individuals.
3. A breeding strategy that would enable sufficient numbers of QTN to be identified for genome editing and have their causality proven using breeding data.

Planned Impact

(i) The academic community. Scientifically, the project constitutes a step change in genetic engineering for animal breeding delivered by the application of quantitative genetics. It will bring together genetic engineers, who work with single causal variants, with statistical geneticists, who work with thousands. This impact will be delivered via publication in journals, presentations at conferences, seminars, and by making data and software available.
(ii) Animal breeding companies, breed societies, and levy boards. The biological insights about efficient use of genome editing to enhance socioeconomically important traits in a sustainable way will underpin the design of a new generation of scientific breeding programmes. The software and scripts that we will use to generate and analyse the data in this project will be made available to these organisations.
(iii) The entire chain of users of animal products. The entire chain of users of animal products, including meat packers, milk processors, egg and wool suppliers, retailers and consumers will benefit because the knowledge generated will equip animal breeding companies with tools to deliver a higher quality product, which costs less, and is more environmentally friendly, healthier and suited to individual requirements of stakeholders in the supply chain.
(iv) Plant breeding organisations. The methods, data sets of this scale, and biological insights are also highly relevant to plant breeding organisations. Therefore the benefits to plant breeding organisations, in the developed and developing world, will be similar to those outlined for animal breeding companies, breed societies, and levy boards.
(vi) UK Treasury will benefit from increased tax revenues through increased profitability of UK based breeding companies, the farm animal supply chain, other UK agricultural users should they adopt the method, and UK based sequence and genotype and genome editing technology providers.
(vii) UK science infrastructure and capacity. The proposed methods and data set will provide a platform for increased R&D capabilities in the UK, maintaining its scientific reputation and associated institutions, with increased capability for sustainable agricultural production. The proposed research will be embedded within training courses that the PI and co-PI are regularly invited to give, and the post-docs working on the project will have the opportunity to be trained at a world-class institute in a cutting edge area of research that unifies two fields.
(viii) Policy. Pure genome editing mimics natural evolutionary processes. Its availability is likely to drive significant changes in societal attitudes to genome editing and in ethical and regulatory frameworks.
(ix) Society. This project will demonstrate the value of genome editing for increasing the sustainability of breeding populations and for preserving genetic variation, which will help the general public to understand and appreciate the great value of genome editing technology. In addition, people who work to improve or depend upon the competitiveness and sustainability of agriculture will benefit from the downstream practical applications outlined above. The application of the outcomes by breeding organisations will lead to faster and more sustainable genetic progress, leading to healthier food, and food production that is more resource-efficient and affordable. Increased efficiencies in agriculture have direct societal benefits in greater food security with less environmental impact. The knowledge will also feed into educational programs.

Publications

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Gorjanc G (2018) Optimal cross selection for long-term genetic gain in two-part programs with rapid recurrent genomic selection. in TAG. Theoretical and applied genetics. Theoretische und angewandte Genetik

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Hoyos-Flight M (2017) Genome Editing and the Future of Farming meeting report. in Transgenic research

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Johnsson M (2019) Removal of alleles by genome editing (RAGE) against deleterious load. in Genetics, selection, evolution : GSE

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Johnsson M (2018) Sequence variation, evolutionary constraint, and selection at the CD163 gene in pigs. in Genetics, selection, evolution : GSE

 
Description We can use genome editing technology to produce disease resistant pigs.
Exploitation Route Driver for commercial development of genome editing in livestock
Sectors Agriculture, Food and Drink

 
Description Driver for commercial development of genome editing in livestock
First Year Of Impact 2013
Sector Agriculture, Food and Drink
Impact Types Societal,Economic

 
Description Nuffield genome editing project
Geographic Reach Multiple continents/international 
Policy Influence Type Membership of a guideline committee
 
Description RSB genome editing
Geographic Reach Multiple continents/international 
Policy Influence Type Membership of a guideline committee
 
Description A strategic approach to identifying and combating porcine reproductive and respiratory syndrome virus outbreaks and other porcine viral diseases
Amount £787,016 (GBP)
Funding ID BB/R013187/1 
Organisation Biotechnology and Biological Sciences Research Council (BBSRC) 
Sector Public
Country United Kingdom
Start 04/2018 
End 03/2021
 
Description General Scheme - Bruce Whitelaw - Editing RELA S531P
Amount £30,000 (GBP)
Organisation Genus plc 
Sector Private
Country United Kingdom
Start 03/2017 
End 12/2019
 
Description General Scheme - Christine Tait-Burkard - PRRSV study at Moredun to evaluate CD163 edited pigs
Amount £48,812 (GBP)
Organisation Genus plc 
Sector Private
Country United Kingdom
Start 03/2017 
End 09/2017
 
Description Research Grant - Christine Tait-Burkard - Nanobodies as antiviral PRRSV agents
Amount £59,802 (GBP)
Organisation Eco Animal Health Ltd 
Start 03/2018 
End 03/2019
 
Description Responsive Mode - Christine Tait-Burkard - Understanding the CD163 - PRRS virus interaction to improve genetic engineering for resistance
Amount £674,353 (GBP)
Funding ID BB/R004463/1 
Organisation Biotechnology and Biological Sciences Research Council (BBSRC) 
Sector Public
Country United Kingdom
Start 12/2017 
End 11/2020
 
Description Pig breeding with Genus 
Organisation Genus plc
Country United Kingdom 
Sector Private 
PI Contribution Developed and demonstrated gene editing in pig zygotes.
Collaborator Contribution Supply of animal resources and funds.
Impact Several publications, presentations at scientific meetings, media opportunities and joint research grants.
Start Year 2010
 
Description Surrogate Sires 
Organisation Genus plc
Country United Kingdom 
Sector Private 
PI Contribution Design and strategy to produce germless pigs and cattle
Collaborator Contribution Project design and implementation
Impact publication and patents
Start Year 2015
 
Description Surrogate Sires 
Organisation Washington State University
Country United States 
Sector Academic/University 
PI Contribution Design and strategy to produce germless pigs and cattle
Collaborator Contribution Project design and implementation
Impact publication and patents
Start Year 2015
 
Title Domain 5 of CD163 for Use in Antiviral Compositions Against PRRS and Transgenic Animals 
Description Animals resistant to PRRSV 
IP Reference WO2015011483 
Protection Patent application published
Year Protection Granted 2014
Licensed Commercial In Confidence
Impact scientific publications
 
Title Gene edited pigs with altered RelA activity 
Description production of pigs with altered NFkB activity 
IP Reference EP1216564.3 
Protection Patent application published
Year Protection Granted 2012
Licensed Commercial In Confidence
Impact scientific publications and research funds
 
Title Nanos knock-out that ablates germline cells 
Description Animals that lack spermatogonial cells as recipient for SSCs 
IP Reference WO2016011029 
Protection Patent application published
Year Protection Granted 2015
Licensed Commercial In Confidence
Impact scientific publication
 
Title Use of transgenic techniques to manipulate sex ratio or progeny 
Description Using genetic engineering to alter sex ration of offspring in farm breeding 
IP Reference US61/971,869 
Protection Patent application published
Year Protection Granted 2014
Licensed Commercial In Confidence
Impact research funds
 
Title genetically edited swine 
Description production of animals resistant to ASFV 
IP Reference WO2017055844 
Protection Patent application published
Year Protection Granted 2015
Licensed Commercial In Confidence
Impact scientific publications and research grants
 
Description BBC Country File interview 
Form Of Engagement Activity A broadcast e.g. TV/radio/film/podcast (other than news/press)
Part Of Official Scheme? No
Geographic Reach National
Primary Audience Supporters
Results and Impact TV interview on genetically engineered pigs on mainstream BBC Country File programme
Year(s) Of Engagement Activity 2013
 
Description Costing the Earth 
Form Of Engagement Activity A broadcast e.g. TV/radio/film/podcast (other than news/press)
Part Of Official Scheme? No
Geographic Reach National
Primary Audience Public/other audiences
Results and Impact BBC radio interview on genetically engineered livestock for BBC Radio 4 Costing the Earcth
Year(s) Of Engagement Activity 2013
 
Description Cutting edge Festival 
Form Of Engagement Activity A talk or presentation
Part Of Official Scheme? No
Geographic Reach International
Primary Audience Public/other audiences
Results and Impact Talk on genome edited livestock at international science festival
Year(s) Of Engagement Activity 2016
 
Description DBT workshop 
Form Of Engagement Activity A formal working group, expert panel or dialogue
Part Of Official Scheme? No
Geographic Reach International
Primary Audience Policymakers/politicians
Results and Impact Indian Department of Biotechnology workshop on GM Livestock in Bangalore
Year(s) Of Engagement Activity 2016
 
Description Hendrix Genetcic workshop 
Form Of Engagement Activity A formal working group, expert panel or dialogue
Part Of Official Scheme? No
Geographic Reach International
Primary Audience Industry/Business
Results and Impact Closed industry workshop on application of genetic engineering technology
Year(s) Of Engagement Activity 2016
 
Description Midlorthian Science Festival Debate 
Form Of Engagement Activity A talk or presentation
Part Of Official Scheme? Yes
Geographic Reach Local
Primary Audience Public/other audiences
Results and Impact Constructive and lengthy debate

Invited back to next festival
Year(s) Of Engagement Activity 2014
 
Description Nuffield Council bioethics workshop 
Form Of Engagement Activity A formal working group, expert panel or dialogue
Part Of Official Scheme? No
Geographic Reach National
Primary Audience Professional Practitioners
Results and Impact Workshop exploring bioethics of genome editing technology and applications
Year(s) Of Engagement Activity 2015,2016
 
Description Our Changing World Series 
Form Of Engagement Activity A talk or presentation
Part Of Official Scheme? No
Geographic Reach Regional
Primary Audience Public/other audiences
Results and Impact University of Edinburgh showcase lecture on genome editing animals for food security
Year(s) Of Engagement Activity 2016
 
Description RSB Teachers Annual Meeting 
Form Of Engagement Activity A talk or presentation
Part Of Official Scheme? No
Geographic Reach Regional
Primary Audience Schools
Results and Impact Talk on genome editing to teachers conference
Year(s) Of Engagement Activity 2016
 
Description SUSS 
Form Of Engagement Activity A talk or presentation
Part Of Official Scheme? No
Geographic Reach Regional
Primary Audience Schools
Results and Impact Talk on impact of genome editing technology on society at annual Scottish universities science school.
Year(s) Of Engagement Activity 2018
 
Description The Food Chain 
Form Of Engagement Activity A broadcast e.g. TV/radio/film/podcast (other than news/press)
Part Of Official Scheme? No
Geographic Reach International
Primary Audience Public/other audiences
Results and Impact BBC World Service radio interview on genetically engineered livestock for The Food Chain
Year(s) Of Engagement Activity 2018
 
Description named biotechnology speaker on US Ste |Department Economic Bureau Outreach Fund 
Form Of Engagement Activity Participation in an activity, workshop or similar
Part Of Official Scheme? No
Geographic Reach International
Primary Audience Policymakers/politicians
Results and Impact International workshop top engage stakeholders in genetic engineering technology and applications
Year(s) Of Engagement Activity 2015