Genome editing for quantitative traits in livestock

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.

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.

(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.