Empowering sheep breeding by identifying variants associated with growth traits using allele-specific expression

Sheep are a vitally important animal for global food production, providing a source of meat, milk and fibre. The UK is the largest producer of lamb and mutton and the largest exporter of sheep products in Europe. There are approximately 13.1 million breeding ewes currently being raised in the UK producing 300,000 tonnes of meat annually.

This project will use genomics to unravel the complex genetic control of characteristics (or 'traits') in sheep that are desirable to the sheep production industry.

The trait that we will focus on for this project is growth because understanding how genetics can drive growth traits can provide farmers and animal breeders with crucial information they can use in genetic improvement strategies designed to enhance the quality and quantity of sheep products.

The sheep genome is ~2.6 billion bases (or letters) in size. We are only beginning to understand which parts of the sheep genome are functional, at what time during development, and the role that they play in generating healthy and productive animals.

Gene expression is the process by which information from a gene is used in the synthesis of a functional gene product. Genetic variation is the difference in DNA sequences between individuals within a population. Genetic variation that affects gene expression has been shown to influence 'traits' (e.g. growth) in livestock. Therefore, measuring gene expression in any given tissue or cell type can provide insight into genetic variation.

We know that in Texel sheep genetic variation in a specific region of the genome affects muscling characteristics, but only when it is inherited from the sire and not from the dam. This is called a 'parent-of-origin' effect. This parent-of-origin effect in Texel sheep was discovered over many years by focusing on specific regions of the genome using classical genetics techniques. In this proposal we will use new sequencing technologies to measure gene expression across the whole genome.

In the first stage of the project we will measure gene expression in tissues that are important for growth at relevant developmental stages in crossbred Texel x Scottish Blackface sheep. This will allow us to measure gene expression at each base in the genome and identify variants where the expression is unbalanced in the direction of the sire or the dam.

In the second stage of the project we will use statistical prediction models to associate these variants exhibiting unbalanced expression with regions of the genome that are associated with growth traits in sheep. This will allow to predict how likely these variants are to be contributing to some of the growth characteristics observed in sheep.

The outcome of the project will be a set of variants associated with growth traits in sheep. Some of these will have parent-of-origin effects similar to the muscling variants in Texel sheep. In the UK these variants will be of particular economic importance as they will underlie inheritance of the desired muscling traits from the Texel which is commonly used as terminal sire in British commercial lamb production.

The variants we discover in this project can be incorporated in genetic improvement programs for sheep. The information generated by this project will be of huge value to sheep breeders and producers, who can priortise particular important variants, to enhance their breeding programmes. Genetic improvement is widely used in sheep and genomics enabled breeding schemes such as those, which have been established in New Zealand are increasingly common in the UK and across the globe.

We have focused on sheep and growth traits as an example but the outcomes of the project could be applied to other livestock and other traits of interest to improve the efficiency of animal production.

This project will combine isoform and allele-specific expression analyses to identify variants associated with growth traits in sheep.

Allele-specific expression is caused by a genetic variant that effects the expression of an allele on the same gamete. It is important in animal breeding programmes because small but significant changes in allelic imbalance of expression have been linked to complex phenotypes in livestock.

In this project we will use RNA-sequencing and full-length isoform sequencing (Iso-Seq) to fully characterise allele-specific expression across multiple developmental stages in Texel x Scottish Blackface sheep. We will then associate variants with allele-specific expression with growth traits using information from Genome Wide Association Studies (GWAS).

This will allow us to identify allele-specific expression variants in genomic regions associated with growth (e.g. within the QTL associated with muscling characteristics in Texel sheep on chromosome 18). Using statistical prediction models we will determine how likely the variants with allele-specific expression are to be causal for growth traits. These variants can then be incorporated as weighted biological priors in genomic prediction strategies to improve persistency and accuracy and maximise our ability to turn genetic variation into sustainable genetic gain in sheep.

Genetic improvement is widely used in sheep and genomics enabled breeding schemes such as those which have been established in New Zealand are increasingly common in the UK. However, current genomic prediction values for most traits in sheep are low (<0.4) with considerable scope for improvement using new sources of genomic information such as those outlined in this project.

We will build on close links with the Texel Society and wider sheep sector to facilitate implementation of the results and methodology in their breeding programmes ensuring the project will have impact beyond the completion of the grant.

This project will identify variants associated with growth traits in sheep by combining isoform and allele-specific expression analyses. These variants could then be incorporated in breeding programmes to improve the accuracy of genomic prediction in sheep.

The potential non-academic beneficiaries of this research include sheep breeding companies, sheep producers and ultimately the entire chain of users of sheep products, including retailers and consumers. There are also potential benefits to animal breeding companies more generally and to the wider livestock sector.

Sheep are very important to the rural and agricultural sectors providing economic value, resources including meat, milk and fibre, and utilizing grassland that may not be suitable for any other use. There are approximately 13.1 million breeding ewes currently being raised in the UK producing 300,000 tonnes of meat annually. The total value of the sheep sector in the UK is estimated at £1.15 billion nationally.

Genetic improvement is widely used in sheep and genomics enabled breeding schemes such as those which have been established in New Zealand are increasingly common in the UK and across the globe. However, genomic breeding values for most traits are low (<0.4). Defra has recently funded "The Sheep Genetic Improvement Scoping Study" to recommend innovations in sheep breeding to maximise genetics, environmental gain and flock profit. This reflects the direction of the industry in the application of genomic technologies and emphasises the benefits that the research outcomes of this project will bring to the sheep sector. By building on close links with the Texel Society and wider sheep sector we will facilitate implementation of the results and methodology in breeding programmes for sheep to ensure the project will have impact beyond the completion of the grant.

Ultimately all stakeholders in the sheep sector will benefit from efficient genomics enabled breeding programmes through sheep that are more profitable, better adapted, with improved welfare, and that use less environmental resources.

Animal breeding companies will also benefit from the project because the majority of their breeding goals are quantitative traits. The aim of their breeding programmes are to efficiently utilise genetic variation for genetic improvement. The methodology from this project could be applied as one means to accelerate genetic improvement in animal breeding programs and enable animal breeding companies to utilise genetic variation in a sustainable way. We will use sheep as an example for this project and as such the direct impact is focused on the sheep sector but the methodology we develop will be transferable to other livestock sectors using genomic selection strategies.

The academic research community, particularly researchers in animal breeding and genetics and livestock functional genomics, will benefit directly from the new knowledge, new data and new methodology generated via this project. Groups of researchers who will benefit directly include those engaged in the international collaborative efforts to characterise the genomes of farmed animals to provide a rational basis for genetic improvement through breeding. By providing functional annotation information for the expressed regions of the genome in tissues related growth at multiple developmental stages this project will benefit researchers across the globe working on sheep via an improved sheep genome annotation. Researchers working in quantitative genetics and animal breeding will also benefit as the project will contribute novel methodology and ideas for the integration of functional annotation information (i.e. variants with allele-specific expression) with GWAS and eQTL/aseQTL analysis to define the genetic basis of complex traits.