Exploitation of genomic selection technologies in the UK sheep population

Lead Research Organisation: Aberystwyth University
Department Name: IBERS

Abstract

'Omics - development of novel tools and techniques to better access, understand and enable the exploitaiton of genomic, transcriptomic, proteomic and metabolomic information.

This proposal aims to enable innovations that will enhance the supply of more efficient and productive breeding stock to the UK sheep sector through the development and exploitation of new genomic technologies by a consortium comprising key innovators within the UK lamb supply chain and from other disciplines (e.g. plant genomics). The resulting technology will be capable of application throughout the Industry so that the economic, social, and environmental benefits can be further exploited across the UK sector and will provide important new information that may be applied in other species

The proposal aims to yield complex genomic and phenotypic information on a quality and scale that has not been attempted before in UK sheep. This will lead to the use of Genomic Breeding Values (GBVs) which will enable genetic improvement of the more difficult to improve traits that cannot currently be easily, quickly or cheaply measured in vivo. In doing so it fits with the call remit as it:
1. Is inspired by the latest developments in genomic technologies following the publication of the sheep genome and development of SNPs capable of identifying new production traits in sheep
2. Will endeavour to use a very large number of measured traits in a large animal population to develop new tools that can be used to apply these technologies so that they can be exploited in commercial sheep populations in the UK for the first time.
3. Will use novel approaches to relate specific haplotype blocks and copy number variations to phenotypic variation and in doing so support the development of future sheep SNP technolgy.
4. Will improve the yield and quality of lamb from the same cost base and in doing so support economic growth and environmental sustainability throughout the lamb supply chain
5. Will enable Innovis and subsequently the UK sheep industry to utilise genomic selection to safeguard its markets against overseas competition.

Technical Summary

This proposal aims to enable innovations that will enhance the supply of more efficient and productive breeding stock to the UK sheep sector through the development and exploitation of new genomic technologies by a consortium comprising key innovators within the UK lamb supply chain and from other disciplines (e.g. plant genomics). The resulting technology will be capable of application throughout the Industry so that the economic, social, and environmental benefits can be further exploited across the UK sector and will provide important new information that may be applied in other species
The proposal aims to yield complex genomic and phenotypic information on a quality and scale that has not been attempted before in UK sheep. This will lead to the use of Genomic Breeding Values (GBVs) which will enable genetic improvement of the more difficult to improve traits that cannot currently be easily, quickly or cheaply measured in vivo. In doing so it fits with the call remit as it:
1.Is inspired by the latest developments in genomic technologies following the publication of the sheep genome and development of SNPs capable of identifying new production traits in sheep
2.Will endeavour to use a very large number of measured traits in a large animal population to develop new tools that can be used to apply these technologies so that they can be exploited in commercial sheep populations in the UK for the first time.
3.Will use novel approaches to relate specific haplotype blocks and copy number variations to phenotypic variation and in doing so support the development of future sheep SNP technolgy.
4.Will improve the yield and quality of lamb from the same cost base and in doing so support economic growth and environmental sustainability throughout the lamb supply chain
5. Will enable Innovis and subsequently the UK sheep industry to utilise genomic selection to safeguard its markets against overseas competition.

Planned Impact

We will aim to:

1) Identify & where appropriate protect & commercialise IPR from project results by: a) identifying ownership & content of background IPR, b) establishing a consortium IPR agreement including legacy plan for IPR after end of grant, c) ensuring all data are recorded to meet IPR requirements.

2) Develop awareness of project existence in wider commercial, academic & general public stakeholder communities. This will involve a) assessment of IP potential of output from project and regular PMC meetings, b) identification & evaluation of IP - preparation of data for filing if appropriate, c) developing IP exploitation plan with consortium, d) exploitation by partners if possible, e) identification of non-consortium exploitation routes via attendance at technology fairs etc & consortium networks, f) developing new links & licensing of technology, g) exploitation of technology via new company, h) ensuring execution of legacy plan for IP.

3) Communicate & exploit research results in lay format to wider stakeholder community. This will be conducted by: a) setting up a project website, b) Publication of lay articles indicating start of project, c) communicating plans and activities of project via workshops/information events, d) communication about project including media interviews.

4) Communication of results to academics, professional practitioners & bodies, educational & training organisations via: a) developing protocols and producing new knowledge, b) preparation of lay material for dissemination articles, c) holding dissemination/training workshops & attending trade shows. d) regular contact with appropriate media.

Publications

10 25 50
 
Description The research undertaken identified genomic markers that can be used to predict the performance of an individual lamb (meat quality, quantity, various carcass traits) without having to measure the lamb throughout its life. This enables the breeders to predict which parents will yield good quality lambs and saves time and effort, as well as increasing the overall performance of the flock. This is estimated to boost the profit from the breeding stock by 30% by 2020. In addition, recent analysis of lipid profiles from 564 animals has enabled use of the genetic data to identify regions within the sheep genome that are associated with lipid/fatty acid composition in the meat, which affects eating quality and healthiness of the product. For example, we could breed sheep for healthier levels of linoleic acid, which is important to the human diet. Innovis are currently scaling to incorporate prediction data in their latest flock.
Exploitation Route Innovis and IBERS are working to encourage other breeders to make use of genomics-based breeding technology within the UK. There is also significant scope to expand the methodology into other breeding systems, such as pigs or goats. Our recent identification of candidate markers for lipid content could be used in sheep breeding for producing better-tasting and healthier meat in terms of fatty acid profile, and could inform other animal production systems where fat content of the meat is a concern. Innovis are currently scaling to incorporate prediction data in their latest flock.
Sectors Agriculture, Food and Drink

 
Title Fatty acid profiles from meat samples for 564 animals across ~100 FA compounds 
Description Samples of meat from 564 animals genotyped as part of this project were subjected to GC/MS analysis of fatty acid compounds 
Type Of Material Database/Collection of data 
Year Produced 2018 
Provided To Others? No  
Impact This dataset has been used to undertake GWAS analysis to identify markers for genomic selection and candidate gene identification in sheep. Several of these markers are expected to be novel. 
 
Title GWAS results from lipid analysis of 564 sheep 
Description Data from fatty acid profiling of 564 sheep was combined with the 50K genotyping dataset to perform genome-wide association study (GWAS). 
Type Of Material Database/Collection of data 
Year Produced 2019 
Provided To Others? No  
Impact GWAS identified between 1-20 significantly associated SNP markers for many of the most important lipids involved in healthy diet. In particular, a QTL on chromosome 2 appeared to be associated with multiple fatty acid compounds. Candidate gene analysis for these markers is ongoing. 
 
Title Genomic prediction pipeline for Innovis dataset 
Description Colleagues at University of Edinburgh (Prof John Woolliams, Dr. Janez Jenko, Dr. Ricardo Pong-Wong) developed a pipeline for taking PLINK format datasets of Illumina iSelect genotyping information (from multiple chip types) and generating genomic estimates of breeding value (GEBVs) 
Type Of Material Data analysis technique 
Year Produced 2016 
Provided To Others? No  
Impact Pipeline is available for Innovis to use for future genotyping within their flocks. Should be possible to develop into user-friendly version for non-specialists to access. 
 
Title NGS data for 30 sheep samples 
Description Next-generation whole genome shotgun sequencing was completed to 12x depth per animal for 30 key sires/offspring within the Innovis flock. This was used to validate the accuracy of data imputation from lower-density SNP assays to a total of 12 million variants identified in the NGS data when aligned to the published Ovis aries genome. Data also remains available for study of copy number variation in the sheep genome and correlation to performance. 
Type Of Material Database/Collection of data 
Year Produced 2016 
Provided To Others? No  
Impact Validated imputation model used in genomic selection pipeline also developed as part of this work. 
 
Title SNP resource for 1600 sheep 
Description SNP genotype data was recorded for 600 animals across 50,000 markers and 1000 animals across 15,000 markers. Various phenotypic datasets exist for these animals and can be used for genome-wide association studies. 
Type Of Material Database/Collection of data 
Year Produced 2016 
Provided To Others? No  
Impact Data was used to identify genomic estimates of breeding value (GEBVs) and predictions of performance in Innovis sheep flock. Data has also been used for M.Sc projects to teach students bioinformatic analysis and look at breed/phenotype differences. 
 
Description Meeting with visiting group from Ag Tech New Zealand 
Form Of Engagement Activity Participation in an open day or visit at my research institution
Part Of Official Scheme? No
Geographic Reach International
Primary Audience Professional Practitioners
Results and Impact Drs. Shannon Clarke and Kathryn McRae of Ag Tech NZ visited IBERS alongside other members of their company to give a talk, after which they engaged with Dr Hegarty and discussed the use of genomic selection technologies in sheep breeding, including the outcomes of this project. The broad uptake of genomics by NZ farmers was conveyed and passed on to UK parties.
Year(s) Of Engagement Activity 2017
 
Description Presentation and tour for Welsh Government Food Division Team, Project Helix, Cywain and Food Skills Cmryu 
Form Of Engagement Activity Participation in an open day or visit at my research institution
Part Of Official Scheme? No
Geographic Reach National
Primary Audience Industry/Business
Results and Impact Visit for policymakers and stakeholders on Welsh Government Future Foods programme (~20 individuals) which informed on ongoing/past IBERS food-related programmes that could advance academic/industrial ties.
Year(s) Of Engagement Activity 2018
 
Description Presentation to Jersey Cattle Youth Society (4th April 2017) 
Form Of Engagement Activity Participation in an open day or visit at my research institution
Part Of Official Scheme? No
Geographic Reach National
Primary Audience Professional Practitioners
Results and Impact A presentation of genomics technology and its use for carcass verification and genomic selection in both cattle and sheep was given to the Jersey Society Youth team along with a tour of the IBERS Translational Genomics labs and the National Plant Phenomics Centre. Following this, there was a discussion lunch of the potential for genomic improvement in cattle. The Society reported an increased interest in genomics and usage in breeding systems.
Year(s) Of Engagement Activity 2017
 
Description Presentation to Southdown Sheep Society (Dr. Matt Hegarty) - 7th Oct 2017 
Form Of Engagement Activity Participation in an activity, workshop or similar
Part Of Official Scheme? No
Geographic Reach International
Primary Audience Industry/Business
Results and Impact Presentation of genomic research into sheep breeding to Southdown Sheep Society AGM - approx 100 in attendance total but around 50 attended session. Discussion of need for good performance measures by farmers to underpin the genetics, costs, implications, etc. Invited to write layperson's article for Society newsletter.
Year(s) Of Engagement Activity 2017
 
Description Presentation to visitors from Dunbia Ltd 
Form Of Engagement Activity Participation in an open day or visit at my research institution
Part Of Official Scheme? No
Geographic Reach National
Primary Audience Industry/Business
Results and Impact Informing visitors from industry on genomics technology in animal breeding and improvement
Year(s) Of Engagement Activity 2019
 
Description Visit by Welsh Assembly government members (26th April 2017) 
Form Of Engagement Activity Participation in an open day or visit at my research institution
Part Of Official Scheme? No
Geographic Reach National
Primary Audience Policymakers/politicians
Results and Impact A delegation from Welsh Assembly government toured the IBERS Translational Genomics lab on 26th April 2017 and were presented with information on Welsh-focused projects including the Innovate UK award. This led to brief discussion and positive feedback about the quality of scientific work undertaken.
Year(s) Of Engagement Activity 2017