16AGRITECHCAT5: Carcass trait phenotype feedback for genomic selection in sheep

Lead Research Organisation: SRUC
Department Name: Research

Abstract

The challenges are to improve the quality and efficiency of primary lamb production and build new objective data feedback from meat processor to farmer on carcass quality and animal health phenotypes. Only around half of UK-produced lambs meet the target EUROP conformation and fat classification specification resulting in waste at the farm and processor levels. Farmers are not rewarded for producing higher quality lamb carcasses, for example with higher saleable meat yield, or a greater proportion of higher value cuts such as the loin. Crucially, genetic improvement is undertaken in purebred flocks with a 'disconnect' between their crossbred progeny performance and carcass data from the abattoir, which could potentially inform selection decisions further up the breeding 'pyramid' in the purebred sector. Additionally, improving carcass quality and yield in lambs must be undertaken without compromising their own health and welfare, and that of their purebred sires and dams (as it is likely that these two groups of traits are antagonistic at a genetic level). It is also important because some 1.75 million ewes (52.5%) that were mated to Texel sires were mated to sires from which replacements were retained for breeding (2012 figures).

This livestock genomics project addresses key issues in primary livestock production by collecting, analysing, and exploiting state-of-the art genomic and new phenotypic data from meat sheep on hard to measure (HTM) traits. Building on the existing infrastructure of phenotype farms, data collection protocols and success of the current Agritech Catalyst project 'Using genomic technologies to reduce mastitis in meat sheep' (Innovate Project no. 131791), we will extend the range of HTM phenotypes to include abattoir-derived disease and condemnation data with new carcass and meat quality data in pure and crossbred Texel lambs. We will use Computer Tomography (CT) and newly-created Visual Image Assessment (VIA) and carcass condemnation data to exploit the information to generate wealth using single nucleotide ('SNP') genomic technology. By combining HTM disease and meat quality traits in tandem, we can ensure that genomic selection for carcass merit in crossbred Texel lambs does not take place by compromising disease status in the breeding ewe population.
The aim is to use genomic technology to sell genomically-enhanced rams for exploitation and put in place the provision of a new genomic service for the future sheep breeding programmes in the wider industry. This will help the UK to become a world leader in agricultural technology, innovation and sustainability by exploiting new opportunities to develop and adopt new genomic technology, to increase productivity, and contribute to global food security.

The project will use new technology and data capture systems to drive new information-led breeding structures on novel, economically-important traits for sustainable breeding of meat sheep. The results of the project will enable farmers to have clearer market (price) signals that adequately reflect the commercial value of their lambs produced, so that a higher proportion of lamb carcasses better meet the required specifications for lamb carcass quality and health. In this way, the UK's food security for lamb meat production will be enhanced, as will export-driven demand for high quality meat. The project will pioneer the use of visual imaging technology for sheep meat in the UK, and through benchmarking it alongside estimates of carcass composition (using CT), the commercial partner, Anglo Beef Processors (ABP) gain commercial intelligence that, ultimately, will be manifested throughout the sheep meat sector.

Technical Summary

Genetic and genomic linkages in 3500 genotyped and phenotyped pure and crossbred Texel sheep will be used for new and exisiting traits, including VIA-predicted primal joint and saleable meat yields, 12 new meat hygiene traits, mastitis, udder and teat conformation, milk quality, hoof lesions. These will be combined with historical data from related animals, the pedigree for which extends to over 1.52M unique animals. The project has 3 core components of on-farm phenotyping and genotyping, abattoir-collected carcass information, and genetic and genomic data analyses that will be delivered in 5 work packages (WP):- WP1 "Live animal carcass and health phenotypes". New data and tissue sample collection (n=3500) will be taken from pure and crossbred 'Phenotype Farm' (PF) flocks of Texel sheep on lamb and ewe performance, health data (mastitis, footrot and other hoof lesions) and in-vivo carcass yield and quality (ultrasound and CT). The genotyping subcontractor will use the new Illumina 'LDchip' (with 17,625 SNPs) to generate genotypes. WP2: "Post-mortem (abattoir) carcass and health phenotypes". A new VIA machine dedicated to lamb carcass quality assessment will be installed by ABP. Crossbred lambs will be used to validate prediction equations of different cuts and saleable meat yield from VIA with CT. 3280 lambs from the PF farms will be VIA-scanned and MH inspection data for 12 new health traits from the 3500 VIA-scanned individual lamb carcasses will be collected by ABP and data analysed by SRUC. WP3: "Data analysis and new trait development" to deliver GEBVs using imputation from 17.6K LDchip to the 50K chip, underpin genome-wide association studies (GWAS) for new traits and provide a platform for imminent international collaboration ('Intersheep'). WP4: "Communication and impact delivery" will include a formal KE strategy and WP5: "Project management" quarterly review of finance and project milestones.

Planned Impact

The main beneficiaries of the project are: 1) Consumers, 2) Society, 2) Farmers and the rural community, 3) Meat processor ABP (and if adopted by wider sheep meat processors, other commercial abattoirs), 4) The tecel Sheep Socirty and it's farmer members, and 5) The academic community

Consumers will benefit as this project puts in place new technology and know-how to improve sheep meat quality that will lead to proportionally less fat and higher lean meat yield. The benefits extend to improving the safety of meat because the utilisation of individul animal identification (EID) linked to individual carass condemnation data and again linked through to the animal selection decisions will have a powerful impact on animal mangement and biosecurity.

Society will benefit through the reduction of risk in carcass contamination, reduction of wastage and contamination from the processing of animals with a higher saleable meat yield.

Farmers benefit as clearer market signals from VIA-predicted carcass assessments drive selection decisions that are linked more closely to the needs of the supply chain. Having higher heritabilities for VIA-assessed carcacss traits will lead to higher rates of genetic gain achievable. More profitable farmers impacts on the fragile rural communities that depend on them, which is critical to sustaining the rural economy and for protecting the environment.

ABP benefits through having more market-orientated specifications for meat and being able to identify superior animals for which premiums paid adequately reflect carcacss value. Benefits also accrue because carcasses are consistently assessed using objective (and indisputable) technology.

The TSS benefits from having access to IP which they can exploit (by providing genomic breeding values, GEBVs) for Texel sheep having no pedigree or performance records. This is done by using the SNP 'key', the suite of algorithms that link genotype to phenotype for the novel traits. This income stream can be used to support the future direction of using genomics in the Texel breed to ensure that the reference population (genotyped cohort) is up to date and suffieciently large enough for robust GEBV prediction.

Academics benefit by having access to new, unprecedented data for the generation of scientific papers and other impact material.

All parties benefit through their interaction with one another to better foster collaborations and understanding of their disparate businesses.

Publications

10 25 50
 
Description we have been able to derive prediction equations for carcass composition using Visual Image Assessment images (that has screened animals in the abattoir) and benchmarked these against Computer Tomography images of the same animals, that provides upwards of 95% accuracy for fat and muscle composition. This information is to be used in the validation of the accuracy of VIA to provide a new tool for use in carcass and meat assessment.
Exploitation Route Other abattoirs may also use VIA in carcass assessment
Sectors Agriculture, Food and Drink,Environment

 
Description The Texel sheep society has taken up the use of the mastitis and footrot screening as part of their technical team activity on-farm. They have created a 'reference population' whereby ongoing phenotyping will continue beyond the lifetime of the project for the purpose of generating genomic breeding values for these diseases. This will be used to select elite breeding animals as parents of future generations with the aim of reducing susceptibility to disease.
First Year Of Impact 2018
Sector Agriculture, Food and Drink
Impact Types Economic

 
Description H2020
Amount € 7,000,000 (EUR)
Organisation European Union 
Sector Public
Country European Union (EU)
Start 11/2018 
End 10/2022
 
Description InnovateUK Agritech - BBSRC
Amount £1,545,697 (GBP)
Funding ID BB/P005098/1 
Organisation Biotechnology and Biological Sciences Research Council (BBSRC) 
Sector Public
Country United Kingdom
Start 02/2017 
End 01/2020
 
Title Validation of Visual Image Asessment benchmarked with Computer Tomography for carcass quality of sheep 
Description We have developed a statistical methodology to validate a new carcass-assessment machine (Visual Image Assessment, VIA), so that it automatically generates predictions of carcass merit from the VIA images. This information can be used by the meat processing sector to better identify carcasses suitable for different market / client destinations. It also enables the sheep meat industry to identify bloodlines that better meet end-user needs for specific carcass qualities so that future lamb crops are produced with such desirable qualities. Benchmarking these with actual body composition using Computer Tomography (of the same carcass) has enabled the precision of the VIA machine to be estimated. This has been done for the major carcass areas (fore, mid and hind) and is being tested by the project Industry partner ABP. 
Type Of Material Physiological assessment or outcome measure 
Year Produced 2019 
Provided To Others? Yes  
Impact The meat processing sector has a new method by which payments can be made to farmers based on the actual carcass composition, rather than a subjective assessment undertaken by human subjective evaluation. It better identifies the different qualities of each of the major carcass areas which in turn differ in their economic value. The potential of this technology can benefit the industry (owner) of the machine in that specific carcasses can be identified, that may display specific qualities (distribution, size, shape, of fat, muscle or bone) relevant to specific customers, markets or processors. Other benefits include high-speed, automatic and objective carcass assessment methods that can reduce the need for human intervention for carcass assessment evaluations. Farmers can benefit from this technology by identifying animals with specific high qualities (e.g. higher killing out percentage, muscle distribution, fat cover), whose data can be used to provide large amounts of carcass information from lambs that are linked genetically to the elite breeding animals (sires) . This information can be used to influence selection decisions on-farm to improve the supply of high-quality lamb through the supply chain. 
 
Description Chair a session at Brtish Society of Animal Science (BSAS) annual conference 
Form Of Engagement Activity Participation in an activity, workshop or similar
Part Of Official Scheme? No
Geographic Reach International
Primary Audience Professional Practitioners
Results and Impact I chaired an industry-focussed session at BSAS
Year(s) Of Engagement Activity 2016
URL http://bsas.org.uk/wp-content/uploads/2015/07/bsas_conference2016.pdf
 
Description Hampshire Down breeder visit 
Form Of Engagement Activity A talk or presentation
Part Of Official Scheme? No
Geographic Reach National
Primary Audience Industry/Business
Results and Impact Enhanced engagement of breeders with performance recording of their animals. Discussion of relevance of using genomic selection in their breeding programme.
Year(s) Of Engagement Activity 2016
 
Description Industry workshop 
Form Of Engagement Activity Participation in an activity, workshop or similar
Part Of Official Scheme? No
Geographic Reach National
Primary Audience Industry/Business
Results and Impact Workshop to describe the project and outcomes and to engage with participating farmers in the research process. We received feedback from them on their involvement in the research process.
Year(s) Of Engagement Activity 2018
 
Description Maternal sheep group 
Form Of Engagement Activity A talk or presentation
Part Of Official Scheme? No
Geographic Reach Regional
Primary Audience Industry/Business
Results and Impact To update 20 farmers on latest research on new maternal traits for sheep
Year(s) Of Engagement Activity 2017
 
Description North Sheep Poster and attendance at SRUC featured stand 
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 The project was featured at both the Texel Sheep Society stand as well as the SRUC stand using a common A0 size poster displayed . Considerable interest was sparked.
Year(s) Of Engagement Activity 2017
 
Description Open day 
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 SRUC Open Day at Kirtkon & Auchtertyre - Livestock Handling, Health & Welfare. SRUC, Kirkton Farm 8/10/15

SRUC Animal Welfare Day: 50 Years of Animal Welfare Science. Roslin Institute- Midlothian 9/9/15

SRUC Upland Sheep Meeting. Bush Farm, Crathie, Aberdeen.3/11/15 (Talk 'Breeding for disease resistance - Mastitis & Footrot')
Year(s) Of Engagement Activity 2015
 
Description Present to Quality Meat Scotland on future plans for the Scottish sheep sector 
Form Of Engagement Activity A formal working group, expert panel or dialogue
Part Of Official Scheme? No
Geographic Reach National
Primary Audience Industry/Business
Results and Impact Invited to give a talk to the Scottish Sheep Strategy committee of Quality Meat Scotland on how the future of maternal progeny testing might look like.
Year(s) Of Engagement Activity 2016
 
Description Presentation at conference 
Form Of Engagement Activity Participation in an activity, workshop or similar
Part Of Official Scheme? No
Geographic Reach National
Primary Audience Industry/Business
Results and Impact A conference was organised by the Texel Sheep Society (17 November 2018; 'iTexel') to showcase the research undertaken as part of the two InnovateUK/BBSRC-funded R&D projects that have been funded.
SRUC delivered 5 presentations about the funded R&D being undertaken including an SRUC-funded PhD that is associated with the data that has been generated from these projects.
There were industry articles written in the Farmers Weekly and Scottish Farmer periodicals and video clips about the work are on YOUTUBE.
Around 130 participants were there and the feedback was very positive. An additional day was organised for young sheep farmers that focussed on the technical aspects of the projects, amongst others.
Year(s) Of Engagement Activity 2016,2017,2018
URL https://texel.uk/our-society/itexel-conference-2018/
 
Description Scotsheep event 
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 Scotsheep is a bi-annual event and 2 posters were featured on the project at 2 different locations at the event.
They generated a lot of discussion with the farmers that came onto the SRUC or Texel Sheep Society stands at the event. It was a very successful interaction with both schools, prospective students , the public and also interested farmers that engage in genetic improvement.
Year(s) Of Engagement Activity 2016
 
Description Sheep Breeders' Round Table 
Form Of Engagement Activity A talk or presentation
Part Of Official Scheme? No
Geographic Reach International
Primary Audience Industry/Business
Results and Impact Invited presentation on the project to audience of farmers, policy makers and industry practitioners at the biennial Sheep Breeders' Round Table which sparked questions and discussion afterwards
Year(s) Of Engagement Activity 2017