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

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.

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.

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.