Development of new tools for genetic selection for a sustainable poultry industry (CHIPSUS)

UK public policy is demanding reductions in greenhouse gas emissions and ammonia to meet international targets. In poultry breeding there is a need to maintain competitiveness, and to reduce costs arising from wastage of feed and non-productive birds. Addressing these breeding goals implicates traits such as feed conversion ratio, fertility, performance in commercial traits, and liveability associated with disease resistance and animal welfare. It is these same traits that affect greenhouse gas and ammonia emissions per kilogram of product in broilers or layers. Life Cycle Assessment (LCA) of the impact of broiler production on the environment suggests feed accounts for 80% of supply chain energy use, 82% of greenhouse gas emissions, 98% of ozone depleting emissions, and 96% of acidify and eutrophying gases. In contrast, farm inputs and emissions, mostly from heating and ventilation, only contribute towards these impacts to only a minor degree. Such a breeding goals with this combination of traits has proven difficult to improve through standard trait recording; with sex and age limitations, low heritability and costs of measurement all contributing barriers to progress. Recent developments in DNA technology promise to overcome these barriers, in particular in high throughput processing of dense single nucleotide polymorphisms (SNP). Concurrently, the idea of genomic selection has emerged, in which dense marker information is used primarily as a predictor of the whole breeding value. Progress in developing genomic selection in poultry is hampered by the need to develop and implement a dense and relevant chicken genotyping chip assay, based upon an extensive catalogue of SNP variants. To develop this requires a new research initiative, as proposed here. The overall aim of this project is to develop and implement sustainable evaluation and selection tools using a genome-wide chicken SNP panel and in so doing accelerate the reduction in greenhouse gas and ammonia emissions in the UK and worldwide, and provide the route map and key tools for the whole sector to follow. This will be achieved through five tasks: (i) create a database of genomic variation within and between poultry breeds by high throughput sequence analysis of DNA samples; (ii) design and validate a novel, high-throughput genotyping assay; (iii) genotype broilers with well characterised EBVs for relevant traits; (iv) develop and validate genomic predictors, and (v) optimise methods to implement these tools into the breeding system. The direct benefits of this project lie in the reduction of greenhouse gas potential and ammonia per unit product in poultry, maintaining the competitiveness of the UK industry, and in the improvement of animal welfare through increased liveability, but also opportunities will be created for releasing grain and associated land for other purposes through the improvement of FCR. The acceleration of genetic gain is anticipated to be of the order of 20 to 40% depending on the trait. Benefits accrued by genetic selection will be permanent and accumulate over time, and are achieved at low risk.

Our current understanding of the genetic variation in the chicken genome is mostly based on between-line comparisons. Yet, it is within-line variation that is crucial for genetic improvement in commercial poultry. Therefore in this project we will expand this resource to encompass extensive polymorphisms within breeds. Whilst this will provide a larger catalogue of SNP for chip design, the power of genomic selection also depends critically upon the properties of the marker set, for example, spacing of markers, allele frequency and level of inter-marker association due to linkage disequilibrium. Therefore we will finalise the design of the 500K SNP panel in the light of this information to maximise its utility for genotyping within/between lines. The accuracy, and hence the value of trait information depends on N*h2, where N is the number of individuals with records and h2 is a measure of the genetic accuracy of these records. Therefore we will develop genomic predictors for specific traits by genotyping, with the new 500K panel, 1000's of individuals with highly accurate breeding values as a training set. These genomic predictors will be validated and their accuracy estimated for selection of both target traits and potential undesired correlated responses. The final part of this project will explore the optimisation of breeding procedures for its implementation into commercial operations. We will consider the use of the technology both to more accurately achieve current breeding goals, with their positive impact on greenhouse gas emissions, and expand these goals with further environmental benefits. This consideration of genetic gain will account for undesirable consequences, including animal welfare, the costs of recording and genotyping strategies. It will also need to be translated into commercial gain and environmental impacts over time, in the UK and globally, using the multi-billion multiplication that is possible in the poultry sector in the UK and globally.

Summary of Potential Impacts of Research Programme relevant to BBSRC mission Resources generated will have a major impact on avian genetics throughout the world. For example, the tools to genotype over 500,000 genetic markers with known map location and allele frequencies from a database of possibly 20 million SNPs from a diverse set of chicken breeds will change forever our approach for mapping genes that control traits in experimental lines. These may be lines with differences in (i) disease resistance, and so will contribute towards our understanding of host-pathogen interactions, or (ii) physiology, animal behaviour or metabolic disease. Farming/Agricultural/Verterinary communities: This project will provide information on 100,000's of genetic markers of great utility and the cheap, rapid assay to genotype them in a timely manner. This project will provide a practical route to implement genome selection, where in principle, all genetic variation in the genome for a given trait can be utilised. This approach is expected to revolutionise the way we breed animals in both the poultry and other livestock sectors. For the farmer and poultry producer we can expect new products, decreased costs and increased competiveness on a global scale. We can also expect for traits such as feed efficiency to have a reduced impact on the environment and land use. Stakeholders and Policy Makers: UK-based government bodies such as DEFRA, BBSRC and FSA will be better informed on the latest progress in genome wide applications such as genome sequencing, genotyping and genome selection in poultry and other livestock species. In addition they will have access to new tools and approaches to solve national problems, such as impact of poultry industry on the climate and environment (gas emission and land use), welfare of animals (genetic solutions), susceptibility to infectious disease (genetic solution) and human health (contamination of food by pathogens). General Public: Consumers are demanding safe food that is produced cost-effectively from animals maintained in a welfare-friendly environment. They are also demanding an industry with minimal impact on the climate and land use. This project will achieve these aims through the creation and application of novel genetic selection tools capable of acting on traits (e.g. feed efficiency, animal welfare, disease susceptibility and fertility) that have an impact in these areas. Communications and Engagement: Initially, the grant will be announced in the UK and overseas via our Public Relations Departments who will highlight the research through local media and publications. The research will be showcased to academics and industry at national and international meetings. Data and tools from the research will be made publicly available via the Affymetrix web site and public databases at EBI (Ensembl) and NCBI (dbSNP). Exploitation and Application: Consortium IP will be organised based on the collaboration agreement. University of Edinburgh will exploit outcomes, through training opportunities, projects based upon putative QTL and scientific publications. The implementation of the results will give public benefit through enhancement of production efficiency and reduced greenhouse gas emissions, which will be treated as a new trait for selection within the poultry industry. Further public/poultry sector exploitation arises from (i) a greatly extended open access catalogue of SNPs with greater industrial utility (the current resources only address between breed variation based on limited sequence data and our proposal is to expand this greatly to assess within breed variation - the raw material for genetic gain in poultry breeding), (ii) a 500K SNP genotyping chip assay for open use, which will facilitate the comparison of data world-wide and (iii) a route map for the poultry sector to gain from the experience of the Consortium in the use of genome selection.