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

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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.