QUANTOMICS will deliver a step-change in the availability of cutting edge technologies and tools for the economic exploitation of livestock genomes. We will provide the tools to identify rapidly the causative DNA variation underpinning sustainability in livestock and for industry to exploit high-density genomic information. Our adaptable quantitative and genomic tools each based on cutting-edge technologies and valuable in itself, will together form a powerful integrated pipeline with wide application. To deliver these outcomes we will; i) use comparative genomics to annotate putatively functional features of the genomes of the EU’s key farmed animal livestock species; ii) enhance existing molecular genetic tools (to include copy number variation, CNV); iii) deliver computationally optimised tools for genome-wide selection (GWS) to include CNV; iv) apply these tools to important health and welfare traits in commercial populations of dairy cattle and broiler chickens, determining the benefits and constraints; v) use hyper-parallel resequencing of DNA within identified genomic features underlying loci of large effect in significant numbers of animals to catalogue variation; vi) develop new visualisation tools to make this variation publicly available via the Ensembl genome-browser; vii) develop tools to prioritise the likely functionality of identified polymorphisms; viii) validate the utility of the putative causative haplotypes within commercial populations; ix) test the potential advances from combined GWS and gene assisted selection in breeding programmes; x) explore new methods to manage molecular biodiversity; xi) assess the implications of these new tools for breeding programme design, and xii) disseminate results of the project achieving major competitive, animal health and welfare impacts across the EU livestock industry and ultimately consumers. QUANTOMICS will have wide application in all farmed species and leave a legacy of resources for future research.