Knowledge Based Bio-Economy


Advanced genetics for improving livestock

Project Title: From sequence to consequence - tools for the exploitation of livestock genomes
Project acronym: Quantomics
Project number: 222664
EC contribution: €5 999 000
Duration: 54 months
Starting date: 01/06/2009


Quantomics is a large collaborative research project exploring “From Sequence to Consequence – Tools for the Exploitation of Livestock Genomes”. This €8.14 million project involves 17 leading research groups and businesses and is co-financed by the European Commission’s 7th Framework Programme.

Quantomics will deliver a step-change in the availability of cutting edge technologies and tools for the economic exploitation of livestock genomes. The project will provide the tools to identify rapidly the causative DNA variation underpinning sustainability in livestock and for industry to exploit high-density genomic information. Its 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 in all farmed species. The project is expected to leave a legacy of resources for future research.

Problem (background):

The sequencing of the genomes of the major livestock species places animal agriculture on the threshold of a new era. The development of genomic tools has provided the ability to map genes associated with health, welfare, productivity and product quality. However, the application of these findings in breeding programmes has been hampered by two factors:

  1. The problem of finding genetic markers sufficiently closely associated with the causative DNA sequence differences to be fully effective in selective breeding.
  2. The challenge of identifying the causative DNA polymorphisms themselves to provide an optimally informative and portable tool for selection, breeding and understanding of trait biology.

In this project we have selected a set of technologies and tools to develop that are designed to maximise our ability to bridge the gap between trait variation and DNA sequence and hence remove the two identified bottlenecks.

Aim (objectives):

Quantomics has five high-level Objectives:

  1. To provide the tools to combine information from reference genome sequence, mapping, comparative genomics, annotation, functional studies and dense sequence data from the latest hyper-parallel re-sequencing technologies to identify rapidly the causative DNA variation underlying important traits in livestock species.
  2. To provide the methodologies and software tools to exploit effectively and efficiently genomic information in sustainable breeding programmes.
  3. To determine the benefits and constraints relating to the effective application of these tools to health and welfare traits in chickens and cattle - hence providing information across contrasting breeding schemes that span the breadth of livestock improvement.
  4. To provide a framework for moving from genome sequence to commercial application for all livestock species which can be expanded to include other forms of information such as epigenetic effects when their importance has been established.
  5. To disseminate results of the project to ensure broad and long-term beneficial impact on European competitiveness and EU policy on animal health and welfare and sustainable agriculture.

This project will have a wide application in all farmed species and leave a legacy of resources for future research. Generating quantitative and genomic tools based on cutting-edge technologies, it will form a powerful integrated pipeline with a wide application. It should provide the methodologies and software tools necessary to enable genomic information to be used efficiently in sustainable animal-breeding programmes. It will provide and test various genomic tools that will be of value in improving strains of dairy cattle and broiler chicken. It will provide information on re-sequencing of DNA within identified genomic features underlying loci of large effect from a significant number of animals, resulting in the ability to catalogue variations. Other tools that will be developed will make this information freely available via the Ensembl genome-browser that provides genome databases for vertebrates and other eukaryotic species. The work will prioritise the likely functionality of identified polymorphisms and validate the utility of the putative causative haplotypes within commercial populations. New methods should be tested to manage molecular biodiversity, and the potential advances from combined GWS and gene assisted selection in breeding programmes evaluated

Application of the new genomic tools in the dairy cattle populations will greatly increase the effectiveness of procedures that are currently supported more modestly by existing biometrical tools. Going far beyond this, successful application of these new genomic tools to commercial broilers will provide a completely novel approach to genetic improvement of commercial, crossbred breeding stock – by applying genomics at the level of the commercial crossbred animal, instead of at the level of the parent pure lines. This ‘inverted-pyramid design’, if effective, will be truly revolutionary in its impact in farm animal species where crossbreeding is common.


Key words: Genomics, Genome Sequence, DNA Tools, Software, Ensembl, Breeding, Sustainability, DNA, SNP, CNV, QTL, Quantitative Genomics, Quantomics, Diseases, Mastitis, APEC, Livestock, Broilers, Poultry, Avian, Cattle, Bovine, Pigs, Porcine

Coordinator: Biosciences KTN, The Roslin Institute,