Work Package 3: Genomics and Bioinformatics

Rationale: The development of breeeding tools in Work Packages 4 to 9 was dependent on the identification of SNPs which are functional mutations or are in close Linkage Disequilibrium (LD) with functional mutations. Work Package 3, together with Work Package 1 (Numerical Genomics), provided the underpinning technologies for Work Packages 4 to 9 to reach this goal. Work Package 3 provided SNPs, LD information, and tools for annotating genes; Work Package 1 focused on statistical and breeding support.

A genome sequence is the key resource to develop SNPs. At the start of SABRE the genome sequence  was available for the chicken, was shortly to become available for cattle, but was not foreseeable (by common quality standards) for the pig. This Work Package therefore aimed to provide the genome sequence for 2 key chromosomes in pig.

Together with genome sequences (from SABRE and elsewhere) a set of bioinformatics tools and concurrent information was needed to fully support Work Packages 4 to 9, including: the in silico mining of SNPs, validation and exchange of information on SNPs, generation of LD maps, and tools to support the annotation of genes. Annotation of genes in animals was largely based on comparative information, therefore phenotype ontologies were developed to allow across species data mining. Finally, the focus on functional genomics in Work Packages 4 to 9 was supported by providing tools for pathway analysis.

Objectives for WP3 at start of SABRE

• Sequence and annotate 2 targeted porcine chromosomes (7 and 14)
• Generate SNPs in silico, collect and archive SNP information and coordinate the development of SNP panels for general use
• Generate linkage disequilibrium maps in chickens, pigs and cattle
• Develop, and coordinate development, of phenotype ontologies to facilitate comparative genomics in Work Packages 4 to 9
• To provide pathway analysis tools and collect and distribute pathway data suitable for annotation of transcriptomics studies in Work Packages 4 to 9

Results: Please see the results links on the right side of this page.

WP Leader: Dr Martien Groenen (Wageningen University)

Partners involved:

• Wageningen University
• ID-Lelystad
• Institute National de la Recherche Agronomique
• The Roslin Institute and R(D)SVS, University of Edinburgh
• University of Aarhus Faculty of Agricultural Sciences
• The Wellcome Trust Sanger Institute
• University of Copenhagen Faculty of Life Sciences