Work Package 3: Genomics and Bioinformatics

Rationale: In order to develop breeding tools in Work Packages 4 to 9, SNPs need to be identified which are functional mutations or are in close Linkage Disequilibrium (LD) with functional mutations. This Work Package, together with Work Package 1 (Numerical Genomics), provides the underpinning technologies for Work Packages 4 to 9 to reach this goal: This Work Package provides SNPs, LD information, and tools for annotating genes; Work Package 1 focuses on statistical and breeding support. To develop SNPs, a genome sequence is the key resource, which is now available for the chicken, will shortly become available for cattle, but is not foreseeable (by common quality standards) for the pig. This Work Package therefore will 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 is 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 will largely be based on comparative information, therefore phenotype ontologies will be developed to allow across species data mining. Finally, the focus on functional genomics in Work Packages 4 to 9 is supported by providing tools for pathway analysis.

Objectives

·       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

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

Sanger Institute

University of Copenhagen Faculty of Life Sciences