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Saturday, February 04, 2012  About SABRE » SABRE's Scientific Research » Genomics & Bioinformatics- WP3   Login
 Pig Genome Sequence Minimize

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SABRE’s Work Package 3 (Genomics and Bioinformatics) and the Wellcome Trust Sanger Institute made substantial contributions towards 6x coverage of Pig Chromosomes SSC7 and SSC14. Latest progress towards the pig genome can be viewed by clicking on the image above.


      

 Latest Updates Minimize

The final results of the SABRE project have been published

Click on image for further information


    

 Genomics and Bioinformatics - WP3 Minimize

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

      

 WP3 Results Minimize

      

 Work Packages Minimize

      


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SABRE [Cutting-Edge Genomics for Sustainable Animal Breeding] is an Integrated Project supported by funding under the 6th Research Framework Programme of the European Union European Commission, Directorate E03 – Security of food production systems. Scientific Officers: 1 April 2006-15 February 2007: John Claxton. From 16 February 2007: Jean-Charles Cavitte.

This website represents the views of the Authors, not the European Commission. The Commission is not liable for any use that may be made of the information.

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