As it was announced in July 2010, the International Goat Genome Consortium federates existing projects on SNP detection in order to produce a high density SNP chip. The deadline for ordering this 50K SNP is September the 30th, 2011 and the chip will be available at the end of year 2011. This first effort to give access to a high density genotyping tool may be completed in the future by other contributions and the tool may evolve regarding the needs of the International Community. If you are interested in ordering this tool, please contact (IGGC co-coordinator, INRA), (IGGC co-coordinator, IMAU/KIZ/BGI) and (Illumina Scientist/Agriculture Consortia Manager Illumina, Inc.)

Data Contributions

  • University of Utrecht, Netherlands (H. Heuven / M. Groenen)
    Reduced Representation Libraries of 17 Saanen dairy goats. 120 millions of 32 bp paired-ends sequences i.e. 3 Gb
  • Malaysian Agricultural Research and Development Institute, Malaysia & DNA Landmarks, Canada (JJ. Abdullah / TP. Yu)
    Over 1 million SNP detected on whole genome sequencing of 3*20 Boer, Savanna and Kacang meat and indigenous goats
  • French National Institute for Agricultural Research (INRA), France (Ph. Mulsant / R. Rupp / C. Moreno-Romieux)
    Whole genome sequencing of 13 Alpine, Saanen and Creole goats i.e. 150 Gb
  • Bejing Genome Institute / Kumming Institute of Zoology / Inner Mongolia Agricultural University, China (W. Zhang, W. Wang)
    de novo assembled goat contigs

Data Processing

  1. Essential Steps
    • Centralisation of the data at INRA, France
    • Data processing with INRA pipeline
    • Sigenae & T. Faraut
    • Data access to all partners: detected SNPs, flanking sequences and allele information
  2. Detailed steps
    • Alignment of the different sequences on de novo assembled goat contigs (BWA software)
    • Ordering of contigs on bovine genome reference sequence
    • SNP discovery and annotation using public and private expressed sequence tags
    • Determination of the final SNP panel

Timeline / Pricing

  • Illumina chips available by beginning of December 2011
    Milestones: First of July SNP Permission letter from all content contributors, Final SNP list and all orders due by 30th of September
  • Pricing for 60,000 attempted beadtypes is estimated to range from ~97 to ~180 USD
Final price will depend upon the sample commitment from the community with these lower prices corresponding to a higher sample commitment. The range (3800-10000) is based upon conversations with community members and estimates of how many samples might be possible in the first year

Frequently Asked Questions:FAQ

Acknowledgements to French organizations:
UNCEIA (Federation of AI centers), Capgenes (Goat breeding company), Valogene (company licensed to promote genomic evaluation to the breeders) and Apis-gene (funding company for research on genomics)