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United States Department of Agriculture

Agricultural Research Service

Research Project: GENETIC AND GENOMIC APPROACHES TO IMPROVE EFFICIENCY OF SWINE PRODUCTION AND PRODUCT QUALITY Title: Design of the Illumina Porcine 50K+ SNP Iselect(TM) Beadchip and Characterization of the Porcine HapMap Population

item Groenen, Martien -
item Crooijmans, Richard -
item Ramos, Antonio -
item Amaral, Andreia -
item Kerstens, Hinri -
item Bendixen, Christian -
item Hedegaard, Jacob -
item Rohrer, Gary
item Smith, Timothy
item Van Tassell, Curtis
item Taylor, Jeremy -
item Rothschild, Max -
item Hu, Zhiliang -
item Nonneman, Danny
item Beever, Jon -
item Archibald, Alan -
item Law, Andy -
item Milan, Denis -
item Hansen, Mark -
item Schook, Larry -

Submitted to: Plant and Animal Genome Conference Proceedings
Publication Type: Abstract Only
Publication Acceptance Date: December 1, 2008
Publication Date: January 10, 2009
Repository URL:
Citation: Groenen, M.A., Crooijmans, R.P., Ramos, A.M., Amaral, A.J., Kerstens, H., Bendixen, C., Hedegaard, J., Rohrer, G.A., Smith, T.P., Van Tassell, C.P., Taylor, J.F., Rothschild, M., Hu, Z., Nonneman, D.J., Beever, J., Archibald, A., Law, A., Milan, D., Hansen, M., Schook, L. 2009. Design of the Illumina Porcine 50K+ SNP Iselect(TM) Beadchip and Characterization of the Porcine HapMap Population. Plant and Animal Genome Conference Proceedings. 1/10-14/09, San Diego, CA. Abstract W493.

Technical Abstract: Using next generation sequencing technology the International Swine SNP Consortium has identified 500,000 SNPs and used these to design an Illumina Infinium iSelectâ„¢ SNP BeadChip with a selection of 60,218 SNPs. The selected SNPs include previously validated SNPs and SNPs identified de novo using second generation sequencing on the Illumina Genome Analyzer (Solexa) and Roche 454 FLX sequencer. Towards this end, 16 reduced representation libraries (RRL) were prepared using pooled DNA samples from individuals from five breeds (Duroc, Landrace, Large White, Pietrain, Wild Boar) digested with four restriction enzymes (AluI, HaeIII, MspI and DraI). Fragments in the size range of 150-200 bp were selected for sequencing. The ends of these fragments (36 bp) were sequenced to a 30X coverage on the Genome Analyzer and in case of the AluI libraries complemented with 2X sequencing of the complete fragment using 454 technology. For 41,667 SNPs coordinates on genome build 7, representing approximately 70 % of the porcine genome are available. Of the remaining 18,545 SNPs provisional predicted positions on the porcine genome based on the human-pig comparative map are available for 4,497 SNPs. The BeadChip was used to genotype a panel of 576 individuals representing the original discovery panel as well as representative trios from a variety of pig breeds. First results on the validation of the SNPs, linkage disequilibrium and breed characteristics will be presented.

Last Modified: 8/24/2016
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