Design of the Illumina porcine 50K+ SNP Iselect™ beadchip and characterization of the porcine HapMap population

M.A.M. Groenen, R.P.M.A. Crooijmans, A.M. Ramos, A.J. Amaral, H. Kerstens, C. Bendixen, J. Hedegaard, G. Rohrer, T. Smith, C. Van Tassel, J.F. Taylor, M. Rothschild, H. Zhiliang, D. Nonneman, J. Beever, A. Archibald, A. Law, D. Milan, M. Hansen, L. Schook
Plant and Animal Genome XVII Conference, January 10-14, 2009, San Diego, CA


Using next generation sequencing technology the International Swine SNP Consortium has identified 500,000 SNPs and used these to design an Illumina Infinium iSelect™ 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.