Plant & Animal Genomes XVII Conference Plant & Animal Genomes XVII ConferenceJanuary 10-14, 2009
Town & Country Convention Center
San Diego, CA
Brian P. Dalrymple1 , on behalf of the International Sheep Genomics Consortium2
To complement the sheep SNPs discovered from the 454 skim sequencing of the sheep genome deeper, reduced representational sequencing (RRS) was also undertaken using the Illumina Genome Analyzer. Three size ranges of HaeIII digested sheep DNA (pooled from sixty diverse animals) were sequenced to an average depth of ~20 fold. After extensive filtering of the Illumina sequencing reads and mapping to the sheep genome assembly 76,000 high quality SNPs were identified. The 1536 pilot chip SNPs (identified using Sanger resequencing) along with the 454 and RRS-derived SNPs were then remapped to the sheep genome assembly. All SNPs were scored for probability of assay conversion by Illumina and minor allele frequency was calculated for the 1536 and Illumina-derived SNPs. SNPs with an assay conversion score of less than 0.8, and/or a minor allele frequency of less than 0.2 were excluded. SNPs for the BeadChip were then selected from adjacent windows of the assembled genome sequence with as close to equal spacing as possible. A hierarchy of selection criteria was applied in each window, choosing Sanger before Illumina before 454, Infinium II (requires one bead on the BeadChip) over Infinium I (requires two beads on the Beadchip), highest assay conversion score and minor allele frequency closest to 0.5. In a final quality control SNPs with identical oligonucleotide sequences and SNPs with oligonucleotides with multiple hits to the sheep genome assembly were removed and replaced with the closest adjacent SNP that met the selection criteria. The final Beadchip carries 59,494 sheep SNPs.