Plant & Animal Genomes XVII Conference

January 10-14, 2009
Town & Country Convention Center
San Diego, CA

Skim Sequencing The Sheep Genome, And SNP Discovery, Using Roche 454 FLX Sequencing

John C McEwan¹ , on behalf of the International Sheep Genomics Consortium²

¹  AgResearch, Invermay Agricultural Research Centre, PB 50034, Mosgiel, New Zealand

²  www.sheephapmap.org

The sheep genome was "skim" sequenced to ~3X coverage (9.74Gbp) using a whole genome shotgun approach with Roche 454 FLX sequencing. Six animals (Romney, Texel, Scottish Blackface, Merino, Dorset and Awassi) were used each sequenced to approximately 0.5X coverage. The subsequent assembly was estimated to cover in excess of 42% of the ovine genome and represent 82% of the non repetitive fraction. The assembly procedure was bovine genome assisted, but then reorganized into sheep order using the virtual sheep genome. Using sequence depth as a criteria numerous potential copy number variants were identified. The assembly process also identified 594,681 putative SNPs. Of these 273,348 were high quality SNPs where both alleles had been observed in two or more animals. Testing a sample of 112 these putative SNPs with the Sequenom iPlex system identified that 76% of these had a MAF>0.05, call rate >85% and no gross Hardy-Weinberg or inheritance failures. These SNPs were subsequently used to aid creation of a 50K+ Illumina Infinium iSelect™ SNP BeadChip.