Plant & Animal Genomes XVI Conference

January 12-16, 2008
Town & Country Convention Center
San Diego, CA

Using Roche 454 Flx Sequencing For SNP Discovery In Sheep

John C. McEwan¹ , Gemma M. Payne¹ , Rudiger Brauning¹ , Alan F. McCulloch¹ , Jo-Ann Stanton² , V. Hutton Oddy³ , Frank W. Nicholas⁴ , Brian P. Dalrymple⁵ , International Sheep Genomics Consortium⁶

¹  AgResearch, Invermay Agricultural Centre PB 50034, Mosgiel, NZ

²  Anatomy and Structural Biology, University of Otago, Dunedin, New Zealand

³  University of New England, Armidale, NSW 2350, Australia

⁴  University of Sydney, Camden, NSW 2570, Australia

⁵  CSIRO Livestock Industries, Brisbane, Queensland 4067, Australia

⁶  http://www.sheephapmap.org

One of the International Sheep Genomics Consortium’s aims is to skim sequence the ovine genome, and identify SNPs in order to produce a 60K SNP chip^†. Roche 454 FLX sequencing technology is a new technology based on pyrosequencing. Simulations based on the limited ovine genomic sequence available, and results from a pilot ovine resequencing project, identified that using 454 FLX technology to produce a 3X genome coverage consisting of 0.5X shotgun sequence coverage from 6 ewes, each representing a different breed, assembled using the bovine genome as a framework should be able to provide assembled and ordered sequence for approximately 60% of the ovine genome. It would also detect 286,000 probable SNPs with defined genomic locations of which 180,000 would potentially be useful to select from for construction of a 60K ovine SNP chip comprising equally spaced SNPs. Based on available information this would provide a resource where the mean linkage disequilbrium (r2) between adjacent SNPs would be in excess of 0.3, and would therefore be suitable for whole genome association studies. Sequencing is currently underway with New Zealand sequencing the Romney, Texel and Scottish Blackface breeds.
^†John C. McEwan et al. 454 sequencing and SNP discovery in sheep: project design and interim results PAG XVI