Plant & Animal Genomes XVI Conference

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

Preliminary Survey Of SNP Variation Within The Sheep Genome

James Kijas¹ , David Townley¹ , Brian Dalrymple¹ , Sean McWilliam¹ , Dave Tang¹ , Peter Wilson² , Annette McGrath² , Frank Nicholas³ , Hutton Oddy⁴ , Roxann Ingersoll⁵ , The ISGC^1,2,3,4,5

¹  CSIRO Livestock Industries, Brisbane, Queensland 4067, Australia.

²  Australian Genome Research Facility, Brisbane, Queensland 4067, Australia.

³  University of Sydney, Sydney, NSW 2006, Australia.

⁴  University of New England, Armidale, NSW 2351, Australia.

⁵  Johns Hopkins University, Institute of Genetic Medicine, Baltimore, MD USA.

The International Sheep Genomics Consortium used Sanger re-sequencing to search for single nucleotide polymorphisms within the sheep genome. A total of 3000 genomic targets were selected from available BAC end sequence (2294) or ESTs (706). Re-sequencing of each was performed using a panel of nine individuals, each drawn from a different breed. The average target size was 510 bp meaning approximately 1.5 Mb of the ovine genome was scanned for the presence of SNP. A total of 6022 SNP were independently identified using two SNP-calling packages. The location of each SNP within the virtual sheep genome, accompanied by access to the aligned sequence reads, is available at www.livestockgenomics.csiro.au/vsheep/. A subset of 1536 SNP was selected to represent each ovine chromosome and 901 of the 1172 contigs which comprise the virtual sheep genome. The first high throughput SNP genotyping experiment was subsequently performed for sheep using Illumina's BeadArray platform. Ten individuals from two species of wild sheep were genotyped to determine the ancestral allele for each locus. In addition, a collection of 308 animals from 19 domestic breeds drawn from Africa, Europe, North America, Asia, Australian and New Zealand was used to determine minor allele frequency both within and between sheep populations. The result is a preliminary view of the single nucleotide polymorphic component of the ovine genome.