Whole Genome Sequencing for Variant Detection, Disease Gene Identification and an HD SNP Chip for Sheep

Identification of the genomic variation responsible for phenotypic differences remains a central aim for geneticists. For sheep researchers, the last few years has seen genome wide association studies (GWAS) successfully identify disease genes as well as genomic regions linked with variation in production traits. To move these studies into the next phase, the International Sheep Genomics Consortium (ISGC) has embarked on a whole genome sequencing project. The aims include (i) discovery of approximately 50 million SNP (ii) characterization of genome wide structural variation (iii) construction of a high density SNP chip rich in exonic, low MAF and tag SNP (iv) provision of whole genome sequence to improve the accuracy of genomic selection (v) a SNP chip for wild sheep and (vi) identification of causal mutations that underpin disease. To initiate the experiment, 81 animals were selected from 41 breeds developed in Africa, Asia, Europe and the Americas. Most animals were drawn from 2819 sheep genotyped at 50,000 SNP as part of the recently completed ISGC HapMap experiment. Sequencing has commenced using Illumina paired end reads and guided assemblies are being generated using the sheep genome assembly version 2.0 as the reference. An early priority for the project is the identification of sequence variants that cause disease. Results will be presented from four GWAS studies, along with preliminary data from affected animals undergoing whole genome sequencing.