Study SRP000982 Download

TitleBuilding the sheep SNP50 BeadChip and a draft genome assembly.
Abstract**Background** For genomic selection in sheep a high density single nucleotide polymorphism (SNP) chip of at least 50,000 evenly spaced SNPs was required. In other species, this step had been preceded by genome sequencing, followed by SNP discovery and selection. The sheep community had no assembled genome and limited resources so a one step 3X skim sequencing and comparative assembly methodology utilising 6 widely divergent breeds was used. **Results** Six sheep were sequenced with a Roche 454 FLX producing 9.7Gbp of sequence. An ordered and orientated comparative genome assembly was generated that comprised 1.49 Gbp or 52% of the estimated ovine genome length consisting of 2.3M contigs averaging 654bp. Sized gaps were spaced with Ns. Using bos taurus reference sequences over 90% of genes had more than 60% sequence coverage in the assembly, suggesting preferential assembly of the unique fraction of the genome. Subsequent SNP discovery identified 594,681 SNPs. A separate reduced representational sequencing strategy using an Illumina GAII analyser generated 3.7 Gbp of sequence and identified a further 76,044 high quality SNPs. Using a variety of criteria 59,464 equally spaced SNPs were selected to create an Illumina HD BeadChip. The result was 53,000 assayable polymorphic SNPs with an average minor allele frequency of 0.31 with little ascertainment bias. **Conclusions** The procedure outlined in this paper resulted in a high quality 50K ovine SNP chip. Modified versions of this methodology allowing for advances in next generation sequencing methodology have great potential for other as yet unsequenced organisms of agricultural and aquacultural importance
Referencesno content
OrganismsOvis aries
TypeWhole Genome Sequencing
Descriptionno content
SubmitterAgResearch Limited
Related objects
SubmissionsSRA009241
LinksInternational Sheep Genomics Consortium (ISGC)
authors ISGC guys(John)