A cutting-edge new tool to pinpoint the genetic differences responsible for a variety of commercially important traits in sheep is about to be released by an international consortium of researchers in the US, Australia and New Zealand.

Designing this first generation, Single Nucleotide Polymorphism (SNP) genotyping chip will enable scientists to characterise the genetic variations at approximately 60,000 different positions in the sheep genome. The new SNP chip has the potential to revolutionise the future selection and breeding of sheep globally.

The International Sheep Genomics Consortium undertook this work using two of the latest sequencing technologies. 454 sequencing was used to construct an assembly of the sheep genome from six animals derived from different breeds.

This draft assembly was based on a virtual sheep genome framework, itself constructed using the genome sequence of the cow which is closely related to sheep. Solexa sequencing was used to sample about 5% of the sheep genome from 60 different animals at much greater depth to identify SNPs with a high level of confidence. A larger number of SNPs of lower confidence were also identified from the genome assembly.

Sequencing was undertaken at New Zealand's University of Otago and in two different locations in the US - Baylor College of Medicine, Texas and Illumina in California. The Australian CSIRO was likewise involved while large amounts of data (numerous files of multiple gigabytes) were transferred to AgResearch in Otago and the CSIRO in Brisbane.

During the course of the project, sequence data and analysis results were repeatedly transferred between Australia and New Zealand over the joint AARNet/KAREN network, providing a significant saving of time over the alternative, slower networking routes.

Most of the analysis in Australia was undertaken using the CSIRO Bioinformatics Cluster facility in Canberra and the HPSC in Melbourne again involving transfer of considerable amounts of data between these sites and Brisbane over AARNet.

The results of the analyses will soon be available to researchers around the world via a number of websites, including the sheep genome browser, enabling researchers to view the SNPs in the context of the sheep genome assembly.

The sheep genome is the first mammalian genome to be assembled in the Southern Hemisphere and by researchers not affiliated with a large sequencing facility. The work was funded by an International Science Linkages grant (Australia), Ovita (New Zealand), Sheep Genomics (a joint venture between Meat and Livestock Australia and Australian Wool Innovation Ltd) and Genesis Faraday.

AARNews, August 2008


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