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Sheep Genomics Consortium Develops SNP Chip with Illumina

NEW YORK (GenomeWeb News) — The International Sheep Genomics Consortium and Illumina have completed part of a project aimed at developing a SNP microarray for characterizing variations in sheep genomes, and during 2009 ISGC plans to sequence the genomes of as many as six sheep, ISGC said this week.

IGSC is an international group of institutes and companies funded by AgResearch of New Zealand, Australia, the UK, and the US Department of Agriculture, and is aimed at developing tools to explore the sheep genome.

Initial sequencing for the project was conducted in parallel at Otago University in Dunedin, New Zealand, and the Human Genome Sequencing Center at Baylor College of Medicine, while Illumina provided additional sequencing.

The genome assembly, SNP detection, and selection was conducted by AgResearch and Australia's Commonwealth Scientific and Industrial Research Organization. Illumina used this data to create the OvineSNP50 BeadChip for use in selecting traits for breeding.

The goal of this part of the project was to develop a chip that could collect data from over 60 breeds of sheep that could be used in pinpointing traits that may be important economically, ISGC said.

"Groups will use the chip for a variety of objectives ranging from whole-genome association studies to unraveling the process of domestication and impact of selection," ISGC Secretary James Kijas said in a statement.

"We took the opportunity to use new DNA sequencing technologies which allowed us to identify over 300,000 SNPs," AgResearch's John McEwan said.

The ISGC, which began in 2002, still plans to produce a reference sequence of the sheep genome and a preliminary study of copy number variation in sheep.

"We began this work by creating what we called a virtual sheep genome, which contained the best bet about where the sheep's vast amount of hereditary information could be found on its 26 chromosomes," ISGC researcher Brian Dalrymple said in a statement.

"We drew on the work that had already been done to sequence the human, cow, horse and dog genomes to create our virtual sheep genome assembly," Dalrymple added.

As sequencing costs decrease over the coming year, Dalrymple continued, "We plan to complete the sequencing of six individual sheep genomes."

"During 2009, as sequencing costs continue to decline, we plan to complete the sequencing of six individual sheep genomes. This will be really important as the availability of reference genome sequences will open up a range of possibilities."