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Release of a high-density SNP genotyping chip for the sheep genome

An international team has developed a powerful new tool that can be used to test a sheep’s genetics and predict its productivity and meat quality.

FarmIQ in conjunction with Illumina and the International Sheep Genomics Consortium (ISGC) are today announcing completion of the “Ovine Infinium® HD SNP BeadChip”.

This new chip is capable of identifying up to 600,000 points across the sheep genome (otherwise known as single nucleotide polymorphisms or SNPs) and allows room for researchers to customize the chip or to update with new SNP discoveries. It is one of the first high-density chips developed for sheep and follows the release in January 2009 of the OvineSNP50 BeadChip, which can identify over 50,000 points.

FarmIQ commissioned the HD Chip as part of its mission to add value to red meat by improving linkages between animals’ meat yield and quality, and what happens on the farm and in the processing plant.

During testing since May, the HD Chip has been used to test 5000 animals from a range of breeds and has proved “very accurate and robust,” says John McEwan of AgResearch, who led the chip design work with Rudi Brauning.

Development of the HD Chip started with sequencing of the whole genome (gene map) for 75 individual sheep by Kim Worley and Richard Gibbs’s team at the Baylor College of Medicine Human Genome Sequencing Center (BCM-HGSC). DNA samples and measurements were also taken from 12,000 New Zealand lamb carcasses. The sheep tested represent a broad range of breeds.

Teams at AgResearch, BCM-HGSC, the Department of Primary Industries Victoria, USDA and CSIRO then collaborated to finalise the identification of more than 20 million sheep gene sequence variants.

John McEwan says the new HD chip is more than an expanded version of the OvineSNP50 chip and it will dramatically increase the power to identify key genes. “The HD chip includes 53,000 of the DNA variants that are known to affect proteins and therefore determine the animal’s measurable traits.

“We have also intentionally included some of the more rare genetic variations distributed across the genome to give a better sense of the layout. It’s the equivalent of giving a street map to someone who only knew the location of the city before.”

The HD chip provides the basis for the next generation of genomic selection when used in combination with other genotyping tools, says James Kijas of CSIRO. “For speed and cost-effectiveness, we expect researchers will probably use the high-density chip for key animals and a combination of the SNP50 BeadChip, whole genome sequencing and the low-density 7000 array for others.”

The HD chip development used technology, including the sheep genome, created by ISGC. The work was underwritten by FarmIQ (http://www.farmiq.co.nz/ ) a joint New Zealand government and industry Primary Growth Partnership programme. Illumina was selected as the genotyping platform provider after evaluation of the various technologies available.

The chief executive of FarmIQ, Collier Isaacs, says the SNP chip will provide the next step for genetic improvement in sheep. “FarmIQ is primarily interested in its application to improve sheep meat yield and quality, but the HD Chip will also be used to improve on-farm production and disease resistance traits. For instance it is already being used as part of investigations into how genetics could be used to reduce sheep greenhouse gas emissions.”

Researchers interested in using the ovine HD chip should contact Illumina (www.illumina.com).

For further information concerning the Ovine Infinium HD SNP BeadChip or associated ISGC resources contact:

John McEwan, AgResearch, New Zealand. Ph +64 29 489 9227

Cindy Lawley, Illumina, Inc., San Diego, California, USA Ph +1 619 379 9360

James Kijas, CSIRO Animal, Food and Health Science, Australia Ph +61 732142442

Kim Worley, Baylor College of Medicine, Houston, Texas, USA Ph +1 713 798 8292

Hans Daetwyler, Department of Environment and Primary Industries, Victoria, Australia +61 3 9032 7037

Michael Heaton, USDA, ARS, Clay Center, Nebraska, USA +1 402 762 4362

Collier Isaacs, FarmIQ, New Zealand Ph +64 27 444 5412

Or visit http://www.sheephapmap.org