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). 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 5,000 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 carcases. 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 is designed to enable researchers to customise it or to update it with new SNP discoveries.
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 7,000 array for others.”
The HD chip development used technology, including the sheep genome, created by ISGC. The work was underwritten by FarmIQ (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).
Genotyping chip a milestone for sheep industry
The new sheep genotyping tool puts the sheepmeat industry at the forefront of breeding technology says Collier Isaacs.
The new chip will speed up genetic gain, he says. FarmIQ played a significant role in getting the international development proejct underway, including committing two years ago to taking a consignment of the high-denisty chips when completed.
“Along with the meat yield and quality that FarmIQ is interested in, it will be used to improve performance in the areas of on-farm productivitiy and reducing greenhouse gas emissions.”
Eleanor Linscott, consortium manager for Ovita, says being able to use the new chip will take its work to lift on-farm productivity to a new level.
“We have been working with the lower density chip for the past five years and can correlate 28 on-farm traits to the DNA variants on that chip. So that means we can predict a sheep’s performance for these 28 traits based on its genetics. These are traits for things like reproduction, growth, disease resistance and longevity on commercial farms.
“This new chip will now give us far more detail on those traits.”
The new chip will also assist research by the Pastoral Greenhouse Gas Research Consortium and the New Zealand Agricultural Greenhouse Gas Research Centre into reducing sheep emission of methane, says PGgRC manager Mark Aspin.
“Research has shown that genetics do have an influence on how much gas an animal will emit from a given amount of feed. We have used the lower density chip to test 170 sires and the new chip will further improve our understanding of the genetics.”
Farm IQ’s focus meanwhile is on getting more sheep with known meat yield and eating quality tested with the chip, to build a database of the correlation between genotype and these expressed traits. It will then be used to determine sire breeding values for these traits.
Already the AgResearch team at Invermay, led by McEwan and Shannon Clarke, have tested 5,000 animals using the new chip.
[copy supplied by FarmIQ]
FarmIQ is a Primary Growth Partnership programme, jointly funded by Government and industry. Its goal is “to create something that doesn’t currently exist: a demand-driven, integrated value chain for New Zealand red meat.” This will result in better-informed decisions and more value along the chain, from plate to paddock. www.farmiq.co.nz.