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SNP Chip For The Sheep Genome

Fuseworks Media
Fuseworks Media
SNP Chip For The Sheep Genome

An international team of scientists has today released a new genomic tool which is set to transform the future selection and breeding of sheep around the world.

Called the Ovine SNP50 BeadChip, this cutting-edge tool will enable researchers to characterise the genetic variation at more than 50,000 Single Nucleotide Polymorphisms (SNP) in the sheep genome. This will pinpoint the small genetic differences that produce a variety of commercially important traits in sheep, fast-tracking the rate of genetic gain in the industry.

The research has been undertaken by the International Sheep Genomics Consortium (ISGC), a partnership of scientists and funding agencies which is developing a range of publicly available genomic resources. Access to these resources will help researchers find genes associated with traits that are important to their industries.

Working in partnership with Illumina, Inc., a global company headquartered in San Diego California, the Ovine SNP50 BeadChip has been made available for use by research groups around the world to identify DNA markers associated with traits such as disease resistance and improved and healthier meat products.

According to ISGC Secretary, Dr James Kijas, there has been extremely strong demand for the SNP chip.

"The availability of this tool means that researchers have much more power to identify important genes. As a result, initial demand for the chip has been very high."

"Groups will use the chip for a variety of objectives ranging from whole genome association studies to unravelling the process of domestication and impact of selection. The major aim of the ISGC is to use the chip to collect data from over 60 breeds of sheep and their wild relatives. This will tell us a lot about the history of the species and reveal which parts of the genome have been under selection for economically important traits."

John McEwan (AgResearch, New Zealand) led the team which identified the majority of the SNP. "We took the opportunity to use new DNA sequencing technologies which allowed us to identify over 300,000 SNP. This really energized the project and has resulted in a high quality research tool. The success of the project was only made possible through extensive, international scientific collaboration".

The initial sequencing was performed in parallel at the Otago University, Dunedin, New Zealand and the Human Genome Sequencing Centre at the Baylor College of Medicine, Houston, Texas, with additional sequencing subsequently undertaken by Illumina.

The genome assembly, SNP detection and selection of SNP was undertaken jointly by groups at AgResearch and Australia's CSIRO (Commonwealth Scientific and Industrial Research Organisation) and used by Illumina to create the Ovine SNP50 BeadChip.

Commonwealth Scientific and Industrial Research Organisation

The Baylor sequencing, Illumina sequencing and Australian contribution to the data analysis was financed by an Australian Government International Science Linkages Grant, SheepGenomics (a joint initiative of Meat and Livestock Australia and Australian Wool Innovation Ltd), CSIRO and the University of Sydney. The New Zealand work is part of Meat & Wool NZ and AgResearch's Ovita investment. Additional contributions were provided by Genesis-Faraday from the United Kingdom and USDA funding to Utah State University.

The work of the consortium is not yet completed, and plans are already well advanced for production of a reference sequence of the sheep genome and a preliminary study of copy number variation in sheep. Key ISGC researcher Dr Brian Dalrymple, explained the importance of comparative approaches.

"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.

"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.

"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.

"In the meantime, availability of the Ovine SNP50 BeadChip will mean sheep breeders can expect to access improved ways to increase genetic gain in their animals".

Professor Frank Nicholas, from the University of Sydney, who coordinated much of the Australian funding, summed up the achievement. "This ISGC project shows just what can be achieved when interested groups and countries combine resources to reach a common objective of benefit to all."

NOTE: AgResearch has footage available of the new genomic tool. Television media requiring this footage can contact AgResearch's Media Advisor (Details below).

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