Collaboration key to success for NZ sheep genome
Collaboration key to success for NZ sheep genome researchers
Monday 31 March, 2008
Meat & Wool New Zealand, AgResearch and Ovita today announced that an important phase of an international project to map the sheep genome has taken a big step forward.
Following completion of the sequencing of the sheep genome to three-fold coverage, the first assembly of a draft sequence of the sheep genome has now been achieved. When fully completed, the entire project will provide significant benefits for both farmers and human health researchers.
Meat & Wool New Zealand R&D Manager Max Kennedy says the initial assembly of the interim low coverage sequence of the sheep genome is one step towards identifying DNA variants and also allows scientists to use the sheep genome sequence directly for the first time.
“This will enable researchers to accurately position DNA variants on the genome. The identification of these variants is the primary goal of the next phase of the project.”
When the project is complete, it will allow the development of tools to help farmers identify genes associated with important production, quality and disease traits in sheep, he says.
AgResearch Senior Scientist, John McEwan said the project has generated more than 9,700,000,000 bases (97 Giga bases) of sequence from 6 sheep. While modest by world standards, this is by far the largest sequence assembly project attempted in Australia and New Zealand.
The assembly has been created by New Zealand and Australian researchers who are part of the International Sheep Genomics Consortium (ISGC). The ISGC is a collaboration between scientists (and their organisations) from 16 countries including Australia, New Zealand, the United States, and United Kingdom that contributed to the current work. The purpose of the Consortium is to develop genomic resources in the public domain. Access to these resources helps researchers in each country find genes associated with traits that are important to their industries.
Such a complex project demands a collaborative approach. “The skim sequencing of the genome has been completed in only seven months and utilised the latest “next generation” sequencing methods. It was conducted simultaneously at Otago University in Dunedin and at the Human Genome Sequencing Centre at the Baylor College of Medicine, Houston, Texas. The New Zealand component, led by Jo Stanton of Otago University, was the first use of the technology in New Zealand and required both commissioning of the sequencing machine and staff training.
“We are very appreciative of the efforts undertaken by the team from Baylor, led by Prof Richard Gibbs, which has sequenced several other species. They have been very generous in sharing their skills,” says John McEwan.
The New Zealand work is part of Meat & Wool New Zealand and AgResearch’s Ovita Investment. The sequencing by Baylor and the Australian contribution to the assembly were financed by CSIRO, an Australian Government International Science Linkages Grant, Sheep Genomics (Meat and Livestock Australia and Australian Wool Innovation Ltd) and the University of Sydney with additional support for sequencing by Genesis Faraday from the United Kingdom. The support of Meat & Wool New Zealand enables Ovita to participate in and contribute to the best in international sheep genome research. This ensures New Zealand remains a leader in the field. It also increases the opportunity for greater returns to the New Zealand sheep industry at lower cost.
Max Kennedy says the importance of this funding should not be underestimated; it is a costly exercise but down the track, the benefits to farmers will be significant.
By late 2009 the researchers hope to have mapped production traits to specific regions of the genome. In turn this knowledge will be used commercially to select better animals
In the current project AgResearch staff have been involved in sequencing strategy simulations, have undertaken a major part of the sequencing using the Otago facility, have developed a database to store all the sequences collected and are undertaking sequence assembly and subsequent SNP detection in conjunction with Australian researchers.
The sequence will be used by all sheep researchers. As the sheep is used widely as a human medical model for a number of diseases such as osteoporosis, the flow-on effects of this research should have considerable benefits in the area of human health as well.