Healthier and more productive sheep are on the way thanks to an international sheep gene mapping programme.

AgResearch is one of 19 organisations from Australia, New Zealand, United States, United Kingdom, France and Kenya that make up the International Sheep Genomics Consortium (ISGC). The purpose of the Consortium is to develop public genomic resources that will help researchers find genes associated with production, quality and disease traits in sheep.

AgResearch Senior Scientist John McEwan and international collaborators are currently working on a project to sequence and assemble the sheep genome. This means identifying the entire hereditary information of sheep contained within its DNA.

The objective is to find single nucleotide polymorphisms (SNPs). These are very minor genetic differences that act like a predisposition for productive capabilities or disease.

“Once found the team will create a SNP chip. This chip will be able to scan for some 60,000 variants (or predispositions) in the genome in one pass, rather than needing to perform separate tests for each variant,” says John.

This process known as ‘whole genome selection’ has great potential to speed up the rate of genetic gain in the industry.

“We will quickly be able to weed out predispositions to negative traits like facial eczema and ensure positive traits such as parasite resistance and meat production are carried through the gene pool.”

AgResearch plays host to international sheep database

This will be the first in a series of projects that will allow researchers from AgResearch, Commonwealth Scientific and Industrial Research Organisation, Baylor and the Human Genome Sequencing Centre to share resources and datasets on an ever increasing scale.

Over a last few months of 2007, a team of researchers at AgResearch scanned the sheep genome one and a half times, creating a100Gb database of raw sequence files.

Previously each organisation would have separate databases and spend a large amount of time keeping them synchronised and transferring data between them.

But now, because of KAREN, AgResearch will play host to a single database which will actively assemble, process, and annotate the data collected. The team are also developing an identity and access management solution to regulate access to the data.

“The single database means that data is available to users in an accessible format. Tools will also be developed to ensure the data is analysed appropriately to get the greatest value from it,” says John.

The high speed, high capacity connection that KAREN provides ensures that the database and the organisations’ computer processing capacity are accessible to each collaborator.

“KAREN has effectively shrunk distance and time, enabling us to host this sophisticated, internationally significant resource and harness the computing power of our international partners from right here in Invermay.”

Collaboration cuts the cost of science

While the costs of genome sequencing are dropping as technology develops, the investment required is still beyond most single research groups. This has seen the rise in international consortium-based collaborations such as this project. This trend is beginning to place enormous pressures on data transfer between collaborating scientists around the world and this is why networks like KAREN are vital.

“The scale of this collaboration has brought significant cost savings to all organisations involved, largely due to reductions in the duplication of efforts and resources. And as new technology comes onboard, as KAREN did for us recently, we will see the costs of genome sequencing dropping even further,” says John.

John says the project to create a sheep SNP chip should be completed by July 2008 and his team hopes to have first generation tools developed for New Zealand ram breeders available by mid 2009.

More information

Consortium website: http://www.sheephapmap.org

AgResearch media release: http://www.agresearch.co.nz/anm2Net/templates/agrnews.aspx?articleid=628&zoneid=3 

[Image: The AgResearch team of Russell Smithies, Rudiger Brauning, Gemma Payne, John McEwan and Alan McCulloch (seated) that are using KAREN as a critical part of the process of skim sequencing, assembly and display of the ovine genome]

Updated: 14 January 2008