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

A new genomic tool is now available that will transform sheep breeding.

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 to develop the chip was carried out by the International Sheep Genomics Consortium (ISGC). AgResearch is one of 19 organisations from around the world that make up the ISGC, that is developing public genomic resources to help researchers find genes associated with production, quality and disease traits in sheep.

Assembling the sheep genome

AgResearch Senior Scientist John McEwan and international collaborators first sequenced and assembled the sheep genome, identifying the entire hereditary information of sheep contained within its DNA. Once this was completed the team were able to identify 'single nucleotide polymorphisms' (SNPs). These are very minor genetic differences that act like a predisposition for productive capabilities or disease.

“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," says John.

AgResearch plays host to international sheep database

This will be the first in a series of projects that will allow researchers from AgResearch and partner organisations from across the world to share resources and datasets on an ever increasing scale.

During 2007, a team of researchers at AgResearch scanned the sheep genome one and a half times, creating a 100Gb 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 hosts a single database that assembles, processes, and annotates the data collected.

“The single database means that data is available to users in an accessible format. Tools were also 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 on board, as KAREN did for us recently, we will see the costs of genome sequencing dropping even further,” says John.

More information

SNP Chip video on YouTube: http://www.youtube.com/watch?v=hoHv3E6FmCQ

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

SNP chip for the sheep genome - AgResearch news, 14 January 2009

Collaboration key to success of sheep genome project - AgResearch news, 7 January 2008

[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: 28 April 2009