Collaboration key to success for sheep genome
Collaboration key to success for sheep genome project
7 January, 2008
In less than five months AgResearch has completed its share of an international sheep genome mapping project that will help farmers identify genes associated with important production, quality and disease traits in sheep. AgResearch is one of 19 organisations from Australia, New Zealand, the 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 such traits. Over the last few months a team of AgResearch scientists based at the organisation's Invermay campus, near Dunedin, has scanned the sheep genome one and a half times.
The data will be used to identify single nucleotide polymorphisms (SNPs), which are small genetic differences and indicative of the traits that can separate a productive or disease resistant animal from the rest of the flock.
The science team has created the underlying information that will allow a device known as an SNP chip to scan the genome for 60,000 variants in a single pass, rather than having to conduct separate tests for each variant. The work is part of AgResearch and Meat & Wool New Zealand's Ovita Investment.
"It's a step on the way to creating tools that will allow sheep breeders to select animals based on DNA markers that can indicate useful traits from birth. Historically farmers have had to record the pedigree and production traits of livestock to ascertain their value. The tools we are helping develop will enable them to determining this faster and more accurately," says AgResearch Senior Scientist John McEwan.
He says the milestone could not have been achieved so quickly without collaboration from the University of Otago, which has allowed AgResearch scientists to use the University's recently purchased genome sequencing machine.
"It is also a great example of AgResearch working jointly with a university where both parties benefit from an infrastructural investment," he says.
John McEwan says access to the recently established KAREN telecommunications network that provides high capacity, ultra high-speed connectivity between New Zealand's tertiary institutions, research organisations and the rest of the world, has also enabled the team to work seamlessly with collaborators all over the world and store information on a single database based at AgResearch's Invermay Campus, rather than having to use several in disparate locations.
John McEwan 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.
Otago's Genomics Sequencer Manager Dr Jo-Ann Stanton says that the collaboration with AgResearch has been incredibly productive and highly enjoyable.
"This work has allowed us to fine tune techniques of using the machine, allowing us to take full advantage of its tremendous capabilities. We are now well placed to offer a top-notch nationwide service for researchers seeking high quality, rapid and accurate high throughput sequencing," says Dr Stanton.