Sheep SNP chip

The team produced 42 million reads and a total of nine gigabytes of DNA sequence. AgResearch and CSIRO researchers put it all together by jointly reconstructing a first pass of the sheep genome.

CSIRO bioinformation Dr Wes Barris says the approach involved using their previously-computed virtual sheep genome information to rearrange bovine chromosomes into virtual sheep chromosomes.

Sequence-comparison tools are then applied to map the millions of short sheep sequences onto the temporary virtual chromosomes, which provide a guide for locating and orienting the sheep sequences.

"We end up with sheep chromosomes made up of pure sheep sequence data," Barris says. "The procedure requires a lot of computing power. We have access to two computing clusters and have kept them busy around the clock doing sequence comparisons."

To increase the number of SNPs available to the international community, the consortium performed a second SNP discovery experiment. Kijas led a collaboration with Illumina, using its Solexa technology, which yielded nearly 50 million sheep sequence reads in a single machine run.

"We wanted to identify SNPs and obtain an estimate of their frequency within sheep populations at the same time," Kijas says. "To do this we collected a diverse set of 60 sheep, pooled their DNA into a single tube and then sequenced it with Solexa technology to search for additional polymorphic sites".

An immediate effect from the consortium's work will be the creation of a SNP chip carrying approximately 60,000 of the best SNPs. Kijas says researchers expect this new tool will dramatically accelerate the pace of gene discovery.

Australian researchers will be focusing on traits influencing disease resistance, meat quality, meat yield and wool fibre diameter in the Merino. Meat and Livestock Australia (MLA) and Australian Wool Innovation (AWI) have constructed large research flocks which will be used for the research.

"We're fortunate in having large flocks with highly accurate records for traits such as disease resistance, carcass parameters and even behavioural differences," Kijas says.

"The SNP chip will enable us to perform a genome-wide search for genes underpinning each of these traits."

Kijas says early work has shown that the level of genetic diversity present within sheep breeds is high compared to cattle.

"The ability to collect data from 60,000 SNPs across a large sample of breeds will give us detailed information about the origin and relationship between sheep populations." The consortium is now collecting 2000 sheep representing nearly 40 breeds for the experiment.