Gentec’s Canadian Cattle Genome Project (CCGP) and researcher, Paul Stothard played an important role in the hot-off-the-press paper in Nature Genetics revealing the Phase I results of the 1000 Bull Genomes project.
Briefly, the goal of the project is to obtain extensive DNA sequence information on key ancestor bulls to increase the rate of genetic progress in cattle through improved genomic selection tools and to identify problematic mutations that lead to health issues. Project “HQ” is in Australia, but there are partners around the world. The University of Alberta and the University of Guelph, through the CCGP, are the current Canadian partners.
Although the CCGP includes a large Canadian team, it’s Stothard and Xiaoping Liau’s names that appear on this paper, due in part to their role in laying the groundwork with which to analyze the results.
“When the sequence data was processed, the result was a list of nearly 30 million SNPs,” he explains. “It’s very hard to connect biology or performance to particular SNPs based on that information alone, so we created software to help us better predict the functional consequences of each SNP (for example, which genes may be affected, how severe the changes might be). This is called a SNP annotation.”
Stothard and his team made the SNP annotation available to project members to “tie the story together.” The paper identifies SNPs for chondrodysplasia, early embryo death, and curly coat (which makes the animal susceptible to ticks and parasites). In each case, the annotations help to support the reported associations; for example, by revealing that the affected gene controls related traits in another species or that the SNP alters an important part of a protein. Stothard anticipates that these annotations will continue to be used widely as new traits are explored.
Those were the results of Phase 1 of the project using 234 animals. Today, we’re in Phase 4. Over 1,000 animals have been sequenced, including over 300 provided by Gentec and CCGP (which also makes Phase 4 data very relevant to breeds in the Canadian beef industry). And the annotation will continue to be of high value.
Teams have to contribute a certain amount of sequence data to the project, then get all the data back on all 1000 bulls. The 300 bulls Gentec/CCGP contributed is the largest input so far. Genome Canada gave CCGP a one-year extension to continue working with the data and convert it into new tools for animal breeding.
“Traits like the chondrodysplasia may be closer to adoption,” says Stothard. “That SNP could be incorporated into a panel fairly quickly to help producers avoid breeding animals that carry that mutation in future. Mostly though, the data are still raw, and more work is needed to translate the information into something that will benefit industry.”
All the participants in their various countries are taking project data back to their industry partners. Certainly, CCGP has many partners that it aims to benefit.Posted in Uncategorised