New sheep genomic tool released
A cutting-edge genomic resource is now available which will enhance research in sheep beyond anything that was dreamed possible just two years ago. Through combined efforts and support of several groups, including the International Sheep Genome Consortium, USDA and the American Sheep Industry Association (ASI), a highdensity single nucleotide polymorphisms (SNP) array for sheep was released on Jan. 14, 2009. The ovine Illumina iSelect BeadChip will allow screening of almost 60,000 markers on an animal’s DNA in a single day, dramatically improving the identification of chromosomal regions and genes that have an influence on phenotypic variability.
A recent grant that was awarded by USDA’s National Research Initiative Competitive Grants Program to Utah State University (USU) will ensure that information obtained from the SNP array will contribute to the ovine whole genome assembly. This comprehensive, high-resolution assembly will underpin the discovery of genes and genetic regions that influence important and useful traits in sheep.
“One of the first and most exciting avenues that will be explored is the possibility of using single SNP to enable whole genome selection for traits important in the overall breeding objectives,” says Noelle Cockett, Ph.D., USU
College of Agriculture dean and vice president for extension and agriculture and the sheep genome coordinator for the U.S. The SNP chip will also be used to determine genomewide linkage disequilibrium in several U.S. breeds, representing wool, meat and parasite-resistant breeds.
This linkage information will be included in the worldwide ovine HapMap project and allows the exploration of unique and important characteristics within U.S. germplasm.
“We began this work by creating a virtual sheep genome, drawing on the work that had already been done to sequence the human, cow, horse and dog genomes,” explains Cockett. “As the sequencing costs continue to decline through 2009, the team plans to partially sequence the genomes of six individual sheep for discovery of additional genetic variation. In the meantime, the beadchip can translate into improved ways to increase genetic gain in sheep.”
The next step in the project includes collecting blood samples from animals within the U.S. sheep industry. “We are looking to collect as many as 2,000 blood samples from sheep with breeding values, and can use the assistance of producers,” Cockett explains.
Sheep producers interested in providing blood samples are urged to immediately contact Cockett at USU by e-mail (Noelle.email@example.com) or by phone (office: 435/797-2201 or lab: 435/797-2875).
ASI has aggressively supported funding from USDA for the project to ensure progress in this exciting program and that the results and products will be available for American sheep producers. ASI President Burdell Johnson, who met with the secretary of Agriculture several times with this request in 2008, emphasized the industry support for the U.S. role in this international program, citing future competitiveness of the American industry.
Sequence data used to generate the chip were initially collected in parallel at Otago University, Dunedin, New Zealand, and the Human Genome Sequencing Center at the Baylor College of Medicine, Houston, TX, with additional sequencing subsequently undertaken by Illumina.
The Baylor sequencing and the Australian contribution to the assembly were financed by an Australian Government International Science Linkages Grant, SheepGenomics (a joint initiative of Meat and Livestock Australia and Australian Wool Innovation Ltd.), CSIRO and the University of Sydney. The New Zealand work is part of AgResearch and Meat and Wool New Zealand’s Ovita investment.
Additional contributions were provided by Genesis- Faraday from the United Kingdom and USDA funding to USU.— WLJ