Harnessing the Power of Genomics for Beef - A Collaborative Approach

A previous article in this series in OMAFRA Virtual Beef introduced the field of genomics and how it will revolutionize beef cattle genetics, and in turn the beef industry. This area involves the direct analysis of the differences that exist amongst animals' DNA, and how these differences relate to the traits that we care about. Examples are reproduction, growth rate, feed efficiency and meat quality. The science of genomics is rapidly changing - tests are now available that allow an animal to be tested for 50,000 (50K) of these genetic differences called SNPs ("snips")!. Please refer to the previous article for a primer on this emerging field: www.omafra.gov.on.ca/english/livestock/beef/news/vbn0708a3.htm

This article will provide insight into how the successful use of this technology is transforming the dairy cattle breeding industry, and will shed light onto the need for more collaboration and coordination that will be required to fully harness this technology in beef cattle.

Will Genomics Work?

Before the industry fully embraces a plan to harness the opportunities that genomics provides, some concrete evidence that this technology will work in practice is required. There are now a number of genetic marker tests that have been independently validated and have been proven to work for cattle producers. Producers can use these tests now. However, the new technology discussed here is a result of a new large panel of 50K SNP, also known as the "Whole Genome Scan" or "Genomic Selection" approach. Proof now exists in recent developments in the field of dairy cattle breeding that this technology does work.

The Canadian Dairy industry, through the Canadian Dairy Network, the Centre for the Genetic Improvement of Livestock at the University of Guelph and the USDA is poised to introduce genetic evaluations to the Canadian Dairy industry in April 2009 (pending final approval) incorporating genotypes from the 50K SNP chip. The research to validate that this technology will work is already complete. And the results are quite impressive!

The benefit of this technology will be the greatest for young animals, who do not have progeny yet, or when we are trying to predict the genetic merit of an animal for a trait that we do not routinely measure, such as feed efficiency. Currently, when a young dairy sire is chosen to enter an AI stud and have semen drawn for the purposes of 'proving' him through his daughters' performances, the accuracy of the available genetic evaluations by which these young sires are chosen is quite low. The average reliability of a genetic evaluation on a bull at birth, which is based solely on his parents' proofs is 0.38 for production traits, as this young bull has no progeny and no record on himself. However, if we can add the information from genomics (50K SNP) to the prediction, this reliability increases to 0.67, an increase of 29 points in reliability.. This represents a huge increase of 76% in reliability in the genetic selection of these young sires! [(.67-.38)/.38 = .76]. This technology is poised to have a major impact on the dairy cattle breeding industry. The technology will also have a major impact on the beef cattle breeding industry, but considerable work still lies ahead to realize the benefit.

The Need for Collaboration

The results from dairy cattle breeding represent a collaborative effort, as Canada and the USA are exchanging genotypes on sires and dams. A total of 4000 proven sires were used to derive the prediction equations which relate the 50K SNP genotypes to the production traits. These 4000 proven sires (semen straws used as source of DNA) are the result of a central repository from a number of participating AI studs in the USA, of which Semex is a member. Preliminary results from the USA also indicate that the increase in reliability due to genomics would be even greater if more than 4000 sires were available to determine the required prediction equations. This genotyping technology is very powerful, in that we can genotype a single animal easily for 50K SNP. However, it is now clear that the data requirement - the number of animals with DNA and measured traits that we need to derive useful predictions from these large numbers of genotypes is also quite large. The need for collaboration to exploit the full benefit of this technology is clear.

Canadian University partners Alberta and Guelph, represent the Canadian activities with the 50K SNP technology with a goal towards genomic selection for the beef industry.

Figure 1. Measuring feed efficiency
Figure 1. Measuring feed efficiency

Our project includes 1250 animals genotyped with extensive data available. The project is providing some very useful results that will enable improved genetic selection technologies for beef cattle. However, although the project is of substantial size, it is acknowledged that the tools developed would be more powerful with a resource that includes more animals genotyped. The dairy example includes over 4000 progeny tested sires, with fairly accurate proofs, and evidence there suggests more bulls would still be advantageous. With beef cattle, we are dealing with many traits for which an animal has its own record (such as feed efficiency), but are not typically progeny proven bulls in most cases, as bulls are not proven in large numbers for all the traits we are interested in improving with genomics, such as feed efficiency and beef tenderness.. In fact we will need about 5-10 animals with their own records to get the same power as a progeny proven sire. So we can expect that increasing our numbers to 20,000 animals with complete performance information and genotypes will still be advantageous.

The resources required to exploit the full benefit of this technology are extensive and not likely to be completely met by one organization. For this reason Canadian University partners, Alberta and Guelph have entered into a collaborative data sharing agreement with both the Cooperative Research Centre for Beef Cattle in Australia and the USDA Meat Animal Research Centre, to combine the collective data in this area. All three organizations are involved with similar 50K SNP experiments in beef cattle. Data was exchanged in Dec 2008. The next step is to identify how additional resources can be coordinated across the 3 countries. This will require a combined effort with various industry groups such as Cattlemen's Associations and Breed Associations, University, Government and research organizations working collaboratively in a pan-Canadian effort to accomplish this goal. The effort and work before us is significant, but the potential benefits to the beef industry are also significant and must be pursued!

Like the dairy industry, genomics will significantly change the landscape of genetic improvement and the resulting beef animals used for production.

Figure 2: Genomics is unravelling the secrets of DNA
Figure 2: Genomics is unravelling the secrets of DNA

Acknowledgements

This world class genomics research would not be possible at the University of Guelph without the funding and research stations (along with their cattle and staff) made possible by the partnership with the Ontario Ministry of Agriculture, Food and Rural Affairs. Funding from the Ontario Cattlemen's Association and the Agriculture Adaptation Council is also gratefully acknowledged. Insights into the impact of genomics on dairy cattle breeding were obtained from Dr. Flavio Schenkel who is leading the research in this area from the Centre for the Genetic Improvement of Livestock at the University of Guelph in conjunction with the USDA, Canadian Dairy Network and funding from NSERC, and L'Alliance Boviteq (Semex Canada).

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