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Friday General Session

Whole Genome Analyses: Where are we now?

Understanding the beef genome offers tremendous potential value in making genetic improvement in selecting for economically relevant traits for which expected progeny differences (EPDs) don’t exist or are of low accuracy. Speaking May 1 at the 2009 Beef Improvement Federation (BIF) symposium in Sacramento, Calif., Dorian Garrick, Lush Chair in animal breeding and genetics at Iowa State University, presented an overview of current activities and progress made in whole-genome analyses.

Dorian Garrick

Dorian Garrick
Iowa State University

Garrick first explained that genomics evaluation consists of three phases: 1) training, also called discovery, in which you analyze either individual single nucleotide polymorphisms (SNPs) or analyze the entire genome looking for markers of value; 2) validation, in which you confirm whether or not those markers are in fact valuable; and 3) commercialization of those validated markers.

Garrick said there are two primary training populations currently available, both of which are dominated by Angus genetics. These include a dataset at the University of Missouri from Angus artificial insemination (AI) bulls that have published EPDs, and a multi-breed dataset developed by the U.S. Meat Animal Research Center (USMARC) at Clay Center, Neb. Numerous universities across the country are also working to collect data for specific goals such as detecting markers for carcass and meat attributes, including beef healthfulness, feedlot health, performance data and female fertility.

“Collectively, these projects represent major intellectual and economic investments in beef cattle improvements through funding by Pfizer Animal Genetics, Merial, land-grant universities and the U.S. Department of Agriculture,” Garrick said, noting that these investments will deliver improved selection tools to the U.S. beef industry and answer important questions we have in understanding the beef genome.

Specifically, he said three questions may be answered within the next 12 months: 1) what is the upper limit for predictive ability using a high-density genomic panel with 50,000 markers; 2) how is that predictive ability influenced by genetic distance; and 3) can a sample of just a few hundred markers offer similar predictive ability for substantially less cost?

These questions are the current focus of whole-genome analyses in U.S. beef cattle based on the Bovine Illuminaâ„¢ 50K Panel, a panel of 50,000 SNP markers that was developed using federal funds and made commercially available by Illumina in January 2008.

The 50K panels have also been used to make predictions for both the breed they were based on and other breeds. The most extensively analyzed dataset has again been those of Angus AI bulls, and correlation between discovered markers and existing EPDs have been calculated at 0.5-0.7. This correlation rate is equivalent to genomic predictions that account for between 25% and 50% of genetic variance.

“When you put that in perspective, that means that the 50K genomic prediction is equivalent to about six to 16 offspring in a progeny test if that trait had a heritability of 25%,” Garrick said. However, he said that when genomic predictions are made across breeds the information is far less reliable, often equal to observations based on only one progeny.

The 50K panels have also been analyzed to determine if fewer markers can be used without sacrificing predictive ability. Garrick said that for within breed predictions a sample of the best 600 SNPs taken from the 50K panel may actually offer information that is “almost as good” as the more expensive, larger panel.

Editor’s Note: This summary was written under contract or by staff of Angus Productions Inc. (API). To request reprint rights contact Shauna Rose Hermel, editor, at 816-383-5270. PowerPoints are posted with permission of the presenter and may not be reproduced in whole or in part without the express permission of the presenter.

The 41st BIF Research Symposium and Annual Meeting was hosted by the California Beef Cattle Improvement Association and the California Cattlemen's Association. For more information, visit www.bifconference.com or www.calcattlemen.org/bif2009.html.


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