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Genomics - the New Buzzword of the Beef Industry • Angus Genetics Inc. and IGENITY to Introduce Industry's First Genomic-Enhanced EPDs for Multiple Traits • Steer Feedout Program • Save the Date

Genomics - the New Buzzword of the Beef Industry

Genomics, you may have heard the term thrown around in the popular press, but what does it mean? Genomics is the study of the genomes of organ isms. The field includes inten sive efforts to determine the entire DNA sequence of organisms and fine-scale genetic mapping efforts. The field also includes studies of phenomena such as heterosis, epistasis, pleiotropy and other inter actions between loci and alleles within the genome. In contrast, the investigation of the roles and functions of single genes is a primary focus of molecular biology and is a common topic of modern medical and biological research. Research of single genes does not fall into the definition of genomics unless the aim of this genetic, pathway and functional information analysis is to elucidate its effect on, place in and response to the entire genome's networks.

What role will molecular biology and genomics play in your operation? There are several commercial companies that are marketing genetic marker products to beef producers. If you have read any industry magazines or newsletters, you probably have seen advertisements for these companies. If you have been to bull sales lately, you probably have seen results of these tests published in the sale catalog. How does a producer decide when it is appropriate to use these tests and how do you interpret the results?

The first step to understanding genetic marker technology is to look at basic genetic principles. There are traits in cattle that are controlled by just one gene; the horned/polled locus is a good example of this. The polled allele is always dominant to the horned allele, so the inheritance and expression of this trait is straightforward and easily predicted. Most of our important production traits are polygenic, or controlled by many genes. Weaning weight is an example of a polygenic trait. We know it is controlled by many different genes, but we don't know how many - it could be 10 or 10,000. So the important lesson here is that knowing the result of a marker for one gene that controls weaning weight is important, but it does not tell us all there is to know about that animal's potential weaning weight. We are learning that some genes may play a bigger role in determining outcomes for traits such as weaning weight, so if these results are from one of those more influential traits, the test may even be more valuable than if it comes from a gene that plays a minor role in determining an animal's weaning weight.

Illumina SNP Chip

The second step to this question is to understand the technology. What are genetic markers? Markers themselves usually consist of DNA that does not contain a gene; however, they can tell a researcher the identity of the person a DNA sample came from. This makes markers extremely valuable for tracking inheritance of traits through generations of cattle. Although there are several different types of genetic markers, the type most used on genetic maps today is known as a microsatellite map. However, many of the new tests are being constructed using single-nucleotide polymorphisms, or SNPs (pronounced "snips"). Both types of markers are easy to use with automated laboratory equipment, so researchers can rapidly map a disease or trait in a large number of family members.

The discovery of new genetic markers is rapidly increasing and companies are bringing new tests to the market at a rapid pace. One key to this rapid increase in the number of markers developed goes back to the completion of the sequencing of the bovine genome and the development of a system called the SNP chip. The results of the bovine genome project were published in April 24, 2009, and will continue to play an important role in beef cattle genetic studies as well as human genome research. The use of the Illumina SNP chip, a test that can determine the genotype of 50,000 SNP markers at a time, is generating huge amounts of data that will lead to more discoveries of new markers in beef cattle. On the human side, the technology is already up to 1.2 million markers at a time.

The third step is to understand how the use of genetic markers in your herd will benefit you. Right now there seem to be two uses for genetic markers: 1) as a marketing tool and 2) as a genetic improvement tool. Many purebred breeders use this technology as a marketing tool, mainly as a way to seemingly add value to the animals they are selling.

The real benefit of the technology is as a genetic improvement tool. We now have the technology to incorporate genetic marker information into the calculation of EPDs, which will increase their accuracy. This is the best way to incorporate this technology into your herd. Many of the tests that are available now are multiple marker "panels," or many different markers that are assembled into one test that all have significant links to the trait the test was designed around. For example, several companies market a test to predict marbling or quality grade, and you will get a single result for marbling on the report you get back from that company, whether it be in "stars" or molecular breeding values (MBVs). More than likely, that result is a combination of results from many different genetic marker tests. The problem you now face is that now you have a marbling EPD and a genetic test result for marbling, how do you utilize both forms of information to make a selection decision? The answer is to combine them, and that is what many breeds are working towards.

Are you interested in evaluating the use of genetic markers in your herd? If so, please contact your local county Extension agent to set up a time to discuss genetic markers.

What is going on at the University of Arkansas in the area of cattle genomics?

Effects of a Single Nucleotide Polymorphism in the Interleukin-8 Receptor on Susceptibility of Dairy Cattle to Mastitis. R.W. Rorie and M.D. Person. http://arkansasagnews.uark.edu/563-35.pdf

Relationship of Lactate Dehydrogenase Activity with Body Measurements of Angus x Charolais Cows and Calves. M.L. Looper, T.P. Neidecker, C.W.Wall, S.T. Reiter, R. Flores, A.H. Brown, Jr., Z.B. Johnson, and C.F. Rosenkrans, Jr. http://arkansasagnews.uark.edu/553-2.pdf

Associations Between Cattle Breed and Heat Shock Protein 70 Gene. M. Lamb, R. Okimoto, M. Brown, and C. Rosenkrans, Jr. http://arkansasagnews.uark.edu/545-50.pdf

Identification of Polymorphisms in the Enhancer Region of the Bovine Prolactin Gene. S.G. Black, R. Okimoto, and C.F. Rosenkrans, Jr. http://arkansasagnews.uark.edu/522-25.pdf

Marker-Assisted Selection
http://www.ansci.cornell.edu/nbcec/producers/
marker_assisted_selection.pdf

Validation of Marker Tests
http://www.ansci.cornell.edu/nbcec/producers/Validation.pdf

Basics of DNA markers and genotyping
http://www.ansci.cornell.edu/nbcec/producers/
basics_DNAMarkers&Genotyping.pdf 

Whole Genome Selection
http://www.ansci.cornell.edu/nbcec/producers/
whole_genome_selection.pdf

Guide to DNA Markers
http://www.ansci.cornell.edu/nbcec/producers/dna_markers.html

DNA-Based Progeny Testing and Development of Commercial Ranch EPDs
http://www.ansci.cornell.edu/nbcec/producers/
DNAbased_progenytesting.pdf

Angus Genetics Inc. and IGENITY to Introduce Industry's First Genomic-Enhanced EPDs for Multiple Traits

I don't want this to sound like a commercial or an endorsement for either Igenity® or the American Angus Association®, but I am including this story because it is the first time any breed has taken advantage of multiple genetic markers in increasing the usefulness and accuracy of the EPDs they produce. Angus producers will have first access to breed-specific DNA profiles, but I am certain that this will not be the only press release we see on this topic.

DULUTH, Ga., July 14, 2009 - Angus Genetics Inc.® (AGI) and Merial have entered into an exclusive agreement to provide American Angus Association® breeders with genomic-enhanced expected progeny differences (EPDs) powered by IGENITY®. This will be the first time beef producers have access to genomic-enhanced EPDs for multiple traits at once - and from an Angus-specific DNA profile.

Bill Bowman, president, AGI, says this agreement joins two groups committed to advancing genetic improvement in the beef industry.

"AGI and IGENITY share a common vision to provide beef producers with the most advanced solutions to their genetic selection and management needs," Bowman says.  "This represents a significant milestone for our industry - one our board has directed us to pursue aggressively for the past two years and supported with collaboration and research dollars."

The combination of a breedspecific DNA profile with the Angus National Cattle Evaluation (NCE) will result in higher-accuracy EPDs. This will be an especially powerful tool for evaluating young animals, as cattle will now have accuracies that were previously only possible once they had multiple progeny on the ground, Bowman says.

Dr. Stewart Bauck, executive director of research and development, IGENITY, commends AGI and its parent company, the American Angus Association, for leading this charge.

"The American Angus Association has set the standard in data collection and embracing cutting-edge technologies," he says. "We appreciate the work the Association has done to keep the breed at the forefront of the beef industry by helping bring this advancement to Angus breeders."

Bowman says the selection of a DNA technology partner was a logical decision.

"IGENITY has a robust profile of analyses, including the industry's only DNA analyses for reproduction and maternal traits in combination with all of the economically important carcass traits," he says. "Plus, the addition of the genomic tools from IGENITY into our NCE system provides us the ability to improve the accuracy of Angus EPDs - especially in young animals."

Dr. Bauck adds that genomic-enhanced EPDs for multiple traits have become a reality after years of collaboration among beef industry leaders.

"The industry agreed that genomic-enhanced EPDs were the next advancement in DNA technology," he says. "It was our responsibility as the leading DNA technology provider to take action and move the topic of genomic-enhanced EPDs from an industry discussion to a user-friendly solution."

The list of available genomic-enhanced EPDs is being finalized by the American Angus Association. It's expected that Angus producers will be able to tap into this offering with the availability of the test this fall. The spring 2010 Sire Evaluation Report, available online in December 2009 and in print January 2010, will be the first report to include genomic-enhanced EPDs. These EPDs are enhanced by analyses from IGENITY; however, producers will continue to communicate and work with the trusted team at the American Angus Association.

In addition to genomic-enhanced EPDs for Angus producers, IGENITY offers analyses for more than 15 economically important traits producers can use to make more confident selection, management and marketing decisions. IGENITY also offers user-friendly information management software and expert consultation to help producers customize this advanced information to their individual herd goals.

Save the Date!

The Beef Improvement Federation will host their annual meeting in Columbia, Missouri, on June 28-July 1, 2010. This meeting is a blend of producers, academia and breed associations that discuss breeding and genetics issues affecting the industry. It is a great chance to hear the cutting edge research and meet the scientists that are conducting the research. The meeting travels around the country, so take advantage of it being this close to home. So, mark your calendars now - I'll send out more info on the meeting as I get it.

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