Bovine DNA sequencing offers insight for researchers, beef producers
March 22, 2017
Though DNA is microscopic, the sequencing of it carries enormous implications for cattle producers.
The U.S. Meat and Animal Research Center recently announced the genomic sequencing of a panel of 96 bulls, and the data is now accessible online at http://www.ars.usda.gov/plains-area/clay-center-ne/marc/wgs/main/
"Our current set of cattle breeds for which we are producing whole genome sequence currently includes 46 breeds," said Michael Heaton, Agricultural Research Service microbiologist who works at USMARC located in Clay Center, Neb. "Researchers can analyze the DNA sequences of genes known to cause disease, and then look for mutations that may affect the gene's function. This type of careful analysis can identify previously unknown mutations, and help estimate the prevalence of an already-known mutation in other breeds. We did this with EPAS1, a gene previously associated with brisket disease in cattle."
"Although anyone can access the DNA sequence information, it was not designed for use directly by producers," Heaton said. However, producers can benefit from the discovery of new gene markers that affect traits in beef cattle. Once the gene markers are discovered and validated, they can be incorporated into existing DNA tests like those currently being used to select breeding stock."
In addition to the most popular breeds such as Angus, Hereford, Limousin, Charolais and Maine Anjou, the USMARC catalog of genome profiles also includes breeds such as Corriente, Highland, Indu Brazil, Wagyu and Beefmaster, just to name a few.
"I have a Beefmaster ranch, and Heaton approached me about obtaining some samples for his research," said Randy Goode, owner of Goode Cattle Co. in Damon, Texas. "I realized what he was trying to accomplish, so I kind of volunteered to travel the country and help him explain to producers in layman's terms what the sequencing would do for the industry and encourage them to donate samples."
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Over the course of 10 years, Goode traveled from Florida, where he obtained samples of water buffalo, to Washington for dairy cattle samples, and everywhere in between, working with Watusi breeders and individual cattlemen to procure a catalog of samples for Heaton's work.
"I traveled to different areas trying to collect as many samples as I could," Goode said. "Most of the time, we stuck to tail hair follicles because they were the easiest to collect. The lab at USMARC is truly fantastic. These guys are incredible researchers, and they really accomplished something pretty important for the beef industry through this sequencing. These codes can be used over and over again to troubleshoot new problems. It's pretty amazing."
In addition to Goode's travels to individual producers, Heaton collected samples from SEK Genetics, Inc., ABS Global, Inc., Bovine Elite, Inc., Accelerated Genetics, the Braunvieh Association of America, North American Corriente Association and the American Tarentaise Association. This broad sampling enabled Heaton to capture the true diversity of the U.S. beef cattle germplasm, which will now serve as a valuable resource for the industry.
"I am continuously amazed by what can be found in the cattle genome every time a new region is analyzed," Heaton said. "The genetic code is fascinating, and in some ways, can be read like a book. By reading and comparing the genetic code from different species (like cattle, humans and fish), we can get a peek at what has happened over millions of years of cattle evolution. Some genes never seem to change, while others never seem to stay the same. It's a great time to be studying cattle genomics."
Heaton said the online resource was designed for researchers and technicians from universities, companies, and government laboratories and genetic testing and diagnostic laboratories around the world.
"We also provide reference DNA samples from these 96 bulls to DNA testing laboratories, so they can regularly calibrate their in-house tests for things like parentage determination, SNP chips, coat color and various traits," Heaton said. "This helps ensure the companies provide cattle producers with accurate test results."
For example, when the Limousin breed discovered discrepancies in its homozygous black tests, a commercial testing lab approached Heaton about helping them get to the root of the problem. With DNA sequencing, USMARC found a variant in the black coat gene, which would result in red calves.
"The genetic test results indicated that bulls should be producing 100 percent black calves when bred to red cows," Heaton said. "However, some black bulls kept producing some red calves. With the DNA sequence from these 96 bulls, we quickly saw that the key gene for red-black coat color was a little different in some Limousin bulls. With knowledge of this difference in hand, the company redesigned their test and had it working perfectly within a week. The black bulls producing red calves turned out to be 'heterozygous black' and would be predicted to throw 50 percent red calves when bred to red cows."
Genomic sequencing opens up a whole new world of discovery for the beef cattle industry, and the catalog of samples offers a valuable library of information for USMARC to reference.
"In terms of using cattle genetics to ward off disease, there is still a lot we don't know about disease mechanisms," Heaton said. "However, as the mysteries of diseases are unraveled, the role of host genes will become more clear and will hopefully lead to novel genetic solutions."
For more information on USMARC's genomic sequencing, check out https://agresearchmag.ars.usda.gov/2017/mar/cattle/.