Online cattle database aids genome analysisOnline cattle database aids genome analysis
Publicly viewable genomics resource of a broad cross section of U.S. beef cattle makes it easier for scientists to identify genes associated with traits that are important to breeders and ranchers.
March 8, 2017
U.S. Department of Agriculture scientists have made available a online genomic database of U.S. beef cattle.
The complete genomes of 96 bulls, representing 19 different U.S. cattle breeds, were sequenced by researchers at the Agricultural Research Service's (ARS) U.S. Meat Animal Research Center (USMARC) in Clay Center, Neb.
The result is a searchable and publicly viewable genomics resource of a broad cross section of U.S. beef cattle that will make it easier for scientists to identify genes associated with traits that are important to breeders and ranchers.
“Our goal was to include animals that represent the breadth of diversity in U.S. beef cattle, not just the top breeds,” said Michael Heaton, a USMARC microbiologist.
Heaton started building the panel in the 1990s but only began the genomic sequencing of all 96 animals in the last two years, with help from USMARC chemist Timothy Smith. The web-based platform was designed by Theodore Kalbfleisch, an associate professor at the University of Louisville in Kentucky.
These 19 cattle breeds are represented in the online cattle genomes for finding disease mutations. The numbers indicate how many animals per breed were included.
“Our primary interest is infectious disease and animal health,” Heaton says. “Typically, diseases affect only a small percentage of animals, but the loss of any animal can be expensive. We wanted to see if we could root out those relatively rare genetic defects that cause a few animals to get sick and die. To do that, we had to gather all the genetic diversity in U.S. cattle to find those ‘bad’ genes.”
Using the panel, Heaton and his colleagues analyzed a bovine gene associated with brisket disease. Also known as pulmonary hypertension, mountain sickness and dropsy, the disease results from elevated pulmonary arterial pressure caused by lack of oxygen. It commonly occurs in cattle raised on ranches at altitudes of at least 5,000 ft. above sea level. There is no cure for pulmonary hypertension, which also occurs in people.
Scientists were able to identify previously unpublished mutations in a gene associated with brisket disease. Such an analysis used to take 3 months at a cost of $3,000 and can now be done in 3 hours for free, Heaton said.
The idea is that if a certain version of the gene is “bad,” it can be added to a genetic test for selecting the best breeding animals. Producers can test their animals and make sure they choose breeding stock with the “good” version, Heaton said. “This is important to producers, because brisket disease is occurring more frequently at lower altitudes. The cattle panel genomes can be used to discover gene mutations that escalate this problem.”
In addition to analyzing gene mutations influencing disease, the panel of genomic profiles also helps in the evaluation of genes affecting production traits such as growth and reproduction.
The sequence is accessible at https://www.ars.usda.gov/plains-area/clay-center-ne/marc/wgs/main/.
“Many producers are using DNA testing to decide which animals to breed, so adding this gene or future genes to tests is a natural,” Heaton said.
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