A rancher’s guide to genomics | TSLN.com

A rancher’s guide to genomics

Photo by Susie Thompson"When genomics first came into the marketplace, bull sale catalogs were filled with a plethora of information," says Matt Spangler. "A lot of that information was useless, because the ratios, EPDs and accuracy were too low."

The added value of genomic information to expected progeny differences (EPDs) in beef cattle may produce more accurate EPDs, especially in young, unproven bulls. The evolution of genomic information isn’t designed to replace EPDs, but will make EPDs more accurate says Matt Spangler, University of Nebraska beef geneticist.

Spangler discussed the implementation of marker-assisted EPDs during the 2011 Range Beef Cow Symposium in Mitchell, NE. His take-home message to seedstock producers was to continue to collect and routinely record phenotypic information, even if they collect genomic data.

“If you are a seedstock producer, you still need to weigh your calves at birth,” he says. “Genomic technology only makes these tools stronger; it does not replace them.”

Spangler says he sees genomic predictions being particularly valuable to seedstock producers with young, unproven bulls. Before genomics were available, producers used EPDs to select a sire and wait for his offspring to be born to improve the accuracy of his traits.

“Genomics and the corresponding marker-assisted or genomic-enhanced EPD, have become a reality,” Spangler explains. “Within a breed, genomic predictions based on 50K genotypes have proven to add accuracy for several traits, particularly to young bulls.”

The problem with genomic testing, Spangler says, is it tends to be breed specific.

“If a test was developed for Angus, it will work best for Angus cattle. The test will not be as accurate if it is used in other breeds. An Angus test used on Charolais will not work as well, and you will be really disappointed if you use it in Bos indicus cattle,” he explains.

Spangler highlights a study where the application of a 50K-based genomic prediction test developed for Angus was used on closely-related Red Angus. The results showed a substantial amount of variation, and were deemed inaccurate, he says.

The American Angus Association (AAA) leads the pack in developing and providing this genomic technology for their members, Spangler says. AAA currently focuses on correlated traits, which means developing genomic information and correlating that data to the trait of interest, such as weaning weight.

The American Hereford Association (AHA) is also in the forefront of utilizing this new technology by working to develop a database of genomic information for their members. AHA focuses on blending genomic information with an index of EPDs currently available.

A third option of implementing this technology, which is currently used by the dairy industry, is the genomic relationship. Markers are used to help supplement pedigree information. No relationships are based on genomic information, he says. “In order to do that, the industry would have to have access to those genotypes.”

Spangler tells producers if their breed association isn’t looking into how to develop genomic information specific to their breed, he would be very concerned about the long-term viability of the breed.

“Genomics work, but how well it works is the question,” Spangler says. “The adoption of this technology follows the breeding pyramid. Unfortunately, it isn’t as well accepted in beef cattle as it is in other species, like swine and poultry.”

Genomics were originally developed to help researchers pinpoint genetic defects like marble bone. Before genomic testing was available, Spangler says animals were purged based on their pedigree.

“We can now use genetic testing to pick out the carriers and determine what to do with them,” he explains. “Without this testing, some breeds would have been decimated in the past few years.”

Genomic testing has also been used as parentage testing to ensure animals have the correct pedigree, but has now evolved into collecting data for complex traits, which are traits controlled by numerous genes that impact EPDs.

“When genomics first came into the marketplace, bull sale catalogs were filled with a plethora of information,” Spangler says. “A lot of that information was useless, because the ratios, EPDs and accuracy were too low.”

For breeds like Angus, who have developed a test for their specific breed, a DNA sample can be collected and sent to the breed association. The breed association sends the sample to a genetic lab for evaluation, and that data is sent back to the breed association, where it is incorporated into a database to produce genomic-assisted EPDs.

Nucleus breeders that produce seedstock for other seedstock operators need to be the first to implement genomic information into their programs, Spangler says.

“Within each breed, the nucleus population is what drives genetic change,” Spangler explains. “Seedstock producers can utilize this information to make genetic change quicker. They can use fewer animals because they have more accurate data and more confidence in the animals they use.”

Spangler also sees the use of genomic information being useful to commercial cattlemen in evaluating nearly identical yearling bulls.

If additional genomic information is available that shows one bull has a calving ease of +11, while the other is -2, that producer could have made a serious mistake without genomic-enhanced additional information, he adds. This technology can really be useful in younger animals that don’t have much EPD data available.

Spangler says he sees genomic information expanding in the future to not only improve accuracy of EPDs, but also identify more complex traits. Data may soon be available for disease susceptibility, feed efficiency, adaptation, reproduction and environmental traits.

“We need phenotypes to be able to develop these tests,” he explains. “We also need to be able to validate the data before we can use it. Collective phenotypes are critical for this to happen.”

Spangler says genomic testing will also continue to be developed and used to identify genetic defects in cattle. “There are many more genetic defects out there,” he says. “We just haven’t identified them all yet.”

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