Spangler: Genomic information can produce more accurate EPDs

The added value of genomic information to EPDs (expected progeny differences) 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 to make the information more accurate, according to Matt Spangler, University of Nebraska beef geneticist. 

Spangler discussed the current application of genomic tools including testing for genetic defects, paternity, genomic enhanced EPDs and the potential for marker-assisted management during a recent University of Nebraska webinar. 

Record keeping

Spangler’s 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 said. “Genomic technology only makes these tools stronger; it does not replace them.”

Spangler said 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 then had to test the bull by producing many offspring to improve accuracy for the traits carried by that bull. 

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

Problems with genomics

The problem with genomic testing, Spangler continued, is that 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 explained. 

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

Using genomics

Because the testing is breed specific, Spangler said the American Angus Association is leading the pack in developing and providing this technology for their members. Spangler said they are currently focusing 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 is also in the forefront of utilizing this new technology by developing a database of genomic information for their members, Spangler continued. They are focusing more on blending of genomic information with an index of EPDs currently available.

The American Simmental Association has adopted a method of treating genomic information as an external EPD, which allows individual molecular breeding value (MBV) accuracies, Spangler added.

A fourth option of using this technology, which is currently used by the dairy industry and some swine companies, is the genomic relationship, Spangler explained. Markers are used to help supplement pedigree information. 

No relationships are based on genomic information, he said, adding, “In order to do that, the industry would have to have access to those genotypes.”

Are genotypes better?

Many producers question whether a genotyped bull is better. 

“His EPDs should be more accurate, but it does not make him a better bull,” Spangler explained. “As accuracy increases, some bull’s EPDs will go up, and some will go down. You don’t need to understand genomic test results. They are supposed to be incorporated into the EPDs to make them more accurate. Just look at the EPD.”

Breeds that have released or are close to releasing EPDs enhanced by genomics-use markers to supplement their EPDs are Angus, Hereford, Simmental, Red Angus, Gelbvieh, Limousin and Maine Anjou. 

“Genomics work, but how well it works is the question,” Spangler said. “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.” 

Identifying carriers and lineage

Originally, genomics was first developed to help researchers pinpoint genetic defects like marble bone. Before this testing was available, Spangler said 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 explained. “Without this testing, some breeds would have been decimated in the past few years.”

Genomic testing has also been used as parent 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 have EPDs. 

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

Implementing genomics

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. Genomic testing can cost $10 to $15 an animal.

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

“Within each breed, the nucleus population is what drives genetic change,” Spangler explained. “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. 

“If a commercial producer is evaluating two yearling bulls with identical EPDs, which should he choose?” Spangler asked. 

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 this additional information, he added. This technology can really be useful in younger animals that don’t have a lot of EPD data available.

Spangler sees genomic information expanding in the future to not only improve accuracy, 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 explained. “We also need to be able to validate the data before we can use it. Collective phenotypes are critical for this to happen.” 

Spangler said 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 said. “We just haven’t identified them all yet.”

Gayle Smith is a correspondent for the Wyoming Livestock Roundup. Send comments on this article to roundup@wylr.net.