Practical use of genetic tests allows commercial cattle producers profit opportunities
Megan Rolf of Kansas State University says genetic tests can provide producers with additional information when selecting bulls to improve the likelihood of achieving their desired results.
Many people think of genomic testing in terms of testing for quantitative, production traits.
“When we do that, we’re usually talking about marker panels that include SNP markers, or SNP chips,” Rolf says. “Basically, a SNP (single nucleotide polymorphism) is a single base change in the DNA.”
Essentially, she says a SNP is a single “typo” in the DNA.
“These tests have a lot of application for both commercial and genetic producers,” she comments. “The other thing we can use this type of market for is parentage testing, and there’s a lot of value available.”
Other tests looks for causal mutation, which is a mutation that causes a particular outcome.
“For this type of testing, we’re probably talking about things like red versus black coat color or a genetic abnormality,” she comments.
“When we talk about testing for genetic production traits, these are generally going to be higher density SNP chips when we’re talking about the seedstock industry,” Rolf explains.
DNA is collected as a blood sample or hair follicle.
“The importance of this step is sometimes understated. It’s really important we get a high quality sample, and seedstock producers need to make sure they follow the breed association’s guidelines for the submission of these samples,” she adds.
Rolf continues, “The other really important process is these genotypes get incorporated into the breed association’s national cattle evaluation. That information is included into expected progeny difference (EPD) predictions, as well, to get a genomic-enhanced EPD.”
Particularly for younger animals, EPD accuracy is increased based on the added information.
“This information can be utilized as a marketing tool, but what genetic testing is designed to do is to enhance our ability to make genetic improvement,” Rolf comments. “We can use the data to make selection decisions to make genetic progress more rapidly.”
For example, the dairy industry has achieved substantial increases in genetic gain in their net merit index and in the swine industry, about a 35 percent increase in genetic gain for the PIC index.
How it works
Briefly, Rolf explains the information can be used in two ways.
“The first way is to estimate the effects of causal mutations or QTN,” she says.
SNP markers, which are fairly well distributed across the genome, can be utilized to identify what is going on specific segments of the genome.
“This provides information on causal mutations,” Rolf explains. “The other way we can use this information is in defining relationships between animals.”
She continues, “What drives traditional genetic evaluation are the pedigree relationships between animals. That is why maintaining the integrity of the pedigree is so important.”
In her master’s degree project, Rolf looked at relationships based on pedigree information that was available. In a parallel study, they estimated the same information based on SNP evaluation.
“There were a lot of points where the pedigree data did not match the genomic data,” she comments.
Use of genomic tests
The gold-standard of genetic testing is a high-accuracy, genomic EPD from a proven bull that has lots of data to back up the EPD prediction.
“Unfortunately, though, when we buy a yearling bull, we’ve got a low-accuracy EPD,” Rolf comments. “It’s useful, and it’s the best estimate that we have with all of the information we have available. However, it’s not much.”
If a genomic test is available, the information is useful, but there are holes present.
“A genomic test doesn’t necessarily explain every bit of genomic variation in that animal,” she explains. “The ideal thing we can do is add them together to get a higher accuracy EPD.”
As additional data is collected, higher accuracy is achieved.
“One of the obvious ways commercial cattlemen can capitalize on genomic data is by taking advantage of seedstock suppliers who have invested the time and effort into generating the genomic-enhanced EPDs for customers,” Rolf says, noting that producers must decide what the genomic information is worth.”
Rolf suggests separating purchasing decisions into several categories.
“First are the traits that are absolutely critical for the operation,” she says. “For example, if we choose a bull to breed to heifers, it is critical that we have a reasonable value for calving ease direct (CED).”
In a specific example, a young bull and proven sire may have the same EPD for CED, but the accuracy is where the information differs.
“Basically the accuracy tells us the confidence we have in that number and how much it might change over time,” Rolf comments. “For a highly proven sire, we can look up possibly change values in any breed sire summary information, and it can help us form a 68 percent confidence interval around the EPD.”
Specifically, the EPD plus or minus the change value, creates a 68 percent confidence interval for the EPD, which is a really narrow range.
“On the younger herd sire, we have a much wider range,” she says. “The EPD accuracy helps us manage the risk that we have in that selection division.”
For the young sire, a genomic test can increase the confidence producers have in a particular bull’s EPDs.
Rolf emphasizes, “That confidence has value.”
Saige Albert is managing editor of the Wyoming Livestock Roundup. Send comments on this article to firstname.lastname@example.org.