Phenotype Matters

More Than a Genetic Spreadsheet

A combination of the right phenotype and EPDs (Expected Progeny Differences) is moving U.S. cattle herds to new levels of productivity.(DTN/Progressive Farmer photo by Karl Wolfshohl)

Genetic tests are available for everything from birthweight to carcass weight, so it's tempting to select your next herd bull based on those results alone. Just think, no more driving all across the country to look at pen after pen of yearling bulls. Or, you could build your dream herd of females off a spreadsheet of genetic predictions for maternal traits. Then again, maybe not.

"Phenotype is more critical now than ever," seedstock producer Dave Nichols says. "It is what you can see and measure. In order to make gene discovery for growth and carcass merit, we have to have birthweight, weaning weight, performance and ultrasound or carcass data. Genomics add to the accuracy of what we already know."

As an example of the importance of phenotype, the Bridgewater, Iowa, cattleman cites a multiyear National Beef Cattle Evaluation Consortium (NBCEC) study designed to find genetic markers for susceptibility to bovine respiratory disease (BRD), or pneumonia.

Researchers first identified sick cattle the old fashioned way, by observing them. Then, they took nasal swabs to confirm the diagnosis. Without first identifying sick cattle by phenotype, they probably wouldn't be able to find genetic markers responsible for resistance to the costly disease.

Phenotype The Bull. Just as phenotype continues to be critical for researchers, it should also be high on producers' lists when selecting bulls.

University of Georgia animal scientist Ronnie Silcox stresses "even genomically enhanced, expected progeny differences (GE-EPDs) don't tell you everything you need to know. When I talk to commercial producers, I tell them EPDs are the first thing they need to look at. Use them to narrow down to a smaller group."

Down to a manageable few, make the final bull selection with the eyes of an experienced cattleman.

"They must be functionally sound," Silcox says. "Do both eyes work? Look at their feet and legs. Make sure they've had a Breeding Soundness Exam. It doesn't matter how good a bull is, he's not going to do you any good if he can't get a cow bred."

And, because most commercial producers sell feeder calves, Silcox says it's important to consider whether a bull has enough muscle to grade like a No. 1 feeder calf. The same approach applies when selecting replacement heifers, whether those heifers come from your own herd or another producer. Narrow your selection using EPDs, then look hard at the heifer. If she can't carry and raise a calf, she isn't going to help your herd.

A Strong Combination. Phenotype continues to be vital in cattle selection. However, it's the combination of EPDs and phenotype that's moving herds to the next level. "EPDs are better than they've ever been. If you add the results of DNA tests to actual performance data, it can increase the accuracy to that of a bull that has produced eight to 10 calves," Silcox says, describing what's commonly known in the industry as GE-EPDs.

Consider a calving-ease yearling bull to use on heifers. If all you have are EPDs based on pedigree, and he is an embryo-transfer calf (his own birthweight doesn't factor in) expect accuracy of just 5%. Add genomic test results to that, though, and accuracy can shoot up to around 40% for the same bull.

The less heritable the trait, the more genomic testing can improve accuracy. Auburn University animal scientist Lisa Kriese-Anderson says, "With lowly heritable traits like the reproductive traits, fertility, gestation length, age at first calving, genomic testing increases the accuracy of the EPD value as if the animal has had 10 to 12 calves on the ground."

She says with the moderately heritable traits like weaning weight and average daily gain, adding genomic test results to the EPD analyses is like looking at 5 to 8 progeny of the animal. With highly heritable traits like carcass traits, or rib-eye area, marbling and fat thickness, genomic tests increase the accuracy at a rate of 2 to 3 progeny.

Even with this boost in accuracy from GE-EPDs, Kriese-Anderson believes, like Dave Nichols and Silcox, that there remain compelling reasons to keep phenotype in the selection process.

"We don't know what every gene in the bovine genome is doing yet. We find a panel of markers that go with a trait, but not every gene that affects that trait is known. We still need actual measurements," she says. "Not every purebred animal will get DNA-tested. We have to have the phenotype information to validate and compare with the genomic information. Someday, we may be able to just take DNA samples. But for now, we need both, and that's OK."

Dairy Selection Is Out Ahead:

While beef breeders say producers need to keep phenotype in their selection process, dairy breeders are already depending heavily on genomic information alone.

University of Nebraska professor emeritus Dale Van Vleck says, "The dairy industry has half a million animals with genotype information. The accuracy of that is very, very good."

For example, out of the 214 top Holstein bulls in the industry, the veteran animal breeder says 213 have only genotypic information available. The accuracy is high, at 70 to 73%.

Van Vleck explains the dairy industry uses a different measure of accuracy, known as "reliability."

"Reliability of 72% from genomic analysis without progeny information is equivalent to an accuracy of a progeny proof with 40 to 50 progeny for a trait such as weaning weight," he says.

The one dairy bull he mentioned that does have progeny has 6,531 daughters in production and almost perfect reliability.

"Beef people just don't have the numbers like that," Van Vleck says. "They don't have it as easy as the dairy people."