Demystifying Genomics in the Commercial Herd

By Troy Rowan, PhD, University of Tennessee Institute of Agriculture

No scientific development in the last 20 years has had a larger impact on livestock genetics than the introduction of genomic testing. The ability of genomics to identify exceptional young sires before they’ve ever sired a calf is an invaluable tool to both seedstock and commercial herds. Compared with the single-gene tests of the late 1990s and early 2000s, genomic tests use markers spread across the cattle genome (>3 billion DNA bases) to capture the complete genetic makeup of animals. Integrating genomics into our conventional methods for predicting genetic merit has led to an incredible increase in the rate at which we are making genetic progress in the seedstock sector. This has helped increase profitability across the cow-calf, feedlot, and packing sectors.

The unknowns of genetic inheritance

The motivation for genomic tests is built on the assumption that an animal inherits its parent’s genetics in a random and unpredictable manner. Mating a good bull with a good cow makes a good calf likely but not guaranteed. Despite sharing 50% of their DNA with each parent, full siblings can have major discrepancies in their overall genetic merit. One sibling may get an exceptional sample of its parents’ genetics, while the other can get a sample that is below average. Identifying the animals that receive favorable samples of parent genetics ensures that we continue to make the next generation better than the last. Bulls play an outsized role in driving genetic progress in commercial herds, so tools that help accurately identify animals with higher genetic potential are invaluable.

Traditionally, we have accomplished this by using Expected Progeny Differences (EPDs), which leverage phenotypes, pedigrees, and contemporary groups to estimate an animal’s likely genetic potential. EPDs are our best statistical guesses, so adding information, particularly on an animal’s progeny, increases our confidence that the value correctly represents a bull’s genetic potential. This is a challenge for commercial operations that almost always purchase bulls that have yet to sire a calf. Even when using their pedigree-based EPDs, our lack of knowledge about which parental genes an animal inherited makes the accuracy of our decision far from perfect. As a result, we assume a fair amount of risk when buying young bulls. Bulls whose actual genetic potential is not well-represented by their EPD can cause us problems and sacrifice our intended genetic gain.

Genomics to the rescue!

Genomics allows us to track the inheritance of DNA directly. This means that as soon as an animal is born, we can understand which favorable or unfavorable genetics it inherited from its parents, rather than waiting for it to be expressed in its offspring years in the future. Integrating genomics into an evaluation does not change the EPDs that are reported or how we interpret them; it only increases our confidence that they represent an animal’s true genetic potential.

When an animal’s genomics is added to the calculation of its EPD, we see an increase in accuracy equivalent to what would be generated by adding over an entire calf crop’s worth of information to the evaluation. Adding genomics can change an animal’s EPD considerably, particularly if they received a very good or bad sampling of parental genetics. While we expect animals to look similar to their parents, over 50% of the genetic variation in traits can come from variation in sampling of the parental DNA.

An important thing to remember about genomics is that whether or not the EPD value increases or decreases after testing, it is ALWAYS a better estimate. Genomics helps move our prediction closer to the animal’s true potential. This allows us to reduce the risk of making a decision based on an animal’s EPD that does not match parental expectations. For example, an animal whose two parents have above-average calving ease could be below average due to a poor sampling of genes. Without genomics, we might also select this bull to breed heifers, not knowing that it is a less-than-ideal candidate. Genomics would identify this poor sampling of calving ease genes in the bull and direct us toward another more suitable option.

When the accuracy of an EPD is increased, we make the “correct” selection decision more often. This ultimately leads to an increased rate of genetic progress. Due to their large impacts on commercial herds, this is particularly important in bull selection decisions. Commercial herds should always purchase bulls that have genomically-enhanced EPDs. The cost of testing is relatively low (<$40), but the information it provides on an animal is invaluable! Options for genomic testing are also becoming more readily available for commercial replacement heifer selection decisions, but that article is for another issue!

Dr. Troy Rowan is an Assistant Professor and state extension specialist at the University of Tennessee Institute of Agriculture. His research uses genomics to understand the biology that underlies a wide range of economically important traits in beef cattle. He is particularly interested in local adaptation, heterosis, and genomic approaches to increasing beef cattle sustainability. His work aims to deliver tangible solutions to U.S. beef cattle producers. Additionally, Dr. Rowan serves as the state extension beef cattle genetics specialist, performing producer education and outreach in Tennessee and nationwide.