How can I use DNA tests for complex traits?

Beef genomics DNA tests can be divided into two types, based on the trait being predicted: DNA tests for simply inherited traits and DNA tests for complex traits.

Michael G. Gonda

Examples of simply inherited traits include red/black Angus coat color and genetic abnormalities (e.g., curly calf, fawn calf syndrome, TH, PHA). These traits are not affected by environmental conditions, and their expression is dependent on alleles at a single gene.

For example, cattle can carry zero, one or two “curly calf” alleles at the gene, causing the curly calf abnormality. If the animal carries zero curly calf alleles, then the animal is a non-carrier and cannot pass the allele that causes curly calf to his or her progeny.

If the animal carries one curly calf allele, then the animal is a carrier and, if mated to another carrier, can produce calves with the curly calf abnormality. If the animal carries two curly calf alleles, then the animal has the curly calf abnormality. Genomic predictions for simply inherited traits will perfectly predict phenotype; these tests are 100 percent accurate.

A complex trait can be influenced by the animal’s environment, and trait expression is dependent on hundreds of genes. Examples of complex traits include yearling weight, heifer pregnancy rate and marbling. If an expected progeny difference (EPD) is available for a trait, then the trait is complex.

We use EPDs to describe genetic merit for these traits because their genetics cannot be explained by a simple genotype. The EPD calculations account for the potential of hundreds of genes to affect traits while removing, as much as possible, environmental factors that obscure our ability to estimate genetic merit. These EPDs are never 100 percent accurate, however. The accuracy of an EPD depends on the trait and number of performance records available.

Genomic tests for complex traits can increase accuracy of these EPDs. When included as part of the EPD calculations, these EPDs are renamed genomically enhanced EPDs. Genomically enhanced EPDs are usually (but not always) estimated for bulls produced by seedstock producers. Using bulls with genomically enhanced EPDs reduces selection risk, i.e., the EPDs on these bulls will be more accurate.

However, genomically enhanced EPDs are usually not available on heifers because the cost is prohibitive. Further, many heifers are crossbred, and current technology has not progressed to the point where we can calculate genomically enhanced EPDs on crossbred animals.

Fortunately, stand-alone DNA tests marketed primarily for heifers and commercial cattle are available from two companies: Zoetis Animal Genetics and Neogen/Geneseek. Although these tests cannot be used to calculate genomically enhanced EPDs, they can provide useful information on the genetic merit of females in commercial herds.

Both companies market tests specifically for predominantly Black Angus cattle and Bos taurus cattle of all breed compositions. Each DNA test predicts genetic merit for a suite of traits depending on the company, target breed (Black Angus or Bos taurus) and cost. Zoetis Animal Genetics reports DNA test results on a zero to 100 scale, where “100” is the best possible score. In contrast, Neogen/ Geneseek reports results on a 1 to 10 scale; whether a score of “10” or “1” is desirable depends on the trait (e.g., “10” favorable for marbling and “1” favorable for birthweight).

The primary application of these genomic tests is for selection of replacement heifers. Other applications of these DNA tests do exist; for example, DNA tests could be used to make mating decisions or qualify for feeder calf certification programs. An example of a feeder calf certification program that uses DNA test results is Top Dollar Angus.

As of July 29, 2016, six DNA tests are available for animals greater than 75 percent Black Angus: GMX Focus, GMX Cow Advantage, GMX Feeder Advantage, GMX Total Advantage (all Zoetis Animal Genetics products), Igenity Gold and Igenity Silver (Neogen/ Geneseek). Three additional tests are marketed for Bos taurus cattle (purebreds and crossbred): Igenity Gold, Igenity Silver and PredicGEN (Zoetis).

No comparison of the efficacy of these products is available. A general rule is that more expensive tests will tend to be more accurate and test for a larger number of traits. Below are a list of general guidelines to follow when using these DNA tests to select replacement heifers in a commercial herd.

Identify your economically relevant traits. For example, PredicGEN tests for marbling, tenderness and yield grade, which may be traits of economic relevance for a producer who retains ownership of his or her cattle through the feedlot.

In contrast, these traits will be of significantly less importance to a producer who sells all of his or her calves at weaning. This producer may be better served selecting a genomic test focused on preweaning and fertility traits. The DNA test you choose must be relevant for your operation.
Match the DNA test to the breeds you own. Genemax Focus and Advantage are only marketed for cattle that are more than 75 percent Black Angus. If you raise non-Black Angus or crossbred Bos taurus calves, you should not use these tests. Instead, you should consider one of the three available DNA tests focused on Bos taurus cattle. Similarly, owners of predominantly Black Angus calves should use an Angus-specific DNA test.
Don’t over-interpret DNA test results. Imagine you are at a bull sale where you are deciding between purchasing two bulls. The first bull has an EPD of +35 pounds for weaning weight, and the second bull has an EPD of +36 pounds for this trait.

Would you automatically select the second bull? Probably not; the difference between these EPDs is negligible, and other criteria would be used to select the bull you want. You can apply this lesson to the interpretation of DNA test results. My recommendation is to bin heifers into one of three categories based on their test results: superior, acceptable and unacceptable.

Select your heifers from the superior and acceptable categories while also focusing on traditional heifer selection criteria (e.g., EPDs if available, performance data and conformation). Genomic tests are another tool in the toolbox; they are not designed to replace traditional selection criteria.
Use your DNA test results. I have heard stories of producers purchasing genomic tests faithfully each year, reading their results carefully and then placing them inside a file, never to see the light of day again. If you are going to purchase a DNA test, use the results to make selection decisions among your heifers.

You don’t need to make selection decisions overly complex. Bin heifers into superior, acceptable and unacceptable categories, and then make selection decisions from the superior and acceptable categories.
Don’t forget about bull selection. Bull selection is far more important than heifer selection in the long run. Bulls can produce many more progeny than females over the course of a lifetime. Their progeny will end up as replacement heifers in your herd if you raise your own replacement females, meaning the majority of the genetic make-up of your herd is determined by which bulls you select.

Use bulls with genomically enhanced EPDs whenever possible, as these bulls will have more accurate estimates of genetic merit.

Selection using genomic tests is no different than selection with any other tool. You need to have a thorough understanding of what traits are economically relevant for your operation and purchase DNA tests that match well with your economically relevant traits.

You should also not rely on genomic testing alone for selection decisions, but instead integrate genomic testing into your selection scheme. Despite their limitations, these genomic tests allow you to fine-tune your heifer selection decisions, leading to faster genetic improvement in the long run.