Sales literature claims DNA tests can be used to accurately evaluate genetic potential of cattle at birth, and ultimately improve your bottom line. While it is evident that animals can be genotyped at a young age, producers often ask me, “Do DNA tests work?” The answer to that question is, as with many questions, “It depends.”

It depends on your motive for testing, and what you mean by “works.” DNA-based tests can be used for various purposes: selection and breeding decisions, feedlot sorting, pedigree verification, and as a marketing tool. Their utility for these applications requires knowledge of both how well they work in cattle populations where they are to be applied, and the cost of testing. In the absence of these two pieces of information, it isn't possible to evaluate the costs and benefits associated with the use of these tests, and so it's not possible to determine if they “work.”

Some seedstock producers are testing their bulls to provide potential buyers with DNA information. The value of that information to the buyer is determined by the market. If the value is deemed to be more than the cost of testing and is reflected in the bull purchase price, then the test “worked,” at least as a marketing tool.

However, many people are interested in using DNA test results for marker-assisted selection (MAS) — using the results of DNA-marker tests to assist in selecting individuals to become parents of the next generation. Therefore, as a geneticist, I interpret the real question being posed when producers ask whether DNA tests work as whether they “work” to improve the accuracy of genetic predictions sufficiently to justify the expense.

The answer to that question is again, “It depends” — on which trait is being examined, which test is being used and how much it costs, and in which breed or population the test is going to be used.

Breed differences

Traditional methods of DNA marker discovery have focused on finding genetic markers in locations on chromosomes that are experimentally known to have an effect on the trait of interest. Rarely has the marker been the actual DNA sequence causing the effect; rather, the marker flags the approximate location of the causative or “good” sequence.

However, the relationship between the marker and the good sequence may differ among breeds. For one breed, a marker might be linked to the DNA sequence causing the desirable effect on the trait; in other breeds, there may be no effect of that marker on the trait, or the marker might even flag the “bad” sequence. The predictive value of a DNA test decreases when markers are incorrectly associated with the trait of interest in a given breed or animal.

The U.S. National Beef Cattle Evaluation Consortium (NBCEC) has been involved in the process of independently validating commercial DNA tests for quantitative beef quality traits since their first appearance on the U.S. market in the early 2000s (results are posted at www.NBCEC.org). Validation is a critical activity to test the strength of support for the genotyping company's published claims based on independent data. This process sometimes revealed that tests did not perform as expected; in certain cases, companies chose to withdraw those tests from commercialization.

Problems arose as the DNA-testing industry matured from single marker tests to multiple-marker “panels” with effects on numerous traits. The NBCEC and DNA testing companies struggled to find appropriately phenotyped populations that were not involved in the discovery process for validation studies. Such populations are rare, as they are expensive to develop and phenotype.

Additionally, results from different breeds and cattle types (e.g., Bos taurus, Bos indicus) genotyped with the same single-nucleotide polymorphism (SNP) panel were often inconsistent with respect to the significance of the association between the test and the trait(s), and sometimes even with respect to the direction of the association (i.e., a good DNA test result in one breed was the least desirable result in a different breed).

This complicated the interpretation of validation results, and created confusion as to whether “validation” meant a test “worked” (was significantly associated with the trait) in all or some breeds, or whether the test had simply been evaluated by an independent third party. This exposed the process to marketing zeal and left producers confused and somewhat stymied because the data reported (significance of the association) did not really help to inform decisions about the value associated with investing in specific DNA tests.

Accuracy

The accuracy of a DNA test at predicting the true genetic merit of an animal (improving accuracy) is primarily driven by the amount of additive genetic variation accounted for by the DNA test. Current estimates of the proportion of genetic variation accounted for by existing tests are generally low (0.0-0.10), although this number is not readily available for all tests.

A key criticism of the currently available tests is that their ability to predict genetic merit is limited. The exception is tenderness DNA tests, where available estimates for the proportion of genetic variation range from 0.016 to 0.299 (www.beefcrc.com.au/Aus-Beef-DNA-results). Over time, it's envisioned that genetic tests will have markers associated with the majority of important genes influencing a trait. In other words, it is hoped that in the future, genotyping results will be highly predictive of the true genetic value of an animal.

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