PUTTING GENOMICS TO WORK

by Troy Rowan, Ph.D., Assistant Professor and Extension Specialist (Beef Genetics), Departments of Animal Science and UTCVM Large Animal Clinical Science, UTIA Genomics Center for the Advancement of Agriculture, University of Tennessee, Knoxville

When we breed cattle, we’ve engaged in the “long game” of genetic progress. Our goal is to make this generation better than the last one. This sustained genetic progress is built on making the right decisions more often than not. By the “right decision,” I mean that the animals (AI sire choice, bull purchase, replacement heifer selection), we are choosing are the animal(s) with the best actual genetic merit for the traits that align with our breeding goal.

EPDs are our best tool for ensuring that our selection decisions are “right” more often. Darrell discussed at length in the March issue that EPDs allow us to break an animal’s phenotype into its environmental and genetic components. This allows us to make selection decisions only on our statistical estimate of an animal’s genetic potential. This month, Darrell discusses the concepts of accuracy and possible change, two values associated with an EPD that directly affect selection accuracy.

In March’s issue, J.R. Tait described the differences between pedigree and genomic relationships. We know that siblings receive 50% of their DNA from each parent. WHICH 50% they get differs. Anyone with a brother or sister (who isn’t an identical twin) knows that significant phenotypic differences (I don’t know about you, but I’m sure better looking than my little brother) can exist between full siblings raised in the same environment. This is a function of what we call Mendelian Sampling, or more simply put, the random sampling of genes. This randomness of passing on of genes from parents to their offspring is why we resemble our relatives but don’t look identical to them. Our goal with EPDs is to estimate which genes an animal inherited from its parents. Typically this has come from information on offspring or relatives (i.e., a bull with larger progeny is likely to have inherited more favorable DNA chunks that control size). The more information on an animal, the more accurate our estimate of that value (and their EPD) will be.

Genomics has revolutionized the way that we calculate EPDs and make selection decisions. As Darrell discussed, traditionally, the way that we’ve seen EPD accuracies increase is through the addition of progeny or relative records into the genetic evaluation. This means that for producers who buy young bulls, the limited amount of information makes accuracy relatively low. Genomic tests can increase

the accuracy of EPDs without progeny being added to the evaluation.

When we genomically test an animal, we directly observe the genotype at a huge number of positions in an animal’s DNA. While most cattle share the exact same genotype at a given position (over 99.9% of DNA bases are the same), the differences that exist can tell us a lot about an animal and how it is related to other members of the population.

We can use genomic testing to increase the accuracy of EPDs because it allows us to quantify the amount of DNA shared between individuals directly. In the figure below, you’ll see that three full siblings share 50% of their DNA with each parent. However, WHICH 50% that they share is different. Instead of assuming an animal shares 25% of its DNA with each grandparent (the assumption we make in pedigree-based EPDs) and that they’ll inherit 25% of each grandparent’s genetic potential, genomics allows us to directly observe which DNA chunks were inherited.

Using genomics can better understand the relationships between individual animals in EPD calculations. The advantage is a boost in accuracy without waiting for offspring information to roll into the evaluation. Genomics allows animals that don’t share a pedigree link to “borrow” information from animals with which they share chunks of DNA.

A genomic evaluation works almost identically to a traditional pedigree-based evaluation. The only difference is that genomics account for relationships when available as opposed to pedigree relationship estimates. The result is more accurate EPDs, especially for younger, unproven animals. Having a genomic test on an unproven animal is equal to having that animal with performance records plus a few progeny on the ground. This can take the animal from having a weaning weight accuracy of around 0.05 up to a 0.25 accuracy or above. The accuracy boost that an EPD receives from genomics will differ based on the trait. The increase in accuracy will usually come along with a shift in the EPD itself. While these are typically modest shifts, they can sometimes be large. Further, an increase in accuracy doesn’t guarantee that the EPD will improve in the favorable direction, just that it is a better estimate of the animal’s true genetic merit. One important thing to remember is that a genomic evaluation ALWAYS needs phenotypes reported on individuals to be successful. Genomics helps us boost accuracy, but reliable phenotypes on animals with genotypes are essential to the long-term success of a genetic evaluation.