A Chromosome’s Worth of Difference

  • By Sean McGrath, Genetics and Beef Consultant and Rancher

While EPD’s have been around for several decades there is still a lot of confusion about where they come from and their use. A lot of comments I hear relate to the confusion between actual performance of a seedstock animal and the EPD for said animal. So, to understand the difference let’s go back to the beginning.

An EPD is an Expected Progeny Difference and it uses all the available information we have to describe an animal’s DNA for a specific trait. The EPD uses the animal’s own performance in its’ calculation but it is not describing the performance of the animal, it reflects the predicted performance differences of the OFFSPRING. Let’s look at the following example. We know that DNA is arranged in chromosomes and that chromosomes come in pairs. (Cows have 30 pairs or 60 chromosomes total). For this example, let’s simplify and only look at one chromosome.


In this example, we can see full sib calves (Calf 1 and Calf 2), that wind up with completely different chromosomes from the parents, and thus they could have completely different DNA for various traits. A good example of this in the real world is that of bulls and heifers. We know that bull calves get an X and a Y chromosome at pair number 30 and heifers receive 2 X chromosomes. We could have full sib calves, but a heifer and a bull have obvious differences caused by having a completely different chromosome.





To further complicate things, when the sire and dam are replicating their DNA, parts of the various chromosomes can swap places. If we were to use our example, we could end up with a calf that looks like Calf 3. The multitude of potential combinations runs into the billions, even if we are talking about a single sire & dam mating. This is the reason that we need EPD’s.

On average a calf is somewhere in the middle of the sire and dam, however the parents genes are not inherited equally between siblings, so obtaining more information allows us to better predict which DNA that calf is carrying and thus can pass on to their offspring.

As we add information, we can do a better job of predicting differences between cattle and we are more sure of the results. We express the amount of information included in an EPD in terms of accuracy. Since an EPD is a reflection of DNA that can be passed on to progeny, measuring progeny is the ultimate information, but measuring the actual animal is a good first step. As we add progeny measures, the impact of pedigree, DNA and the animal’s own performance declines in overall importance.

So, to back up a step, each animal is the result of the DNA they receive/contain, interacting with their environment. We call the actual performance/appearance of the animal the phenotype. Initially we know pedigree information on each bull. If we take performance measurements of phenotype we can determine their performance relative to other animals that are managed in the same way (the same environment).

This same environment is what we refer to as a management group. A contemporary group is a further refinement. It includes animals of the same sex, of roughly the same age and raised in the same environment. If the environment is the same, then a lot of the differences we see between phenotypes are due to genetics or differences in DNA. This is why performance data can create dramatic changes in an animal’s EPD that are predicted from pedigree alone. Once we know the genetic component of those performance differences, we can compare these differences across herds by using pedigree ties.

We can now further refine this, by looking at DNA directly using a genomic panel. This obviously also tells us a lot of information about what DNA the animal received from its’ parents and thus can change the EPD significantly as well.

Finally, since the EPD’s are “Expected Progeny Differences” once an animal becomes a sire/dam and passes on its DNA, we can measure the offspring and see what differences are expressed in the progeny.

Let’s go back to Calf 1, 2 and 3 again. From their pedigree we would predict that they would have identical EPD’s, but we can see that they have different DNA. Let’s for a second assume that they were in the same herd, are all bull calves, born in 2020 and were raised together. They are a contemporary group. Their weaning information is shown in Table 1. Based on the weaning information we would predict that Calf 1 has DNA that is superior for growth from either Calf 2 or 3, and that Calf 2 has a genetic combination that is even lower for growth. A DNA test may further confirm this and provide more accuracy or certainty to that prediction. This is shown the example in Table 2. for these three calves.

Table 1. Weaning Weight Performance of Calf 1, 2 and 3

Calf Weaning Weight Deviation
1 700 +50
2 600 -50
3 650 0
Average 650 0


Table 2. Weaning Weight EPD and Accuracy () of Calf 1, 2 and 3 as information is added to their profile

  Information in the EPD
Calf Pedigree Performance DNA
1 61 (0.15) 70 (0.30) 70 (0.50)
2 61 (0.15) 54 (0.30) 50 (0.50)
3 61 (0.15) 61 (0.30) 62 (0.50)


If these calves were to become sires, then we could measure performance of their progeny and further refine our knowledge of their DNA.

Information in an EPD  
Pedigree Starting point. Accuracy of 0.10 to 0.15
Individual Performance within Contemporary Group Provides a good indication of the genetics of the animal. Accuracy of 0.15 to 0.35 depending on the trait
DNA Markers Contributes a lot of accuracy to young animals (animals without progeny records) Accuracy of 0.30 to 0.60 depending on the trait.
Progeny/Daughter Records Provides a true measure of progeny differences. Accuracy of 0.30 to 0.99 depending on number of progeny


Where to From Here?

A Bull cannot pass on their own performance. The performance of an individual is merely an indication of what DNA they might be carrying that they can pass on to their offspring. While individual performance is useful, management will dictate the expression of genetics, so performance alone can be somewhat misleading. We are really interested in what DNA the animal possesses that it can pass on to offspring.

I have heard the statement made that trade buyers don’t pay for EPD’s, and this is correct. Since we are not expecting any progeny from our steer calves or market animals, we only care about their performance and that is what we are paid on. In the same vein though, commercial breeders are not paid for the individual performance of a sire, they are paid for the expression of his DNA in the marketed offspring or retained females. EPD’s can’t help us with every trait of interest or importance, but they can provide us some insight into the DNA that each animal possesses and will pass on to their offspring.

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The Shorthorn breed is truly unique, from their distinctive roan colour, to their rich breed history and most importantly, the wonderful community of breeders, there is nothing else quite like a Shorthorn.

The key to the Shorthorn breeds advantage lies in their balanced genetic profile, driven by market participation that has been developed and refined, after more than 200 years of genetic selection under Australian conditions.

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