GENETIC EVALUATIONS, HISTORY AND IMPROVEMENTS: PART 2 – PHENOTYPES, ANIMAL RELATIONSHIPS AND GE-EPDS

FEATURE ARTICLE by J R Tait, Ph.D., Director of Genetics Product Development, Neogen Genomics, Lincoln, NE; Jamie Courter, Ph.D., Beef Product Manager, Neogen Genomics, Lincoln, NE and Chuanyu Sun, Ph.D., Associate Director of Bioinformatics, Neogen Genomics, Lincoln, NE

In our previous article we highlighted the biology of Mendelian inheritance with examples of how the pedigree based assumed relationships between animals and their ancestors were great insights for characterizing genetic merit of animals. But in that article we also highlighted that with today’s genomic technologies we can have a more accurate representation of relationships between animals. In this article we will use a simplified example of three half-sib progeny out of a sire to highlight how the phenotypic performance information gets calculated through the pedigree as expected progeny differences (EPDs) or genomically enhanced EPDs (GE-EPDs).

As a reminder, the adjusted phenotypic data in conjunction with the heritability of the trait is used to calculate each animal’s estimated breeding value (EBV). In the United States we express genetic merit of animals on an EPD basis, where EPDs are ½ of EBVs. In this example (Table 1) we will use weaning weight as an example trait with a heritability of 0.30 and 3 half-sib calves from the same contemporary group, two of the calves had above average performance and 1 calf had below average performance. A fourth, unrelated calf whose performance was 60 pounds below the contemporary group average would represent the full contemporary group’s weaning weight data.

In order to calculate each calf’s EPD you take the individual adjusted weaning weight deviation from contemporary group average, multiply that by the heritability to get the EBV and then take half of the EBV to get the EPD. For Calf 1, this is: +40 × 0.30 × 0.50 = +6.0 for weaning weight EPD. Those steps can be done with each calf’s performance data to calculate their own EPDs. Then to get

the Sire’s EPD, you average the 3 calves’ EPDs and then double that average to represent that he passed ½ of his genetics to each calf. In this case the average EPD for the 3 calves is +3.0 EPD thus making the Sire’s EPD for weaning weight +6.0. You will also notice that the Sire’s EPD is the same as the average EBV of the 3 calves [(12 + 9 - 3) / 3]. This is expected based on the definitions of breeding values (own performance) vs. progeny differences (progeny performance). The insight which is not shown in the Table is that the average of the 3 dam’s EPDs for weaning weight will be 0.0, further supporting the concept that the group of calves are the average of their dams’ and sire’s EPDs.

In the pedigree scenario, we expect that the Paternal Grand Sire and Paternal Grand Dam each contribute equally to the Sire’s EPD of +6.0 and therefore we calculate the Paternal Grand Sire’s EPD to be +6.0 and the Paternal Grand Dam’s EPD to be +6.0. However, in the Genomic Enhanced genetic evaluation (Table 2) we see different genomic relationships between the Paternal Grand Sire and each of the 3 calves. Since those genomic relationships are variable each calf’s phenotypic performance contribution to the Paternal Grand Sire’s GE-EPD is now adjusted by the strength of the genomic relationship. You see stronger genomic relationships between the above average performance of Calf 1 and Calf 2 and a weaker genomic relationship between the Paternal Grand Sire and Calf 3. This leads the Paternal Grand Sire to have a higher weaning GE-EPD (+8.0) than was calculated in the pedigree only analysis. It is important to keep in mind that since the Sire received ½ of his genetics from the Paternal Grand Sire and ½ from the Paternal Grand Dam, that those genomic relationships of the Paternal Grand Sire are complemented by genomic relationships to the Paternal Grand Dam. Meaning that the Paternal Grand Dam will have a lower genomic relationship to Calf 1 and Calf 2 and a higher genomic relationship to Calf 3, which will lead to the Paternal Grand Dam having a weaning GE-EPD of +4.0 so that the Sire still represents the average of Paternal Grand Sire and Paternal Grand Dam.

While this example was presented to demonstrate how genomic relationships between phenotyped animals and their genomically tested ancestors can adjust the GE-EPDs of those ancestors, it is important to also remind you as a producer that the information can be carried down the pedigree instead. In the case of an animal not being old enough to get a phenotype yet, genomic profiling and calculating the genomic relationship of a calf can inform which grand parents it inherited more genetic material from which may deviate away from the assumed 25% contributions of each of the grand parents. Which will move the calf’s GE-EPDs closer to the EPDs of the grand parents it inherited more DNA from. This is one of the strengths of genomic testing in young calves, producers get insights on the Mendelian inheritance of a young calf for several traits it has not yet been able to express its own phenotype for.