GENETIC EVALUATIONS, HISTORY

GENETIC EVALUATIONS, HISTORY AND IMPROVEMENTS: PART 1 – GENOMIC RELATIONSHIPS

by JR Tait, Ph.D., director of genetics product development, Neogen Genomics, Lincoln, Nebraska and Jamie Courter, Ph.D., beef product manager, Neogen Genomics, Lincoln, Nebraska

Genetic evaluation systems which brought us Expected Progeny Differences (EPDs) leverage variations in performance of individual animals from their contemporaries and expected relationships between those individual animals based on the pedigree relationship amongst animals. These expected relationships are both the average relationship and the most commonly observed relationships. However, the fact that each calf inherits a random half of the sire’s DNA combined with a random half of its dam’s DNA means that the true relationships between animals may equal those expectations, or they may be different. The benefit of genomics is that they tell us what those relationships actually are between individual animals instead of an assumption.

The pedigree expected relationship between all full sib calves is that they share 0.50 (50%) of their DNA with each other. This expectation is often correct, but in reality there is variability around that expectation. In Figure 1 the relationships between calves within some of the potential calf combinations are: Calf 1 to Calf 2 = 0.50; Calf 1 to Calf 3 = 0.50; Calf 1 to Calf 4 = 0.00; Calf 2 to Calf 3 = 0.00; Calf 2 to Calf 4 = 0.50; Calf 3 to Calf 4 = 0.50. In this case Figure 1 only shows 4 potential calves, which are only 25% of the 16 possible combinations of calves. There are (number of pairs chromosomes)2 combinations of the chromosomes possible from each parent; in this example that is 22 = 4 chromosome combinations from the sire and 4 combinations

Figure 1. Chromosomal inheritance example simplified to 2 pairs of chromosomes. In these examples the chromosome on the left is from the sire of the individual and the chromosome on the right is from the dam of the individual.

of chromosomes from the dam. When the 4 possible chromosome combinations from the sire are considered with the 4 possible chromosome combinations from the dam, that leads to 16 (4sire x 4dam) possible calf chromosome combinations.

When you get into real animals, there are many more pairs of chromosomes than just 2 as represented in Figure 1. In those cases of many pairs of chromosomes, the relationships between full sibs are no longer classified as 0.00, 0.25, 0.50, 0.75, or 1.00. A real example of the observed relationships amongst a population of over 15,000 full sib chickens is presented in Figure 2. There is a slight shift to be below the expected 0.50 relationship, but most animals are close to the pedigree estimate of 0.50 relationship amongst full sibs. What I take away is that around that expected relationship, there is a noticeable amount of variability which is possible and does exist in these groups of animals. Many times, full sibs are genetically quite similar, but occasionally they can be quite diverse.

The extension of this concept goes to the grandparent generation relationships to calves as well. The pedigree expected relationship between each calf and the four grandparents is 0.25 for each grandparent. By looking at Figure 1 and recognizing that the colored chromosomes in the sire and dam are ordered with grand sire of calves on the left and grand dam of the calves on the right for each chromosome pair, we can characterize the true relationships between calves and some of the grandparents.

In this example the relationship between Calf 1 and the paternal grand sire = 0.50 (red and yellow chromosomes both came from the sire’s sire) and the relationship between Calf 1 and paternal grand dam = 0.00 (green and gray chromosomes were not transmitted to Calf 1). In another example the relationship between Calf 4 and the paternal grand sire is 0.00 (red and yellow chromosomes were not transmitted to Calf 4) and the relationship between Calf 4 and the paternal grand dam = 0.50 (green and gray chromosomes both came from the sire’s dam). The other possibilities are not shown in Figure 1, but red chromosome 1 inherited with gray chromosome 2 would represent 0.25 proportion of genetic material in common with each of the paternal grandparents. Likewise, green chromosome 1 inherited with yellow chromosome 2 would represent 0.25 relationship between the calf and each of the paternal grandparents.

Through this article, the intention is to show gratitude for the power of the genetic evaluations which were based on expected pedigree relationships. However, I hope that it also shows how the biology of Mendelian inheritance introduces deviations from those assumptions which can be characterized with genomic profile tools. Cattle breeders who leverage the data and tools provided from pedigree relationships in the genetic evaluation have shown that tremendous progress can be made. As tools such as genomics allow more precise characterizations of relationships amongst animals, even more progress will be possible.

Figure 2. Distribution of genomic relationships for 15,748 full sib genomic tested chickens. Adapted from: Lourenco et al. (Genet Sel Evol 47, 56, 2015)