Data in a Genetic Evaluation

By Ryan Boldt, Director of Breed Improvement This article is the second of a three-part series discussing different data types that are included in the genetic evaluation and the importance of each.

Within the genetic evaluation, phenotypes are king and are truly the driving force behind the EPD calculation process. Last issue, the importance of pedigree information was discussed. While that is the main mechanism that is used to link data together, it is important to have different data points for the EPD calculation process.

Phenotype data collection starts in beef cattle on the day the animal is born. Originally data collection focused on weighing animals. The RAAA was the first breed association to require phenotypic data collection, so, subsequently, those measurements were available to make selection decisions.

While this approach is somewhat effective for generating genetic improvement, progress using just the phenotypic measurements is slow because each phenotype is influenced by both the genetics and the environment that an animal experiences. So, while there is a genetic factor associated with it depending on the trait’s heritability, the phenotype has a varying level of predictability of the genetic value that the animal has for the trait of interest.

The next progression was to move to within-herd comparisons using ratios. While this added more information, it still did not bypass the challenge of selection decisions based on a metric that had environmental influence. This was the main reason for using EPDs because it allowed for the separation of the phenotypes into genetic effects and environmental effects. In genetic evaluation, all phenotype information is compared within the contemporary group. A contemporary group is a group of animals from the same herd, age and sex that were managed similarly. Within the genetic evaluation, each contemporary group is defined differently depending on the trait. For example, there is a different definition of how measurements for birth are compared versus traits collected at weaning or yearling.

While these groups may be defined differently, their function in the genetic evaluation is the same. The contemporary group is used to help define environmental influences over resulting phenotypes in that group. Take, for example, two groups of animals. One group has a very favorable environment with an average weaning weight of 600 pounds. The second group did not experience as favorable of an environment and has an average weaning weight of 500 pounds.These contemporary or environmental effects can then be accounted for in the EPD calculation process.

If we looked at the resulting EPD values in both groups, we may see that they end up being similar and the animals that were above each of the averages in the group receive more favorable EPDs compared to their parental average, and those below average for these phenotypes could see the EPD values move in a less favorable direction. Therefore, it is important to collect as many phenotypes on as many animals in a specific contemporary group as possible. Doing so gives a more accurate picture of the environment influencing the observations in the group and a more accurate picture of each animal’s ranking within the group.

These phenotypes and comparisons really are the basis of the genetic evaluation process. Recording and reporting this information is key to improving the accuracy of EPD information within a herd. Therefore, it becomes important to plan and make data collection a priority in seedstock animals. Table 1 gives an outline of different phenotypes that can be collected on animals at different time points throughout the animal’s life.

Looking at the table, it becomes apparent that there are numerous phenotypes that can be recorded on an animal. While all of the phenotypes are not currently used in genetic evaluation, collecting this information can be used within a herd to help with management decisions or could be used for potential future genetic evaluations.

Figure 1 shows the number of records that are available in the IGS genetic evaluation. The largest number of records available in the IGS database is the pedigree information. In terms of phenotypic measurements, the most reported are weight measurements,

Table 1. Time windows for collecting phenotypes. Birth Weaning Post Weaning/ Yearling

Birth Weight Weaning Weight

Yearling Weight Calving Ease Dam Mature Weight Ultrasound Measurements Dam Teat and Udder Score Dam Body Condition Score Feet and Leg Scores Dam Hip Height Dry Matter Intake Foot and Leg Score of Hip Height Mature Females Docility Scores Breeding Soundness Exam Reproductive Track Scores Carcass Measurements Heifer Exposure Records Docility Scores

followed by calving ease, docility, ultrasound measurements, genotypes and harvest records.

Each of these different phenotypes is important and used in one or, in a few cases, multiple genetic evaluations, that are performed. In all genetic evaluations, multiple phenotypic measurements are used to contribute to the EPD calculation process through what is known as multiple trait models. Take for example, the carcass weight EPD. In this EPD calculation, the following phenotypic data is used; weaning weight, yearling weight, ultrasound rib eye area, carcass rib eye area and the carcass weight phenotypes, which all contribute to this EPD calculation. This information is incorporated by using genetic correlations among traits. These genetic correlations signify the strength or the genetic differences that are common amongst the different traits. Therefore, all of these different data points can be linked together and be used to calculate EPD values that contain more information than may be available on the individual phenotypes for traits. However, it is still vitally important to collect as many of the different phenotypes as possible because these correlated traits do not share perfect genetic relationships with one another. Therefore, multiple data points that can be provided on all these phenotypes leads to the most accurate prediction of genetic merit for each trait. Collection and submission of phenotypic data are one of the most vital portions of a genetic evaluation. This data is the basis of the EPD calculation process. Therefore, it is important to

Figure 1 collect and submit as much data as possible for each animal. By doing this, the process of the genetic evaluation will not only improve the overall accuracy of the evaluation within each herd, but across the population in general. In the next part of this threepart series, how genomic information is included in the genetic evaluation will be covered. //