8.3: Optimising the phenotypic information

Phenotypes of animals may be systematically influenced by, for example, the (management on the) farm the animals are kept in, or whether they were born in summer or winter, or whether they are male or female, etc. For a fair comparison of animals based on their phenotypes it is important to be aware of these systematic influences and to take them into account when defining the phenotypic superiority of an animal. For example, if males on average are 5 kg heavier than females then correction for effect would involve subtracting 5 kg from the weight of each male, so that males and females can be compared directly on their weight again.

The effect of correcting phenotypic superiority for systematic effects is that the resulting ‘cleaned’ phenotype will better resemble the genetic superiority. The clean phenotypes thus allow for a better prediction of the regression coefficient. This is illustrated in figure 2. In the figure on the left the cloud of data points indicates the ‘raw’ data: the data without correction for any systematic effects. When fitting a regression through these data, the regression coefficient would be 0.3. The figure on the right indicates the situation after ‘cleaning’. The regression coefficient has increased, indicating that the phenotypic information has become a better predictor of the true breeding value.

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In the figure on the left is the phenotypic superiority uncorrected for systematic influences. In the figure on the right is the data corrected for systematic effects, resulting in better resemblance to the genetic superiority, and thus a higher regression coefficient.