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Thus far we have been discussing the optimal situation in which someone decides on which animals are allowed to breed and which are not. There are two main points where the breeder has influence: the selected proportion and the accuracy of selection. For good predictions of the genetic response it is essential that these the assumptions for the  selected proportions and the accuracy of selection are correct. How realistic is that? This is fairly realistic in case this someone owns all potential breeding animals, such as in commercial pig and poultry breeding. The selected proportion may depend somewhat on the expected market situation, but at least changes are recorded. The accuracy of selection of the breeding animals also is in the hands of the breeding company. Animals are selected based on performance of other animals (sibs, offspring), and the exact number depend on the number available and may vary a bit between animals. The influence of this small fluctuation on the predicted genetic gain will be very limited. But even in those breeding companies there may be unexpected practical events, such as a disease outbreak, that prevent selecting the intended proportion. However, in general in these species the prediction equations as presented in this chapter are very useful.

In dairy cattle breeding the situation becomes a bit more difficult as the large part of the cows are owned by individual farmers. Each farmer will have his or her own breeding goal, though in general terms these will resemble that of the breeding company, who owns the bulls. The selected proportion in bulls is in the hands of the breeding company, but the subsequent use of those bulls is in the hands of the farmers. There are popular bulls and not so popular bulls. Even though both are selected for breeding, the popular bull will have a larger number of offspring in the next generation than the not so popular bull. The assumption when predicting genetic response to selection is that all selected bulls will have equal chance of ‘spreading their genes’. This obviously is not the case. Depending on which bulls are used more often than expected, this will lead to an over or under prediction of the genetic response. Popular bulls obviously also will have a more accurate EBV than not so popular or young bulls. This difference in accuracy needs to be taken into account when predicting the response to selection. On the females side there may be very little effect of selection in cows because of two reasons: first of all the selected proportion is very large as most cows are used to produce replacements. Second, the farmers may have slightly different selection criteria that result in an overall even smaller effect of selection in the cows. In practice, this selection path can be ignored.

In horses the situation is a bit more complicated than in dairy cattle. The stallions are approved for breeding if they live up to the standards that are defined by the studbook. However, the approved stallions do not necessarily represent a well-defined selected proportion because not all males foals are selection candidates because not all owners are willing to present their colt (young stallion) at the stallion inspection. The selected proportion based on the number of colts selected in the stallion inspection thus may not represent the true selected proportion. As in dairy cattle, some stallions will be much more popular and, consequently, will have more offspring in the next generation than others. As in dairy cattle, the accuracy of selection will depend on the information that is available and may differ between stallions. That can be taken into account when predicting the response to selection. In most studbooks, as in dairy cattle, all mares are allowed to breed. However, different from dairy cattle is that it are not necessarily only the best mares that are used for breeding. Some owners of a very good mare do not want to breed with her, and some owners of poor mares do want to breed a foal. In mares it seems a fair approximation that the selected proportion is 100%. Accuracy of selection generally will be low because of the generally limited number of foals. Some mares with a popular father potentially have a large number of half sibs.

In dogs the situation is more complicated again. The breeding associations and the ‘Raad van Beheer’ have defined some basic prerequisites for males to be allowed to breed. Females in some breeds are also required to present a health certificate related to some potential breed specific health issues. So far so good. However, in males there is no selected proportion because very few people enjoy having a breeding male, and this is not necessarily related to the quality of the dog. Similarly, few owners of a bitch want to breed a litter, despite the quality of the bitch. Consequently, prediction of genetic response based on selected proportion and accuracy of selection is not feasible in dogs. Exception to this is the breeding of working dogs, where quality of the dog is the selection criteria and selected dogs are used for breedingnot always the case and is different in the different species as will be outlined in the subparagraphs for pigs and poultry, dairy cattle, horses and dogs.

So what to do with these situations where selected proportion and accuracy of selection cannot be defined established very well? One solution can be to predict the average genetic potential in the offspring of each mating based on the EBV of the sire and the dam. As we have seen in the chapter about genetic models, knowing the EBV in the parents only gives you some idea about the EBV in the offspring due to the Mendelian sampling: A_offspring = ½ A_sire + ½ A_dam + MS. It will depend on the accuracy of the EBV in the parents to what extend the inaccuracy of the prediction of the genetic response will be further increased.

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