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Critical issue in correcting for systematic effects is that it only works well if genotypes are sufficiently spread across systematic environmental influences. So the animals on both different farms need to be related, for example because the same fathers were used, or because the fathers used on each farm were brothers. If the animals on both different farms are unrelated, then part of the reason of the difference in weight may be a difference in genetic potential. And that is what you want to estimate so you do not want to lose that by correcting the weight. Artificial insemination allows for genetic links between farms because the same sires are used in many farms. In farm animal species where natural mating is common practice, such as in beef cattle and sheep, it often is not possible to estimate systematic farm effects accurately because lack of exchange of animals between farms results in poor genetic links between farms. In species where the sires are brought to their mates on various locations, as can be the case in horse or dog breeding, genetic links will not be a limiting factor. Provided , provided that the sires are used frequently.
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