Selection changes the frequencies of genes that affect the traits of interest. Frequency changes can raise or lower the means of traits and also increase or decrease the genetic variability of traits. Genes may affect more than one trait, directly or indirectly, so that selection will directly affect the traits of interest and will indirectly affect many other traits (i.e., correlated responses) that may not be observed in traditional record keeping. For example, many years of selection for increased milk yields in dairy cattle have caused a correlated decrease in reproductive performance. There could also have been changes in immune responses and other traits that were not observed or recorded while selection was applied to milk production.
Selection tends to choose animals that are related (because they share the same favorable genes). Breeding related animals leads to an animal that may have the same gene allele on both chromosomes. This is called homozy-gosity. The proportion of gene loci in an individual that are homozygous is an inbreeding coefficient. Greater homo-zygosity results in lower genetic variability. Inbreeding can decrease performance and increase the likelihood of undesirable genes becoming homozygous, which could result in death or greater susceptibility to diseases. Mating programs can be designed to maximize the ratio of selection response to level of inbreeding, or to minimize the increase in inbreeding per generation. Such programs dictate which males should be mated to particular females.
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