For some traits, the gene of interest has been discovered and the presence of desirable alleles can be directly assayed with a high level of confidence. However, if the gene of interest is not known, markers linked to the gene of interest can still be used to select for individuals with desirable alleles of the gene of interest.
In some instances, the specific gene responsible for a particular characteristic has been discovered and can be directly examined. Nevertheless, when this is not feasible, linked markers can still be utilized to select for individuals possessing favorable versions of the gene of interest.