The genetic manipulation of this trait can produce new varieties with novel combinations of desirable characters. A good example of genetic manipulation of a trait in ornamental plants is the modification of flower color. The most important pigments in floral coloration are the flavonoids. Certain flavonoids, the anthocyanins, are responsible for the familiar reds and blues of many flowers. Anthocyanins have been studied extensively using molecular, biochemical, and genetic methods.
Plant breeding using marker assisted selection is a second way to use a gene map.
If you know where a gene is on a gene map, DNA markers that flank the gene of interest can be identified. Just like mileage markers on an interstate highway indicate where you are on the highway, the presence of the DNA markers would infer the presence of the desirable gene in the offspring. DNA markers can be detected soon after seed germination, as soon as a few leaves are available to use for DNA marker analysis. This process makes early detection of the presence of the gene possible even though the actual expression of the trait does not occur until much later in maturation. This is especially valuable, for example, when working with genes that control flowering in plants that take many years to bloom and fruit or traits such as disease resistance that take several years to evaluate.