A genetic marker is a phenotypic variant due to a variation in the nucleotide sequence of a genome, or the phenotypic manifestation of an allele. The term is used frequently as a synonym of allele.
Genetic markers may affect the morphology, behavior, physiology, or chemistry of the organism, and they are defined in relation to the phenotype of the standard wild type. A marker gene is a gene whose phenotypic variants are used as genetic markers.
From a practical viewpoint we can distinguish four groups of genetic markers: 1. Selectable markers which enable the individuals that carry them to grow under experimental conditions that hinder similar individuals lacking the marker. Selectable markers are nearly indispensable in the genetic analysis of very large laboratory populations of viruses, bacteria, unicellular eukaryotes, and cultured cells. Particularly useful are the selectable markers that are also counterselectable; that is, certain experimental conditions allow the growth of individuals that lack them and hinder individuals that carry them.
2. Genetic markers that are easily recognized by visual inspection of the shape, the color, and sometimes the movements of cells and organisms. They have been particularly useful in the analysis of small populations of plants and animals.
3. Genetic markers whose detection requires specific tests. Conditional lethal markers impede growth under normal conditions, but are rescued by special circumstances of the environment or the genetic background. Chemical analyses are often indispensable—for example, to detect the presence or absence of a metabolite or to distinguish the electrophoretic variants of a protein. Behavioral markers usually require their own specific tests. Onerous analyses can be avoided in a few cases. For example, some of the adenine auxotrophs of Saccharomyces cerevisiae develop a pink color under certain growth conditions; the presence of certain chemicals or certain enzymes in a cell may be revealed when they produce a colored product with certain reagents.
4. Variations in the DNA sequence that have no other phenotypic expression than the results of direct tests on the DNA (eg, restriction maps, PCR). Their main advantage is that they occur all over the genome, even in regions in which no other genetic markers have been located.