A genetic map of an animal or plant species is an abstract model of the linear arrangement of a group of genes and markers. Development of various DNA marker systems has greatly facilitated the construction of dense genetic linkage maps.

A genetic map is based on homologous recombination during meiosis, so genetic map is also a meiotic map. Co-segregation analysis of genetic markers in progenies derived from single or two parents are used to construct the linkage maps. Markers that are present on different chromosome or are physically distantly located on the same chromosome will exhibit independent assortment during meiosis. In comparison, markers derived from same chromosome and closely placed, will exhibit linkage except when separated by recombination. Since recombination frequency is inversely related to physical distance between two loci/marker, the measure of recombinant events between different markers will reveal their relative order of arrangement and their distance from one another. Molecular maps constructed on this principle, are thus a linear arrangement of genetic markers, the distance between each representing the recombination frequency in terms of centimorgan (cM) units. In order to generate these linkage maps mapping population such as those derived by selfing (F2, F3, NILs), by backcrossing to recurrent parent (BCn, RILs) and double haploid plants have been employed.

Genetic maps help us to examine directly the genotype of the species rather than the phenotypes leading to an understanding of the genetic basis of morphological variation and development, study the distribution of genes, the pattern of inter-generic/inter-specific gene flow and genome evolution. The practical applications of these maps are in generating markers linked to traits of agronomic importance. These markers then have the potential to be employed for map based cloning and marker-assisted selection. Genetic maps based on molecular markers have been constructed or are in progress for a number of diverse plants such as Arabidopsis, Brassica, Rice, Maize, Barley, Pea, Pine and Poplars to name a few. As genome information accumulates for plant species genetic mapping can be carried out by comparing genome maps among species. Comparative mapping (Synteny mapping) thus allows transfer of mapping information across species and better understanding of the evolution of genome structure.