In several earlier topics of genetics on Biocyclopedia.com, we described methods used for preparation of genetic maps in a variety of organisms. In all these cases recombination data involving morphological, biochemical or nutritional traits were primarily utilized for preparing genetic or linkage maps. However, in using these traits, one is always handicapped due to non-availability of mutants for many genes, which therefore, can not be mapped. Linkage maps are thus often incomplete with gaps at many places. This limitation has largely been overcome in recent years due to the availability of molecular markers in the form of Restriction Fragment Length Polymorphisms (RFLPs), Random Amplified Polymorphic DNA (RAPD, pronounced as rapid), minisatellites (also called VNTRs = variable number of tandem repeats) and microsatellites (also called SSRs = simple sequence repeats), etc. These molecular markers are unlimited in number and would thus allow complete saturation of genetic maps giving a high resolution of a few centiMorgans only. Further the genetic maps prepared through estimation of recombination frequencies do not exactly correspond to the physical features either on the chromosomes, or on the DNA molecules, which are parts of the chromosomes. The recombination frequencies, though are function of distances between genes, but are not completely independent of the nature of mutants used, the position of these mutants on chromosomes, the genetic background, the environmental conditions and a variety of other factors.
In view of the above, at the molecular level, the mapping may involve small DNA segments, where recognition sites of many restriction enzymes may be mapped through a technique described as restriction mapping.
This may later be extended to complete chromosomes through a technique called chromosome walking.
This is described as physical mapping because restriction sites are separated by actual distances measured in terms of nucleotide pairs (or base pairs) and not in terms of recombination frequencies or centiMorgans. In other cases, positions of DNA fragments (called restriction fragments) are located through recombination data, so that these molecular maps
are genetic in nature as described above. These molecular maps have now been, prepared in several crops like maize, tomato, potato, rice, barley, etc. and also in animals like Drosophila,
mouse and humans. The technique for preparing these maps (restriction maps and RFLP/ RAPD maps) and also the results obtained so far, will be briefly described in this section.