A gene is a set of instructions for making a molecule given through a set of nucleotides in a molecule of DNA or RNA, with most of the DNA existing on the 23 pairs of chromosomes in the nucleus of each human cell. The bases of the nucleotides are adenine, cytosine, guanine, and thymine which define the information in the gene and the molecular product, often a protein.

Gene mapping refers to one of two different ways of definitively locating the gene on a chromosome. The first type of gene mapping is also called genetic mapping. Genetic mapping refers to the use of linkage analysis to determine how two genes on a chromosome relate in their positions. Physical mapping, the other type of gene mapping, locates genes by their absolute positions on a chromosome using any technique available. Once a gene is located, it can be cloned, its DNA sequence determined, and its molecular product studied.

The first report of mapping a gene to a human Autosomes was published in 1968 by Roger Donahue and associates. Using a linkage analysis, he was able to estimate the genetic distance of 2.5 map units between two loci or gene locations on chromosome 1. In 1971, chromosome banding techniques were developed, which opened the way for researchers to be able to identify more types of alterations, included insertions, deletions, and translocations, as well as mapping to position. In connection with this, restriction fragment length polymorphism (RFLP) analysis was developed and led by the early 1990s to the identification of a number of genes associated with disease in humans. A complementary technique, fluorescence in situ hybridization, developed about the same time, also contributed to the mapping efforts.

An example of this process in application is the work done with the gene for cystic fibrosis. The cystic fibrosis gene was mapped by linkage analysis in 1985. This paved the way for its cloning in 1989 by Francis Collins and his associates. This led to a better understanding of the cause of the disease.

The foundation of gene mapping also laid the foundation for the Human Genome Project. The idea of sequencing the entire human genome was explored in the 1980s, but was not universally thought to be feasible. Impetus from the U.S. Department of Energy along with the National Institutes of Health (NIH) helped foster the 1990 launch of the project. The technical achievements mentioned above contributed to the project’s momentum. The project was completed in 2003.

Two different ways of mapping are distinguished. Genetic mapping uses classical genetic techniques (e.g. pedigree analysis or breeding experiments) to determine sequence features within a genome. Using modern molecular biology techniques for the same purpose is usually referred to as physical mapping.

Physical Mapping

In physical mapping, the DNA is cut by a restriction enzyme. Once cut, the DNA fragments are separated by electrophoresis. The resulting pattern of DNA migration (i.e., its genetic fingerprint) is used to identify what stretch of DNA is in the clone. By analyzing the fingerprints, Contigs are assembled by automated or manual means into overlapping DNA stretches. Now a good choice of clones can be made to efficiently sequence the clones to determine the DNA sequence of the organism under study.

Macrorestriction is a type of physical mapping wherein the high molecular weight DNA is digested with a restriction enzyme having a low number of restriction sites.

There are alternative ways to determine how DNA in a group of clones overlaps without completely sequencing the clones. Once the map is determined, the clones can be used as a resource to efficiently contain large stretches of the genome. This type of mapping is more accurate than genetic maps.

Genes can be mapped prior to the complete sequencing by independent approaches like in situ hybridization.

Restriction endonuclease

A restriction enzyme (or restriction Endonuclease) is an enzyme that cuts double-stranded or single stranded DNA at specific recognition nucleotide sequences known as restriction sites. Such enzymes, found in bacteria and archaea, are thought to have evolved to provide a defense mechanism against invading viruses. Inside a bacterial host, the restriction enzymes selectively cut up foreign DNA in a process called restriction; host DNA is methylated by a modification enzyme (a methylase) to protect it from the restriction enzyme’s activity. Collectively, these two processes form the restriction modification system. To cut the DNA, a restriction enzyme makes two incisions, once through each sugar-phosphate backbone (i.e. each strand) of the DNA double helix.

Restriction enzymes recognize a specific sequence of nucleotides and produce a double-stranded cut in the DNA. While recognition sequences vary between 4 and 8 nucleotides, many of them are palindromic, which correspond to nitrogenous base sequences that read the same backwards and forwards.

Molecular Cloning

Molecular cloning refers to the procedure of isolating a defined DNA sequence and obtaining multiple copies of it in vitro. Cloning is frequently employed to amplify DNA fragments containing genes, but it can be used to amplify any DNA sequence such as promoters, non-coding sequences, chemically synthesized oligonucleotide and randomly fragmented DNA. Cloning is used in a wide array of biological experiments and technological applications such as large scale protein production.


A Contig (from contiguous) is a set of overlapping DNA segments derived from a single genetic source. A Contig is also sometimes defined as the DNA sequence reconstructed from a set of overlapping DNA segments.

A Contig in this sense can be used to deduce the original DNA sequence of the source. A Contig map depicts the relative order of a linked library of contigs representing a complete chromosome segment. Fragmentation of a Contig into 1-2kb pair segments provides suitably sized DNA segments for sequencing. Special software must be used to assemble the segments back to one single un-interrupted piece (Contig).

Insitu Hybridization

In situ hybridization (ISH) is a type of hybridization that uses a labeled complementary DNA or RNA strand (i.e., probe) to localize a specific DNA or RNA sequence in a portion or section of tissue (in situ), or, if the tissue is small enough (e.g. plant seeds, Drosophila embryos), in the entire tissue (whole mount ISH). DNA ISH can be used to determine the structure of chromosomes. Fluorescent DNA ISH (FISH) can, for example, be used in medical diagnostics to assess chromosomal integrity. RNA ISH (hybridization histochemistry) is used to measure and localize mRNAs and other transcripts within tissue sections or whole mounts.