Mapping techniques helps to determine the location of elements within a genome with reference to identifiable markers. Mapping helps to identify the exact position of the gene, the distance between two genes
There are different techniques of mapping like genetic mapping, physical mapping and comparative mapping. Physical mapping further includes restriction mapping, somatic cell mapping, cytogenetic mapping and radiation hybrid mapping.
1. Genetic Mapping.
Genetic mapping techniques make use of recombination events to find the distance between genetic markers.
RFLP or Random Fragment Length Polymorphism studies the variations in homologous DNA sequences to identify the distance between two markers. The DNA segment is digested with the restriction enzymes into restriction fragments which are cleaved at specific restriction sites. These fragments are separated via gel electrophoresis based on the length of the segments. For genetic mapping, two or more RFLP loci are employed. The parental and recombinant fragments are identified by southern blotting and their frequency is observed. The resulting analysis of frequency of recombinants reveals the distance between the two RFLP loci.
Short tandem repeat polymorphisms (STRP) are currently used for gene mapping studies involving single gene disorders. The homologous genomes differ in the number of repeats of STR loci between individuals. The gene map is the result of identification of repeats. STRP genome scan of 10cM is ideal for such studies though for disorders involving multiple genes and linkage disequilibrium require higher STRP density.
SNP (Single Nucleotide Polymorphism) is used in genetic studies employing linkage analysis and genome wide association. The inheritance of a trait and genetic signatures such as microsatellites and SNPs are used to study the linkage analysis. For best results, researchers may need to use the data from several generations.
Genome Wide Association (GWA) consider the population as a single family and try to establish relationships between traits and markers such as microsatellites and SNPs. There is no need for the researchers to find accurate data from several generations as in the linkage analysis. The technique is used for mapping functions of genes of common diseases. With SNP mapping, it is possible to considerably reduce the number of samples thus reducing the time and cost of gene mapping.
The mapping technique involves the calculation of recombination fraction expressed as
ө = number of recombinants / number of total progeny.
Genetic mapping requires informative markers which are polymorphic in nature. The mapping can be done only in a population with known relationships. The distance estimation is accurate if done between markers which are closer.
The distance is measured in units of centimorgans (cM) where 1 cM represents 1% chance of recombination between markers
2. Physical mapping
Physical mapping techniques depend on the observable experimental results involving processes such as hybridization and amplification. The mapping does not need to have a distance measure.
Restriction mapping is one of the oldest techniques of gene mapping based on cleavage by restriction enzymes. These enzymes cut the DNA at specific sites which are often palindromic sequences of DNA. The mapping is done by identification of relative position of these restriction sites along a linear or circular DNA.
Cytogenetic mapping depict the order and map location in reference to a chromosomal banding pattern. The map visualizes the stained chromosomes as seen under a microscope and hence comparison is easier with the homologous chromosomes. The light and dark bands allow the karyotyping of these chromosomes and therefore chromosomal alterations are easier to be identified.
Somatic cell mapping uses rodent cells to integrate the genome from other species. The technique is used to map a gene to the specific potion of the chromosome with the highest resolution. Target genome cells are fused with the rodent cells and screened for the presence of hybrids with the target genome incorporated. Finer mapping with higher resolution is possible if the hybrids contain cells partial chromosomes as a result of translocation of genome. The process is costlier since it involves screening of numerous hybrids.
Radiation hybrid mapping is a cost-effective and high-resolution alternative method of gene mapping. The principle is the same as the somatic cell hybrid mapping. The comparison of results from various groups is relatively difficult. The data is usually in vector format with 1 or + depicting retention of target genome, 0 or - for absence, 2 or '?' for unknown genome.
Whatever method you choose, the recombination frequency is generally non accurate when calculated over large distances. Hence mapping functions are used to define the relationship between map distance and recombination frequency.
About Author / Additional Info: