Deoxyribonucleic Acid (DNA) holds a small portion of the bigger genetic process that keeps occurring in our body. The genome holds the center of life and it, in turn, produces generations of new similar yet variant offsprings of the ancient ones. There are different aspects of viewing this genomic activity and that not only involves a view through simple DNA programming alone.
Certain identifiable locations in the genome can be traced across generations, they are called Genetic markers. They are nothing but specific DNA sequences with a known location on a chromosome that holds the essential tools for linkage and association studies.
There are several techniques involved for detecting genetic variations in a living being, most of them are incorporated with forensic DNA profiling. Genetic markers were used to a greater extent to create livestock linkage maps using microsatellite markers.
Evolution of Genetic Markers
The history of genetic markers goes back to years. The first genetic marker was identified by Thomas Hunt Morgan from the species of fly drosophila. Since then its evolution has been tremendous.
Around the 1980s morphological and allozyme markers were identified and studied from common buckwheat (Fagopyrum esculentum). It was used to construct linkage maps and is widely used in population genetics. In the early 2000s, advances in PCR technology led to the development of various DNA marker systems for use in linkage mapping.
However, PCR-based markers did not completely cover the genome, making genetic analysis of buckwheat challenging. The subsequent development of next-generation sequencing, a game-changing technology, has allowed genome-wide analysis to be performed for many species.
The idea of mapping the human genome began in 1950 intending to associate a particular chromosome with a specific physical trait. Geneticists created linkage maps, looking especially at large families with an aberration in a chromosome.
The development of technology has underlain the search for genetic markers. Restriction enzymes were first used to map DNA in 1971. In 1975 two simple techniques sequenced DNA in gels and transformed bacteria.
E.M. Southern developed a technique for gel electrophoresis, in which, using an electric field, light bases travel farther along with a gel plate than heavier bases. More complicated techniques were later developed for protein electrophoresis. For example, high throughput analysis combines many techniques involving microchips and spectrographic analysis.
In addition, each October the magazine Science produces a full-color page of known gene locations on the genome. The map is thus slowly becoming complete.
For many years, gene mapping was limited to identifying organisms by traditional phenotype markers. This included genes that encoded easily observable characters
Types of Genetic Markers
There are mainly three types of genetic markers in the human genome.
1. Single Nucleotide Polymorphism(SNPs)
A germline substitution of a single nucleotide at a specific position in the genome, resulting in a genetic variation among people is referred to as Single Nucleotide Polymorphism. This difference could be completely normal and occurs throughout a person’s DNA, with an approximate count of once in every 1000 nucleotides.
An example of the SNP phenomenon could be explained as, at a specific base position in the human genome, the G nucleotide appears in most individuals, but in a minority of them, the position is occupied by an A. This denotes that there is an SNP at this specific position and the two possible nucleotide variations G or A is said to be the alleles of this specific position.
One of the major contributions of SNPs is in clinical research under genome-wide association study. It has created multiple opportunities to identify disease-causing phenotypes and traits.
2. Short Tandem Repeats(STRs)
It is a microsatellite marker, which is tandemly repeated DNA sequences that are 2-7bp in length with a highly mutative polymorphism. They are widely used in biological research; certain trinucleotide repeats associated with these STRs can be traced back to their involvement in human neurodegenerative diseases.
STR analysis is a common molecular biology method applied to compare the allele repeats at specific loci in DNA between two or more samples. STR analysis is a major tool in the forensic evaluation of evidence from a crime scene.
It evaluates specific STR regions found on the nuclear DNA. The polymorphic(variable) nature of these regions intensifies the discrimination between one DNA profile and another. Forensic DNA profiling performed by law enforcement agencies such as the FBI however modifies this analysis slightly and uses it as Autosomal Short Tandem repeat Markers to establish the identity of missing personnel be it a suspect or victim.
At present, there has been no demonstration of forensic STR variants directly causing or predicting disease, due to its legal and ethical implications.
3. Restriction Fragment Length Polymorphisms(RFLPs)
They are the results of variation in the DNA sequence recognized by restriction enzymes. These are bacterial enzymes used by scientists to cut DNA molecules at known locations. RFLPs are used as markers on genetic maps.
Typically, gel electrophoresis is used to visualize them. It works on a basic principle, if two organisms differ in the distance between sites of cleavage of a particular restriction endonuclease, the length of the fragments produced will differ when the DNA is digested with a restriction enzyme.
Other major genetic markers include SSLP (Simple sequence length polymorphism), AFLP (Amplified fragment length polymorphism), RAPD (Random amplification of polymorphic DNA), VNTR (Variable number tandem repeat), SSR Microsatellite polymorphism(Simple sequence repeat), SFP (Single feature polymorphism), DArT (Diversity Arrays Technology), RAD markers (Restriction site associated DNA markers) and STS Sequence-tagged sites).
Applications of Genetic Markers
- Genetic markers are employed in genealogical DNA testing for genetic genealogy to determine the genetic distance between individuals or populations.
- Uniparental markers (on mitochondrial or Y chromosomal DNA) are studied for assessing maternal or paternal lineages.
- Autosomal markers are used for all ancestry. It can also be used to study the relationship between an inherited disease and its genetic cause (for example, a particular mutation of a gene that results in a defective protein).
- It is known that pieces of DNA that lie near each other on a chromosome tend to be inherited together. This property enables the use of a marker, which can then be used to determine the precise inheritance pattern of the gene that has not yet been exactly localized.
- Genetic markers helps vastly in connceting one person to other on a biological basis.
- It helps in study of human population diversity.