Taxonomy: Genetic Marker

What is marker?

  • Marker may be defined as “Mark of identification”.
  • In Biology three major types of markers are used:
  • Morphological marker (also called “classical” or “visible” markers) which are phenotypic traits.
  • Biochemical markers, which are called isozymes- multiple forms of enzymes, including allelic variants of enzymes.
  • A genetic marker is a gene or DNA sequence with a known location on a chromosome.

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What is Genetic Marker?

  • A genetic marker is a gene or DNA sequence with a known location on a chromosome that can be used to identify individuals or species. It can be described as a variation (which may arise due
    to mutation or alteration in the genomic loci) that can be observed.
  • A piece of DNA that lies on a chromosome so close to a gene that the marker and the gene are inherited together. A marker is thus an identifiable heritable spot on a chromosome. A marker can be an expressed region of DNA (a gene) or a segment of DNA with no known coding function.
  • A genetic marker may be a short DNA sequence, such as a sequence surrounding a single base-pair change (single nucleotide polymorphism, SNP), or a long one, like minisatellites.


  • For many years, gene mapping was limited to identifying organisms by traditional phenotype markers. This included genes that encoded easily observable characteristics such as blood types or seed shapes. The insufficient number of these types of characteristics in several organisms limited the mapping efforts that could be done. This prompted the development of gene markers which could identify genetic characteristics that are not readily observable in organisms (such as protein variation).

Types of genetic or molecular marker

Some commonly used types of genetic markers are:

  • RFLP (or Restriction fragment length polymorphism)
  • SSLP (or Simple sequence length polymorphism)
  • AFLP (orAmplified fragment length polymorphism)
  • RAPD (or Random amplification of polymorphic DNA)
  • VNTR (orVariable number tandem repeat)
  • SSR Microsatellite polymorphism, (or Simple sequence repeat)
  • SNP (or Single nucleotide polymorphism)
  • STR (or Short tandem repeat)
  • SFP (or Single feature polymorphism)
  • DArT (or Diversity Arrays Technology)
  • RAD markers (or Restriction site associated DNA markers)

sequences that are repeated multiple times and the number of repeats varies from person to person. Another reason why every individual has a unique DNA fingerprint is because of regions called variable number tandem repeats, or VNTR’s. A VNTR is a sequence that is repeated multiple times. The number of repeats varies from person to person. This example shows the sequence GATC repeated 5 times in one individual and only 2 times in a second individual.


Applications genetic markers

Molecular markers have several advantages over the traditional phenotypic and biochemical markers in plant.

  • The main uses of DNA markers in agricultural research such as Cultivar identity/assessment of ‘purity’/ Hybrid Testing
  • to study the evolutionary relationships among individuals
  • Genetic markers are employed in genealogical DNA testing for genetic genealogy to determine genetic distance between individuals or populations.
  • Genetic Diversity Analysis
  • Genetic Linkage Map Construction
  • Mapping of quantitative trait loci (QTLs)
  • Map based cloning of genes
  • Mapping of mutations
  • Marker-assisted selection (MAS)
  • Marker assisted backcross breeding (MAB)
  • Marker-assisted pyramiding
  • Mapping major genes
  • Genetic markers can be used to study the relationship between an inherited disease and its genetic cause
  • Characterization of transformants
  • Genetic markers can 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 are employed in genealogical DNA testing for genetic genealogy to determine genetic distance between individuals or populations. Uniparental markers (on mitochondrial orY chromosomal DNA) are studied for assessing maternal or paternal lineages.Autosomal markers are used for all ancestry.
    Genetic markers have to be easily identifiable, associated with a specificlocus, and highly polymorphic, because homozygotes do not provide any information. Detection of the marker can be direct by RNA sequencing, or indirect using allozymes.
  • Some of the methods used to study the genome or phylogenetics are RFLP, AFLP, RAPD, SSR. They can be used to create genetic maps of whatever organism is being studied.
    There was a debate over what the transmissible agent ofCTVT (canine transmissible venereal tumor) was. Many researchers hypothesized that virus like particles were responsible for transforming the cell, while others thought that the cell itself was able to infect other canines as an allograft. With the aid of genetic markers, researchers were able to provide conclusive evidence that the cancerous tumor cell evolved into a transmissible parasite. Furthermore, molecular genetic markers were used to resolve the issue of natural transmission, the breed of origin (phylogenetics), and the age of the canine tumor.
  • Genetic markers have also been used to measure the genomic response to selection in livestock. Natural and artificial selection leads to a change in the genetic makeup of the cell. The presence of different alleles due to a distorted segregation at the genetic markers is indicative of the difference between selected and non-selected livestock.

Using Antibiotic Resistance Genes As Markers

There is some concern about using antibiotic resistance genes as markers. The antibiotic resistance genes spread to other bacteria, producing strains of pathogenic (disease-causing) bacteria that it could not kill with antibiotics. In insulin production, the risk is probably very small, because the genetically modified bacteria are only grown in fermenters and not released into the wild. But now there are many different kinds of genetically modified bacteria around, some of which are used in situations in which their genes might be passed on to other bacteria. If these bacteria were pathogens, then we might end up with diseases that are un-treatable.

Because of the risk of creating pathogenic antibioticresistant bacteria, there is now much less use of antibiotic resistance genes in this way, and other ways have been developed in which the successfully transformed bacteria can be identified. One method uses enzymes that produce fluorescent substances. For example, enzymes obtained from jellyfish make a protein called GFP (green fluorescent protein) that fluoresces bright green in ultraviolet light. The gene for the enzyme is inserted into the plasmids. So all that needs to be done to identify the bacteria that have taken up the plasmid is to shine ultraviolet light onto them. The ones that glow green are the genetically modified ones. The same marker gene can be used in a range of organisms. Figure (A).

Fig (A) : 6 A transgenic mouse expressing a gene for a fluorescent protein.

Another marker is the enzyme β-glucuronidase (known as GUS for short), which originates from E. coli. Any transformed cell that contains this enzyme, when incubated with some specific colourless or non-fluorescent substrates, can transform them into coloured or fluorescent products. This is especially useful in detecting the activity of inserted genes in plants, such as the sundew
in fig (B).

Fig (B) : Sundews are carnivorous plants that use sticky hairs to catch insects. On the left is a leaf of a transgenic sundew plant which is expressing the gene for GUS. The leaf has been placed in a solution of a colourless substance and the enzyme GUS has converted it into this dark blue colour. This indicates that the plant has been genetically modified successfully. On the right is a normal sundew leaf.

So, genetic markers are useful in identification of various genetic variations. The development of DNA-based genetic markers has had a revolutionary impact on genetic studies. With DNA markers, it is theoretically possible to observe and exploit genetic variation in the entire genome. These markers can be used to study the evolutionary relationships among individuals. Popular genetic markers include allozymes, mitochondrial DNA, RFLP, RAPD, AFLP, microsatellite, SNP, and EST markers. The application of DNA markers has allowed rapid progress in investigations of genetic variability and inbreeding, parentage assignments, species and strain identification, and the construction of highresolution genetic linkage maps for aquaculture species. The advent of nextgeneration sequencing (NGS) has revolutionized genomic and transcriptomic approaches to biology. The new sequencing tools are also valuable for the discovery, validation and assessment of genetic markers in populations. This review focuses on importance and uses of genetic markers with advent of modern technologies.


This Article is completely based on by the lecture of Dr. Mohammad Zashim Uddin, Professor, Department of Botany, University of Dhaka

 Some info and pictures have been added by author

Reference used for info: Cambridge International Biology Cource Book by Mary Jones

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About Abdul Bari Chowdhury

A Biology maniac who is interested in fundamental research attempt to explore and explain the underlying mechanisms that govern the functioning of living matter............ E-mail: abchowdhuryy@gmail.com. Minimum monthly resolution: Publish (1), Revise(3), Share (5).

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