DNA Markers: Overview & Application

DNA Markers: Overview & Application

DNA Markers: Overview

Have you ever thought about how scientists identify the species of an organism?

By using DNA markers.

DNA markers, also known as genetic markers or molecular markers, are short DNA sequences with a known location on chromosomes — a structure made of DNA and proteins. The marker is extensively used in labs as an identification tool for experiments like genetic mapping, DNA fingerprinting, genotyping, and genetic analysis.

In the genomes of organisms, DNA markers are most commonly found in regions that do not encode proteins. That’s why they are considered neutral elements of the genome.

Generally, genes and genetic markers close to each other on a chromosome are inherited together. This trait of genetic markers is mainly useful to identify a nearby gene that causes a particular disease or trait within a family.

Among the significant practical advantages of DNA markers are their abundance across genomes, which has made them predominantly useful. In addition, environmental factors usually have very little or no effect on the DNA markers of an organism during its development.

A few examples of DNA markers include restriction fragment length polymorphisms (RFLPs), microsatellites, variable number of tandem repeats (VNTRs), single nucleotide polymorphism (SNPs), and copy number variants (CNVs).

Polymorphic molecular markers can be classified as dominant or co-dominant based on their inheritance of the mode of gene action. Further, they may or may not have a known function.

However, you must know that DNA markers also have good or bad qualities. So, how can you identify them?

Here’re a few characteristics present in a good-quality DNA marker:

  • They should be highly polymorphic in nature.
  • They should be selectively neutral.
  • They should be highly reproducible.
  • There should be a high frequency of genetic markers in the genome.
  • The genetic marker (gene) should show a codominant inheritance pattern.
  • When using multiple markers at once, they should not interact with each other.
  • An easy-to-use and rapid assay should be used for detecting markers.

In this article, we will review the types of DNA markers, their functions, and their applications in molecular biology and molecular genetics studies.

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Types of DNA Markers

Genetic polymorphism of DNA has wide applications in human genome research, phylogenetics, and studying genetic diversity as a DNA biomarker.

Based on variations in the length of the DNA sequence or the presence of different identities of nucleotides located at specific positions in chromosomes, polymorphic DNA markers are of different types:

PCR-based genetic markers

It involves in vitro amplification of particular DNA sequences or loci using a thermostable DNA polymerase enzyme and specific or random chosen oligonucleotide sequences (primers). The amplified fragments are separated using agarose gel electrophoresis and identifying banding patterns.

  • Random Amplified Polymorphic DNA (RAPD): Refers to the genetic variations within a specific DNA fragment generated through a specific endonuclease. The reaction proceeds after the primer anneal to two different sites on the complementary strand of the DNA template. RAPD has applications in genome mapping, individual genotyping, and linkage analyses.
  • Inter Simple Sequence Repeat (ISSR) markers: Obtained after DNA segments present between two microsatellite regions are amplified using PCR.
  • Expressed Sequence Tags (ESTs): It’s a small piece of DNA with a known sequence and location on the chromosome. They consist of only exons, which code for proteins in an RNA transcript.
  • Microsatellites or simple sequence length polymorphisms (SSLPs): Also known as simple sequence repeats. They are tandemly repeated nucleotide sequences/motifs and consist of codominant alleles. The marker can detect variation in DNA length by the amplification of tandem arrays followed by visualization in an electrophoretic gel. It’s hypothesized that SSRs either occurred due to the mobility of transposable genetic DNA molecules, double-strand DNA recombination, or nucleotide disparities.
  • Cleaved Amplified Polymorphic Sequence (CAPS): Variations in restriction fragment length due to INDELs or SNPs. In PCR amplicons, they alter restriction endonuclease recognition sites generated by oligonucleotide primers specific to a particular location.
  • Amplified Fragment Length Polymorphism (AFLP): Involves amplifying a specific DNA fragment followed by restriction digestion of the organism’s whole genome.

Hybridization-based genetic markers

In hybridization-based markers, restriction enzyme digested DNA is hybridized to a labeled probe to visualize DNA profiles.

  • Restriction Fragment Length Polymorphism (RFLP): One of the first techniques used for DNA analysis. It involves generating distinct fragments by cutting at a specific site on the chromosome using a specific endonuclease.
  • VNTRs: In this method, restriction enzymes are used to digest the target gene, and then hybridized with RFLP probes.

What are DNA Markers Used For?

DNA markers are typically polymorphic nucleic acids found in individuals or populations. They are a useful tool used in labs for a range of research studies, including crop improvement, disease diagnosis and treatment, and phenotyping and genotyping of organisms.

Gene Identification

DNA markers have essential roles in gene mapping. It identifies the location of linked genes on chromosomes. Further, it also identifies any alterations in the organism’s genome or DNA sequence, which helps in identifying the genes associated with the genetic disorders.

DNA markers also help in identifying the species of newly discovered organisms and its family. Further, its applications in the determination of characters in a DNA sequence to differentiate between individuals, populations, or species.

Disease Identification

Many disease-resistance genes have been identified using DNA markers. The markers are some inherited traits that help in disease identification. In many crops, quantitative trait loci (QTLs) have been identified that explain phenotypic variation in disease responses.

Developing disease response-linked DNA markers requires converting identified markers into simple user-friendly protocols, which is followed by validation across different genetic backgrounds.

What Industries Use DNA Markers?

DNA markers have extensive applications in molecular biology labs and industries for the role it plays in identifying genes and genetic diversity among organisms.


Biotech industries and labs are used to study the alterations in the genome, causes of disease, and mutations that occur frequently in our bodies. Point mutations, such as substitutions, deletions, and insertions or alterations like inversions or duplications within the genome can be identified using RFLP, a PCR-based DNA marker.

Further, DNA markers are also useful in understanding the genotypic differences in the same or different species. Also, maternal or paternal lineages are assessed using uniparental markers (on mitochondrial DNA or Y chromosomes).


Molecular markers have a crucial role in disease identification and analysis. RFLP has applications in identifying disease carriers, genetic mapping, disease, inheritance, and heterozygous detection. Further, single nucleotide polymorphism is used in biomedical research to compare the difference between diseased and control groups during an experiment.  


DNA markers have been widely used in plant breeding experiments. ISSR markers are used for phylogenetic analysis and identifying genetic diversity. It’s also used to detect the proximity of cultivars and analyze somaclonal variation. Further, ISSR’s simple setup allows it to be used for parental recognition, gene tagging, gene mapping, and strain identification.

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DNA markers are also known as genetic or molecular markers. They are DNA sequences with a known location on chromosomes. They have a range of applications in molecular biology and biotech labs and industries for gene mapping, identifying species, detecting genotypic differences, and studying gene loci-associated diseases.

The studies are performed using workflows like agarose gel electrophoresis, next-generation sequencing, PCR, etc. These high-throughput workflows require researchers to equip their labs with high-throughput equipment and high-quality reagents. However, for small or established labs having low funds, acquiring such expensive equipment is not easy. That’s why leasing is considered to be an effective option.

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