Different type of genetic markers

“Genetic markers are known DNA sequences which can be used for studying any kind of polymorphism”.


Image credit: SFGate

A pen marker is used to mark some important sentences from the entire textbook and we can use it in exams, papers and other assignments. Similarly, genetic markers are some important and know regions in a genome by naming it as a specific marker we can apply it in polymorphism study.

Genetic markers can be widely used in cancer genetics, disease diagnosis, carrier detection, heterozygous and homozygous identification, maternal cell contamination, paternity verification, linkage analysis, population genetics and plant breeding programs.

Let us understand it with an example







Can you identify something? 11 basepair sequence is repeatedly observed at several intervals, in the sequence and it is present in all three species. A wide collection of data set indicates that this sequence is abundantly frequent in all organism on earth (assume it). Let us give some name to this marker by using its characteristics.

  • It is observed one after another, tandemly.
  • It is repeatedly observed after regular interval of sequences hence it is a repeat sequence. 
  • Though the sequence is same, sequence numbers are different in all three species i.e, 4 repeats in species A, 5 repeats in species B and 7 repeats in species C. So the number of the repeats are variable.

Now collect all three characters in a single set: it is a sequence, arranged tandemly, repeated one after another and variable so we can name it as variable numbers of tandem repeats.

As it varies from species to species, we can use it for identification of species.

RFLP (Restriction Fragment Length Polymorphism)

Firstly, let us understand the terminology RFLP, alteration (polymorphism) in the length of different fragments (of DNA) can be analysed using restriction digestion.

Restriction digestion is performed by restriction endonuclease enzymes. It cuts DNA at its specific restriction site. Millions of restriction sites are present for individual RE in the human genome.

RFLP is used for studying alteration in gene or allele. DNA is isolated from the study organism. A gene of interest in isolated and amplified using polymerase chain reaction in a thermocycler. PCR product or amplified gene is digested with specific enzyme or enzyme of our interest.

The image represents an overall process of RFLP. In step 1- DNA sample is amplified using PCR primers. step 2- multiple copies of DNA is generated after the end of PCR reaction. step 3- Restriction endonuclease cuts DNA, it creates 1 cut in AA allele and 2 cuts in aa allele.

Different fragments of allele AA, aa and Aa in gel.

Here if restriction site is present on a gene, RE will cut it, if not the gene remain uncut. So if any alteration (polymorphism) is produced, RE will not cut the sequence and we can observe distinct band pattern in electrophoresis.

The length of different fragments is identified using blotting, which is now replaced by sequencing. RFLP is applicable in disease identification, genetic mapping, heterozygous detection and carrier identification. 

RAPD (Randomly Amplified Polymorphic DNA)

It amplifies randomly into the genome at any position. Here a fixed set of PCR arbitrary primers are used to amplify random segment in a genome of the different organisms. RAPD is routinely used in plant genomic studies. A set of different primers are used to amplify DNA of plants of the same species and by using RAPD, a diversity or polymorphic genetic tree is created.

RAPD is a simple and most reliable method for genomic study. No prior information of sequence is required for analysis. However, we cannot distinguish homozygous from heterozygous by using RAPD.

VNTR (Variable Numbers of Tandem Repeats)

We already have discussed VNTR. It is a highly polymorphic marker and repeated sequences are arranged one after another. VNTR is an important tool in parental verification. It is a simple technique,  known VNTR primers are used to amplify a specific region of the genome. D1S80, ApoB, D17S30 are some important markers routinely used in maternal cell contamination. 

VNTRs are highly variable sequences. Repeat numbers almost vary among individuals. One VNTR allele is inherited from father, while one allele is inherited from mother. Both alleles have different numbers of the repeat because our parent is not closely related.


The image represents the VNTR patterns of father, mother, child and unrelated DNA sample.

If our parents are genetically unrelated, repeat number is more variable. Though we have two alleles of which one allele is matched with father and one is matched with mother, repeat number is slightly different. But it can not be detected in agarose gel electrophoresis.

Traditionally, VNTR markers are most acceptable tool for parental verification and for checking maternal cell contamination in CVS or AF sample.

Structurally, VNTR repeats are 10-100bp long sequences, it varies from species to species and among the species. The repeat number is ranging from 5-50 repeats.

Read the article: Sex differentiation

SNP (Single Nucleotide Polymorphism)

SNP is the most commonly observed polymorphism in the genome. Under the influence of some environmental condition, chemical or radiation, millions of SNPs are arisen and repaired daily, however, it depends on the type of the origin of SNP. Most probably, if it is in the non-coding region, it is safe and can be repaired.

Though SNP is easily detected and repaired by DNA repair mechanism, some life-threatening disorders occur as a result of SNP. Thalassemia, sickle cell anaemia and cystic fibrosis are the most common type of genetic disorders, originated due to SNPs.

SNP analysis is most commonly used in linkage disequilibrium studies, haplotyping and disease trait identification. In the future, SNP may be a useful tool for personalized medicine.

STR (Short Tandem Repeats)

Short tandem repeats are another type of tandem repeat marker but it is more specific and accurate than VNTR. For the identification of some important samples combination of STRs and VNTRs are used for a reliable result.

Structurally, it is 1-6 bp long and 5-50 repeats are present. It is a kind of microsatellite. The short repeats are dinucleotide, trinucleotide or so on. But dinucleotide repeat is most common in the human genome. Approximately 1 lakh dinucleotide repeats are present in non-coding microsatellites.

Attend class: Mutation

Other common markers are SSR (simple sequence repeat), AFLP (amplified fragment length polymorphism), SSLP ( simple sequence length polymorphism) which are important in genetic research and diagnosis.

Genetic markers can be widely used in cancer genetics, ARMS PCR, disease diagnosis, carrier detection, heterozygous and homozygous identification, maternal cell contamination, paternity verification, linkage analysis, population genetics and plant breeding programs.


Article written by: Tushar Chauhan

Article reviewed by: Ravi Parmar