What is a Molecular Marker? 

A known DNA sequence or gene sequence is present on a chromosome, and it is associated with a specific trait or character. It is mainly used as a genetic marker of the molecular marker. The first genetic map was done in a fruit fly, using genes as the first marker. In two categories, molecular markers are classified, classical marker and a DNA marker. A molecular marker is also known as a genetic marker. 


The process of finding differences in the genetic make-up of individuals is genotyping. First, through genotyping, single nucleotide polymorphism is identified. Then, through genotyping, the difference in the DNA sequence is identified. 

The collection of genes is genotype. The genotype is responsible for giving any trait to organisms. 

Types of Classical Marker 

Morphological Markers 

The morphological marker is also known as a visible marker. Phenotypic traits or characters such as the color of the flower, the shape of the seed, pigmentation, and growth habits are visually characterized by the morphological marker. Morphological markers are not associated with quality and yield. Instead, environmental factors affect these markers. 

Cytological Marker 

The cytological markers represent unique structural features of chromosomes like bands, secondary constrictions. For the characterization of normal chromosomes and detection of chromosomal mutation, its features are used. In addition, it is widely used in the mapping and identification of linkage groups. However, cytological markers are rarely used. 

Biochemical Marker 

Biochemical markers are gene products. It can be easily identified by electrophoresis and particular staining. Isozymes and allozymes are enzyme variants that are commonly used as biochemical markers. Allozymes are enzymes, and different alleles encode them; they have the same function or catalytic activity. By using electrophoresis, allozymes can be separated. Other separating techniques are also used, which separates based on shape, size, and charge. Allozymes and isozymes are different. Enzymes that perform the same catalytic function but different non-allelic genes encode them are known as isozyme. Protein markers are biochemical markers. They are present in a limited number.

DNA Marker 

A DNA marker is a specific segment of DNA by which differences at the genomic level are represented. DNA marker is also known as molecular marker. DNA marker and protein marker both are molecular markers. DNA markers do not have any biological effect. Therefore, they are not considered normal genes. However, they are easily identified and are located at particular locations of the genome. The common law of inheritance does the transmission of DNA markers from generation to generation. 

An ideal marker should have the following characteristics. 

  • It shows a high degree of polymorphism. 
  • It is present in the whole genome in an even way. 
  • Its expression is codominant. 
  • In distinct phenotypes, the linkage is present. 

Types of Molecular Marker 

Various types of molecular markers are present. In two classes, they have been divided based on their detection method. 

Hybridization-based (RFLP) 

RFLP: RFPL is Restriction Fragment Length Polymorphism. It is the hybridization-based molecular marker. In 1975 it was first used for the identification of DNA sequence polymorphisms for genetic mapping. However, due to mutation, the sites identified by particular restriction enzymes can be created or destroyed; that is why RFLP arises, ultimately leading to differences between individuals in the length of restriction fragments produced from identical genome regions. 


The PCR-based are sub-divided into two subcategories. 

  • Sequence non-specific techniques such as RAPD, AFLP. 
  • Sequence targeted PCR-based techniques such as SSLP, SNP. 
  • A polymerase chain reaction amplifies genomic DNA. Therefore, after the isolation of genomic DNA from organisms, it is amplified. 

RAPD: RAPD is known as Random Amplification of Polymorphic DNA. It is a kind of PCR. PCR is a polymerase chain reaction. In this, random fragments of DNA are amplified. In RAPD, the information about the DNA sequence of target organisms is not known. Primers used are short, and the template of genomic DNA is large. The targeted gene sequence is not known. The binding of the primer is random.  

The quality and quantity of template DNA influence the reproducibility of RAPD.  

AFLP: AFLP is known as Amplified Fragment Length Polymorphism. AFLP is developed to overcome the limited reproducibility of RAPD. The preliminary information about DNA sequence is not required in AFLP. Therefore, the reliability and reproducibility of AFLP are high. In AFLP, the first step is by using restriction enzymes digestion of genomic DNA. Designing a double-stranded oligonucleotide adaptor is done so that after ligation, the restoration of the initial restriction site cannot be done. The adaptors are ligated at both ends of fragments to be used as a known fragment for identification in PCR amplification. When primers can anneal the fragments, PCR amplification can be done.  

SSLP: SSLP is (Simple Sequence Length Polymorphisms). It is an arrangement of repeat sequences that shows high variations. Two types of SSLP are present. 

  • Minisatellites: It represents a Variable Number of Tandem Repeats. In this, up to 25bp repeat units are present. Many alleles are present in minisatellites and show high heterozygosity. The distribution of minisatellites is not even across the genome. For the construction of QTL mapping, genetic linkage maps, marker-assisted selection SSR is widely used. SSR is a polymorphic marker 
  • Microsatellite: It is also known as Short Tandem Repeat Polymorphism. In microsatellites, the repeats are shorter. A microsatellite is hyper-variable, high reproducibility, specificity for locus. Microsatellites can easily be analyzed by PCR and easily detected by PAGE. In microsatellite, primer designing information about nucleotides should be known. The microsatellite is used in the construction genetic linkage map. The microsatellite is used in marker-assisted selection. 

SNP: SNP is (Single Nucleotide Polymorphisms). It is a place in the genome where an individual is seen with one nucleotide different from another nucleotide. In every genome, a large number of SNPs are present. From these SNPs, RFLP also arises sometimes. SNPs are generally present in the non-coding region. It may be present in introns or intergenic sequences. In molecular markers, the most abundant contribution is done by SNPs. For an individual to qualify as polymorphic, at least 1 % of an individual's SNPs should be present. Due to base-pair substitution mutation, SNPs arise.  It is a codominant marker linked to genes. It is a very potential genetic marker in the study of genetics and breeding. SNP shows high efficiency for identifying polymorphism. It is also known as a new generation marker. 

Context and Application 

This topic is important for various examinations 

  • Bachelors in botany and zoology 
  • Masters in botany and zoology 

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