Marker and its Application in Crop Improvement
Authors: Prasenjit, D., Anirudha, S. K., Gautam, V., Jaya, B. and Sonam, M.
Sr. M.Sc.(Agri.), Dept. of Biotechnology, UAS, Dharwad, Karnataka, PIN-580005
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Recent generation is facing a threat of food security because of an unprecedented increase in population and decrease in cultivable land. Conventional breeders are doing their best to get the ultimate yield from the crop varieties but nowadays global warming and other constraints like biotic and abiotic factors have also shown up those create a huge problem. So to overcome all these mess; molecular breeders have taken the assistance of different biotechnological tools, among which the genetic markers are the most exploited ones.

From the last two decades, the world has witnessed an exponential increase in the number of gene sequences available in the nucleotide sequence databases of plants and our understanding of molecular and physiological roles of these genes is increasing day by day.

Genetic markers are a bunch of advanced key players in the ‘genomics era’ of agriculture breeding. A Genetic marker is a molecular tool that differentiates between various traits of any particular character within individual organisms or species. Generally, they do not represent the target genes themselves but act as a ‘sign’ or ‘‘flag’ at a nearby location of the gene/genes. Genetic markers that are located in close proximity of genes (i.e. tightly linked) may be referred gene ‘tags’. Such markers themselves do not affect the phenotype of the trait of interest because they are located only near or ‘linked’ to genes controlling the trait.

Presence or absence of a marker indicates the presence or absence of a particular gene. Marker is a piece of DNA molecule that is associated with a certain trait of an organism which is used as a land mark or tag or benchmark showing the presence of that trait within the genetic backbone of the organism.

Mainly markers are classified in to three different categories like phenotypic marker, cytological marker, biochemical marker and molecular marker.


Different types of markers

Phenotypic marker

These are the traditional markers. Morphological mutant traits in a population are mapped and linkage to a desirable or undesirable trait is determined and indirect selection is carried out using the physically identifiable mutant for the trait. There are several undesirable factors that are associated with morphological markers.

Advantages of phenotypic marker

1. Readily available
2. Require simple equipment to screen
3. Visible to naked eyes.

Disadvantages of phenotypic marker

1. They usually exhibit dominance, sometimes they exhibit deleterious effects.
2. They exhibit pleiotropy and epistasis.
3. They exhibit less polymorphism, need experts.
4. Number of this type of markers is less eg.,seed coat colour, flower colour, fruit shape.
5. They are highly influenced by the environmental factors. Often the environmental condition can influence the expression of a particular characteristics which leads to a selection of false positive plants.
6. Limited genomic coverage.
7. Performing breeding experiments with phnotypic marker is labour intensive, time consuming, cost effective, required lots of plant population to screen to detect the desirable plants.

Cytological marker

Markers that are related to variation in chromosome number, shape, size and banding pattern are referred to as cytological markers. In other words, it refers to the chromosomal banding produced by different stains; for example, G banding.

Advantages of cytological marker

1. Readily available
2. Requires small equipments

Disadvantages of cytological marker

1. Limited in number
2. They exhibit less polymorphism, need experts.

Biochemical marker

Proteins are products of gene action. The product of a gene can be used as a marker for the presence of a gene. Different alleles of a gene may produce different proteins. Sometimes, different forms of a protein with same catalytic activity but with different molecular weight and electrophoretic properties may be produced by different alleles. Such enzymes are called isozymes. The difference in enzyme mobility is caused by point mutations resulting in amino acid substitution. The differences in banding patterns observed on electrophoresis can be used for comparison and selection. Easily assayable isozymes have been widely used for the characterization of germplasm. However, the availability of useful protein markers is a limitation. Isozymes are used as biochemical markers in plant breeding. Isozymes are common enzymes expressed in the cells of plants. The enymes are extracted, and run on denaturing electrophoresis gels. The denaturing component in the gels (usually SDS) unravels the secondary and tertiary structure of the enzymes and they are then separated on the basis of net charge and mass. Polymorphic differences occur on the amino acid level allowing singular peptide polymorphism to be detected and utilized as a polymorphic biochemical marker.

Advantages of biochemical marker

1. Require simple equipments
2. A vigorous complement to the morphological assessment of variation.

Disadvantages of biochemical marker

1. The main weakness of allozymes is their relatively low abundance.
2. Low level of polymorphism.
3. Allozymes are in fact phenotypic markers and they may be affected by environmental conditions.
4. Profiling of a particular allozyme markers may change on the type of tissue used for the analysis.

Molecular markers (DNA-based markers)

Molecular markers have become important tools for genetic analysis and crop improvement. DNA-Markers, which are phenotypically neutral and literally unlimited in number, have allowed scanning of the whole genome and assigning landmarks in high density on every chromosome in many plant species. Different types of molecular markers have been developed.

Advantages of molecular markers among other markers

1. Molecular markers are more in number.
2. They are not influenced by the environment.
3. They are more reliable (marker should be tightly linked to target loci, preferably less than 5cM genetic distance).
4. Level of polymorphism is high.
5. Easily excessable marker sequences.
7. Highly reproducible.
8. Multiple alleles for each markers.

The main challenge for researchers lies in selecting one or more of these markers for their specific purposes. The ideal type of genetic marker should be highly polymorphic, show codominant inheritance and be evenly distributed throughout the genome. Molecular markers somehow full fill the requirements of scientist. Molecular markers are more reliable than other markers. So scientists are using these markers regularly during breeding programmes.

Different types of molecular markers are listed below-

Molecular marker are further divided in to two categories
1. Hybridization based marker
2. PCR based marker

1. Hybridization based marker :- The variation in the length of the DNA fragments generated by specific restriction endonucleases in two or more individuals is due to the difference in the pattern of occurrence of specific restriction sites (of the corresponding restriction endonucleases) on the genomic DNA detected in the hybridization experiment and thus the markers are called hybridization based markers.

Example : Restriction Fragment Length Polymorphism (RFLP)

2. PCR based marker :- Markers which shows polymorphism based on the pcr amplification is called PCR based marker.

Example : Simple Sequence Repeat (SSR) or microsatellites, Cleaved Amplified Polymorphic Sequences (CAPS), Amplified Length Polymorphism(AFLP), Sequence Characterized Amplified Regions (SCARS), Expressed Sequence Tags (ESTS), Single Nucleotide Polymorhism (SNPS ).


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3. Marker assisted Plant breeding-Principles and practices by B. D. Singh and A. K. Singh.
4. Anonymous, 2017,Genetic marker. Wikipedia: The Free Encyclopedia,

About Author / Additional Info:
M. Sc. Agri in Molecular Biology and Biotechnology, IABT, UAS Dharwad.
Research Area " Molecular Breeding.