Simple Sequence Length Polymorphism (SSLP)


Molecular markers also called genetic markers can be defined as the part of DNA that provide specific information about a certain location in the genome. In a pool of unknown DNA, they are used to locate the sequence of interest. Molecular markers are used in the field of genetics for linkage analysis and also diagnosis of certain diseases.

There are many types of molecular markers of which simple sequence length polymorphism is a type that uses polymerase chain reaction. Polymorphism refers to the condition in which two or more variants of a particular DNA sequence are present in different individuals. The most prevalent type of polymorphism is the variation at single nucleotide sequence which is referred to as simple sequence length polymorphism.

Simple Sequence Length Polymorphism (SSLP)

Simple sequence length polymorphism can be defined as variation found in a single nucleotide sequence in genomic DNA. This technique uses PCR amplification and is generally used to study the genetic linkage between two individuals of the same species or different species. They are also referred to as microsatellites.

Characteristic Features of SSLP

  • They are generally short sequences of length in the range of 1 to 6 base pairs. That is why they are also called microsatellites.

  • They can be found in many locations in the genome which ranges up to 1000.

  • They generally have hypermutable sites which can lead to the diversity in organisms. These are rich in guanine and cytosine residues which are tandemly repeated several times.

  • They are found in the non-coding regions so they do not code for any protein but control the expression of genes in the coding regions.

  • They can be found in the form of dinucleotide repeats like TATATA repeated around 45-50 times or can be found as trinucleotide repeats like GTCGTCGTC repeated many times.

  • The mutations that occur in these regions may not produce any variations and can be passed from one generation to another unhindered because of their presence in the non-coding regions. But the variations produced in these regions can be utilized in the DNA fingerprinting of the organism.

  • SSLP that are present in the flanking regions that is the regions present near the borders of the 5’ end of the transcription unit can be used in the diagnosis of certain diseases.

Effects of SSLP Mutations

  • SSLP mostly occurs in the non-coding regions of a DNA and can pose no changes after the mutations also but if mutations occur in SSLP that are found in the coding regions it can result in changes in the phenotype of the organisms or may even lead to some diseases.

  • If mutations occur in the protein coding regions it can cause changes in the properties of the proteins that can result in inactive proteins or proteins with altered function which can in turn cause certain abnormalities.

  • Mutations in the SSLP of the intron region can cause phenotypic changes which have to be studied deeply and also, they can cause leukemia or sarcomas.

Procedure for SSLP Analysis

  • First DNA is extracted from the nucleus by lysing the cell using a suitable detergent. Then the DNA is purified to get rid of the cellular debris, proteins, and RNA attached to it.

  • The specific polymorphic regions are then analyzed using a polymerase chain reaction in which primers are selected based on the sequences of the flanking region.

  • DNA is denatured at high temperature and then cooled this assist in the annealing of the primer to the single-stranded DNA. Then amplification is done by selectively programming the PCR cycle. Once amplification is done DNA fragments are resolved using agarose gel electrophoresis.

  • As DNA molecules are negatively charged, they will move towards the positively charged anode and get separated, which can be visualized using dye like ethidium bromide.

Limitations of SSLP

  • More error prone as primers get attached to alternate sites, which leads to incorrect scoring.

  • If the primers of interest are not available, the whole procedure will become expensive.

  • Sometimes, because of converging evolution some characters may be present in some divergent species but may be absent in common ancestor. This condition is known as homoplasy.

Applications of SSLP

  • Mutations in the flanking sequences can be determined using SSLP. This will help in the diagnosis of several diseases like leukemia, colorectal cancer, sarcoma, etc. They can also be used to detect the progression of tumor cells.

  • They can be used in DNA profiling or genetic fingerprinting of an individual. This is helpful in paternity testing and the determination of criminals from a very minute sample.

  • SSLP have been used to study the linkage of certain closely related species and their evolution.

  • SSLP has been widely used in plant breeding programs to study the linkage of the trait of interest like disease resistance, quality of yield, etc.


In recent years, new research and advancements in the field of molecular biology led to the use of codominant markers like single nucleotide polymorphism (SNPs), simple sequence length polymorphism (SSLP), etc. But still, some areas need to be explored in relation to sequences of wild plant varieties and cultivated varieties, and deeper research in this field can lead to better crop development.

Updated on: 17-May-2023


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