Types of molecular markers (genetics) ITS ADVANTAGES AND DISADVANTAGES What is a genetic marker? RFLP: Restriction fragment length polymorphism AFLP: Amplified fragment length polymorphism RAPD: Random amplification of polymorphic DNA ISSR: Inter simple sequence repeat STR: Short tandem repeats SCAR: Sequence characterized amplified region SNP: Single nucleotide polymorphism SSR: Simple sequence repeat

1. TYPES OF MOLECULAR
MARKERS
Submitted by MOHAMMED ANFAS K T
anfasnellikuth@gmail.com
https://www.linkedin.com/in/mohd-anfas-5409431a0

2. MOLECULAR MARKERS
Molecular markers are specific fragments of DNA that can be
identified within the whole genome
Molecular markers are found at specific locations of the genome
They are used to 'flag' the position of a perticular gene or the
inheritance of a perticular character
Molecular markers are phenotypically neutral

4. RFLP: Restriction fragment length polymorphism
Restriction fragment length polymorphism (RFLP) is a type of polymorphism
that results from variation in the DNA sequence recognized by restriction
enzymes.
With the help of the Restriction digestion by REase, alterations in the same/
homologous DNA sequences can be detected by analysing fragments of
different length, digested with a restriction enzyme.
A single restriction endonuclease gives more specific results by cutting at one
specific locus and produces fragments of different length.

5. RFLP: Restriction fragment length polymorphism
Advantages
1. High reproducibility
2. Show Codominent allele
3. Detect coupling phase of DNA
4. Reliable marker in linkage and breeding analysis
5. Easily determine a linked trait present in both homozygous and
heterozygous

6. RFLP: Restriction fragment length polymorphism
Limitations
1. Require large quantities of high molecular weight DNA
2. Expensive process
3. Time consuming
4. Labour intensive
5. Ratio active probe

7. AFLP: Amplified fragment length polymorphism
The AFLP technique was developed by Zabeau and Vos in the
year 1993. The method is based on the amplification of the
selected fragments followed by the digestion of the total
genomic DNA of the selected organism.
The process of the AFLP is restriction digestion of the
genomic DNA, adapter ligation of the digested DNA fragments
and amplification of DNA fragments in PCR using the adapter
specific primers.
The method was originally developed by the keygen in 1990.

8. AFLP: Amplified fragment length polymorphism
Advantages
No prior sequence information is required in the AFLP.
Also, the sensitivity, reproducibility and resolution of AFLP
marker are higher as compared with other markers.
Disadvantages
The AFLP marker is not co-dominant hence it can not
distinguish homozygous from the heterozygous.

9. RAPD: Random amplification of polymorphic DNA
By using the short, arbitrary DNA primers, the part of the genomic
DNAs is randomly amplified.
Pronounced as a “rapid”, it does not require any previous
sequence information, the primer of 8 to 12mer randomly amplifies
the region of the genomic DNA.
If any mutation or alteration occurred in the region of the primer
binding site, the primer can not bind to that location or the
amplified fragment length decreases or increases.
A different pattern of amplification is observed in different sample
types. Hence the RAPD can help in the polymorphism studies.

10. RAPD: Random amplification of polymorphic DNA
Advantages
1. The RAPD markers are abundantly present into the genome
and are distributed throughout the genome.
2. No previous sequence information is needed.
3. It can amplify low quantity of DNA.

11. RAPD: Random amplification of polymorphic DNA
Disadvantages
1. The marker is not locus-specific.
2. The sensitivity of the RAPD is also lower.
3. The reproducibility is also very low.
4. Homozygous and heterozygous are not easily distinguished.
5. The RAPD results are difficult to interpret because the short
primer can amplify any of the random sequences presents into
the genome.

12. ISSR: Inter simple sequence repeat
The ISSR marker is the inter simple sequence repeat, the method
is based on the PCR agarose gel electrophoresis, detected using
the single primer amplification reaction.
Between the oppositely oriented microsatellites, the sequence of
100 to 3000bp fragment of a sequence is called the ISSR.
Here the advantage of using the ISSR is that no prior sequence
information is required for constructing the primers.
Multiple loci are amplified because of the random distribution of
ISSR within the genome.

13. STR: Short tandem repeats
The short tandem repeats/ simple sequence repeats are also called
a microsatellite. The microsatellite is the shorter repeats
sequences present into genome thousands or millions of times.
In other words, we can say that the STRs are tandem repeats but
are much shorter than the VNTR. The repeats in STR are 2 to 6
base pairs per repeats.
The STR is highly polymorphic, the number of repeats differs
between individuals even though the loci are homologous.
Because of this reason, the STR marker is the first choice in
forensic analysis.

14. SCAR: Sequence characterized amplified region
The SCAR stands for sequence characterized amplified region.
It is easy to use, reliable and reproducible.
The present marker is based on the PCR-agarose gel
electrophoresis, uses longer primers of 15-30 nucleotides hence
the reproducibility increases anonymously.
It is a locus-specific and co-dominant marker.
Unlike the RAPD, it required sequence information for designing
the primer for SCAR.
It is widely used in the plant marker assistance selection studies.

15. SNP: Single nucleotide polymorphism
SNP is a single nucleotide polymorphism, type of unique marker in
comparison with other markers enlisted here.
Due to the addition or deletion of a single nucleotide in a genome, the SNP
originated.
Millions of SNPs are present in the genome, however, it may or may not be
pathogenic.
The SNP marker is used in the Genome-wide association studies.
By comparing the case and control groups, the association of particular SNP
associated with particular disease can be determined.

16. SSR: Simple sequence repeat
Simple sequence repeat is a microsatellite repetitive DNA
marker, typically ranging from 5 to 50 times in a genome.
The marker is highly variable. It is more similar to the short
tandem repeats. We had discussed STR in the above segment.
The SSR marker or the microsatellite marker is co-dominant and
restriction digestion is not involved in this process thus,
advantageous over the RFLP.
It is a marker based on the polymerase chain reaction.

17. THANK YOU
Submitted by MOHAMMED ANFAS K T
anfasnellikuth@gmail.com
https://www.linkedin.com/in/mohd-anfas-5409431a0