this slides contains lots of information about molecular marker and their types

1. TOPIC – MOLECULAR MARKER
Course no.-PBG 401 & 402
Submitted to:
Dr.Shalini Purwar
Submitted By:-
Gaurav verma
I.D.- 457

2. MARKER
Marker is an object used to mark or to
indicate a position , place or location
Types of marker:-
1.Morphological marker
2.Biochemical marker
3.Cytologgical marker
4.Molecular marker or DNA marker

3. Morphological marker
These are related to shape ,size ,colour and
surface of various plant parts.
Such character is used for the
varietal identification.
Demerits:-
1.They generally express late into the
development of an organism.
2.They usually exhibit dominance.
3.They exhibit pleiotropy and epistasis.

5. Biochemical marker
Such marker is related to variation in
protein and amino acid banding
pattern.
A gene encode a protein that can be
extracted and observed. Eg..—
isozymes and storage protein.
Gel electrophoretic studies are used
for identification of biochemical
markers.

6. Cytological marker
• Marker that are related to variation in the
chromosome number .,shape ,size and
banding pattern are referred to as the
cytological marker.
• Other words ,it refer to chromosomal
banding produced by different strains.
• Example :-G banding

7. DNA Marker
• A DNA marker is a small region of DNA
showing sequence polymorphism in
different individuals with in a species (or)
among different species.
• DNA marker is also known as molecular
marker or genetic marker.
• DNA marker is the most widely used type
of marker due to their abudence.

8. Types of molecular
marker
Two types of molecular marker:-
1. Non PCR based marker eg.- RFLP
2. PCR based marker eg;- RAPDs
AFLPs, SSRs, CAPs, SNPs, SCAR
etc…..

9. Restriction fragment length
polymorphisms (RFLP)
• First type of DNA marker developed in 1980
before the discovery of PCR and based on
southern hybridizing technique.
• This technique is based on restriction
endonuclease.
RFLP technique consist of three major techniques:-
1.- Cutting genomic DNA with specific restriction
enzymes.
2.-Seprating different size DNA fragment on
electrophoresis gel(Agarose) and
3.-Hybridizing a labelled radioactive DNA probe to
complementary DNA fragment on gel in order to
visualize them.

10. RFLP
Advantages of RFLPs:-
• Simple and cheaper technique
• It does Not required special instrumentation
• These are co-dominance and highly locus specific
• Help in the development of other marker like CAPS &
INDEL
Disadvantages:-
1. Required large amount of high quality DNA.
2. The multiplex ratio is low , 1 per gel.
3. Developing sets of probes and marker is labour
intensive.
Uses:-
1. can be used to determine the disease status of an
individual.
2. Used in gene mapping
3. Used in DNA fingerprinting

11. Random amplified
polymorphic DNA(RAPD)
• This is PCR based technology.
• In 1991 Welsh and maclelland developed this technique/
• This procedure detect nucleotide sequence polymorphism in
DNA.
• This is used to analyze genetic diversity of an individual by
random primer.
• The RAPD marker are dominant.
USES;-
1. For assessment of genetic variation in breeding populations,
germplasm,and different species of a cross.
2. For DNA fingerprinting of cultivars and germplasm.
3. For gene tagging and construction of linkage map.

12. Amplified fragment length
polymorphism (AFLP)
• It was developed by Zabeau and Vas in 1993.
• This technique provide very high multiplex ratio.
• This is Codominant type of marker.
• This technique is widely used in the construction
of genetic maps contaning high densities of DNA
marker.
• In plant breeding and genetics AFLP marker are
used in varietal identification ,germplasm
characterization ,gene tagging and marker
assisted selection.

13. Simple sequence repeats
(SSRs)
1. SSRs also called microsatellites.
2. The SSR marker tend to be highly polymorphic.
3. This is simple PCR based technique.
4. Most of the SSR marker are Co dominant and
locus specific.
5. The SSR marker can be multiplexed using PCR.
6. The use of microsatellites or SSR marker has
been proposed for genetic mapping of
eukaryotes (Backman and Soller)

14. Single Strand Conformation
polymorphism (SSCPs)
1. This is simple PCR based assay.
2. Most SSPs are co dominant and locus specific.
3. Many SSCPs marker are multi allelic and highly
polymorphic.
4. SSCPs have been widely used in human genetics
to screen disease genes for DNA polymorphism.
5. SSCP analysis can be a powerful tool for
assessing the complexity of PCR products.

15. Single nucleotide
polymorphisms (SNPs)
• These are highly polymorphic and mostly biallelic.
• These are locus specific
• Small ammount of DNA is required for SNPs.
• SNP are useful in gene mapping and identification
of disease causing genes.
• SNPs are being used in generating genetic maps.
• In plant SNPs have been not extensively used so
far.
• Development of SNPs is the labour oriented.

16. Expressed sequence
Tags (EST)
• Expressed sequence tags are the small
piece of DNA and their location and
sequence are known .
• This term is 1st used by Venter and
Colleagues in 1991.
• EST are the commonly used to map gene of
known function.
• ESTs are used for polygenetic studies.

17. Sequence tagged sites
(STS)
• STSs is a short DNA sequence that has copy in a
genome and whose location and base sequence are
known.
• STSs are usually 200- 500 base pair long.
• STSs is derived from cDNAs.
• STSs is most powerful physical mapping
technique.
• STSs are used as standard marker to find out the
gene in any region of the genome.
• It is used for constructing detailed map of large
genome.

18. Sequence characterized
amplified region (SCAR)
• SCAR are DNA fragment amplified
by the PCR using specific 15-30 bp
primer designed from nucleotide
sequence established from cloned
RAPD fragments linked to a trait of
interest.
• low quantity of temple DNA is
required.

19. SCAR
• Strength:-
high reproducibility and locus
specific.
. Application:-
Gene mapping studies and in marker
assisted selection
used in quarantine department for
checking of disease.

20. Reference
• Principal of biotechnology notes of
NG ranga university.
• Wikipedia
• Slide share
• Plant Biotecnology by Phundan singh
• Biotechnology by B D Singh
• Class notes