MOLECULAR MARKERS

TYPES AND
APPLICATIONS

V. M. PRIYADARSHINI
I Ph. D., (Horticulture)
2050190002
MARKER
A marker is a DNA
sequence with a known
physical location on a
chromosome.
 WHAT IS AN IDEAL MARKER?

• Highly Polymorphic in nature.

• Co-dominant inheritance
• Frequent occurrence in genome.
• Selective neutral behaviour.
• Easy access.
• Easy and fast assay.
• High reproducibility.
• Easy exchange of data between laboratories.
 CYTOLOGICAL MARKERS

Any distinct or heritable feature of chromosome

structure that can be used to follow the chromosome or
chromosome region in breeding experiments.
 BIOCHEMICAL MARKERS
• Markers related to protein and amino acid variations.

Biochemical markers:

• Monoterpenes – role in disease resistance and pest

attack

• Allozymes – controls metabolic activity of organism

• Isozymes – different variants of the same enzyme having

identical function and present in same individual.
 MOLECULAR MARKER
• Molecular marker is a DNA or gene sequence within a recognized
location on a chromosome which is used as identification tool.

• In the pool of unknown DNA or in a whole chromosome, these

molecular markers helps in identification of particular sequence of
DNA at particular location.

• Molecular marker is identified as genetic marker.

• Unlike morphological markers, abundant in number and

phenotypically neutral.
CLASSIFICATION OF MOLECULAR
MARKERS

PCR BASED TECHNIQUES

1. RAPD - Random Amplified Polymorphic DNA

2. AFLP – Amplified Fragment Length Polymorphism
3. ISSR – Inter-Simple Sequence Repeat
4. SSR – Simple Sequence Repeats
5. SCAR – Sequence Characterized Amplified Region
6. CAPS – Cleaved Amplified Polymorphic Sequence
7. SNP – Single Nucleotide Polymorphism
NON – PCR BASED TECHNIQUES/ HYBRIDIZATION:

1. RFLP – Restriction Fragment Length Polymorphism

2. VNTR – Minisatellites or Variable Number of

Tandem Repeats.
 CLASSIFICATION OF MARKER SYSTEM
MARKER SYSTEM ABBREVIATIONS USEFUL/SPECIFIC FEATURES

A. First- generation marker based on restriction fragment detection

RFLP Restriction fragment length polymorphism Physical mapping of genes

B. Second – generation markers based on PCR

RAPD Random amplified polymorphic DNA Gene tagging

AFLP Amplified fragment length polymorphism Gene tagging

SSR Simple sequence repeat (microsatellite) Highly informative mapping

STS Sequence tagged sites Gene mapping

SCAR Sequence characterized amplification region Gene tagging & physical mapping

CAPS Cleavage amplification polymorphism Allelic diversity

MARKER SYSTEM ABBREVIATIONS USEFUL/SPECIFIC FEATURES

C. Third- generation marker based DNA sequencing

SNP Single nucleotide polymorphism High throughput system

D. Gene scanning for expressed genes

EST Expressed sequence tag

SRAP Sequence – related amplified polymorphism

TRAP Target recognition amplification protocol

E. Markers using array technology

Microarrays (arrangements of small spots of DNA fixed to Whole genome scanning
glass slides)

(DArT) Diversity array technology Dominant marker, germplasm

characterization
 RFLP

Restriction Fragment Length Polynorphism (RFLP) – 1970’s

& 1980’s.

DEFINITION:

Genetic markers resulting from the variation or change in

the length of defined DNA fragments produced by digestion
of the DNA sample with restriction endonucleases.
PROCEDURE

Isolate high quality DNA

Digest with a combination of restriction enzymes

Fractionate digested samples by electrophoresis

Transfer fragments to membrane

Hybridize with radioactively labeled DNA probe(s) detect by

autoradiography.
ADVANTAGES AND DISADVANTAGES OF DIFFERENT MARKERS
CHARACTERISTICS OF DIFFERENT MARKERS
 APPLICATIONS
• Gene mapping

• Detect alterations in sequence of DNA.

• Determine different characters in DNA.

• Genetic diversity.

• Finger printing.

• Genotypic pyramiding.

• Marker – Assisted Selection.

• Identification of Genotype.