3. • A molecular marker is a molecule
containing within a sample taken from an
organism or other matter
4. • A genetic marker is gene or DNA
sequence with a known location on a
chromosome that cam be used to
identify individual or species
• It may be a short DNA sequence
5. Should be easy, fast and cheap to detect
Should be reproducible
Should be polymorphic
Should have co-dominant inheritance to
allow discrimination between homo and
heterozygote in diploids
6. RFLP - Restriction Fragment Length Polymorphism
AFLP - Amplified Fragment Length Polymorphism
RAPD - Random Amplification of Polymorphic DNA
SSLP - Simple Sequence Length Polymorphism
7. VNTR - Variable Number Tandem Repeats
SSR - Simple Sequence Repeats
SNP - Single Nucleotide Polymorphism
STR - Short Tandem Repeats
RAD - Restriction site Associated DNA
8. RFLP
• Termed by Botstein-1980
• Combination of a probe and restriction
enzyme (RE) to identify polymorphic
DNA sequence using Southern blotting
9. STEPS
1. DNA is isolated
2. DNA is digested with RE
3. Electrophoresis
4. Blotted on a membrane and probed with a
labeled clone
5. The fragments to which the probe has
hybridized are detected by autoradiography
12. RAPD
• PCR based molecular technique
• It is used to analyze the genetic
diversity of an individual by using random
primers
13. STEPS
1. An arbitrary oligonucleotide primer, usually 9 to 10
bp long is added to a sample of plant chromosomal
DNA
2. It will pair with the chromosomal DNA at many
sites, sometimes including opposite strands on the
target DNA
3. DNA region will be amplified via PCR
4. Products are by visualized following polyacrylamide
gel electrophoresis
5. Analysis of data
14.
15. ADVANTAGES
The same (universal) set of
oligonucleotide primers can be used for
all plant species
No genomic libraries, radioactivity,
Southern transfers, or DNA
hybridization reactions are required, so
a large number of samples may be easily
and rapidly characterized
The process can be automated
17. • It involves PCR amplification of genomic
restriction fragments generated by
specific RE and oligonucleotide adaptors
of few nucleotide bases
18. STEPS
1. DNA fragments obtained from digestion
with restriction enzymes
2. Ligation of oligonucleotide adapters to
the digestion products
3. Selective amplification by the PCR
4. Gel electrophoresis
5. Analysis of data
19.
20. RAPD RFLP
1.Quantity of DNA required for analysis is
small(10-50 ug )
1.Large quantity of purified DNA required
i.e.2-10 ug
2.Same primers with arbitrary sequence
can be used for different species
2.Different species specific probes are
required
3.Fewer steps in procedure therefore it is
rapid
3.Comparitively slower processing due to
more steps involved
4.Technique comparatively less reliable 4.Technique comparatively reliable
5.Cannot detect allelic variants 5.Can detect allelic variants
6. 1-10 loci detected 6. 1-3 loci detected
7.Method involves
a) Extraction of DNA
b) Amplification by PCR using
random primers
c) Gel electrophoresis of amplified
DNA and visualization of markers
7.Method involves
a) Digestion of extracted DNA by
restriction enzymes
b) Gel electrophoresis
c) Southern blot