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Genetic markers

Genetic marker types
• Morphological marker
• Molecular marker
1
...
DNA marker

MOLECULAR MARKERS

DNA-based Molecular marker
• A DNA sequence that is readily detected and whose
inheritance can be easily monitored
...

• A marker is a gene of known function and location, that
allow the studying of the inheritance of the gene
...

• NB: polymorphism involves existence of different forms of
same gene in plants or population of plants
...
e
...

* Co-dominant inheritance: allow the discrimination between

homozygotes from heterozygotes
* Occurs frequently throughout the genome
* Highly reproducible: can be analyzed by different persons in

different labs
* Easy, fast and cheap to detect
* Selectivity neutral: all alleles have the same fitness
* High resolution with large number of samples

Desirable properties for a good molecular marker
*Not epistatic: one can determine the genotype of a phenotype
irrespective of the genotype of the other loci
...

* Evenly distributed throughout the genome
...


Co-dominant marker
Gel configuration
P1

P2

O1

O2

Dominant marker
P2

O1

Polymorphism
Parent 1 : one band

Gel configuration
P1

Polymorphism
-Parent 1 : one band
-Parent 2 : a smaller band
-Offspring 1 : heterozygote =
both bands
-Offspring 2 : homozygote
parent 1

O2

-Parent 2 : no band
-Offspring 1 : homozygote parent 1
-Offspring 2 : ????

Dominant versus Co-dominant molecular markers
Dominant:
No distinction between homo- and heterozygotes
possible
...

• The technique is mainly based on the special enzyme called
Restriction Endonucleases
...

• Specific binding patterns can be visualized by hybridization
with labelled probes
...


•
•
•
•
•

It is a PCR based technology
...

This procedure detects nucleotide sequence polymorphism in DNA
...

In RAPD the decamer (10 bases) primers will or will not amplify a
segment of DNA depending on the positions that are complimentary to
the primer sequence
...

• Amplified products are separated on agarose gel in presence of ethidium
bromide (ETBR )and viewed under UV
...
e
...
For example, no
fragment is produced if primers annealed too far apart or 3'
ends of the primers are not facing each other
...


How RAPD works

Template
DNA

 Primer binds to many locations on the template
DNA
 Only when primer binding sites are close and
oriented in opposite direction so the primers point
toward each other will amplification take place

RAPD-When can amplification fail?

Template
DNA

Primers point away
from each other, so
amplification
won’t happen

RAPD-When can amplification fail?

Template
DNA

> 2,000 bases

Primers too far
apart, so
amplification
won’t happen

RAPD(Random Amplified Polymorphic DNA)
DNA markers which developed by amplifying random sequence
of specific markers through the used of random primers

Random Amplified Polymorphic DNA (RAPD)

RAPD Polymorphisms among landraces of sorghum
Sequences of 10-mer
(10 nucleotides) RAPD
primers

RAPD gel configuration

Primer name

OP A08
OP A15
OP A 17
M
OP A19
OP D02

Primer Sequence

5’ –GTGACGTAGG- 3’
5’ –TTCCGAACCC- 3’
5’ –GACCGCTTGT- 3’
5’ –CAAACGTCGG- 3’
5’ –GGACCCAACC- 3’

Advantages of RAPD
 Amplifies anonymous stretches of DNA using arbitrary primers
...
Nearly all RAPD markers are dominant, i
...
it is not possible to distinguish
whether a DNA segment is amplified from a locus that is heterozygous (1
copy) or homozygous (2 copies)
...

2
...
Thus, the RAPD technique is
notoriously laboratory dependent and needs carefully developed laboratory
protocols to be reproducible
...
Mismatches between the primer and the template may result in the total
absence of PCR product as well as in a merely decreased amount of the
product
...


Microsatellites (SSR)

Microsatellites (SSR)
• The term microsatellites was coined by Litt & Lutty (1989)and it is
also known as Simple Sequence Repeats (SSRs)
...

• Microsatellite markers, developed from genomic libraries, can
belong to either the transcribed region (exons) or the non
transcribed region (introns) of the genome
...

• If nucleotide sequences in the flanking regions of the microsatellite
are known, specific primers can be designed to amplify the
microsatellite by PCR
...


Microsatellites (SSR)

Microsatellites (SSR)
5 repeats of ACT

DNA
ACT

ACT

ACT

ACT

ACT

4 repeats of ACT

DNA

ACT

ACT ACT

ACT

31

Microsatellites (SSR)
DNA markers which developed by amplifying microsatellite in
the genome
Sequence
ACTGTCGACACACACACACACGCTAGCT
TGACAGCTGTGTGTGTGTGTGCGATCGA

Primer
(AC)7

ACTGTCGACACACACACACACACGCTAGCT
TGACAGCTGTGTGTGTGTGTGTGCGATCGA

(AC)8

ACTGTCGACACACACACACACACACACGCTAGCT
TGACAGCTGTGTGTGTGTGTGTGTGTGCGATCGA

(AC)10

ACTGTCGACACACACACACACACACACACACGCTAGCT
TGACAGCTGTGTGTGTGTGTGTGTGTGTGTGCGATCGA

(AC)12

Primers anneal to the flanking regions
of microsatellites
Forward primer

ACT

ACT

ACT

ACT

ACT

R

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