P.Pandiyammal @ Subathra III B.sc Biotechnology Ayya Nadar Janaki Ammal College, Sivakasi, Tamilnadu.

1. P.Pandiyammal @ Subathra
18UT12
III B.sc Biotechnology

2.  Definition
 Types of markers
 DNA / Molecular markers
 Non PCR Based markers
 RFLP
 PCR Based markers
 RAPD
 AFLP

3.  Characters which can be easily identified are referred to
as marker characters.
 A trait that is polymorphic, easily and reliably identified,
and readily followed in segregating generations and
indicates the genotype of the individuals that exhibit the
trait is called a genetic marker.
 These are character whose pattern of inheritance can be
followed at morphological, biochemical and molecular
levels.

5. Non-PCR Based
 RFLP- Restriction fragment length polymorphism.
PCR Based
 RAPD- Random amplification of polymorphic DNA.
 AFLP-Amplified fragment length polymorphism.
 SCAR-Sequence characterize amplified region.
 STS- Sequence tagged sites.
 EST-Express sequence tags.
 SNP-Single nucleotide polymorphism.
 SSR-Simple sequence repeats
 CAPS-Cleaved amplified polymorphic sequences.

6.  The DNA-based markers represent variation in
genomic DNA sequences of different individuals.
 They are based on naturally occurring polymorphism
in DNA sequence i.e., base pair addition, deletion,
substitution.
 They are detected as differential mobility of
fragments in a gel, hybridization with an array or
PCR amplification, or as DNA sequence differences.
 They are used to ‘flag’ the position of a particular
gene or the inheritance of a particular character

7. RFLP signifies that a single restriction enzyme generates fragments
differing in lengths from the same genomic regions of different
individuals/strains/lines of a given species or of different species.
Strengths:
 Simple technique
 Co dominant
 highly reproducible
Weaknesses:
 Requires large quantities of
high molecular weight DNA.
 Expensive, time consuming
and labor intensive
 uses radioactive probes that
are hazardous.

8. RAPD refers to polymorphism found in the randomly amplified
fragments of DNA generated by using single DNA primer of
arbitrary sequence.
Strengths:
 Simple and quick
 Primers are readily available
 very small DNA samples
Weaknesses:
 polymorphism is limited
 dominant markers in nature
 Reproducibility of results is
low

9. Any difference in the restriction fragment lengths that is detected by
selectively amplifying a pool of restriction fragments using PCR.
Strengths
 Requires small quantities of DNA
 No sequence information required
 Can be applied to any organism
 highly reproducible
 Amenable for automation
Weaknesses
 Dominant markers
 Requires very high quality DNA
 Technically challenging
 Fluorescent AFLPs are difficult to
interpret