Geoscience Reference
In-Depth Information
table 17.1
Comparisons of the most commonly used molecular markers in plants
S. no.
Feature
RFLP
RAPD
AFLP
SSRs
SNPs
1
DNA require
(μg)
10
0.02
0.5-1.0
0.05
0.05
2
DNA quality
High
High
Moderate
Moderate
High
3
PCR based
No
Ye s
Ye s
Ye s
Ye s
4
Inheritance
Co-dominant
Dominant
Dominant
Co-dominant
Co-dominant
5
No. of
polymorphic
loci
1-3
1.5-50
20-100
1-3
1
6
Ease of use
Not easy
Easy
Easy
Easy
Easy
7
Amenable to
automation
Low
Moderate
Moderate
High
High
8
Reproducibility
High
Low
High
High
High
9
Development
cost
Low
Low
Moderate
Moderate
High
10
Cost per
analysis
High
Low
Moderate
High
Low
The first official recognition of RFLP came from viruses
(Grodzicker et al. 1975), followed by a subsequent demonstra-
tion made in the human-globin gene cluster (Jeffreys 1979).
Since then, most organisms have been used for the presence
of RFLP, and the application of this technology has evolved
in various fields. Subsequent to RFLP, several other methods
such as variable number of tandem repeats, allele-specific oli-
gonucleotide, allele-specific polymerase chain reaction (PCR),
oligonucleotide polymorphism, single-stranded conformational
polymorphism (SSCP) and sequence-tagged sites (STS) have
been documented. The PCR-based assay has evolved and can
detect variations at the DNA level by replacing conventional
hybridisation-based assay of detecting DNA-level variations.
Second-generation molecular markers
The second-genera-
tion molecular markers are microsatellite arrays of tandemly
repeated di-, tri-, tetra- and penta-nucleotide DNA sequences,
which are dispersed throughout the genomes of all eukaryotic
organisms investigated to date. These markers are responsi-
ble for various revolutions in the field of molecular breeding.
The microsatellites are also called as sequence-tagged micro-
satellite sites or SSRs. Currently, SSRs are considered as the
molecular markers of choice within the genome mapping com-
munity and are frequently being adopted by plant researchers
