DNA Markers
It is estimated that each
chromosome has 108-1010 base pairs but only about 10% of
the genome is actively coding with the result that a bulk of the genetic
material remains unnoticed through phenotypic analysis. Furthermore, not much
of the coded information may be easily observable that restricts the mapping of
only a small fraction of the genome. The assessment of variation at the DNA
level provides, at least in principle, mapping of each and every point of the
entire genome. Specific spots on DNA molecule both in coding as well as non-coding
regions can be identified as markers. In fact, the detection of naturally
occurring DNA sequence polymorphism is the most attractive application of
molecular biology for the welfare of mankind. A DNA marker is a small region of
DNA showing sequence polymorphism in different individuals within a species or
group of individuals. The interest in DNA based markers started from
surprisingly highl level of variation for sequence changes in DNA from different individuals.
Random Amplified Polymorphic DNAs (RAPDs)
This is a PCR based technique where a single
short oligonucleotide primer which binds to many different loci, is used to
amplify random sequences from a complex DNA template such as a plant genome.
For most plants the primers that are 9-10 nucleotide long are expected to
generate 2-10 amplification products (amplicon). The primers are generally of
random sequence, biased to contain at least 50% GC content and to lack internal
repeats. The products are easily separated by standard electrophoretic
techniques and visualized by UV illumination of ethidium bromide stained gels.
Pollymorphism results from changes in either the sequence of the primer binding
site (e.g. point mutations) or from changes which alter the size or prevent the
amplification of target DNA (e.g. insertions, deletions, inversions). In
inheritance studies, the amplification products are transmitted as dominant
markers (Waugh and Powell, 1992).
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