The molecular techniques have been widely used for typing and assessing the
genetic diversity of microorganisms. The techniques based on polymerase chain
reaction (PCR) fingerprinting have been employed to examine genotypic diversity of
rhizobial populations and to discriminate among rhizobial strains. These techniques
include random amplified polymorphic DNA (RAPD), two-primers RAPD (TP-RAPD),
repetitive sequence based PCR (rep-PCR) and amplified fragment length polymorphism
(AFLP). The 3 main techniques of rep-PCR are enterobacterial repetitive intergenic
consensus (ERIC)-PCR, repetitive extragenic palindromic (REP)-PCR and BOX-PCR.
While RAPD uses a single primer to amplify the segments of DNA randomly
throughout the genome, rep-PCR uses pairs of primers (for ERIC- and REP-PCR) or a
single primer (for BOX-PCR) to amplify the intervals between conserved repeated
sequences present in genome. In AFLP, total genomic DNA is digested and then ligated
to oligonucleotide adapters. A pair of primer is used to amplify the product from
restriction. RAPD, rep-PCR and AFLP are suitable for distinguishing strains at species
or below levels but they are less valuable for taxonomic purpose. TP-RAPD has been
developed for taxonomy purpose as the patterns of strains in the same species have been
found to be identical. The TP-RAPD patterns supported the proposal of novel species of
rhizobia.
Keywords: Amplified fragment length polymorphism (AFLP), BOX-polymerase
chain reaction (BOX-PCR), Enterobacterial repetitive intergenic consensuspolymerase
chain reaction (ERIC-PCR), Genotypic diversity, Polymerase chain
reaction (PCR) fingerprinting, Random amplified polymorphic DNA (RAPD),
Repetitive extragenic palindromic-polymerase chain reaction (REP-PCR),
Repetitive sequence based polymerase chain reaction (rep-PCR), Rhizobia, Twoprimers
random amplified polymorphic DNA (TP-RAPD).
