plant surface microbiology.pdf

Software requirements
– Scoring of the bands: MICROSOFT EXCEL or similar.
– Quantification of genetic diversity within population: ARLEQUIN (Schneider
et al. 1997).
– Measurement of the genetic distances between strains: ARLEQUIN
(Schneider et al. 1997);
NTSYS-pc (Rohlf 1990)
RAPDistance (freely downloaded from http://life.anu.edu.au/molecular/
software/rapd.html)
– Analysis of the genetic structure:
(1) AMOVA: ARLEQUIN (Schneider et al. 1997);
(2) PCA: NTSYS-pc (Rohlf 1990)
– Estimation of genetic relationships among populations: ARLEQUIN
(Schneider et al. 1997)
MEGA (Kumar et al. 1993)
NTSYS-pc (Rohlf 1990)
PHYLIP (Freely downloaded from
http://evolution.genetics.washington.edu/phylip.html)
Many of these softwares exist either as DOS/Windows and as Mac versions.
For ARLEQUIN a Linux version also has been developed.
8 Concluding Remarks
28 Analysis of Microbial Population Genetics 563
Several techniques for the analysis of genetic diversity of bacterial populations
have been proposed. RAPD, ITS and AFLP are effective technologies able
to show intra-population polymorphism and to detect phylogenetic relationships
among strains belonging to the same or closely related bacterial species.
RAPD is a suitable technique in that it is fast, cheap and the amount of polymorphism
displayed is high. RAPD has the disadvantage of requiring accurate
setting up of the conditions to obtain high reproducibility. ITS-RFLP analysis
on the contrary, shows less polymorphism, which is linked to a defined DNA
region, being more suitable to define phylogenetic relationships among
strains.
AFLP shows some advantages over the other methods: (1) the high stringency
of the PCR conditions gives robust reproducibility; (2) easy application
to plant, animal and bacterial genomic DNA. AFLP requires more DNA than
RAPD and ITS-RFLP and a more laborious procedure. Nevertheless,AFLP has
a high informational content per single reaction, in fact, up to 100 different
bands can be displayed in a single lane and the scoring can be done with an
automatic sequencer.