The region 4 that
showed variability among the aligned sequences of M.
phaseolina isolates was not considered for further analysis. We also excluded 5.8 S RNA gene sequence
from the analysis. After editing and rearrangement of
aligned sequences and comparison with the sequences
of closely related genera of fungi, region 1
and 5 were selected for the development of speciesspecific
primers for M. phaseolina. Two primers
MpKFI and MpKRI were designed from the specific
nucleotide areas and one oligonucleotide probe
MpKH1 (19 mer) was designed from the conserved
region, adjacent to 5.8 S gene showed in the region 3
(FIG. 2). The designed primers yielded single amplified
product of 350 bp with all the M. phaseolina
isolates tested. The specificity of the primers was
tested on representative species of common soilborne
microbes (TABLE II). The primer pair was
found to be specific for M. phaseolina as none of
the other soil microbes tested could yield any
amplification product under identical conditions of
amplification (FIG. 3).