Item Details

Title: Improved PCR for identification of members of the genus

Date Published: 2013
Author/s: John Adriko & Ernest Rashid Mbega & Carmen Nieves Mortensen & Ednar Gadelha Wulff & Wilberforce Kateera Tushemereirwe & Jerome Kubiriba & Ole Søgaard Lund
Data publication:
Funding Agency : DANIDA
Copyright/patents/trade marks: KNPV
Journal Publisher: European Journal of Plant Pathology
Affiliation: Department of Plant and Environmental Sciences, Faculty of
Science, University of Copenhagen,
Hoejbakkegaard Allé 3, 2630 Taastrup, Denmark, National Agricultural Biotechnology Centre, National
Agricultural Research Laboratories,
P. O. Box 7065, Kampala, Uganda, African Seed Health Centre (AfSHC), Department of Crop
Science, Sokoine University of Agriculture,
P.O. Box 3005, Morogoro, Tanzania
Keywords: Xanthomonas . Identification . ITS . gumD .
TonB dependent receptor . Multiplex PCR


A PCR-based system was developed to reliably
and robustly identify group I and II members of the
genus Xanthomonas. Primer sets developed from three
gene targets namely fyuA, ITS and gumD were evaluated
in the study. Primer sets were evaluated using DNA
extracted from 45 Xanthomonas strains representing 25
species broadly covering the genus. Fifteen non-
Xanthomonas strains of plant-associated bacteria including
phylogenetically closely related species
Stenotrophomonas maltophilia and Xylella fastidiosa
were also tested. The primers targeting fyuA amplified
DNA from all xanthomonads except X. theicola, while
the ITS primers amplified a DNA fragment of 254 bp in all 45 Xanthomonas strains; whereas no amplification
was observed for non-xanthomonads. The gumD
primers allowed efficient amplification of DNA in 38
out of 39 isolates from Group II, whereas no or very
weak amplification occurred with DNA from Group I
members. Internal controls of primers targeting bacterial
16S rDNA or plant 26S mitochondrial rDNA were
successfully applied in multiplex PCRs for testing bacterial
cultures or plant tissue, respectively. The findings
give us a PCR based approach that can reliably and
effectively differentiate xanthomonads from nonxanthomonads
as well as separating the strains belonging
to the two described groups of the genus
Xanthomonas. The study thus offers valuable tools for
disease surveillance and management. It can effectively
be applied in rapid assessment of new disease occurrences,
for which no specific detection tools could be in