Diagnostic primers for the detection of Xanthomonas oryzae pv. oryzicola

Abstract

A previously cloned repetitive element from Xanthomonas oryzae pv. oryzicola, R41 shares 44.8% identity with IS1112 cloned from X. oryzae pv. oryzae. Based on sequences in the non-homologous regions, primers were synthesized and used for polymerase chain reaction (PCR). Two unique fragments amplified from X. oryzae pv. oryzicola by the primer pair R41PR4 and R413 were cloned, sequenced, and used as basis for primer design. Six primer pairs based on the first clone, 2R41-3e, did not yield unique amplified products. From the five primer pairs based on 2R41-1J, the second clone, only the primer pair PR41-1F1 and PR41-1R showed differential patterns for the two pathovars of X. oryzae. When the primer PR41-1R was used alone, an intense 378 bp fragment was amplified in the 39 X. oryzae pv. oryzicola and 26 X. oryzae pv. oryzae strains except for two American, two North American, and three African isolates. Amplification was also observed in other Xanthomonas species, but the banding patterns produced were distinguishable from those observed in the X. oryzae pathovars. The exception was the causal organism of brown blotch, which also produced the 378 bp band. When PR41-1F1 was used alone, X. oryzae pv. oryzicola can be differentiated from the X. oryzae pv. oryzae strains. DNA from other Xanthomonas and other genera were also amplified but with a much different banding pattern. For PCR diagnosis of X. oryzae pv. oryzicola, the PR41-1R primer or the previously reported Hrp primers should first be used to diagnose X. oryzae pathovars; distinction of X. oryzae pv. oryzicola from X. oryzae pv. oryzae is achieved by amplification using the PR41-1F1 primer.

Source or Periodical Title

Philippine Agricultural Scientist

ISSN

317454

Page

408-418

Document Type

Article

Subject

Bacterial leaf blight, Detection, Polymerase chain reaction, Rice disease, Xanthomonas oryzae pv. oryzicola

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