title: Multiplex PCR assay for simultaneous detection of six major bacterial pathogens of rice.
abstract: OBJECTIVE
  The aim of this study was to develop a multiplex PCR (mPCR) assay for rapid, sensitive and simultaneous detection of six important rice pathogens: Xanthomonas oryzae pv. oryzae, X. oryzae pv. oryzicola, Pseudomonas fuscovaginae, Burkholderia glumae, Burkholderia gladioli and Acidovorax avenae subsp. avenae.
  
  
  RESULTS
  Specific primers were designed through a bioinformatics pipeline. Sensitivity of detection was established using both traditional PCR and quantitative real-time PCR on isolated DNA and on bacterial cells both in vitro and in simulated diseased seeds and the parameters were optimized for an mPCR assay. A total of 150 bacterial strains were tested for specificity. The mPCR assay accurately predicted the presence of pathogens among 44 symptomatic and asymptomatic rice seed, sheath and leaf samples.
  
  
  CONCLUSIONS
  This study confirmed that this mPCR assay is a rapid, reliable and simple tool for the simultaneous detection of six important rice bacterial pathogens.
  
  
  CONCLUSIONS
  This study is the first report of a method allowing simultaneous detection of six major rice pathogens. The ability to use crude extracts from plants without bacterial isolation or DNA extraction enhances the value of this mPCR technology for rapid detection and aetiological/epidemiological studies.
authors: State Key Laboratory of Rice Biology, Institute of Biotechnology, Zhejiang University, Hangzhou, China.
authors: Z
authors: Z
authors: Cui
authors: State Key Laboratory of Rice Biology, Institute of Biotechnology, Zhejiang University, Hangzhou, China.
authors: M R
authors: MR
authors: Ojaghian
authors: State Key Laboratory of Rice Biology, Institute of Biotechnology, Zhejiang University, Hangzhou, China.
authors: Z
authors: Z
authors: Tao
authors: State Key Laboratory of Rice Biology, Institute of Biotechnology, Zhejiang University, Hangzhou, China.
authors: K U
authors: KU
authors: Kakar
authors: State Key Laboratory of Rice Biology, Institute of Biotechnology, Zhejiang University, Hangzhou, China.
authors: J
authors: J
authors: Zeng
authors: Chinese Academy of Inspection and Quarantine, Beijing, China.
authors: W
authors: W
authors: Zhao
authors: USDA-ARS-USHRL, Fort Pierce, FL, USA.
authors: Y
authors: Y
authors: Duan
authors: Plant Breeding, Genetics and Biotechnology Division, International Rice Research Institute, Metro Manila, Philippines.
authors: C M
authors: CM
authors: Vera Cruz
authors: State Key Laboratory of Rice Biology, Institute of Biotechnology, Zhejiang University, Hangzhou, China.
authors: B
authors: B
authors: Li
authors: State Key Laboratory of Rice Biology, Institute of Biotechnology, Zhejiang University, Hangzhou, China.|Zhejiang Province Key Laboratory of Plant Secondary Metabolism and Regulation, College of Life Science, Zhejiang Sci-Tech University, Hangzhou, China.
authors: B
authors: B
authors: Zhu
authors: State Key Laboratory of Rice Biology, Institute of Biotechnology, Zhejiang University, Hangzhou, China.
authors: G
authors: G
authors: Xie
mesh_terms: D019117:Burkholderia / Q000235:genetics; D042621:Comamonadaceae / Q000235:genetics; D004269:DNA, Bacterial / Q000032:analysis; D060885:Multiplex Polymerase Chain Reaction / Q000379:methods*; D012275:Oryza / Q000382:microbiology*; D010935:Plant Diseases / Q000382:microbiology*; D018515:Plant Leaves / Q000382:microbiology; D011549:Pseudomonas / Q000235:genetics; D012639:Seeds / Q000382:microbiology; D014974:Xanthomonas / Q000235:genetics
chemical_list: D004269:DNA, Bacterial
keywords: comparative genomics; detection; multiplex PCR; quantitative real-time PCR; rice bacterial pathogens