Real-time Fluorescence PCR Method for Detection of Burkholderia glumae from Rice

doi:10.1016/S1672-6308(08)60073-6

Abstract

Abstract: Burkholderia glumae causing seedling rot and grain rot of rice was listed as a plant quarantine disease of China in 2007. It’s quite necessary to set up effective detection methods for the pathogen to manage further dispersal of this disease. The present study combined the real-time PCR method with classical PCR to increase the detecting efficiency, and to develop an accurate, rapid and sensitive method to detect the pathogen in the seed quarantine for effective management of the disease. The results showed that all the tested strains of B. glumae produced about 139 bp specific fragments by the real-time PCR and the general PCR methods, while others showed negative PCR result. The bacteria could be detected at the concentrations of 1×10⁴ CFU/mL by general PCR method and at the concentrations below 100 CFU/mL by real-time fluorescence PCR method. B. glumae could be detected when the inoculated and healthy seeds were mixed with a proportion of 1:100.

Key words: Burkholderia glumae, bacterial grain rot, detection, real-time fluorescence polymerase chain reaction, rice

FANG Yuan, XU Li-hui, TIAN Wen-xiao, HUAI Yan, YU Shan-hong, LOU Miao-miao, XIE Guan-lin. Real-time Fluorescence PCR Method for Detection of Burkholderia glumae from Rice[J]. RICE SCIENCE, 2009, 16(2): 157-160 .

References

1 Goto M. Fundamentals of Bacterial Plant Pathology. California: Academic Press, 1992.
2 Shahjahan M, Rush M C, Groth D. Panicle blight recent research points to a bacterial cause. Rice J, 2002, 103: 26– 28.
3 Sogou K. The present situation of bacterial grain rot of rice. Plant Prot, 1985, 39: 396–402.
4 Zhu B, Lou M M, Huai Y, Xie G L, Luo J Y, Xu L H. Isolation and identification of Burkholderia glumae from symptomless rice seeds. Rice Sci, 2008, 15(2): 145–149.
5 Luo J, Xie G L, Li B, Xu L H. First report of Burkholderia glumae isolated from symptomless rice seeds in China. Plant Dis, 2007, 91(10): 1363.
6 Sayler R J, Cartwright R D, Yang Y N. Genetic characterization and real-time PCR detection of Burkholderia glumae, a newly emerging bacterial pathogen of rice in the United States. Plant Dis, 2006, 90: 603–610.
7 Xia M X, Zhao W J, Ma Q, Zhu S F. Rapid detection of tomato bacterial canker (Clavibacter michiganensis subsp. michiganensis) with real-time fluorescent PCR. Acta Phytopath Sin, 2006, 36(2): 152–157. (in Chinese with English abstract)
8 Urakami T, Ito Yoshida C, Araki H. Transfer of Pseudomonas plantarii and Pseudomonas glumae to Burkholderia as Burkholderia spp. and description of Burkholderia vandii sp. nov. Int J Syst Bact, 1994, 44: 235–245.
9 Takeuchi T. Specific detection of Burkholderia plantarii and B. glumae using primers selected from the 16s-23s rDNA spacer regions. Ann Phytopathol Soc Japan, 1997, 63(6): 455–462.
10 Yukiko M, Hirosuke S, Akinori K. Phylogenetic study and multiplex PCR-based detection of Burkholderia plantarii, Burkholderia glumae and Burkholderia gladioli using gyrB and rpoD sequences. Int J Syst Evol Microbiol, 2006, 56: 1031–1038.
11 Weinberg J B, Alexander B D, Majure J M, Williams L W, Kim J Y, Vandamme P, LiPuma J J. Burkholderia glumae infection in an infant with chronic granulomatous disease. J Clin Microbiol, 2007, 45: 662–665.
12 Schaad N W, Frederick R D. Real-time PCR and its application for rapid plant disease diagnostics. Can J Plant Pathol, 2002, 24: 250–258.
13 Qi Y X, Xie Y X, Zhang H Q, Zhu S F, Xiao Q M, Liao X L. Detection of Ralstonia Solanacearum by real-time fluorescent PCR. J South China Univ Trop Agric, 2005, 11(1): 1–5. (in Chinese with English abstract)

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