Journal of Proteomics & Bioinformatics
Open Access

Development of a Pcr-Based diagnostic assay for detecting Bipolaris oryzae, the brown spot fungus in rice

Archana B, UdayaShankar A C, ChandraNayaka S, Niranjana S R, Mortensen C N, Lund O S and Prakash H S

: JPB

Abstract :

Bipolaris oryzae is the common causal agent of brown spot in rice (Oryza sativa L.), and infection by this fungal pathogen results in severe yield losses. A polymerase chain reaction (PCR) based diagnostic assay was developed to detect Bipolaris oryzae, the brown spot fungus in rice. Universal primers ITS1 and ITS4 were used to obtain the rDNA sequence of the available B. oryzae isolates of diverse geographic origins of India. Species-specific primers were designed based on B. oryzae ITS sequence data obtained in the present study and in comparison with other Bipolaris spp., Curvularia spp., Drechslera spp. and Exserohilum spp. in NCBI database. The specific primers designed were employed to amplify DNA in PCR from a total of 171 isolates of Alternaria spp., Bipolaris spp., Curvularia spp., Drechslera spp., Exserohilum spp. and Magnaporthe oryzae. The species-specific primers BoVf and BoVr were used in the detection of B. oryzae that amplified a 275 bp fragment from the DNA of all B. oryzae isolates but not the DNA from other species. The primer was also used to detect B. oryzae in rice seed and successfully amplified the predicted size of the DNA fragment in the infected material. PCR detection of as little as 100 ng μl-1 to 1 fg μl-1 of B. oryzae DNA was possible. The method described here requires one day for completion, compared to 10 days required for the cultural method.