Rapid and specific detection of Tilletia indica using loop-mediated isothermal DNA amplification

Karnal bunt in wheat is caused by the fungus Tilletia indica. It is a quarantine disease, and therefore its timely and specific detection is important. Current detection protocols involve DNA amplification by polymerase chain reaction (PCR). However, this technique has encountered specificity issues due to the high DNA homology of T. indica with other Tilletia species, in particular T. walkeri. Here, we report the specific and rapid detection of T. indica DNA using the loop-mediated isothermal amplification (LAMP) at 62 °C. Alignment of the mitochondrial DNA of T. indica and T. walkeri has revealed four major unique regions in T. indica. Six LAMP primers designed in one of these unique regions were able to amplify T. indica DNA. The amplification could be completed in 30 min and was nearly as sensitive as conventional PCR. The amplification was found to be highly specific to T. indica DNA during the screening of 17 isolates of T. indica, T. walkeri, T. horrida, T. ehrhartae and T. caries. The use of the fluorescent chemical calcein has enabled endpoint detection with the naked eye. This method, with its specificity, rapidity and simple visualization, is well suited for the detection of this important disease in wheat.