Scorpion ARMS primers for SNP real-time PCR detection and quantification of Pyrenophora teres.

summary We have developed a quantitative PCR detection method that can be used to determine the seed infection levels of Pyrenophora teres, a seed-borne fungal pathogen of barley. This method uses Scorpion Amplified Refractory Mutation System (ARMS) technology with real-time PCR detection. Scorpion ARMS primers were designed and optimized such that a single nucleotide base mismatch in the primer sequence could distinguish P. teres from P. graminea, a closely related seed-borne pathogen of barley. It is necessary to distinguish between these two agriculturally important pathogens since different disease management decisions are made, based on the presence and level of infection measured for each. The advance in development of sensitive and specific fluorescent probes has enabled the current PCR test to detect Pyrenophora spp. pathogenic on barley to be enhanced with the advantage that it can now specifically detect P. teres in a single reaction, whilst previously, two reactions were required to discriminate P. teres from P. graminea.