Abstract: The invention provides a method and compositions for detecting the presence of viable endophyte in a plant, the method comprising germinating seed and excising a young leaf, optionally preparing an extract from the young leaf, and performing antibody, nucleic acid, or preferably PCR-based methods to detect the viable endophyte, wherein at least one primer hybridizes to the intergenic region (IGS) of the ribosomal repeat region of a specific endophyte when used in a PCR-based method. The invention provides a new method for rapid identification of both viable beneficial endophytes and any viable contaminating endophytes, as opposed to any non-viable endophytes, by detecting the presence of endophytes in the first leaf of germinated plants.

Abstract: The invention provides a methods and compositions for detecting the presence of viable endophyte in a plant, the method comprising detecting the presence of an endophyte in a young leaf or extract thereof, from the plant, wherein detecting the presence of the endophyte in the young leaf or extract is indicative of the presence of viable endophyte in the plant.