Identification of purple blotch pathogen of shallot by PCR using specific primer for Alternaria genus

Purple blotch (Alternaria porri), having symptom similar to stemphylium blight (Stemphylium vesicarium), is one of the important diseases that significantly lowered shallot yield in Indonesia. However, stemphylium blight has never been reported. Purple blotch pathogens from farmers’ crops in Bantul and experimental crop in Centre of Innovative Agricultural Technology Universitas Gadjah Mada (CIAT-UGM) Sleman Regencies were identified to observe whether Stemphylium sp. was found with A. porri. Thirteen isolates obtained showed variability in colony texture, colour and pigmentation. DNA fingerprinting through Polymerase Chain Reaction of BOX and Enterobacterial Repetitive Intergenic Consensus region dispersed those isolates into two main groups. Identification using Alternaria-specific primers, Dir1ITSAlt/Inv1ITSAlt revealed that 10 isolates were Stemphylium sp. and 3 isolates were Alternaria sp. A. porri was only identified from CIAT-UGM. This finding emphasise that the Alternaria-specific primer was able to amplify Stemphylium sp. Besides, stemphylium blight disease may have been occurred in farmers’ crops in Bantul.