Morphological and molecular diversity of Alternaria porri isolates causing purple blotch disease in small onion across Tamil Nadu

Abstract

Purple blotch caused by Alternaria porri is one of the most destructive diseases limiting small onion (Allium cepa L.) production in Tamil Nadu. To understand the prevalence and variability of the pathogen, a comprehensive survey was conducted during 2024 across major onion-growing regions of the state. Disease severity varied considerably among locations, with percent disease index (PDI) values ranging from 9.80–76.80 %, indicating the widespread occurrence of the disease under diverse agro-climatic conditions. A total of 31 isolates of A. porri were recovered from infected onion samples and characterised using cultural, morphological and molecular approaches. The isolates exhibited marked variability in colony characteristics, sporulation, conidial morphology and virulence, suggesting the existence of diverse pathogen populations within the state. Pathogenicity studies identified several highly virulent isolates capable of causing severe disease symptoms. Molecular characterisation based on internal transcribed spacer (ITS) sequencing confirmed the identity of the isolates, showing 90–100 % similarity with reference A. porri sequences available in the National Center for Biotechnology Information (NCBI) database. Species identity was further validated using Alt a1 gene-specific primers. Phylogenetic analysis revealed moderate genetic diversity among the isolates and grouped them into distinct clusters, reflecting their evolutionary relationships. The study highlights the substantial spatial, morphological and molecular variability present in A. porri populations associated with onion purple blotch in Tamil Nadu and provides valuable baseline information for disease surveillance, resistance screening and the development of effective management strategies.