Morpho-molecular and pathogenic variability of <i>Alternaria porri</i> isolates causing onion purple blotch disease in Southern Karnataka, India

Purple blotch disease, caused by <i>Alternaria porri</i>, significantly reduces crop yield and quality while complicating management due to high spore production and pathogenic variability. To investigate pathogen variability, a comprehensive survey was conducted in onion fields across Southern Karnataka, India, assessing the incidence and severity of purple blotch disease. A total of 42 isolates were collected from various districts of Southern Karnataka, India. It was found that disease ranged from 51.98 to 39.14% in surveyed districts. All the isolates underwent cultural, morphological, and molecular characterization. Cultural studies revealed substantial variations in colony diameter, shape, margin, mycelial texture, colour, growth pattern, and pigmentation. Morphological analysis showed notable differences in conidial size, shape, and colour among the isolates. Molecular characterization using ITS sequence analysis revealed significant genetic diversity among the isolates, with genetic distances ranging from 0.00 to 0.099. The lowest distance (0.00) indicates near-identical sequences, while the highest (0.099) between isolates Alt12 (Hiriyur) and Alt36 (Tarikere taluk) suggests notable genetic divergence. Pathogenicity tests identified 12 highly virulent, 19 moderately virulent, and the rest as less virulent isolates. Highly virulent isolates showed rapid growth, high sporulation, and extensive mycelial development. Haplotyping analysis revealed a dominant central haplotype (Hap_1) and highlighted Chikkamagaluru district as a hotspot for genetic variation, suggesting active gene flow and potential evolutionary adaptations. This study provides a detailed understanding of the cultural, morphological, molecular and pathogenic variations of <i>A. porri</i> in Southern Karnataka, India, emphasizing genetic diversity and the need for targeted disease management and breeding strategies for resistant onion varieties.