Survey, Pathogenic Variability and Molecular Characterization of Colletotrichum spp. Causing Anthracnose of Chilli (Capsicum annuum L.) in Tamil Nadu, India

Abstract

Anthracnose caused by Colletotrichum sp. is one of the most destructive diseases of chilli (Capsicum annuum L.), resulting in severe yield and quality losses. The present study was undertaken to assess the disease incidence, cultural and morphological variability, pathogenicity and molecular identity of Colletotrichum sp. isolates collected from major chilli-growing areas of Tamil Nadu, India. A field survey conducted during kharif 2023 revealed that anthracnose was prevalent in all surveyed locations, with the highest percent disease index recorded in Paramakudi, followed by Sivapuri and Attur, while the lowest incidence was observed in Hanumandhapuram. Five isolates of Colletotrichum sp. obtained from different regions exhibited considerable variability in colony characteristics, mycelial growth and conidial dimensions. Pathogenicity tests under pot culture conditions indicated significant differences in virulence among the isolates, with isolate Cc 03 (Paramakudi) being the most virulent, recording the highest fruit rot and leaf infection intensity. Molecular characterization based on internal transcribed spacer (ITS) rDNA sequencing confirmed all isolates as Colletotrichum capsici, exhibiting ≥99% sequence similarity with corresponding GenBank reference sequences and clustering within a single, well-supported clade in the phylogenetic analysis. In addition, amplification of the species-specific β-tubulin and actin genes produced distinct amplicons of 317 bp and 751 bp, respectively, further substantiating the molecular identity of C. capsici. The study highlights the variability and virulence potential of Colletotrichum spp. populations in Tamil Nadu and provides a reliable basis for disease management strategies and future resistance breeding programme in chilli.