Pathogenicity and multigene sequence analysis reveal the widespread distribution of Alternaria alternata causing early blight in tomato

The study investigated early blight, a major fungal disease affecting tomatoes, across two distinct agroclimatic zones in India, resulting in a collection of 90 Alternaria isolates. Morpho-cultural characterization grouped these isolates into 11 putative clusters, which were subjected to further analysis. Pathogenicity tests revealed that all 11 isolates were pathogenic on the Pusa-Ruby tomato cultivar. Molecular analysis, specifically comparing nucleotide sequences of the ß-tubulin (ß-tub), cytochrome-B (cyt-B) and Alternaria major allergen gene (Alt a1) using the MycoCosm and NCBI databases, identified these isolates as Alternaria alternata. The phylogenetic tree, constructed via the Maximum-Likelihood method using the Alt a1 gene, demonstrated that all 11 isolates clustered with A. alternata, Sector—Alternaria, alongside reference strains from the NCBI database. Additionally, Alt a1 showed the capability to differentiate sub-groups within Sect.—Alternaria, indicating its intraspecific discriminatory potential. In conclusion, the study confirms the widespread presence of pathogenic A. alternata on tomatoes and highlights the importance of marker gene, Alt a1 in discerning the identity of Alternaria species.