AbstractAlternaria isolates were collected from onion foliage at different stages of the plant life cycle. Incidence of Alternaria species in cultivars 'Mercedes' and 'Excallbur' was determined during two consecutive growing seasons in fields located In southern Puerto Rico. Leaves showing purple to brown sunken elliptical lesions with chlorotic halos were taken at random. Five leaf sections (0.5 cm) from each sample were superficially disinfested, transferred to culture media and incubated, and isolations were documented. Disease incidence ranged from 25 to 52% in 60- to 100-day-old plants. An increase in Alternaria incidence was observed in response to high relative humidity in the fields. A total of 280 isolates were obtained, and 35 were selected for morphological, pathogenic and molecular characterization. A complex of five different Alternaria species is associated with onion leaf blight on the island. Alternaria destruens, A. tenuissima, A. palandui, A. allii and a group of small-spore Alternaria sp., belonging to a taxonomically undescribed group, were identified. Sixty-two percent of selected isolates belong to this group having an A. arborescens intermediate sporulation pattern. Alternaria destruens and A. palandui have not been previously reported as associated with onions in the Caribbean or in the Western Hemisphere. Pathogenicity tests showed that A. allii, A. tenuissima and Alternaria sp. were pathogenic to onion foliage, with A. allii as the most virulent. Molecular characteristics of the isolates were determined by using the ITS of the rDNA gene. Phylogenetic relationships based on rDNA ITS sequences from Alternaria isolates and other Pleosporaceae distinguished three clades. The first clade of large filiform-beaked spores included A. allii from this study, as well as isolates from the GenBank (A. porri, A. solani, A. macrospora, A. zinniae and A. sesamicola). These formed a monophyletic group, discrete from other members of the genus. The second clade included a diverse group of smallspore Alternaria: A. tenuissima, A. alternata, A. palandui, A. destruens and Alternaria sp.; the third clade included Stemphylium spp.
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