Morphology, phylogeny, and pathogenicity of Colletotrichum siamense associated with leaf blight and pod rot of Theobroma cacao in Malaysia

The incidence of leaf blight and pod rot of Theobroma cacao was observed during a sampling survey conducted in several states of Malaysia from September 2018 to March 2019. This study aimed to identify the causal agent of leaf blight and pod rot of T. cacao using morphological, molecular, and multigene phylogenetic analyses. Three genes were used to delineate the species of the isolates studied, namely internal transcribed spacer (ITS), β-tubulin (tub2), and glyceraldehyde-3-phosphate dehydrogenase (gapdh). Nineteen isolates were obtained from symptomatic leaves (7 isolates) and pods (12 isolates) of T. cacao. The identity of the 19 isolates was provisionally identified as Colletotrichum species on the ground of their morphological characteristics. Furthermore, the identity of the isolates was narrowed down to the species level by a BLAST nucleotide search and multigene phylogenetic analysis. Phylogenetic analysis of ITS, tub2, and gapdh inferred that the obtained isolates resided in the same clade as the reference isolates of Colletotrichum siamense with a high bootstrap support (98%). The pathogenicity assays of C. siamense isolates were performed on healthy leaves and pods of T. cacao. Symptoms of blight and rot developed on the inoculated leaves and pods of T. cacao, respectively, were similar to those observed in the field, thus fulfilling Koch’s postulates.