Morpho-cultural, pathological and molecular variability in Thyrostroma carpophilum causing shot hole of stone fruits in India

Shot hole disease of stone fruits caused by Thyrostroma carpophilum has become a major threat to stone fruit industry of Jammu and Kashmir, India because of the failure in its management with fungicides. To understand the diversity in shot hole pathogen, a combination of conventional (morphological, cultural and pathological) and molecular (ISSR and ITS markers) approaches were employed to discern variability in 25 isolates of T. carpophilum isolated from peach, plum, apricot, almond and cherry leaves collected from Srinagar, Ganderbal, and Baramulla districts of Jammu and Kashmir, India. The studies revealed a high level of variability among the pathogen. Based on the morpho-cultural and pathological studies, the isolates were grouped into different categories based on colony growth, texture, margin and colour besides change in media colour, incubation period, leaf area infected, etc. Using ISSR markers, a high level of polymorphism in different isolates of T. carpophilum was observed which indicated that these markers are suitable for studying the genetic diversity in this pathogen. Based on dendrogram, the isolates were grouped irrespective of their geographical origin or host species. Phylogenetic analysis of the 25 sequences based on ITS region showed maximum similarity with T. carpophilum (Syn. Wilsonomyces carpophilus ) sequences retrieved from NCBI and grouped them in a single clade which proved it as a powerful tool for authentic identification. The pathogen was highly variable based on morpho-cultural, pathological and molecular (ISSR) characterisation.