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Pomegranate fruit rot disease, known as “heart rot” or “black heart,” is a major pomegranate disease that impacts production worldwide. Heart rot is characterized by black rot of the fruit core that spreads from the calyx area, whereas the outer peel and the hard rind retain their healthy appearance. Aims of the present study were to identify the pathogen that causes pomegranate heart rot in Israel and to study the dynamics of fruit-organ colonization by fungi during fruit development, as the first steps toward the development of management strategies. Several fungi were isolated from pomegranate fruits, among which were species of Penicillium, Aspergillus, Botrytis, and Rhizopus, but the causative pathogen of the disease was identified as Alternaria alternata. This fungus was isolated from the pistils of more than 85% of open flowers and ∼20% of the loculi of asymptomatic fruits and from all tissues of the symptomatic fruits. The dynamics of fruit-organ colonization by fungi during fruit development was recorded in six commercial orchards in 2010 and 2011. It was found that A. alternata spores germinate on the stigmata of open flowers and develop into the style. In some fruits, the mycelium grows into the tunnel and reaches the lower loculus, where the fungus becomes latent for about 3 to 4 months pending initiation of fruit ripening. Then, in a small number of fruits, the fungus starts growing and invades the arils, causing black rot of the arils in the lower loculus. At the beginning of disease development, the fungus causes brown soft rot of the arils, which becomes black and dry as the fungus grows. Eventually, the fungus grows from the lower loculus into the upper loculi, causing rot of the entire fruit.

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