Apple varieties susceptible to mouldy core generally have an open sinus extending from the calyx into the core. Flower parts are rapidly colonised by a range of saprophytic fungi as they start to senesce and the open sinus allows these fungi to enter the core region. Several factors can affect the open sinus including weather conditions, irregular fruit growth and use of growth regulators. Wet weather during blossom encourages colonisation of flower parts by fungi and can increase the risk of mouldy core. Mouldy core can be caused by a range of different fungi including Alternaria, Stemphylium, Cladosporium, Epicoccum and Fusarium. In an AHDB Horticulture funded study in the UK in 2008 and 2009 (Project TF 184), the main fungi isolated from the rotted cores were at least three different species of Fusarium, as well as Alternaria and Penicillium. In other countries Alternaria is generally the most important cause of core rots. Limited investigations in the UK on Cameo and Bramley fruits indicate that Fusarium may be important. Identification of the main fungi responsible is important as this can affect fungicide efficacy.
Wet core rots are caused by a range of fungi including Fusarium, Mucor and Penicillium. Wet core rots generally arise from fungi that enter the core when the fruit is drenched post-harvest in anti scald agents contaminated with fungal spores.