Genome-Wide Transcriptomic Analysis Correlated with Superficial Scald Development in Granny Smith Apples (Malus X Domestica Borkh)

The usage of low temperature as strategy to extend storage capacity of climacteric fleshy fruits, often leads to the development of post-harvest disorders related to chilling injuries, which seriously affect the entire marketability. For pome fruits, the most serious disorders is represented by superficial scald, which occurs with the development of diffuse brown areas in the epidermis after the re-establishment of room temperature conditions. Since superficial scald is influenced by environmental, physiological and genetic factors, only the integration of comprehensive approaches would allow the determination of its real etiology. A possible contribution to unveil the physiological mechanisms acting during the development of superficial scald may be offered by NGS based approach, in order to detect the overall functional variation ongoing with the onset of this disorder. In this work, RNA-seq technology was employed to characterize the transcription dynamics in Granny Smith apples affected by superficial scald and treated with 1-MCP (1-methylcyclopropene), an ethylene competitor known to interfere with this physiopathy. This comparison was also carried out over different harvesting dates, investigating also the role of the ripening stage in the development of this phenomenon. In total 14 different conditions were tested, generating more than 650 millions of unique reads. The 68.56% of these reads have been univocally mapped on the genome and 18.000 new transcripts were de-novo assembled. Global transcription dynamics highlighted the effect of 1-MCP on the development of superficial scald, identifying two clusters represented by an equal number of elements, and specifically associated to this functional regulation.