Transcriptome and metabolic survey disclose the mode of action of static and dynamic low oxygen postharvest storage strategies to prevent the onset of superficial scald disorder in fruit of ‘Granny Smith’ apple cultivar

To preserve quality features and ensuring availability of fresh fruit on the market, apples need to be stored after harvest. The low temperature applied during storage, beside avoiding important fruit loss, can also promote the development of serious chilling injury disorders, such as superficial scald. One of the strategies largely employed to prevent the development of this phenomenon is the control of the storage atmosphere by lowering down the oxygen concentration. In this work, a multifaceted survey was carried out to investigate transcriptome variation together with three categories of metabolites (phenolics, lipids and volatile organic compounds ) in fruit of ‘Granny Smith’ apple cultivar stored in both static and dynamic controlled hypoxia atmosphere for five and seven months, respectively. The global transcriptome survey identified a core set of differentially expressed genes in three main functional groups, revealing as the duration of storage had an important effect in the coordination of gene expression. The effect of the length of storage was furthermore highlighted by the DEG-network analysis that identified a distinct number and type of transcriptomic hubs. Samples characterized by the development of superficial scald were distinguished by a higher concentration of chlorogenic acid and a higher expression of phenylalanine ammonia lyase (PAL) and polyphenol oxidase (PPO) in a time-dependent fashion. The prevention of this disorder was instead related to distinctive re-programming events, involving the accumulation of specific antioxidant types of metabolites, very long chain fatty acids (VLCFAs) and the expression of genes coordinating a hypoxia acclimation process, such as RAP2-like and plant cysteine oxidase (PCO). •Cold storage can induce the onset of the superficial scald in apples.•Low oxygen during storage efficiently control the incidence of superficial scald.•Cold storage impact the transcriptional reprogramming in a time dependent fashion.•Metabolite concentration is regulated by both hypoxia and storage duration.•The oxidation of chlorogenic acid by PPO leads to the onset of superficial scald.