Metabolomic and transcriptomic profiling of Red Delicious apple stored under static (CA) and dynamic controlled atmosphere (DCA)

Red Delicious (RD) apples benefit from low oxygen storages, that delay ripening allowing for a better maintenance of fruit quality. However, RD is sensitivity to such conditions and often results in an excessive accumulation of ethanol and other off flavors, as well as the onset of storage disorders, leading to unmarketability and important postharvest losses. To mitigate these effects, dynamic controlled atmosphere (DCA) storage has been adopted particularly for pome fruits. DCA uses extremely low oxygen levels that are adjusted based on the fruit's physiological responses. These conditions induce modulations in both fundamental and specialized metabolisms. To investigate these adaptations, RD apples stored under different CA protocols (normoxia; static 0.3% and 0.8% oxygen; dynamic oxygen modulation from 0.3 to 0.8%) under cold storage at 1 °C. Responses were evaluated for peel and pulp tissues separately focusing on the molecular and metabolic adaptations. For this aim, transcriptomics analysis using both RNA-sequencing (RNA-seq) and RT-qPCR in addition to metabolomics analysis involving VOCs, polyphenols, and primary metabolites were conducted to provide a comprehensive overview of the fruit status. Results confirmed the marked induction of ethanol and subsequent accumulation of ethyl esters and alanine under static 0.3% conditions. Common and tissue-specific responses between peel and pulp have been identified. Both tissues accumulated non-ethyl esters under normoxia, fermentation-related VOCs under static CA conditions, and amino acids like valine and lysine under DCA, along with the retention of higher firmness levels and absence of storage disorders. Among tissue-specific responses, polyphenols appeared to differentially accumulate at higher levels in the pulp under DCA and in the peel under normoxia. Transcriptomics analysis confirmed and aligned the metabolomic findings and highlighted the involvement of ERFs transcription factors in response of apple fruit to different levels of low oxygen stress.

The study provided insight into the metabolic and molecular responses of RD apples to DCA protocols, helping to clarify and deepen the understanding of both common and tissue-specific responses of apple pulp and peel tissues.