Co-expression networks provide insights into molecular mechanisms of postharvest temperature modulation of apple fruit to reduce superficial scald

•Genes were identified for follow-up analyses to understand superficial scald.•Gene activity changes early in apple storage may predict long term outcomes.•Our analysis implicates nearly 1000 genes in a complex postharvest trait. Temperature conditioning is an effective approach for enhancing some aspects of postharvest apple fruit quality, particularly avoidance of chilling injury. The molecular mechanisms of warming regimes that alter apple fruit quality are poorly understood, as is how warming contributes to avoiding development of the peel disorder superficial scald. Here we report transcriptional responses of ‘Granny Smith’ fruit peel during the early phases of long-term cold storage in response to intermittent warming, an ostensibly organic compliant strategy that effectively reduced scald incidence. We observed two temporally distinct classes of gene expression, which were discovered by co-expression network analyses. One profile is largely concordant with recovery from chilling stress, whereas the other reveals transient shifts marked by hormone signaling and transcription and translation machinery. Altogether, our analyses point to novel aspects of superficial scald etiology and circumscribes a list of candidate genes that may be useful to uncover molecular processes that promote, as well as mitigate, the peel disorder.