Biomarker development for external CO(2) injury prediction in apples through exploration of both transcriptome and DNA methylation changes

Several apple cultivars are susceptible to CO(2) injury, a physiological disorder that can be expressed either externally or internally, and which can cause major losses of fruit during controlled atmosphere (CA) storage. Disorder development can also be enhanced using SmartFresh™ technology, based on the inhibition of ethylene perception by 1-methylcyclopropene (1-MCP). Injury development is associated with less mature fruit with lower ethylene production, but the aetiology of the disorder is poorly understood. Here we report on the progress made using mRNAseq approaches to explore the transcriptome during the development of external CO(2) injury. Next-generation sequencing was used to mine the apple transcriptome for gene expression changes that are associated with the development of external CO(2) injury. ‘Empire’ apples from a single orchard were treated with either 1 µL L(−1) 1-MCP or 1 g L(−1) diphenylamine or left untreated, and then stored in a CA of 5 kPa CO(2) and 2 kPa O(2). In addition, susceptibility to the disorder in the ‘Empire’ apples from five different orchards was investigated and the methylation state of the ACS1 promoter investigated using McrBC endonuclease digestion and real-time quantitative polymerase chain reaction. Expression of over 30 000 genes, aligned to the apple genome, was monitored, with clear divergence of expression among treatments after 1 day of CA storage. Symptom development, internal ethylene concentrations (IECs) and methylation state of the ACS1 promoter were different for each of five orchards. With transcriptomic changes affected by treatment, this dataset will be useful in discovering biomarkers that assess disorder susceptibility. An inverse correlation between the frequency of this disorder and the IEC was detected in a multiple orchard trial. Differential methylation state of the ACS1 promoter correlated with both IEC and injury occurrence, indicating epigenetic regulation of ethylene biosynthesis and possibly events leading to disorder development.