Apple Epigenetics

Several commercially important apple cultivars are susceptible to CO2 injury, a physiological disorder that can be expressed either externally or internally, and which can cause major losses of fruit during controlled atmosphere storage. CO2 injury development is associated with less mature fruit with low ethylene production, but the aetiology of the disorder is poorly understood.

A new paper in AoB PLANTS reports on progress using mRNAseq approaches to explore the transcriptome during the development of external CO2 injury. In addition to having an important biological role in the development of external CO2 injury, an epigenetically regulated transcript could provide a predictive marker that can be used by the apple industry. The aetiology of this disorder is rapid, which means that a useful predictive biomarker is probably required at harvest, or within the first few days of storage. Further studies are in place to capture the transcriptomes and methylomes of fruit in an orchard-to-orchard manner. A larger collection of tissue will be required, representing more orchards, to more clearly observe whether the environmental impact on this disorder can be attributed to an epigenetically regulated process, such as DNA methylation, and to mine for suitable epigenetically regulated predictive biomarkers. Certainly, an ‘at harvest’ biomarker, which is epigenetically regulated, would be the most easy to evaluate and would be potentially most useful as an industry tool.

Biomarker development for external CO2 injury prediction in apples through exploration of both transcriptome and DNA methylation changes. (2013) AoB PLANTS 5 doi: 10.1093/aobpla/plt021
Abstract
Several apple cultivars are susceptible to CO2 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 CO2 injury. Next-generation sequencing was used to mine the apple transcriptome for gene expression changes that are associated with the development of external CO2 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 CO2 and 2 kPa O2. 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.