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ARS Home » Pacific West Area » Wenatchee, Washington » Physiology and Pathology of Tree Fruits Research » Research » Publications at this Location » Publication #285420
Title: Biomarker development for external CO2 injury prediction in apples through exploration of both transcriptome and DNA methylation changes

Author
item GAPPER, NIGEL - Cornell University
item Rudell, David
item Giovannoni, James
item WATKINS, CHRISTOPHER - Cornell University

Submitted to: AoB Plants
Publication Type: Peer Reviewed Journal
Publication Acceptance Date: 3/3/2013
Publication Date: 3/20/2013
Citation: Gapper, N., Rudell Jr, D.R., Giovannoni, J.J., Watkins, C. 2013. Biomarker development for external CO2 injury prediction in apples through exploration of both transcriptome and DNA methylation changes. AoB Plants. doi: 10.1093/aobpla/plt021.

Interpretive Summary: Carbon dioxide injury causes economically significant levels of apple crop losses annually on susceptible varieties. Damage can occur on the peel of apple exposed to elevated levels of carbon dioxide during controlled atmosphere storage. Commonly used post-storage treatments include 1-methylcyclopropene, which can enhance disorder development, and diphenylamine, which reduces or eliminates the disorder. Postharvest treatments (1-MCP and DPA) in combination with different levels of carbon dioxide were used to contrast global changes in gene expression preceding or associated with disorder development. Epigenetic factors were also evaluated in one key ripening-related gene indicating the potential for their influence on disorder development. This information will be used in tools that assess risk of apple fruit developing this disorder during controlled atmosphere storage as well as understanding the underlying chemical changes that lead to the disorder.

Technical Abstract: Several apple cultivars are susceptible to CO2 injury, a disorder that can be expressed either externally or internally. The etiology of the disorder is poorly understood. Our focus in on an external injury of 'Empire' apples that causes major losses during controlled atmosphere (CA) storage. Disorder development can also be enhanced by use of the SmartFreshTM technology, possibly resulting from inhibition of ethylene perception provoked by 1-methylcyclopropene (1-MCP) treatment. Here we report on initial progress using mRNAseq approaches to explore the transcriptome during the development of external CO2 injury. Methodology 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 either treated with either 1 µL L-11-MCP, 1 g l-1DPA, or left untreated, and then stored in a CA of 5 kPa CO2 and 2 kPa O2. In addition, susceptibility of the disorder in five different orchards was investigated, and the methylation state of the ACS1 promoter investigated by McrBC endonuclease digestion and real time qPCR. Principal results The expression changes of over 30,000 genes aligned to the apple genome were monitored, with clear divergence of expression pattern for each treatment as early as one day of CA storage. Occurrence of injury, internal ethylene concentrations, and methylation state of the ACS1 promoter were different for each of five orchards. Conclusions With transcriptomic changes caused by treatment, this dataset will be useful for discovering biomarkers that assess disorder susceptibility. An inverse correlation between the frequency of this disorder and the internal ethylene concentration was detected in a multiple orchard trial. Differential methylation state of the ACS1 promoter correlated with both internal ethylene and injury occurrence indicating epigenetic regulation of ethylene biosynthesis and possibly events leading to disorder development.