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United States Department of Agriculture

Agricultural Research Service

Research Project: Genetic, Metabolic, and Physiological Factors Regulating Deciduous Tree Fruit Quality

Location: Physiology and Pathology of Tree Fruits Research

Title: Integrated metabolomic and transcriptomic profiling illustrates successive phases of increasing gene expression associated with chilling-related apple peel cell death

Authors
item Rudell, David
item Gapper, Nigel
item Hertog, Maarten -
item Nicolai, Bart -
item Buchanan, David
item Mattheis, James
item Watkins, C
item Lee, Jinwook
item Leisso, Rachel
item Giovannoni, James
item Johnston, Jason -
item Schaffer, Robert -

Submitted to: Metabolomics
Publication Type: Abstract Only
Publication Acceptance Date: May 24, 2013
Publication Date: July 1, 2013
Citation: Rudell Jr, D.R., Gapper, N.E., Hertog, M., Nicolai, B., Buchanan, D.A., Mattheis, J.P., Watkins, C.A., Lee, J., Leisso, R.S., Giovannoni, J.J., Johnston, J., Schaffer, R. 2013. Integrated metabolomic and transcriptomic profiling illustrates successive phases of increasing gene expression associated with chilling-related apple peel cell death. Metabolomics. 51.

Technical Abstract: Superficial scald is a chilling-related storage disorder of apple caused by the death of peel epidermal and hypodermal cells and associated discoloration. It is controlled using postharvest antioxidant (diphenylamine; DPA) and ethylene action inhibitor (1-methylcyclopropene; 1-MCP), and/or controlled atmosphere (CA) storage treatment. We are using integrated metabolomic and transcriptomic profiling to reveal metabolic processes necessary to develop for diagnostic tools, breeding markers, and novel treatments to mitigate economic impact of the disorder. ‘Granny Smith’ apples were stored for up to 6 months at 1 oC and apple peel sampled periodically. Scald was reduced in apples treated with DPA or 1-MCP compared with untreated apples. GC and LC-MS protocols were employed to profile over 600 discrete identified and unidentified metabolite MSTs and RNA-seq to evaluate the expression of over 36,000 gene models. Initial evaluation of these data using multi-block PLS-DA indicated that changes in both the metabolome and transcriptome were treatment dependent. Changes preceded visible scald symptoms in untreated fruit and a succession of increasing levels of 3 scald-associated metabolites [2,6,10-trimethyldodeca-2,7(E),9(E),11- tetraen-6-ol (CTOL; 12 w prior), then acylated steryl glycosides (ASGs; 8 w prior), then methanol (MeOH; coinciding with symptoms)] representing different metabolic events during storage. Pearson’s correlation (expression-product) networks of individual metabolite changes and summarized transcript data (k-means clustering) revealed clusters of gene models associated with successive increases in the levels of each model metabolite. Gene ontology analysis of early CTOL co-expressed genes are linked with stress response while later MeOH (cell-death) genes include cellular catabolism, cell death, and disassembly. Analysis of individual genes within highly correlated clusters highlights links with metabolites including among MeOH, methyl esters, and putative pectin methylesterase transcripts indicating that cell-death associated middle lamella degradation and an altered volatile aroma profile may be linked.

Last Modified: 8/1/2014
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