Profiling the transcriptomic and metabolomic changes associated with apple fruit controlled-atmosphere storage related peel disorder

'Golden Delicious' (Malus x domestica Borkh.) (GD) is one of the most widely available pome fruit. External CO2-injury, a postharvest controlled-atmosphere storage related peel disorder, significantly impacts long-term storability and fruit quality for fresh apple and pear fruit cultivars, although annual incidence varies greatly. The experiment included 5%CO2-controlled atmosphere (CA), 5%CO2-CA plus 1-methylcyclopropene (CA+1-MCP), and regular air (RA) treatments and peel tissues were sampled at 14, 28, 56, 84 days storage over a three year period. RNA-Seq based transcriptome profiling (2011) and Lipdome profiling by LCMS (2011-2013) were carried out for sampled apple peel tissues. KEGG pathway analysis indicated oxidation/reduction, glycolysis, sodium transporters and glutamate biosynthesis enriched in CA but not RA and CA+1-MCP. Accordingly, gene ontology for CA emphasized the importance of the endoplasmic reticulum (ER), ER stress and the Unfolded Protein Response while CA+1-MCP down regulated these ER stress response and protein folding genes. Multivariate and time course analysis of RNA-seq and LCMS/APCI data provided genes and lipids of interest. SKP2A, an F-box protein known to be involved in severe ER stress, was detected only in CA stored fruit after 28 days storage. Results for the lipidome show (C18:3/18:2) diglyceride, β-SitoGluclinolenate, two monogalactose-diacylglycerol and two triacylglycerols species having a significant differences between treatments. Highly relevant network gene models selected by sparse Partial Least Squares is being validated by RTqPCR using all three years GD peel tissue. These results will determine the key molecular responses of apple peel tissue to high-CO2 controlled-atmosphere storage.