title: Transcriptomic events associated with internal browning of apple during postharvest storage.
abstract: BACKGROUND
  Postharvest ripening of apple (Malus x domestica) can be slowed down by low temperatures, and a combination of low O2 and high CO2 levels. While this maintains the quality of most fruit, occasionally storage disorders such as flesh browning can occur. This study aimed to explore changes in the apple transcriptome associated with a flesh browning disorder related to controlled atmosphere storage using RNA-sequencing techniques. Samples from a browning-susceptible cultivar ('Braeburn') were stored for four months under controlled atmosphere. Based on a visual browning index, the inner and outer cortex of the stored apples was classified as healthy or affected tissue.
  
  
  RESULTS
  Over 600 million short single-end reads were mapped onto the Malus consensus coding sequence set, and differences in the expression profiles between healthy and affected tissues were assessed to identify candidate genes associated with internal browning in a tissue-specific manner. Genes involved in lipid metabolism, secondary metabolism, and cell wall modifications were highly modified in the affected inner cortex, while energy-related and stress-related genes were mostly altered in the outer cortex. The expression levels of several of them were confirmed using qRT-PCR. Additionally, a set of novel browning-specific differentially expressed genes, including pyruvate dehydrogenase and 1-aminocyclopropane-1-carboxylate oxidase, was validated in apples stored for various periods at different controlled atmosphere conditions, giving rise to potential biomarkers associated with high risk of browning development.
  
  
  CONCLUSIONS
  The gene expression data presented in this study will help elucidate the molecular mechanism of browning development in apples at controlled atmosphere storage. A conceptual model, including energy-related (linked to the tricarboxylic acid cycle and the electron transport chain) and lipid-related genes (related to membrane alterations, and fatty acid oxidation), for browning development in apple is proposed, which may be relevant for future studies towards improving the postharvest life of apple.
authors.forename: Ifigeneia
authors.initials: I
authors.lastname: Mellidou
authors.forename: Kim
authors.initials: K
authors.lastname: Buts
authors.forename: Darwish
authors.initials: D
authors.lastname: Hatoum
authors.forename: Quang Tri
authors.initials: QT
authors.lastname: Ho
authors.forename: Jason W
authors.initials: JW
authors.lastname: Johnston
authors.forename: Christopher B
authors.initials: CB
authors.lastname: Watkins
authors.forename: Robert J
authors.initials: RJ
authors.lastname: Schaffer
authors.forename: Nigel E
authors.initials: NE
authors.lastname: Gapper
authors.forename: Jim J
authors.initials: JJ
authors.lastname: Giovannoni
authors.forename: David R
authors.initials: DR
authors.lastname: Rudell
authors.forename: Maarten L A T M
authors.initials: ML
authors.lastname: Hertog
authors.forename: Bart M
authors.initials: BM
authors.lastname: Nicolai
mesh_terms: D015415:Biomarkers; D003080:Cold Temperature; D061353:Food Storage; D005638:Fruit / Q000378:metabolism; D018506:Gene Expression Regulation, Plant; D027845:Malus / Q000235:genetics* / Q000378:metabolism*; D010940:Plant Proteins / Q000235:genetics* / Q000378:metabolism; D060888:Real-Time Polymerase Chain Reaction; D017423:Sequence Analysis, RNA; D013997:Time Factors; D059467:Transcriptome
chemical_list: D015415:Biomarkers; D010940:Plant Proteins