BackgroundApple fruit mealiness is one of the most important textural problems that results from an undesirable ripening process during storage. This phenotype is characterized by textural deterioration described as soft, grainy and dry fruit. Despite several studies, little is known about mealiness development and the associated molecular events. In this study, we integrated phenotypic, microscopic, transcriptomic and biochemical analyses to gain insights into the molecular basis of mealiness development.ResultsInstrumental texture characterization allowed the refinement of the definition of apple mealiness. In parallel, a new and simple quantitative test to assess this phenotype was developed.Six individuals with contrasting mealiness were selected among a progeny and used to perform a global transcriptome analysis during fruit development and cold storage. Potential candidate genes associated with the initiation of mealiness were identified. Amongst these, the expression profile of an early down-regulated transcript similar to an Arabidopsis thaliana pectin methylesterase gene (AtPME2) matched with mealiness development. In silico analyses of this Malus x domestica PME gene (MdPME2) confirmed its specific pattern compared with all other identified MdPME genes. Protein fusion experiments showed that MdPME2 is secreted into the apoplast in accordance with a possible activity on pectin structure. Further microscopic analysis indicated a progressive loss of cell to cell adhesion in mealy apple fruits. Biochemical analysis revealed specific modifications of pectin residues associated with mealiness, without global changes in the degree of methylesterification of pectins.ConclusionsThese data support the role of PME in cell wall remodelling during apple fruit development and ripening and suggest a local action of these enzymes. Mealiness may partially result from qualitative and spatial variations of pectin microarchitecture rather than quantitative pectin differences, and these changes may occur early in fruit development. The specific MdPME2 gene highlighted in this study could be a good early marker of texture unfavourable trait in apple.Electronic supplementary materialThe online version of this article (doi:10.1186/s12870-014-0375-3) contains supplementary material, which is available to authorized users.