Transcriptome analysis integrated with changes in cell wall polysaccharides of different fresh-cut chili pepper cultivars during storage reveals the softening mechanism

[Display omitted] •Hangjiao No. 2 softened more rapidly than Lafeng No. 3.•Changes of cell wall polysaccharide during storage were studied.•Different softening rate was due to the initial difference in pectin structure.•Hangjiao No. 2 showed more pectin solublisation and loss of side chains from RG-I.•Hangjiao No. 2 had higher activities of PG and α-L-Af during the late storage period. Cell wall disassembly and transcriptomic changes during storage of two fresh-cut chili pepper cultivars displaying contrasting softening rates were investigated. Results showed that Hangjiao No. 2 (HJ-2) softened more rapidly than Lafeng No. 3 (LF-3). Compared with LF-3, HJ-2 had a higher content of WSP, more side chains of RG-I in three pectin fractions, and higher activities of PME, PL, and β-Gal at day-0. During storage, HJ-2 showed more markable pectin solubilization, more severe degradation in CSP and NSP, and greater loss of side chains from RG-I in three pectin fractions, which were correlated with increased activities of PG and α-L-Af. Furthermore, the higher up-regulation of PG (LOC107870605, LOC107851416) and α-L-Af (LOC107848776, LOC107856612) were screened in HJ-2. In conclusion, the different softening rate between cultivars was not only due to the fundamental differences in pectin structure but also pectin degradation regulated by related enzymes and gene expression levels.