Morphological, physiochemical, and transcriptome analysis and CaEXP4 identification during pepper (Capsicum annuum L.) fruit cracking

•The cracking-susceptible cultivar‘L92’was subjected to morphological, physiochemical and transcriptome analyses and an assay of postharvest water loss.•The polygalacturonase, peroxidase, and cellulase activity levels and water-soluble pectin and lignin contents were significantly higher in FSC (fruit seriously cracking) fruits than in FNC (fruit without cracking) fruits.•By comparing the FSC with the FNC fruits and analyzing DEG profiles during the fruit cracking process, 45 DEGs were found to be significantly enriched in KEGG pathways related to cell wall metabolism and lignin biosynthesis, which are involved in the fruit cracking process.•The silencing of CaEXP4 induced cells in the epidermal layer to be smaller and more neatly and tightly arranged, with a greater number of cell layers of the sub-epidermal layer compared with control fruit. In pepper (Capsicum annuum L.), fruit cracking is a common physical deformation that not only affects the fruit quality, but also increases the water loss rate during storage and reduces shelf-life and economic value. To comprehensively unravel the putative genes and mechanism underlying fruit cracking, the cracking-susceptible cultivar ‘L92’ was subjected to morphological, physiochemical and transcriptome analyses and an assay of postharvest water loss. The polygalacturonase, peroxidase, and cellulase activity levels and water-soluble pectin and lignin contents were significantly higher in FSC (fruit seriously cracking) fruits than in FNC (fruit without cracking) fruits. The hemicellulose and cellulose contents of FSC fruits were lower than those of FNC fruits; with non-significant differences in chelator trans-1,2-diaminocyclohexane-N,N,N0,N0-tetraacetic acid-soluble pectin and sodium carbonate-soluble pectin levels. By comparing the FSC with the FNC fruits and analyzing differentially expressed gene (DEG) profiles during the fruit cracking process, 1,574 DEGs were identified. Among them, 45 unigenes were significantly enriched in KEGG pathways related to cell wall metabolism and lignin biosynthesis. The silencing of CaEXP4 induced cells in the epidermal layer to be smaller and more neatly and tightly arranged, with a greater number of cell layers of the sub-epidermal layer compared with control fruit. Small structural modifications may lead to changes in cell wall structure and elasticity, which might have caused the fruit cracking. To the best of our knowledge, this is the first morphological, histological, physi