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Fruit cracking is a common physiological disorder in many fruit species. Jujube (Ziziphus jujuba Mill.) is an economically valuable fruit in which fruit cracking seriously affects fruit yield and quality and causes significant economic losses. To elucidate cracking-related molecular mechanisms, the cracking-susceptible cultivars 'Cuizaohong' and 'Jinsixiaozao' and the cracking-resistant cultivar 'Muzao' were selected, and comparative transcriptome analyses of cracking and non-cracking 'Cuizaohong' (CC and NC), cracking and non-cracking 'Jinsixiaozao' (CJ and NJ), and non-cracking 'Muzao' (NM) were conducted. A total of 131 differentially expressed genes (DEGs) were common to the CC vs. NC and CJ vs. NJ comparisons. To avoid passive processes after fruit cracking, we also mainly focused on the 225 gradually downregulated DEGs in the CJ, NJ, and NM samples. The functional annotation of the candidate DEGs revealed that 61 genes related to calcium, the cell wall, the cuticle structure, hormone metabolism, starch/sucrose metabolism, transcription factors, and water transport were highly expressed in cracking fruits. We propose that expression-level changes in these genes might increase the turgor pressure and weaken mechanical properties, ultimately leading to jujube fruit cracking. These results may serve as a rich genetic resource for future investigations on fruit cracking mechanisms in jujube and in other fruit species. [ABSTRACT FROM AUTHOR]

• Analysis of exocarp and endocarp of jujube by HPLC-MS/MS. • ABA and MeJA induced fruit cracking. • Transcriptome analysis before and after exogenous hormone treatment. • Identification of transcription factors and cell wall genes related to fruit cracking. Fruit cracking is a physiological disease that occurs during the development of jujube, abscisic acid (ABA) and jasmonic acid (JA) mainly regulate the cell wall metabolic pathway and induce fruit cracking. Here, we used high-performance liquid chromatography-tandem mass spectrometry (HPLC-MS/MS) to detect phytohormone-related metabolites at different developmental stages in cracking-susceptible (CS-15) and cracking-resistant (CR-04) individuals of full-sibling hybrid offspring. The fruit of 'Pingshunbenzao' jujube was treated with ABA and MeJA at the white-ripening stage, and the 48-h fruit cracking index was significantly increased compared to that of CK (water). Furthermore, RNA-seq of semi-red stage fruits identified several differentially expressed genes, related to the cell wall, such as SBT1.7 (Contig21.0.484), EXPA (Contig12.0.7) and QRT3 (newGene_1935), and transcription factors (TFs). These results reveal the relationship between the levels of different hormones and fruit cracking, identify genes associated with fruit cracking, and provide new insights to solve the problem of fruit cracking through hormonal regulation. [ABSTRACT FROM AUTHOR]