Integrative metabolome and transcriptome profiling reveal key metabolic regulatory networks in Ziziphus jujuba cv. Dongzao pulp

‘Dongzao’ (Ziziphus jujuba ‘Dongzao’) is an economically important fresh fruit well known for its distinctive flavor and significant nutritional benefits. However, dynamic alterations in the genetic and metabolic networks that regulate the development of ‘Dongzao’ pulp are not fully elucidated. In this study, first, a metabolic regulatory network was constructed. Next, the metabolic landscape of the ‘Dongzao’ jujube fruit pulp was established during development and ripening by using a joint analysis of metabolomic and transcriptomic data. This dataset was used to establish a global map of changes in the major metabolites throughout ‘Dongzao’ pulp development. The potential regulatory networks were then dissected, and the key structural genes and transcription factors associated with modulating the metabolism of important jujube fruit ingredients were identified. Further bioinformatics analyses and transient gene overexpression revealed that ZjSHINE3 and ZjNAC29 act as key transcription factors involved in sucrose and malic acid accumulation, respectively. In summary, this study provides novel insights into the metabolic regulatory networks underlying jujube fruit pulp development and generates a useful resource for genetic improvement and breeding studies of jujube.