Genome-Wide Characterization of the bZIP Gene Family in Winter Jujube Highlights ZjbZIP7’s Association with Late Fruit Development

Background: Basic leucine zipper (bZIP) transcription factors function widely in plant development, hormone signaling, and fruit ripening, but the bZIP family and its potential regulatory roles in winter jujube fruit development remain poorly characterized. Methods: a genome-wide analysis was performed using the gapless genome assembly of winter jujube (Ziziphus jujuba Mill. cv. Dongzao), including phylogenetic, chromosomal distribution, gene duplication, synteny, gene structure, conserved motif, and promoter cis-element analyses. Developmental expression patterns were investigated using RNA-seq and RT-qPCR. Weighted gene co-expression network analysis (WGCNA) and a yeast one-hybrid assay were further used to examine the co-expression relationships of ZjbZIP7 and its promoter-binding association with ZjACO1. Results: A total of 52 ZjbZIP genes were identified and classified into nine phylogenetic groups. These genes were unevenly distributed across 11 chromosomes, and 11 segmentally duplicated gene pairs were detected. Comparative synteny analysis identified 46 syntenic bZIP gene pairs between winter jujube and the sour jujube (Z. jujuba var. spinosa) and 42 between winter jujube and Arabidopsis thaliana. Promoter analysis identified 53 types of cis-acting elements associated with light, phytohormones, stress responses, and development; notably, abscisic acid-responsive elements were present in 47 of the 52 promoters. RNA-seq analysis across seven fruit developmental stages showed that 18 ZjbZIP genes accumulated preferentially during the late stages, with ZjbZIP7 showing particularly pronounced transcript accumulation during the late developmental stages. RT-qPCR analysis of eight representative genes broadly confirmed their RNA-seq profiles. Weighted gene co-expression network analysis identified 38 genes tightly co-expressed with ZjbZIP7, including the ethylene biosynthesis gene ZjACO1. A yeast one-hybrid assay further demonstrated that ZjbZIP7 bound to the ZjACO1 promoter in yeast. Conclusions: These findings enhance our understanding of the evolutionary relationships and developmental expression patterns of the ZjbZIP gene family as a whole and provide valuable candidate genes for elucidating fruit-ripening mechanisms that may be useful in improving fruit quality in winter jujube breeding.