Genome-Wide Identification and Expression Analysis of ZjCDPK Genes Related to Ripening of ‘Dongzao’ Jujube Fruit

Calcium-dependent protein kinases (CDPKs) are plant-specific Ca2+ sensors that translate calcium signals into phosphorylation responses. CDPKs coordinate both plant responses to the environment and plant growth, including fruit development and ripening. However, the CDPK gene family and its potential roles in jujube fruit development remain poorly characterized. In this study, 19 ZjCDPK genes were identified in the genome of ‘winter jujube’ (Ziziphus jujuba Mill. cv. ‘Dongzao’) and mapped to 11 of the 12 chromosomes. Phylogenetic analysis classified the ZjCDPK proteins into four groups, with CDPKs from Arabidopsis and tomato. Two intraspecific collinear gene pairs and sixteen orthologous gene pairs between ‘Dongzao’ and Arabidopsis were identified. Most family members exhibited similar organization of exon–intron splicing and contained similar motifs, with all containing a conserved serine/threonine protein kinase catalytic domain and four C-terminal EF-hand motifs. Promoter analysis identified 681 cis-acting elements, with abundant elements associated with abiotic stress, light, and phytohormone responses, including those related to abscisic acid, ethylene, methyl jasmonate, salicylic acid, auxin, and gibberellin. Developmental expression profiling across seven fruit stages, together with qRT-PCR validation, showed that ZjCDPK02, 08, 10, 12, 14, 16, and 19 accumulated preferentially during the late stages of fruit development. Correlation analysis further showed that ZjCDPK14 was strongly co-expressed with ZjCDPK02 (r = 0.96) and positively correlated with both fruit firmness (r = 0.907) and total soluble solids content (r = 0.816). Significant associations with these quality traits were also detected for ZjCDPK02, 04, 08, 15, 16, and 19. These findings provide a comprehensive framework of the ZjCDPK family and identify candidate genes for functional studies of calcium signaling during jujube fruit development, ripening, and quality formation.