Objective To explore the molecular mechanisms underlying the morphological differences in fruits and seeds of Ziziphus jujuba var. spinosa from different sources and to identify key genes influencing the morphological variation in Z. jujuba var. spinosa fruits and seeds. Methods Wild and grafted Z. jujuba var. spinosa fruits and seeds were used as materials. Phenotypic differences in their appearance were analyzed using a phenotypic group approach. Transcriptome sequencing was performed using the Illumina HiSeq platform. After data quality control, assembly, and gene annotation, differentially expressed genes (DEGs) were analyzed and screened. Quantitative real-time PCR (qRT-PCR) was used to assess the expression levels of key genes in different tissues, under gibberellin (GA₃) and drought stress treatments. Results The transverse and longitudinal diameters, as well as the weight of grafted Z. jujuba var. spinosa fruits, were significantly larger than those of wild Z. jujuba var. spinosa fruits. Similarly, the longitudinal diameter, thickness, and weight of grafted Z. jujuba var. spinosa seeds were significantly higher than those of wild Z. jujuba var. spinosa seeds. Transcriptome sequencing revealed that DEGs between grafted and wild Z. jujuba var. spinosa fruits and seeds were related to stress response, transcriptional regulation, plant hormone signal transduction, and phenylpropanoid biosynthesis. Through qRT-PCR, core DEGs influencing the morphological development of Z. jujuba var. spinosa fruits and seeds were identified, including WRKY53, WRKY40, TIFY9, NCED3, TSJT1, NRT3.1, BZIP9, TEN1, BXL1, and LRX4. After treatment with 150 mg/L GA₃, the expression levels of WRKY53, LRX4, NRT3.1, and TIFY9 were significantly upregulated, whereas BZIP9 and NCED3 were significantly downregulated. Under PEG-6000 drought stress, the expression levels of WRKY53, WRKY40, TEN1, TSJT1, and TIFY9 were significantly upregulated, while those of BZIP9 and LRX4 were significantly down-regulated. Conclusion This study preliminarily elucidated the molecular mechanisms underlying the morphological differences between grafted and wild Z. jujuba var. spinosa fruits and seeds. It also identified key candidate genes influencing the morphological development of fruits and seeds and their expression patterns under different stress conditions. These findings provide a theoretical basis and key targets for molecular breeding, environmental adaptability studies, and resource improvement of Z. jujuba var. spinosa.

Ziziphus jujuba Mill. var. spinosa (Bunge) Hu ex H. F. Chow  /  wild  /  grafted  /  fruit  /  Ziziphi Spinosae Semen  /  gibberellin  /  drought