Integrated transcriptome and proteome indicate molecular mechanisms of endogenous hormonal imbalance regulating variation in jujube (Ziziphus jujuba Mill.) embryo fertility

Embryo abortion impedes hybrid breeding and limits development of the economically important Chinese jujube ( Ziziphus jujuba Mill.) industry. To elucidate hormonal regulation of jujube embryogenesis, transcriptomic, proteomic, and hormone content analyses were performed on high- and low-fertility embryos at 30, 40, and 50 days of development. Differentially expressed genes (DEGs) and proteins (DEPs) were screened and subjected to functional enrichment analysis, cluster analysis, and interaction network analysis. DEGs and DEPs were enriched in plant hormone signal transduction. The expression patterns of genes and proteins in the hormone signaling pathways of jujube embryos with different fertility levels varied significantly yet were interrelated. Hormone dynamic analysis indicated a decrease in indole-3-acetic acid (IAA) content and excessive accumulation of abscisic acid (ABA) and ethylene (ACC) in low-fertility embryos, resulting in the imbalance of (IAA + CTK + GA 3 )/(ABA + ACC). These findings provide novel targets for molecular breeding to improve jujube fruit set. • Embryo abortion is a major constraint in jujube breeding and industry development, requiring urgent solutions. • Multi-omics reveals hormone signaling pathways as core regulators of jujube embryo development and abortion. • Hormone genes were dysregulated in abortive embryos and validated by RT-qPCR. • The (IAA + CTK + GA 3 )/(ABA + ACC) ratio serves as a key biomarker for embryo fate determination.