Integrated omics analysis provides preliminary insights into the regulatory network controlling ethephon-promoted calyx abscission in Korla Xiangli (Pyrus × sinkiangensis Yü)

Background Calyx abscission is a key horticultural trait affecting fruit quality in Korla Xiangli (Pyrus × sinkiangensis Yü ). Exogenous ethephon treatment has been shown to significantly promote calyx abscission, but the underlying molecular regulatory network and metabolic mechanisms that regulate ethephon-induced abscission remain poorly understood. Elucidation of these processes is essential to optimize calyx management strategies in commercial Korla Xiangli production. Results This study systematically elucidated the molecular regulatory network of ethephon-induced calyx abscission in Korla Xiangli by phenotypic observation, phytohormone profiling, wide-target metabolomics and high-throughput transcriptomic analyses. Treatment with 300 mg·L⁻¹ ethephon significantly accelerated abscission zone formation by two days, with abscission occurring seven days after pollination. The peak daily abscission rate reached 16.90%, which represented a 5.15-fold increase compared with the untreated control. The results demonstrated that the third day after pollination was the critical period for ethephon-mediated calyx abscission regulation. At this stage, ethylene concentration in the abscission zone significantly increased by 33.09% and indole-3-acetic acid content decreased sharply by 49.30%. In contrast, abscisic acid, salicylic acid, gibberellin A₃, and jasmonic acid levels were strongly upregulated, which suggests extensive hormonal regulation associated with abscission initiation. Transcriptome data showed transient induction of ERF1/2 and repression of AUX/IAA and SAUR genes, limiting polar auxin transport and enhancing ethylene sensitivity. Metabolomic profiling revealed 383 differential metabolites, primarily associated with flavonoid, lipid, and terpenoid pathways, collectively promoting ROS regulation, membrane destabilization, and programmed cell death. Network analyses identified MYB, AP2/ERF, and NAC transcription factors and highlighted key hub genes involved in auxin–ethylene crosstalk. Conclusions In this study, we first conducted phenotypic observations of ethephon-induced calyx abscission in Korla Xiangli, and then measured the levels of plant hormones, metabolites and gene expression in the abscission zone. These results provide a theoretical basis and genetic resources for the precise regulation and molecular breeding of calyx abscission in Korla Xiangli.