The ethylene-responsive miR-99-3p--PvYUC2--PvACS1 signalling hub modulates secondary wall thickening in postharvest common beans

Postharvest deterioration of horticultural crops is profoundly influenced by their responses to the shifting environment after harvest. In common bean (Phaseolus vulgaris) pods, secondary wall thickening is a key determinant of quality loss, a process known to be regulated by the phytohormone ethylene. However, the upstream signalling components and integrated networks that perceive and transduce ethylene signals to orchestrate this cell wall remodelling remain poorly understood. Here, we demonstrate that exogenous ethylene acts as a potent environmental signal, enhancing both secondary wall deposition and ethylene biosynthesis in postharvest pods, whereas the ethylene action inhibitor 1-MCP suppresses these responses. Integrated transcriptome and small RNA sequencing revealed a comprehensive rewiring of gene and miRNA expression under these contrasting ethylene signalling conditions. We identified that ethylene upregulates a suite of genes involved in its own biosynthesis, auxin metabolism, secondary wall biosynthesis, and ethylene-responsive transcription factors. Through protein-protein interaction analysis and yeast two-hybrid assays, we discovered a novel molecular interface between hormone pathways: PvYUC2 , a key auxin biosynthetic enzyme, directly interacts with the ethylene biosynthetic enzyme PvACS1 . Furthermore, we experimentally validated PvYUC2 as a direct target of a differentially expressed miRNA, miR-99-3p. Collectively, our findings unveil a previously unrecognised, miRNA-gated signalling hub—where miR-99-3p fine-tunes the PvYUC2 – PvACS1 interaction—that integrates auxin and ethylene pathways to modulate ethylene-mediated secondary wall thickening. This study provides novel mechanistic insights into how postharvest tissues perceive and transduce hormonal environmental signals to drive specific physiological changes, offering a potential molecular toolkit for managing postharvest quality in legumes and beyond.