Genome-wide identification and expression analyses reveal cell wall degradation gene family networks in kiwifruit...

Understanding the molecular mechanisms underlying fleshy fruit softening holds significant biological importance, as it provides critical insights for enhancing fruit quality, nutritional value, and shelf life while reducing postharvest losses. Although key structural genes associated with softening have been extensively characterized in model fleshy fruits, the gene families regulating kiwifruit (Actinidia chinensis) softening remain incompletely elucidated. Here, we performed genome-wide analyses to identify nine cell wall-related gene families potentially involved in fruit softening in kiwifruit: PL, BXL, CEL, EXP, MAN, PG, PME, TBG/BGAL, and XTH. Systematic phylogenetic, gene structure, and collinear homology analyses, combined with expression profiling and regulatory network construction, revealed the functional divergence of these gene families. Focusing specifically on the PL gene family, we applied AlphaFold3 to generate large-scale predictions of interactions between TF and SG interactions in the regulatory network. High-confidence interactions were selected via rigorous scoring, and the network was optimized with expression profiling. Electrophoretic mobility shift (EMSA) and luciferase reporter (LUC) assays confirmed the network-predicted transcriptional regulation of AcPL26 by AcERF015. Moreover, transient expression of AcERF015 in kiwifruit markedly reduced fruit firmness and elevated water loss rate, accompanied by a significant up-regulation of AcPL26 transcript levels as revealed by RT-qPCR, as well as increased pectate lyase activity and reduced protopectin content, collectively supporting the predictions of the regulatory network. Our findings provide pathway regulatory insights into the PCW degradation gene families governing kiwifruit softening and support improvement strategies.