Genome-Wide Identification of the Polygalacturonase Gene Family and Its Potential Association with Abscission Zone in Capsicum annuum L.

Abstract

Background: Polygalacturonase (PG) genes regulate plant organ abscission by degrading pectin in the cell wall. However, their association with pedicel abscission susceptibility in pepper remains poorly understood. Methods: 47 CaPG genes were identified were identified in the ‘Zunla1’ genome and characterized by structural, evolutionary, and comparative genomic analyses. Their expression profiles across various tissues and fruit development stages were examined using transcriptome data. Ethephon treatment and qRT-PCR were employed to assess gene responses during ethylene-induced pedicel abscission. Results: The 47 CaPG genes were distributed across 12 chromosomes, with CaPG1 to CaPG5 unanchored. Most proteins were hydrophilic, nuclear-localized, and had promoters enriched in light-responsive elements. Collinearity analysis revealed limited segmental duplication, and Ka/Ks values indicated strong purifying selection. Phylogenetic and collinearity analyses showed that CaPG genes are more closely related to those in tomato than in Arabidopsis or maize. Expression profiling revealed tissue- and stage-specific patterns, with 21 CaPG genes associated with pedicel abscission susceptibility. Ethephon treatment enhanced abscission and upregulated several CaPG genes. Conclusions: This study offers insights into the CaPG gene family’s structure, evolution, and function. Specific CaPG genes likely contribute to ethylene-mediated pedicel abscission, providing potential targets for improving fruit-retention traits in pepper.