Comprehensive Characterization of the TCP Gene Family in Punica granatum: Insights into Their Roles in Developmental Dynamics and Stress Adaptation

The plant-specific TCP transcription factor family plays crucial roles in morphogenesis and stress adaptation. While characterized in many species, this family remains unstudied in Punica granatum. We performed the first genome-wide analysis of the TCP family in pomegranate, identifying 24 PgTCP genes classified into the PCF, CIN, and CYC/TB1 subclades, supported by conserved gene structures and motifs. Evolutionary analysis indicated segmental duplication and purifying selection shaped this family. Expression profiling revealed distinct spatiotemporal patterns: PgTCP2/9/14/21 were highly expressed in flowers, with PgTCP21 also notably abundant in fruit tissues (seed coats and pericarp), suggesting roles in reproductive development. PgTCP19, an ortholog of the branching suppressor BRC1, showed dominant expression in dormant buds, implicating it in shoot architecture regulation. Furthermore, PgTCP5 and the miR319-targeted PgTCP22 were leaf-predominant, indicating a function in leaf development. Under abiotic stress, PgTCPs displayed dynamic, treatment-specific responses. A subset of genes was rapidly induced by cold, while PgTCP14 and PgTCP23 showed sustained upregulation during drought. Several light-responsive PgTCPs were suppressed under shading. This study provides a foundational resource, functionally classifies the PgTCP family, and identifies key candidates regulating organ development and stress resilience for future functional validation and molecular breeding in pomegranate. This work provides the first comprehensive overview of the TCP gene family in pomegranate and offers candidate genes for future functional studies related to development and stress responses.