The SlTPL3–SlWUS module regulates multi‐locule formation in tomato by modulating auxin and gibberellin levels in the shoot apical meristem

ABSTRACT Malformed fruits depreciate a plant's market value. In tomato ( Solanum lycopersicum ), fruit malformation is associated with the multi‐locule trait, which involves genes regulating shoot apical meristem (SAM) development. The expression pattern of TOPLESS3 ( SlTPL3 ) throughout SAM development prompted us to investigate its functional significance via RNA interference (RNAi) and clustered regularly interspaced short palindromic repeats/CRISPR‐associated nuclease 9 (Cas9)‐mediated gene editing. Lower SlTPL3 transcript levels resulted in larger fruits with more locules and larger SAMs at the 5 d after germination (DAG5) stage. Differentially expressed genes in the SAM of wild‐type (WT) and SlTPL3‐ RNAi plants, identified by transcriptome deep sequencing (RNA‐seq), were enriched in the gibberellin (GA) biosynthesis and plant hormone signaling pathways. Moreover, exogenous auxin and paclobutrazol treatments rescued the multi‐locule phenotype, indicating that SlTPL3 affects SAM size by mediating auxin and GA levels in the SAM. Furthermore, SlTPL3 interacted with WUSCHEL (SlWUS), which plays an important role in SAM size maintenance. We conducted RNA‐seq and DNA affinity purification followed by sequencing (DAP‐seq) analyses to identify the genes regulated by SlTPL3 and SlWUS in the SAM and to determine how they regulate SAM size. We detected 24 overlapping genes regulated by SlTPL3 and SlWUS and harboring an SlWUS‐binding motif in their promoters. Furthermore, functional annotation revealed a notable enrichment for functions in auxin transport, auxin signal transduction, and GA biosynthesis. Dual‐luciferase assays also revealed that SlTPL3 enhances SlWUS‐mediated regulation (repression and activation) of SlPIN3 and SlGA2ox4 transcription, indicating that the SlTPL3–SlWUS module regulates SAM size by mediating auxin distribution and GA levels, and perturbations of this module result in enlarged SAM. These results provide novel insights into the molecular mechanism of SAM maintenance and locule formation in tomato and highlight the SlTPL3–SlWUS module as a key regulator.