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.

Cold stress induces malformed tomato fruits by breaking the feedback loops of stem cell regulation in floral meristem

“…Alternatively, the homeostasis of GA and ABA in the OC region of FM may also be directly regulated by SlWUS. Previously, it was reported that both SlGA3ox (Solyc03g119910), involved in GA biosynthesis, and SlGA2ox4 (Solyc07g061730), involved in GA metabolism, exhibited upregulation in RNAi‐SlTPL3 tomato lines (Song et al ., 2022). As SlTPL3 acts as the inhibitor of SlWUS in the late stage of floral development (Bollier et al ., 2018), it is reasonable to infer that SlWUS could influence GA biosynthesis or metabolism.…”

New Advances in the Study of Regulation of Tomato Flowering-Related Genes Using Biotechnological Approaches

“…Regulation of the formation of multiple locules in tomato fruits is achieved by modulating the levels of auxin and gibberellin (GA) in apical meristems, for which the transcriptional repressor TPL3 and WUS are responsible [128]. A protein interaction was found between them, ensuring the regulation of auxin transporter genes and enzymes for gibberellin biosynthesis.…”