Genome-edited tomato and cucumber plants with higher yields using CRISPR-Cas9 modulation of the CLAVATA pathway

Overview

This solution applies CRISPR-Cas9 genome editing to tomato and cucumber plants by targeting the CLAVATA signaling pathway, which controls the size and activity of plant meristems—the tissues responsible for producing flowers, fruits, and roots. By modulating specific CLE peptide genes and their receptors, the technology aims to enlarge reproductive meristems and increase fruit yield. The approach is grounded in established research showing that loss-of-function in CLE signaling genes can lead to enlarged flowers and fruits. With a proven transformation pipeline for tomato and a transferable protocol for cucurbit species, this offering addresses a direct need in agricultural productivity for two commercially important crop species.

Technical specifications

• Target pathway: The CLAVATA3 (CLV3) peptide-receptor pathway and related CLE peptide-receptor modules that negatively regulate shoot apical meristem size
• Candidate genes identified in tomato: SlCLV3 and SlCLE9 (orthologs of Arabidopsis CLV3, with conserved meristem function) and SlCLE7 and SlCLE24 (orthologs of Arabidopsis CLE45/CLE33, important for phloem tissue formation)
• Editing approach: CRISPR-Cas9 with guide RNAs designed to create editing events at the beginning of coding regions of target CLE genes
• Editing strategies: Single-gene targeting and multi-gene targeting to test combinations of modifications
• Discovery pipeline: Transcriptomics analysis of isolated meristems combined with bioinformatics to identify the most promising CLE candidate genes in both tomato and cucumber genomes
• Transformation capabilities: Established tomato transformation pipeline and adaptable cucurbit transformation protocol
• Infrastructure: Dedicated cell culture facilities for transformation work and greenhouse space for growing edited plants through fruit harvest

Technology readiness level

The project is at an early-to-mid research stage. The research team has completed bioinformatic identification of CLE gene clusters in tomato and has functional validation evidence for SlCLV3/SlCLE9 in meristem regulation and SlCLE7/SlCLE24 in phloem development. The next phase involves transcriptomics-based candidate prioritization, CRISPR-Cas9 editing, plant regeneration, and yield screening over an estimated three-year project timeline. Genome-edited plants with improved yields have not yet been produced; the technology is currently at the stage of candidate gene selection and editing design, with greenhouse validation as the next milestone.