Tomato mutagenesis platform using transposon activation and gene editing

Overview

This research program delivers a mutagenesis and trait-discovery platform for tomato built on activating dormant retrotransposon systems (GYPSY and COPIA) combined with targeted gene editing. By awakening these natural mobile genetic elements, the platform creates new allelic diversity and enables site-selected gene insertions or knockouts that are difficult to achieve through conventional breeding alone.

The approach has produced two validated proof-of-concept outcomes. First, a COPIA insertion in the xyloglucan endotransglucosylase/hydrolase gene slXTH9 produced a near-complete loss-of-function allele linked to firmer fruit texture and longer post-harvest shelf life. Second, a COPIA LTR-retrotransposon insertion in the intron of Solyc02g079490 generated a hypomorphic allele associated with elevated accumulation of 2-phenylethanol, a volatile responsible for the characteristic floral aroma of heirloom tomatoes.

The platform offers breeders, seed companies, and food industry partners a route to novel tomato varieties with improved post-harvest performance and enhanced sensory quality.

Technical specifications

Core capabilities:

• Transposon activation: Targeted reactivation of endogenous GYPSY and COPIA retrotransposon families in tomato to generate heritable genetic variation
• Site-selected insertion: Precision gene editing to direct transposon insertions into specific genomic loci for targeted gene disruption or regulatory rewiring
• Gene knockout: CRISPR-based editing to inactivate genes of interest for functional studies and trait development
• Validated gene targets: slXTH9 (fruit softening and shelf life) and Solyc02g079490 (2-phenylethanol biosynthesis and aroma)

Key features:

• Leverages natural transposon biology rather than introducing foreign mutagens, preserving genomic context
• Combines transposon mutagenesis with modern gene editing for both random and targeted variation
• Demonstrated utility for both quality traits (texture, shelf life) and flavor traits (aroma volatiles)
• Compatible with introgression line analysis and TIP-GWAS for trait association

Technology readiness level

The platform is at an early-to-mid technology readiness stage. Proof-of-concept has been established through published validation of two distinct trait applications: a loss-of-function slXTH9 allele for fruit firmness and a hypomorphic Solyc02g079490 allele for enhanced 2-phenylethanol accumulation. The next phase involves selecting target genes, constructing editing vectors, and performing genetic transformation, followed by in vitro expression checks in regenerants and progeny from seed. Further validation, including removal of the COPIA insertion through genome editing to formally confirm the role of Solyc02g079490, is planned.