# Comparative Transcriptome Analysis in Tomato Fruit Reveals Genes, Pathways, and Processes Affected by the LEC1-LIKE4 Transcription Factor

## TL;DR

This study identifies genes and pathways influenced by the L1L4 transcription factor in tomato fruit development, impacting traits like color, texture, and flavor.

## Contribution

The study reveals novel regulatory roles of L1L4 in tomato fruit ripening and quality traits through transcriptome analysis of ZFN-edited lines.

## Key findings

- L1L4 disruption affects carotenoid and flavonoid pathways, influencing fruit color.
- L1L4 impacts cell wall modification and sugar metabolism, affecting texture and flavor.
- L1L4 interacts with histones and transcription factors like ERFs and MYBs in regulatory networks.

## Abstract

Tomato (Solanum lycopersicum) is a globally important crop, and enhancing its fruit quality and phenotypic traits is a key objective in modern breeding. This study investigates the role of the LEAFY-COTYLEDON1-LIKE4 (L1L4), an NF-YB subunit of the nuclear factor Y (NF-Y) transcription factor, in tomato fruit development using RNA-sequencing data from zinc-finger nuclease (ZFN)-targeted disruption lines. Differential gene expression (DEG) analyses of two independent l1l4 mutant lines compared to the wild-type line revealed significant alterations in key metabolic pathways and regulatory networks that are implicated in fruit ripening. Specifically, L1L4 disruption impacted the genes and pathways related to the fruit’s color development (carotenoid and flavonoids), texture (cell wall modification), flavor (sugar and volatile organic compound metabolism), and ripening-related hormone signaling. The analyses also revealed multiple differentially expressed histones, histone modifiers, and transcription factors (ERFs, MYBs, bHLHs, WRKYs, C2H2s, NACs, GRAS, MADs, and bZIPs), indicating that L1L4 participates in a complex regulatory network. These findings provide valuable insights into the role of L1L4 in orchestrating tomato fruit development and highlight it as a potential target for genetically improving the fruit quality.