# A single nucleotide substitution in the SlMCT gene contributes to great morphological alternations in tomato

## TL;DR

A single mutation in the SlMCT gene in tomatoes causes significant changes in plant growth and fruit color by affecting key metabolic pathways.

## Contribution

A rare MCT mutant in tomato reveals how a single nucleotide substitution alters plant development and pigment biosynthesis.

## Key findings

- A single nucleotide substitution in SlMCT causes dwarfism, chlorosis, and yellow fruits in tomato.
- Over-expression of wild-type SlMCT restores fruit color and other defective traits in the mutant.
- The mutation affects metabolic pathways, altering levels of carotenoids, hormones, and other compounds.

## Abstract

Terpenoids, a group of metabolites, are important to plant development and color formation, and serve as valuable nutrients for humans. The enzyme 4-diphosphocytidyl- 2 C-methyl-D-erythritol cytidyltransferase (MCT) plays a pivotal role in the methylerythritol phosphate (MEP) pathway for terpenoid biosynthesis. However, the potential lethality of MCT mutants has hindered further exploration into its functional role in terpenoid metabolite families in plants. Here, we characterized a rare MCT mutant yfm with dwarfism, chlorosis, small leaves, and yellow fruits in tomato. Map-based cloning and sequence analysis revealed that a single nucleotide substitution in the SlMCT gene, which resulted in a point mutation (Leu297Pro) in amino acid in the mutant. Over-expression and complementation of the wild-type SlMCTT in the yfm mutant restored the fruit color and the other defective phenotypes. This mutation altered the gene expressions and metabolic components in the MEP and other pathways. Consequently, the total contents of carotenoids, chlorophyll, IAA, GAs, and SA were decreased, while the contents of CK, JA, and ABA were increased. Eventually, these alterations led to changes in plant phenotypes and fruit color in yfm. These findings provide novel insights into understanding the roles of MCT on plant development and pigment biosynthesis.

The online version contains supplementary material available at 10.1186/s43897-025-00159-x.