# Promoter variations of ClERF1 gene determines flesh firmness in watermelon

## TL;DR

This study identifies the ClERF1 gene as a key factor influencing flesh firmness in watermelon, offering insights for breeding improvements.

## Contribution

The study reveals that promoter variations in ClERF1 affect gene expression and fruit firmness in watermelon.

## Key findings

- ClERF1 is a candidate gene for watermelon flesh firmness, identified through QTL mapping and sequence analysis.
- Promoter activity of ClERF1 is stronger in hard-flesh watermelon, leading to higher gene expression.
- ClERF1 regulates cell wall biosynthesis and fruit ripening by binding to promoters of ClAux/IAA and ClEXT.

## Abstract

Flesh firmness is a critical factor that influences fruit storability, shelf-life and consumer’s preference as well. However, less is known about the key genetic factors that are associated with flesh firmness in fresh fruits like watermelon.

In this study, through bulk segregant analysis (BSA-seq), we identified a quantitative trait locus (QTL) that influenced variations in flesh firmness among recombinant inbred lines (RIL) developed from cross between the Citrullus mucosospermus accession ZJU152 with hard-flesh and Citrullus lanatus accession ZJU163 with soft-flesh. Fine mapping and sequence variations analyses revealed that ethylene-responsive factor 1 (ClERF1) was the most likely candidate gene for watermelon flesh firmness. Furthermore, several variations existed in the promoter region between ClERF1 of two parents, and significantly higher expressions of ClERF1 were found in hard-flesh ZJU152 compared with soft-flesh ZJU163 at key developmental stages. DUAL-LUC and GUS assays suggested much stronger promoter activity in ZJU152 over ZJU163. In addition, the kompetitive allele-specific PCR (KASP) genotyping datasets of RIL populations and germplasm accessions further supported ClERF1 as a possible candidate gene for fruit flesh firmness variability and the hard-flesh genotype might only exist in wild species C. mucosospermus. Through yeast one-hybrid (Y1H) and dual luciferase assay, we found that ClERF1 could directly bind to the promoters of auxin-responsive protein (ClAux/IAA) and exostosin family protein (ClEXT) and positively regulated their expressions influencing fruit ripening and cell wall biosynthesis.

Our results indicate that ClERF1 encoding an ethylene-responsive factor 1 is associated with flesh firmness in watermelon and provide mechanistic insight into the regulation of flesh firmness, and the ClERF1 gene is potentially applicable to the molecular improvement of fruit-flesh firmness by design breeding.

The online version contains supplementary material available at 10.1186/s12870-024-05000-z.