A 13-bp insertion in CmAPRR2 gene disrupts its function in regulating the green rind formation of immature melon fruit (Cucumis melo L.).

Melon (Cucumis melo L.) fruit rind color represents a crucial agronomic trait that significantly influences consumer preference, market value, and postharvest quality. Although economically important, the molecular mechanisms regulating rind color variation remain largely unexplored. In this study, we identified and characterized a key gene controlling the immature fruit rind color from two melon inbred lines, TC3 with immature green fruit rind and Tm34 with immature light-green fruit rind. Genetic segregation analysis across multiple populations demonstrated that immature green fruit rind color is governed by a single completely dominant gene, designated as GR. Fine mapping strategies delimited the GR locus to a 27.14 kb region on chromosome 4 containing five candidate genes. Sequence analysis revealed a 13-bp insertion specifically within the seventh exon of CmAPRR2, encoding a two-component response regulator-like protein APRR2. The insertion introduced a premature stop codon, leading to a truncated protein. Allelic diversity assessment among 40 natural melon accessions revealed a strong correlation between rind color phenotype and the CmAPRR2 insertion polymorphism. Expression analysis demonstrated significantly higher CmAPRR2 transcript levels in green rinds compared to light-green rinds during immature fruit development. Consistent with this observation, genes involved in chlorophyll biosynthesis and chloroplast development were also upregulated in green rinds. While the insertion mutation did not affect the nuclear localization of CmAPRR2, it exhibited a significant reduction in its transcriptional activation capacity. Further, employing virus-induced gene silencing (VIGS) to silence the SlAPRR2 gene in tomato led to the development of light-green fruit coloration and a marked downregulation of APRR2 gene expression. These findings provide novel insights into the molecular mechanisms underlying melon rind color formation and identify CmAPRR2 as a promising genetic resource for molecular breeding programs aimed at manipulating rind color traits in melon.