Mutation in CmGhc1 confers the white hypocotyl phenotype in melon (Cucumis melo L.)

Melon is a globally cultivated horticultural crop with a predominantly hybrid commercial seed market in China. Seedling morphology, particularly hypocotyl color, is a valuable trait for rapid F₁ hybrid seed purity assessment. While green hypocotyls are common, white hypocotyls are rare in melon germplasm. This study identified a mutant with white hypocotyl but green leaves from the heavy ion beam mutant library. Genetic analysis revealed that a single recessive gene controlled the white hypocotyl, designated CmGhc1. A single-base deletion in the fifth exon of CmGhc1 led to a truncated CmGhc1 lacking the HTH-MYB DNA binding domain, likely affecting its transcriptional activity. CmGhc1 was localized in the nucleus, and yeast two-hybrid analysis and a dual-LUC assay demonstrated it as a transcription repressor. Furthermore, a KASP marker (hc1) was developed and verified as a functional marker for breeding white hypocotyl germplasms in melon. RNA-seq data revealed that CmGhc1 significantly affected the transcription of genes related to chlorophyll metabolism and photosynthesis in hypocotyl. In summary, these findings contribute to our understanding of chloroplast biogenesis and provide a valuable tool for melon breeding.