Cucumber is one of the world’s most widely cultivated vegetable crops, and immature fruit skin color is a key quality trait for both consumers and breeders. Previous studies have identified several genes involved in cucumber peel color, many linked to chloroplast formation or chlorophyll biosynthesis. However, the regulatory network remains incomplete, especially for naturally occurring yellow-peel mutants. Chloroplasts are central to peel pigmentation because they support photosynthetic pigment production, while iron–sulfur (Fe–S) clusters are essential cofactors in chloroplast biogenesis and electron transport. Based on these challenges, deeper research is needed to uncover new molecular mechanisms controlling cucumber peel color.
Researchers from China Agricultural University, the Sanya Institute of China Agricultural University, the Yantai Institute of China Agricultural University, and the United States Department of Agriculture–Agricultural Research Service (USDA-ARS) reported (DOI: 10.1093/hr/uhag043) the study in Horticulture Research on 2 March 2026. The article investigates how CsYP controls cucumber fruit skin color. The team combined map-based cloning, whole-genome sequencing, ribonucleic acid sequencing (RNA-seq), clustered regularly interspaced short palindromic repeats/CRISPR-associated protein 9 (CRISPR/Cas9), and protein-interaction assays.
The researchers first compared a green-peel cucumber line with a natural yellow-peel mutant. Yellowing became visible around 6 days after pollination and became stronger as fruits developed. Transmission electron microscopy showed that mutant peel cells contained fewer and malformed chloroplasts, while pigment analysis revealed major reductions in chlorophyll a, chlorophyll b, and carotenoids. Genetic analysis showed that yellow peel was controlled by a single recessive gene. Using bulked segregant analysis (BSA) and fine mapping, the team narrowed the locus to a 198.2-kilobase region on chromosome 1 and identified CsYP as the key candidate. A single guanine insertion in the sixth exon caused a frameshift mutation and premature termination of translation. When CsYP was knocked out in green-peel cucumber, the edited yp-1 and yp-2 lines developed yellow peel, confirming its function. Further assays showed that the CsYP protein localizes to chloroplasts and interacts with Cscytb6f, a cytochrome b6-f complex iron–sulfur subunit, suggesting that cucumber peel color is regulated through chloroplast metabolism and Fe–S protein-related activity.
The authors said the discovery offers a clearer view of how cucumber fruit color is built from the inside out. They said CsYP appears to do more than influence pigment levels directly; it links chloroplast development with rhodanese-like sulfur transfer and Fe–S protein function. This makes the study important because it moves peel-color research beyond visible greenness and into the cellular machinery that sustains chloroplast performance. They said the work provides a useful entry point for understanding how fruit appearance, photosynthetic capacity, and nutrient-related pathways may work together in horticultural crops.
The findings provide a new genetic resource for cucumber breeding and a broader framework for improving fruit appearance and market quality. Because peel color is highly visible but molecularly complex, identifying CsYP gives breeders a more precise target for developing cucumber varieties with stable and desirable skin color. The study also suggests that iron and sulfur metabolism may affect fruit coloration by supporting chloroplast health, opening a new direction for crop-quality research. Beyond cucumber, the work may help scientists examine whether rhodanese-like proteins and Fe–S-related pathways regulate chloroplast development and pigmentation in other vegetables and fruit crops.
###
References
DOI
10.1093/hr/uhag043
Original Source URL
https://doi.org/10.1093/hr/uhag043
Funding information
This study was supported by the National Key Research and Development Program ‘Strategic Science and Technology Innovation Cooperation’ Key Special Project (2023YFE0206900), the 2115 Talent Development Program of China Agricultural University.
About Horticulture Research
Horticulture Research is an open access journal of Nanjing Agricultural University and ranked number one in the Horticulture category of the Journal Citation Reports ™ from Clarivate, 2023. The journal is committed to publishing original research articles, reviews, perspectives, comments, correspondence articles and letters to the editor related to all major horticultural plants and disciplines, including biotechnology, breeding, cellular and molecular biology, evolution, genetics, inter-species interactions, physiology, and the origination and domestication of crops.