Jumping Genes Shape the Yellow Peel of Cucumbers, New Study Finds

A cucumber is not always green. As the fruit matures, the peel of some varieties shifts to a striking yellow, while others stay white or pale, and that difference matters far beyond the market stall. Peel color influences consumer preference, signals ripeness, and reflects deep biochemical shifts inside the fruit’s skin cells. For decades, breeders have selected for these colors without fully understanding the molecular machinery behind them. Now, a study published in Theoretical and Applied Genetics has traced one of the most important color switches in cucumber back to an unexpected source: a pair of transposable elements, the so-called jumping genes, lodged inside a single regulatory gene on chromosome 4.

The research, led by Chen Chen and Geng Zhou of the Hunan Vegetable Research Institute at the Hunan Academy of Agricultural Sciences, together with colleagues at Yuelushan Laboratory and Hunan Agricultural University, focused on the gene CsMYB60. This gene encodes an R2R3-MYB transcription factor, a type of DNA-binding protein that acts as a master switch for plant pigment production. Earlier work had already established that CsMYB60 drives the biosynthesis of flavonoids and proanthocyanidins, two classes of plant secondary metabolites, in cucumber fruit spines. More recent studies extended that role to the mature fruit skin, showing that the gene helps control flavonoid accumulation and, with it, the color the peel takes on as the fruit ripens.

To dissect the genetic basis of peel color with precision, the team turned to a powerful experimental resource: a pair of near-isogenic lines. These are two cucumber inbred lines, L14 and L19, that are genetically almost identical except at the region governing peel color. L14 develops a yellow mature peel, while L19, a mutant derived from it, remains white. Because the two lines share nearly all of their genetic background, any difference in peel color can be attributed with high confidence to the small stretch of DNA where they differ, eliminating the noise that usually complicates genetic analysis in diverse varieties.

The researchers combined bulked segregant analysis with high-resolution fine mapping. In bulked segregant analysis, scientists cross the two contrasting lines, then pool the DNA of many offspring that share the same trait, in this case yellow peel, and sequence those pools alongside pools from offspring with the opposite trait. Regions of the genome where the pools diverge sharply are candidate homes for the causal gene. This approach, originally developed for rapid mapping in rice, allowed the team to narrow the peel color locus to a 121-kilobase interval on chromosome 4. Within that interval sat exactly one compelling candidate: CsMYB60.

What the team found when they compared the DNA sequences of the two alleles was the study’s central surprise. The yellow-peel line L14 carries not one but two Mutator-like element insertions, known as MULE1 and MULE2, within the second intron of CsMYB60. The white-peel mutant L19, by contrast, retains only MULE1. Mutator-like elements are a family of transposable elements, mobile DNA sequences that can copy or cut themselves out of the genome and reinsert elsewhere. Far from being genomic junk, transposable elements are now recognized as major drivers of plant evolution, frequently rewiring gene regulation by inserting into promoters, introns, or nearby regulatory regions and altering when, where, and how strongly a gene is expressed.

Here, the double insertion appeared to matter. During the peel color-transition stage, when the fruit’s skin is actively changing, the MULE1 plus MULE2 haplotype showed higher CsMYB60 transcript abundance than the MULE1-only haplotype in the near-isogenic materials examined. In other words, the line carrying both insertions produced more messenger RNA from the pigment-regulating gene, and that line was the one that turned yellow. The authors are careful to note that the causal regulatory contribution of MULE2 itself remains to be determined; the association between the structural haplotype and both expression level and peel color is clear, but precisely how the second insertion boosts transcription is a question for future work.

The team did not stop at correlation. Using CRISPR/Cas9 genome editing, they knocked out CsMYB60 directly in the L14 background. The result was unambiguous: the edited plants lost their yellow pigmentation entirely, confirming that CsMYB60 is required for yellow mature peel formation in this genetic background. This kind of functional validation is the gold standard in plant genetics, because it demonstrates necessity rather than mere association. Delete the gene, and the trait disappears; restore or retain it with the right structural haplotype, and the trait appears.

The findings fit into a broader and rapidly evolving picture of how fruit color is controlled in cucurbits. Cucumber peel and flesh color are governed by a constellation of loci affecting chloroplast development, carotenoid accumulation, and flavonoid biosynthesis. Previous studies have implicated genes such as CsMYB36 in yellow-green immature peel, APRR2 in green immature fruit color, and various chloroplast-related genes in light green phenotypes. The R2R3-MYB family, meanwhile, is famous across the plant kingdom for its role in the MYB-bHLH-WDR transcriptional complexes that regulate flavonoid pathways. What makes the new study distinctive is that it identifies a structural haplotype, a specific physical arrangement of DNA, rather than a simple single-nucleotide change, as the molecular signature associated with the trait.

That distinction has practical consequences for breeding. Structural variation like transposon insertions is often invisible to standard SNP-based genotyping, which means breeders can inadvertently lose or overlook valuable haplotypes when crossing varieties. The authors point out that the molecular marker associated with the MULE1 plus MULE2 haplotype may facilitate tracking of this structural variant in relevant cucumber breeding materials. In practice, that means seed companies and public breeding programs could screen seedlings for the double-insertion haplotype and confidently predict which plants will produce the yellow mature peel that certain markets demand, without waiting for the fruit to ripen.

The study also adds to a growing appreciation of transposable elements as engines of agricultural diversity. In crops ranging from maize to grapevine to tomato, transposon insertions have been shown to create or modulate traits as varied as seed coat color, fruit shape, and ripening behavior. The cucumber peel story is a textbook example of how a mobile element can act as a regulatory rheostat: by landing inside an intron, the MULE insertions appear to tune the output of a transcription factor that sits atop an entire pigment biosynthesis pathway. Whether MULE2 acts by altering chromatin structure, changing intron splicing, or providing novel regulatory sequences remains open, and answering it will likely require additional experiments such as reporter assays and splicing analyses.

For now, the work delivers a complete arc from field observation to molecular mechanism. Two nearly identical cucumber lines, one yellow and one white, led researchers to a 121-kilobase window on chromosome 4, then to a single MYB gene, then to two nested transposon insertions, and finally to a CRISPR experiment that sealed the case. The identification of a previously unrecognized MULE1 plus MULE2 structural haplotype associated with distinct CsMYB60 transcript abundance and mature peel coloration gives cucumber geneticists a new landmark on their maps and gives breeders a practical tool. It also serves as a reminder that some of the most important instructions in a crop’s genome are not written in its genes at all, but in the restless, mobile DNA that has been reshaping those genomes for millions of years.

Subject of Research: Transposon-mediated structural haplotypes at the CsMYB60 gene and their association with mature peel coloration in cucumber

Article Title: Transposon-mediated structural haplotypes at CsMYB60 are associated with peel coloration in cucumber

Article References: Chen, C., Chen, J., Chen, H., Liu, X., Lu, X., Tian, Y., & Zhou, G. (2026). Transposon-mediated structural haplotypes at CsMYB60 are associated with peel coloration in cucumber. Theoretical and Applied Genetics, 139(10), Article 285. https://doi.org/10.1007/s00122-026-05388-2

Image Credits: AI Generated

DOI: 10.1007/s00122-026-05388-2

Keywords: cucumber, peel color, CsMYB60, transposable elements, MULE, structural haplotype, flavonoid biosynthesis, R2R3-MYB transcription factor, CRISPR/Cas9, fine mapping, bulked segregant analysis, plant genetics