Cucumber is a major crop worldwide, ranking as the third most-produced vegetable after tomatoes and onions. Yet breeding improved varieties — plants that are more resilient, produce better-shaped fruit, or are less prone to hollowness — remains highly challenging.
Until recently, most genetic research has focused on single-letter changes in DNA, known as SNPs. A new study in Nature Genetics, however, shows that much larger and previously underexplored forms of genetic variation have been central to cucumber’s history — and could be crucial for future crop improvement.
Led by Boyce Thompson Institute (BTI) Professor Zhangjun Fei, the research team created the most comprehensive cucumber genetic resource to date: a graph-based pangenome. Rather than relying on a single reference genome, this approach integrates genetic information from many different varieties. Built from 39 reference-quality cucumber genomes, the pangenome uncovered nearly 172,000 large “structural variants” (SVs) — DNA rearrangements that have shaped cucumber evolution and can strongly influence key agronomic traits.
“This is the first time we’ve been able to capture the full scope of genetic variation in cucumbers at such a detailed level,” explained Fei. “The pangenome allows us to see these SVs — large insertions, deletions, and rearrangements of DNA — and understand the profound impact they have on the cucumber’s biology and evolution.”
The analysis paints a clear picture of how cucumber’s genome was shaped over time. During domestication, the genetic code appears to have undergone a major “clean-up.” While mildly harmful single-letter mutations (SNPs) were often tolerated and retained, larger and potentially more disruptive structural variants (SVs) were repeatedly eliminated — suggesting these big rearrangements pose greater risks to plant health, according to a press release.
The researchers also traced cucumber’s spread from its origins in India through Asia, Europe, and later the Americas. As the crop expanded geographically, mildly deleterious SNPs accumulated — a pattern known as “expansion load.” Structural variants, however, showed the opposite trend: they continued to be purged over time, and the SVs that remain tend to be younger than SNPs. Together, these findings point to stronger, longer-term selection against large-scale genetic changes.
The study also found evidence of gene flow from wild cucumber populations into European cucumbers. While this introgression may have delivered useful traits, it also appears to have brought along harmful structural variants that “hitched a ride” alongside beneficial genes.
“This is a critical insight for modern breeding,” says Fei. “It shows that when breeders bring in valuable traits from wild relatives, such as drought tolerance, they can inadvertently introduce hidden genetic baggage. Our work provides a resource to help breeders identify and remove that baggage.”
These results have direct value for cucumber breeding. The researchers found that adding information about each accession’s burden of potentially harmful structural variants into genomic prediction models improved predictions for key traits, including fruit shape and susceptibility to hollowness. Incorporating SV data could therefore help breeders select superior lines more accurately and speed up the development of improved varieties.
The impact is not limited to cucumber. The approaches developed in this study provide a framework for exploring genetic diversity in other species, with the potential to accelerate breeding for higher yield, better quality, and greater tolerance to environmental stress.
This research was supported by grants from the USDA National Institute of Food and Agriculture Specialty Crop Research Initiative through the CucCAP project.
