Cucumber is an economically important 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 an enormous challenge.
Until recently, scientists have focused on single-letter "typos" in the genetic code, known as SNPs. However, a new study published in Nature Genetics reveals that previously underexplored large genetic variations have played a critical role in cucumber's history and are a key to its future improvement.
A research team led by Boyce Thompson Institute (BTI) Professor Zhangjun Fei constructed a graph-based pangenome, the most comprehensive genetic map of cucumber ever created. Unlike traditional approaches that rely on a single reference genome, a pangenome combines genetic information from many different varieties. This powerful resource, built from 39 reference-level cucumber genomes, revealed nearly 172,000 large-scale "structural variants" (SVs), DNA rearrangements that have shaped the evolution of this important vegetable crop and can have dramatic effects on 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 revealed a dramatic story. During cucumber domestication, the genetic code underwent a major cleanup. While mildly deleterious single-letter mutations (SNPs) were often tolerated and retained, the more damaging SVs were consistently purged—suggesting that these larger variants pose greater risks to plant health.
The study also tracked the cucumber's global journey, from its origins in India to its spread across Asia, Europe, and the Americas. While mildly harmful SNPs accumulated during this geographic expansion—a phenomenon known as "expansion load"—structural variants followed the opposite pattern: they continued to be purged over time, and the remaining SVs are generally younger than SNPs. Together, these patterns suggest stronger long-term selection against large genetic changes.
The study also uncovered gene flow from wild cucumber populations into European cucumbers. While this introgression may have introduced beneficial traits, it also brought along harmful structural variants that "hitched a ride" with 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 findings have immediate practical implications for cucumber breeding. The team showed that incorporating information on the burden of potentially harmful structural variants carried by each accession into genomic prediction models improved their ability to predict important traits such as fruit shape and hollowness. This could help breeders develop better varieties more efficiently.
The implications extend beyond just cucumbers. The techniques developed in this study could help researchers understand genetic diversity in other species, potentially accelerating the development of crops with better yield, quality, and stress tolerance.
This research was supported by grants from the USDA National Institute of Food and Agriculture Specialty Crop Research Initiative through the CucCAP project .
About thge Boyce Thompson Institute (BTI)
As an independent nonprofit research institute affiliated with Cornell University, our scientists are committed to advancing solutions for global food security, agricultural sustainability, and human health. Through groundbreaking research, transformative education, and rapid translation of discoveries into real-world applications, BTI bridges fundamental plant and molecular science with practical impact. Discovery inspired by plants. Learn more at BTIscience.org .
