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About 400 years ago, a cross between cabernet franc and sauvignon blanc gave birth to cabernet sauvignon. Today, cabernet sauvignon is the world’s most-planted wine grape, dominating vineyards from Napa to Bordeaux. New research from the University of California, Davis, reveals that the grape still carries a kind of gene memory of its parents.

Clones over the centuries

Unlike annual crops such as corn or wheat, grapevines are propagated from cuttings, not seeds. Each new vine is essentially a clone of its ancestor. That means every cabernet sauvignon vine grown today is genetically nearly identical to the original 17th-century plant.

“When you think about it, it’s unusual compared to most crops, which are continuously improved through breeding,” said Professor Dario Cantù, of the UC Davis Department of Viticulture and Enology. “We still cultivate plant material selected hundreds of years ago simply because cabernet sauvignon is so beloved.”

Scientists have long wondered whether chemical “switches” that help control how genes turn on and off, known as epigenetic marks, remain stable across hundreds of years of clonal reproduction. A led by Cantù and published in the journal Genome Biology shows they do. 

“These are modifications that don’t alter the genetic code itself, but sit on top of it,” Cantù explained. “They can be inherited from your parents, but also change as you develop, as you interact with the environment or as you’re challenged by stress or disease.”

The team used advanced genome sequencing to assess the stability of these epigenetic modifications, which can influence traits like fruit quality and stress tolerance. The study is the first to show that this kind of molecular memory can persist for centuries in a clonally-propagated crop.

“It’s like sequencing identical twins at 90 and still detecting the parental signatures they inherited, even though their experiences — and much of their epigenome — has changed with age,” Cantù said.

New genetic analysis tools

To uncover this, scientists assembled highly detailed genome maps of cabernet sauvignon and its parent varieties, cabernet franc and sauvignon blanc. They analyzed multiple clones of each cultivar and developed a sophisticated genomic model, called a phased sequence graph, that captures subtle genetic and epigenetic variations more accurately than traditional reference genomes.

This new framework allowed researchers to trace how epigenetic marks are inherited along with DNA, and to understand how those marks affect gene activity. The study showed clonal plants may show minor differences from one vine to another, but their core epigenetic patterns or “gene memory” remain remarkably stable, even across centuries of clonal propagation.

Clues for climate resilience

This discovery could help scientists understand how long-lived crops adapt to their environments and whether those adaptations leave stable molecular marks. Cantù noted that if some epigenetic responses to heat, drought or other stresses prove to be stable, they could become targets in breeding. 

“If we know which stress-induced epigenetic changes persist, we could potentially introduce them by exposing plants to specific conditions and select vines that retain those beneficial marks over the long term — without altering their genetic makeup and preserving the defining traits of varieties like cabernet sauvignon.”

The framework developed for this research can be applied to many other perennial crops. By identifying which inherited markers endure, scientists hope to guide breeding programs for resilience and quality.

The discovery also carries a historical resonance for UC Davis. In 1997, UC Davis professor and geneticist Carole Meredith  cabernet franc and sauvignon blanc as the parents of cabernet sauvignon. Nearly three decades later, Cantù’s team has shown that the grape still bears molecular traces of that ancestral pairing.

“This work connects a UC Davis classic to a UC Davis first,” Cantù said. “It shows that even after centuries, cabernet sauvignon still holds the molecular memory of where it came from.”

Other authors include Noé Cochetel, Amanda M. Vondras and Rosa Figueroa-Balderas of UC Davis; Joel Liou and Paul Peluso of Pacific Biosciences.

This research was partially supported by the National Science Foundation, the U.S. Department of Agriculture National Institute of Food and Agriculture, the E. & J. Gallo Winery and the Ray Rossi Endowment in Viticulture and Enology.