Written by: Sarah Sharman, PhD
One hundred years ago, if you were hiking the Appalachian Trail, towering trees would have dominated the forest canopy. The American chestnut, often called the “redwood of the East” due to its size, stretched from Maine to Mississippi, feeding wildlife and humans, shading mountain trails, and supplying durable wood for homes and barns. Then, at the turn of the 20th century, a tiny fungus called chestnut blight arrived from Asia and swept through the mountains like wildfire.
By mid-century, almost four billion trees had vanished, surviving only as scattered stumps and sprouts. For decades, the American chestnut seemed gone for good. But in labs and greenhouses across the country, scientists and community volunteers have been working to bring it back.
A new study published in Science shows that the dream of restoration may finally be within reach, and modern genomics is helping lead the way. The research, led by The American Chestnut Foundation (TACF) and HudsonAlpha Institute for Biotechnology, demonstrates that chestnut breeding guided by genetic information can dramatically accelerate restoration efforts while preserving the traits that made the tree an essential part of Appalachian forests.
Mapping the Blueprint of Resistance
Although most American chestnut trees cannot naturally survive blight, some Asian species that coevolved with the fungus are resistant. Over the last century, breeders have sought to leverage that natural resistance by breeding American chestnuts with Asian relatives. This effort has been largely spearheaded by TACF through volunteers and scientists breeding and growing hybrids of the resistant and susceptible varieties across the eastern United States.
The challenge is more complex than only increasing resistance to chestnut blight: breeders must also maintain the American chestnut’s tall, fast-growing form so it can thrive amongst other mature trees in established forests.
Adding to that complexity, trees that show the strongest resistance to blight often grow more slowly, forcing breeders to choose between disease resilience and the height needed to compete for sunlight. This trade‑off has long constrained progress, since scientists lacked the genomic resources necessary to pinpoint and combine genes linked to both traits.
To help solve that puzzle, HudsonAlpha scientists built three of the first and most complete chestnut genome assemblies ever. Led by Faculty Investigator Jeremy Schmutz and Research Faculty Investigator John Lovell, PhD, the team mapped the species’ DNA in great detail, creating reference blueprints that helped reveal how resistance works at the molecular level.
Seeing the chestnut genome in such detail helped the team understand that resistance isn’t controlled by one simple genetic switch. Instead, it’s a network of many genes working together.
HudsonAlpha’s insights showed that natural resistance is a multifaceted defense system that combines genetic and biochemical responses. With these genome resources in place, collaborators at Oak Ridge National Laboratory explored how genes are regulated in response to blight infection and found that resistant Chinese chestnuts produce several compounds that can slow or stop the blight fungus.
“By assembling high-quality genomes for both American and Chinese chestnuts from the TACF breeding program, we’ve begun to untangle the complex genetic architecture of blight resistance,” said Lovell. “These reference genomes now serve as a foundation for pinpointing the specific genes tied to important traits, not only improving TACF’s breeding efforts but also enhancing our understanding of tree resilience more broadly.”
From Seedlings to Forests
Using genome sequencing data from thousands of hybrid trees in TACF’s breeding program, researchers demonstrated that genomic selection can accurately predict which seedlings will show resistance to blight. This breakthrough means that instead of waiting for years for trees to grow and undergo infection trials, scientists can screen for the right genetic combinations early, dramatically speeding up the breeding cycle.
“With genome-enabled breeding, we expect the next generation of trees to have roughly twice the average blight resistance of our current population, with about 75 percent American chestnut ancestry,” said lead author Dr. Jared Westbrook, TACF’s director of science. “These trees are expected to begin producing large quantities of seed for restoration within the next decade.”
For HudsonAlpha, this project highlights how the same genomic tools used in human health and agriculture can be used to restore ecosystems.
“Genomics gives us the blueprint for resilience,” said Schmutz. “Whether we’re restoring an iconic tree, improving a food crop, or protecting biodiversity, the same DNA‑based tools let us understand natural genetic variation and identify solutions to key problems across plants.”
A Long-Term Vision for Forest Resilience
The researchers emphasize that rebuilding the American chestnut isn’t a one-time fix. It’s an ongoing process of gradual improvement, selecting the best trees in each generation until forests once again contain thriving, tall-growing chestnuts that can stand up to blight and other foes.
Rather than simply preserving what remains, this work builds the foundation for resilient forests that can adapt and flourish. It’s a shift from rescue to restoration.
For HudsonAlpha, participating in this effort captures the essence of what the Institute does best: leveraging genomics to tackle complex, real-world problems across agriculture, forestry, conservation, and beyond.
This has been and will continue to be such a fruitful collaboration. By combining HudsonAlpha’s genomic expertise with TACF’s decades of breeding data, we’re building the engine for future chestnut restoration.
The American chestnut may have been functionally extinct for nearly a century, but with each sequenced genome and each new generation of trees, its return feels within reach. The story of the chestnut’s comeback is also the story of modern genomics, where data and collaboration can help heal an ecosystem and reconnect a region to its natural heritage.
