Source: Ars Technica

Restoration

Wiped out in its native range by invasive pathogens, the trees may make a comeback.

Very few people alive today have seen the Appalachian forests as they existed a century ago. Even as state and national parks preserved ever more of the ecosystem, fungal pathogens from Asia nearly wiped out one of the dominant species of these forests—the American chestnut—killing an estimated 3 billion trees. While new saplings continue to sprout from the stumps of the former trees, the fungus persists, killing them before they can seed a new generation.

Thanks in part to trees planted in areas where the two fungi don’t grow well, the American chestnut isn’t extinct. Efforts to revive it in its native range have continued, despite the long generation times needed to breed resistant trees. In Thursday’s issue of Science, researchers describe their efforts to apply modern genomic techniques and exhaustive testing to identify the best route to restoring chestnuts to their native range.

Multiple Paths to Restoration

The American chestnut is functionally extinct—it no longer plays its historic role in forest ecosystems—but it is not truly extinct. Two Asian fungi introduced to North America have devastated the species:

Chestnuts planted outside the species’ historic range—mainly in the drier western United States—have continued to survive because the pathogens are less aggressive there.

Natural Resistance

• Virus‑mediated protection – A virus that infects the blight fungus can suppress its virulence, allowing a few trees to persist where the virus is common.
• Large Surviving American Chestnuts (LSACs) – A handful of mature trees still exist in the Appalachian range. Their survival suggests low‑level, naturally occurring resistance within the original population.

These LSACs are central to one restoration strategy: if enough individuals possess distinct resistance mechanisms, interbreeding them could yield a lineage that both survives the fungi and thrives in its native habitat.

Hybrid Breeding

• The American chestnut can form fertile hybrids with the Chinese chestnut, which co‑evolved with the introduced fungi and therefore carries strong resistance.
• The goal of the back‑cross breeding program is to repeatedly cross hybrids with pure American chestnuts, producing trees that are genetically close to the American species while retaining Asian‑derived fungal resistance.

Biotechnological Approach

• Research identified oxalic acid as a key virulence factor of the blight fungus.
• Wheat naturally produces an enzyme that degrades oxalic acid.
• By inserting the wheat gene encoding this enzyme into the American chestnut genome, scientists created a transgenic chestnut capable of neutralizing the fungus’s attack.

Common Challenges

• Long generation time – Chestnuts grow slowly and may take many years to reach reproductive maturity.
• Self‑incompatibility – American chestnuts cannot self‑pollinate; at least two compatible trees are required for any breeding effort.

Coordinated Research Effort

Because the relative effectiveness of natural resistance, hybrid breeding, and genetic engineering remains uncertain, the American Chestnut Foundation convened a large, interdisciplinary collaboration. The consortium’s objectives are to:

1. Evaluate each resistance strategy under realistic field conditions.
2. Identify the most promising lines for large‑scale reintroduction.
3. Develop best‑practice guidelines for restoring blight‑resistant chestnuts to the wild.

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Tracking Resistance

The scale of the effort is immense. The team infected over 4,000 individual trees with the blight fungus and tracked their growth in Appalachian nurseries for an average of more than 14 years. Trees were scored for resistance on a 0‑to‑100 scale based on the damage caused by the infection.

In parallel, the researchers:

• Produced the highest‑quality chestnut genomes to date (both American and Chinese species).
• Gathered biochemical data on how the trees respond to infection.

Growth‑Rate Findings

When planted at sites where viruses kept the blight in check, distinct growth patterns emerged:

Rapid growth may have been a key factor that allowed the chestnut to dominate the canopy historically.

Genetically Modified (GM) American Chestnuts

• Unexpected insertion effect: The wheat gene used for blight resistance was inserted into a gene important for plant growth.
• Survival & growth impacts:
  • Trees with two copies of the inserted gene survived at ≈ 16 % of the expected rate.
  • Trees with one copy grew ≈ 22 % slower than unmodified trees.

Despite these setbacks, there was notable variability:

• 4 % of the tested GM trees displayed both high blight resistance and growth comparable to unmodified American chestnuts.
• Ongoing work will determine whether this combination of traits persists in subsequent generations.

Progeny Results

• The offspring of surviving GM American chestnuts grew like typical American chestnuts.
• Among 143 progeny, only seven scored above 50 on the 100‑point resistance scale.

Implications:

• Interbreeding the higher‑resistance individuals could further boost resistance.
• However, excessive inbreeding may create a population that lacks the genetic diversity needed to thrive after reintroduction.

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Future research will focus on balancing resistance, growth, and genetic diversity to restore the American chestnut to its historic ecological role.

Root Causes

The research team decided to use their testing to investigate the genetic basis of resistance. There’s a very practical reason for this: if resistance is mediated by just a handful of genes that each have large impacts, it should be possible to continue breeding resistant strains back to regular American chestnuts and selecting for resistance. But if many factors each have relatively small impacts, directed interbreeding of hybrids will be required to maximize both resistance and DNA originating from the American chestnut.

The team completed the highest‑quality chestnut genomes for both the American and Chinese species, identifying about 25 000–30 000 genes in the different assemblies. They then used this information for two types of genetic analysis:

1. Quantitative trait locus (QTL) identification
2. Genome‑wide association study (GWAS)

Both approaches aim to locate regions of the genome associated with specific traits and estimate their impact.

Findings

• Resistance to chestnut blight appears to arise from a relatively large number of sites, each with a modest effect.

  • QTL‑identified sites typically boosted resistance by ~10 points on the researchers’ 100‑point scale.
  • GWAS linked 17 individual genetic differences to about a quarter of the heritable resistance traits.
  • This suggests that, for hybrids (and likely for the weaker blight resistance found in surviving American chestnuts), directed breeding among surviving trees will be needed.

• Root‑rot fungus resistance, in contrast, seems to involve a limited number of alleles with large impacts.

Metabolite Approach

The researchers also compared 100 chemicals produced by resistant and susceptible strains. Among the 41 chemicals detected at higher levels in the Chinese chestnut, they identified:

If the genes responsible for producing these metabolites can be identified, they could guide directed breeding programs or gene‑editing strategies to increase their production.

Future Plan

• Use genomic predictions to select hybrid seedlings for planting in test orchards.
• Identify plants with high growth and resistance, then repeat the selection cycle.

The researchers conclude that all three approaches—selecting resistant American chestnuts, breeding hybrids derived from Chinese chestnuts, and directed genetic modification—can help bring the American chestnut back.

“As environmental disturbances and invasive species continue to push key species toward extinction, we need to get better at this kind of species‑rescue operation.”

Science, 2026. DOI: 10.1126/science.adw3225

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About the Author

John Timmer – Science editor at Ars Technica.

• B.A. in Biochemistry, Columbia University
• Ph.D. in Molecular and Cell Biology, University of California, Berkeley

When not at his keyboard, John seeks out a bicycle ride or a scenic hike.

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