Predicting Blight Resistance from DNA Alone Could Halve the Time to Restore American Chestnuts

The American chestnut has been functionally absent from North American forests for nearly a century. A fungal pathogen introduced in the late 1800s killed billions of trees by the 1950s, and despite decades of breeding programs aimed at restoration, no population of blight-resistant trees with high American chestnut ancestry has yet been established at ecological scale.

The bottleneck is time. American chestnuts take years to reach reproductive maturity. Measuring a tree's resistance to blight requires exposing it to the fungus, then waiting for results - a process that takes additional years. Each generation of selective breeding thus requires a decade or more. A study published in Science by researchers from The American Chestnut Foundation (TACF) and Virginia Tech offers a way to compress that timeline substantially.

Genomic selection: reading resistance from DNA

Genomic selection is a method developed in agriculture and animal breeding that predicts traits - in this case, blight resistance - directly from genome-wide DNA sequence data. Rather than waiting for a tree to demonstrate its resistance in a field trial, breeders can screen a seedling's genetic markers and estimate how resistant it will likely be when mature.

To apply this to chestnuts, the researchers combined genomic sequence data with long-term blight resistance records from thousands of hybrid chestnut trees in TACF's breeding population. They validated that resistance could be reliably predicted from genetic data - a demonstration that now enables breeders to select the most promising seedlings before years of costly and time-consuming field testing.

The practical projection is striking. "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. Those trees are expected to begin producing seed for restoration within the next decade.

Understanding why resistance is complex

Achieving that projection required first understanding why blight resistance is difficult to breed in the first place. The study assembled some of the most complete chestnut genomes to date, using work from the HudsonAlpha Institute for Biotechnology, and found that resistance is not controlled by one or two major genes. It emerges from many genes working together across the genome, with copy number variation - differences in how many copies of specific resistance-associated genes a tree carries - playing a significant role.

Researchers at Oak Ridge National Laboratory added a metabolic dimension: Chinese chestnuts, which evolved alongside the blight fungus over millennia, contain chemical compounds in their tissue that reduce or halt fungal growth. These compounds are not easily transferred to American chestnut hybrids through simple crosses. Multiple generations of selection, guided by genomic data, are needed to accumulate both the genetic variants and the metabolic profile that together confer meaningful protection.

Genetically modified trees: promising but not yet sufficient

The study also evaluated a genetically modified chestnut line designed to neutralize the oxalic acid the blight fungus uses to kill host tissue. Early greenhouse tests showed promise. But field trials revealed variable resistance and slower growth relative to non-modified trees - underscoring that blight resistance in a forest context is more complex than neutralizing a single fungal toxin. The researchers do not dismiss transgenic approaches, but their analysis places genomic selection-guided conventional breeding as the more immediately tractable path.

A framework for tree conservation more broadly

The approach developed for American chestnut restoration reflects a broader shift in conservation biology - away from one-time rescue efforts and toward systematic, generational improvement guided by genetic data. "Each generation becomes stronger and better adapted," said TACF President Michael Goergen. "Genomic tools allow us to build a restoration pipeline that keeps improving over time."

The researchers suggest this framework could apply to other threatened tree species facing introduced pathogens or climate-driven stress - a growing category that includes ash trees, white pines, and several oaks. Conservation breeding has historically operated with less precision than agricultural breeding. Genomic selection narrows that gap.

For the American chestnut specifically, the timeline to restoration remains long. Trees with the projected resistance levels will need to be tested in forest ecosystems before large-scale planting begins, and producing sufficient seed to restore populations from Maine to Mississippi requires many additional years. Genomics accelerates the breeding cycle; it does not eliminate the decades of patient accumulation that forest restoration inherently demands.