The team completed the highest-quality chestnut genomes for both the American and Chinese species, identifying about 25,000 to 30,000 genes in the different assemblies. They then used this information for two types of genetic analysis: quantitative trait locus identification and genome-wide association. Both approaches aim to identify regions of the genome associated with specific properties and estimate their impact.
The work suggested that resistance arises from a relatively large number of sites, each with relatively minor effects. For example, the sites in the genome identified by quantitative trait analysis typically boosted resistance by about 10 points on the researchers’ 100-point scale. In the genome-wide analysis, 17 individual genetic differences were associated with about a quarter of the heritable resistance traits. All of this suggests that, for the hybrids (and likely for the weaker blight resistance found in surviving American chestnuts), directed breeding among surviving trees will be needed.
For the root rot fungus, in contrast, it looks like there are a limited number of important alleles with a large impact.
The researchers also took an alternative approach to identify resistance factors, comparing 100 chemicals produced by resistant and susceptible strains. Among the 41 chemicals detected at higher levels in the Chinese chestnut, the researchers found a metabolite, lupeol, that completely suppressed the growth of the fungal pathogen. Another, erythrodiol, limited its growth. If we can identify the genes involved in producing those chemicals, we could use that knowledge to guide directed breeding programs—or even engage in gene editing to increase their production.
The team’s current plan is to use genomic predictions to select hybrid seedlings for planting in test orchards, aiming to identify plants with high growth and resistance. From there, the process can be repeated. But even after the exhaustive exploration of resistance traits, the researchers seem to believe 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.
The researchers warn, though, that as environmental disturbances and invasive species continue to push some key species to the brink of extinction, we need to get better at this kind of species rescue operation.
Science, 2026. DOI: 10.1126/science.adw3225 (About DOIs).