After more than a century of devastation from deadly blight, the iconic American chestnut tree could be brought back from the brink of extinction thanks to novel genomic tools and carefully bred hybrids, a new study finds. The study included experiments that suggest that breeding trees with an average of 70 to 85% American chestnut ancestry can result in trees with significant levels of blight and root rot resistance. The demise of the American chestnut tree is among the most striking examples of how introduced disease can rapidly destroy an endemic species. In the late 19^th century, the necrotrophic fungus that causes chestnut blight was introduced to North America on Asian chestnuts. Within a few decades, billions of American chestnut trees were lost, erasing this once-dominant tree from forests from Maine to Mississippi. Today, this species is widely considered to be functionally extinct. Efforts to restore the American chestnut have persisted for more than a century, including by breeding trees resistant to disease. Although introgression of resistance alleles from Chinese chestnuts has contributed to the recovery of self-sustaining American chestnut populations, progress has been slow due to the complex and poorly understood genetic architecture of blight resistance.

To address this gap, Jared Westbrook and colleagues generated chromosome-scale genome assemblies for three important founder chestnuts in hybrid breeding programs. By comparing these highly annotated reference genomes, Westbrook et al. found that most protein-coding genes are shared across species, with copy number variation (CNV) appearing to contribute to blight resistance in Chinese chestnut. Moreover, RNA sequencing showed that American and Chinese chestnuts respond very differently to blight infection, and metabolite profiling revealed that Chinese chestnut contains high levels of compounds that inhibit fungal growth, suggesting that enhancing these metabolites could improve resistance in American chestnut. Given this complexity, Westbrook et al. argue that recurrent selection and multigenerational intercrossing are likely to be more effective at creating resistant hybrids through backcross breeding strategies. “It is important to evaluate genetic gains in tree breeding programs in long-term field trials,” Jared Westbrook notes. “Ideally, individual families should be planted at more than one field site to separate the effects of the local environment from the genetic effects on traits.” In a Perspective, Steven Strauss and Gancho Slavov discuss the study in greater detail.