Whole-genome resequencing reveals the population structure, genomic diversity, and demographic history of American chestnut (Castanea dentata)

Abstract

American chestnut (Castanea dentata) was once the most economically and ecologically important hardwood species in the United States. In the first half of the 20th century, an exotic fungal pathogen – Cryphonectria parasitica – decimated the species, killing approximately four billion trees. Two approaches to developing blight resistant American chestnut populations show promise, but both will require introduction of adaptive genomic diversity from wild germplasm to produce diverse, locally adapted reforestation populations. Here we characterize population structure, demographic history, and genomic diversity in a range-wide sample of 384 wild American chestnuts to inform conservation and breeding with blight resistant varieties. Population structure analyses with DAPC and ADMIXTURE suggest that the chestnut range can be roughly divided into northeast, central, and southwest populations. Within-population genomic diversity estimates revealed a clinal pattern with the highest diversity in the southwest, which likely reflects bottleneck events associated with Quaternary glaciation. Finally, we identified genomic regions under positive selection within each population, which suggests that defense against fungal pathogens is a common target of selection across all populations. Taken together, these results show that American chestnut underwent a postglacial expansion from the southern portion of its range leading to three extant populations. These populations will serve as management units for breeding adaptive genetic variation into the blight-resistant tree populations for targeted reintroduction efforts.

A genome-guided strategy for climate resilience in American chestnut restoration populations

“…R package version of the Python sampling method can be found at https://github.com/alex-sandercock/castgen ( 65 ). The R code used to estimate the seed zone shifts due to climate change is available at Zenodo: https://zenodo.org/doi/10.5281/zenodo.10676843 ( 66 ). Genomic Data: The genomic data for the TACF backcross and wild American chestnut samples were submitted to NCBI SRA BioProject PRJNA1070245 ( 67 ).…”

“…Genomic Data: The genomic data for the TACF backcross and wild American chestnut samples were submitted to NCBI SRA BioProject PRJNA1070245 ( 67 ). The climate adaptive VCF file for the wild American chestnut samples is available at Zenodo: https://zenodo.org/doi/10.5281/zenodo.10676843 ( 66 ). Seed Zone files: The shape files and raster files for the wild Seed Zones are available at Zenodo: https://zenodo.org/doi/10.5281/zenodo.10676843 ( 66 ).…”

“…The climate adaptive VCF file for the wild American chestnut samples is available at Zenodo: https://zenodo.org/doi/10.5281/zenodo.10676843 ( 66 ). Seed Zone files: The shape files and raster files for the wild Seed Zones are available at Zenodo: https://zenodo.org/doi/10.5281/zenodo.10676843 ( 66 ). Previously published data were used for this work ( 10 ).…”

European and American chestnuts: An overview of the main threats and control efforts

“…Screening individual trees within a breeding population and identifying the genetic basis of important traits should become faster, possibly reducing the number of BC needed in traditional breeding programs. The de novo transcriptome assembly provided a significant contribution, however, future studies can now rely on genomes of C. mollissima ( Xing et al, 2019 ; Staton et al, 2020 ), C. crenata ( Shirasawa et al, 2021 ), and C. dentata ( Sandercock et al, 2022 ).…”