Published February 18, 2024 | Version v1
Dataset Open

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

Creators

  • 1. ROR icon Virginia Tech
  • 2. Breeding Insight, Cornell University
  • 3. ROR icon The American Chestnut Foundation

Description

The American chestnut (Castanea dentata) is a functionally extinct tree species that was decimated by an invasive fungal pathogen in the early 20th century. An understanding of the genomic architecture of local adaptation in wild American chestnut was necessary in order to deploy locally adapted, disease-resistant American chestnut populations. Here, we characterize the genomic basis of climate adaptation in remnant wild American chestnut, develop new computational methods, and evaluate the adaptive genomic content captured within backcross breeding populations. Whole genome re-sequencing data of 356 trees from Sandercock et al. (2022) coupled with genotype-environment association methods identified 18483 climate associated loci.

Methods

  1. VCF file: The ~21 million SNP dataset from Sandercock et al. (2022) was first imputed using BEAGLE and filtered to remove SNPs with MAF < 0.05. Climate associated loci were then identified using RDA and LFMM2 genotype-environment association methods.
  2. Seed zone shape files: Three seed zones were identified using the ~18k climate associated loci. These regions partition the chestnut range into geographic seed zones that reflect relatively homogeneous areas with respect to multivariate adaptive genomic variation. These regions can be used to conserve germplasm ex situ and guide subsequent breeding crosses that lead to climate-matched restoration populations. 
  3. gmbigxhorn.jtl.map.2022.csv is a genetic map generated from American chestnut backcross genotyping-by-sequencing data.
  4. R code for estimating the average migration distance for each seed zone under future climate change conditions.

 

 

Files

gmbigxhorn.jtl.map.2022.csv

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Additional details

Related works

Is derived from
Publication: 10.1111/mec.16629 (DOI)

Funding

National Institute of Food and Agriculture
GENOME-GUIDED ADAPTIVE INTROGRESSION IN DISEASE RESISTANT AMERICAN CHESTNUT POPULATIONS 1018599
National Institute of Food and Agriculture
ACCELERATING MARKER-TRAIT ASSOCIATION STUDIES IN CHESTNUT (CASTANEA SPP. AND HYBRIDS) 1027966
National Institute of Food and Agriculture
GENOMIC TOOLS TO MITIGATE BIOTIC AND ABIOTIC THREATS TO FOREST HEALTH 1025004
Virginia Tech
Institute for Critical Technology and Applied Science Doctoral Scholar Fellowship N/A
North Carolina Biotechnology Center
Genome-Guided Conservation for Climate Resilience in the Blight Resistant American Chestnut Population N/A

Software

Repository URL
https://github.com/alex-sandercock/castgen/
Programming language
Python, R
Development Status
Active