10.5061/DRYAD.P8CZ8W9KP
Mostert-O'Neill, Marja
0000-0002-6318-3508
University of Pretoria
Reynolds, Sharon
University of Pretoria
Acosta, Juan
North Carolina State University
Lee, David
University of the Sunshine Coast
Borevitz, Justin
Australian National University
Myburg, Alexander
University of Pretoria
Genomic evidence of introgression and adaptation in a model subtropical
tree species, Eucalyptus grandis
Dryad
dataset
2019
Hybrid speciation
ancestry mapping
landscape genomics
Hybrid speciation
ancestry mapping
landscape genomics
2020-11-10T00:00:00Z
2020-11-10T00:00:00Z
en
https://doi.org/10.1111/mec.15615
147998722 bytes
6
CC0 1.0 Universal (CC0 1.0) Public Domain Dedication
The genetic consequences of adaptation to changing environments can be
deciphered using landscape genomics, which may help predict species’
responses to global climate change. Towards this, we used genome-wide SNP
marker analysis to determine population structure and patterns of genetic
differentiation in terms of neutral and adaptive genetic variation in the
natural range of Eucalyptus grandis, a widely cultivated subtropical and
temperate species, serving as genomic reference for the genus. We analysed
introgression patterns at subchromosomal resolution using a modified
ancestry mapping approach and identified provenances with extensive
interspecific introgression, suggesting early hybrid speciation in
response to increased aridity. Furthermore, we describe potentially
adaptive genetic variation as explained by environment-associated SNP
markers, which also led to the discovery of a large structural variant.
Finally, we show that genes linked to these markers are enriched for
biotic and abiotic stress responses.
Seed collected from 193 wild-growing Eucalyptus grandis trees were
germinated and leaves were collected for DNA isolation and SNP genotyping
using the EUChip60K SNP chip. Genotyping was done by the genomics service
provider, GeneSeek, in Lincoln, NE. A total of 596 individuals were
genotyped. Genotype calls were optimised by reclustering the SNPs
according to published standards (see Silva-Junior et al., 2015. A
flexible multi-species genome-wide 60K SNP chip developed from pooled
resequencing of 240 Eucalyptus tree genomes across 12 species).
Furthermore, technical replicates and SNPs with no unique map position on
the E. grandis reference genome v.2 were removed. This data resource is a
.csv file with 596 individuals in rows and metadata, environmental data
and SNPs (for 57,567 markers) in columns. Metadata columns include source
loacation/provenance ("Location"), family ID
("FAMILY_ID"), provenance ID ("PROV_ID"),
"Subpopulation", "Region", and whether or not a sample
was included in the balanced sample set where no family is represented by
more than two half-siblings ("Balanced_sample_set_n362").
Missing data is encoded as "NA".