Cavers, S.; Wachowiak, W.; Perry, A.
Scots pine single nucleotide polymorphisms (SNP) for Axiom array
Cite this dataset as:
Cavers, S.; Wachowiak, W.; Perry, A. (2020). Scots pine single nucleotide polymorphisms (SNP) for Axiom array. NERC Environmental Information Data Centre. https://doi.org/10.5285/cbaa464a-ac18-42bf-8518-c746d8d97270
Download/Access
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This dataset is available under the terms of the Open Government Licence
https://doi.org/10.5285/cbaa464a-ac18-42bf-8518-c746d8d97270
This dataset contains ~50,000 single nucleotide polymorphisms (SNPs, DNA mutations) for Scots pine (Pinus sylvestris) and closely related members of the Pinus mugo complex, which were selected for inclusion on a 50K SNP Axiom array
Publication date: 2020-03-27
View numbers valid from 01 June 2023 Download numbers valid from 20 June 2024 (information prior to this was not collected)
Format
Text
Spatial information
Study area
Spatial representation type
Tabular (text)
Spatial reference system
WGS 84
Provenance & quality
The array comprised 49,829 SNPs from several sources, as follows. The majority (N = 49,052) were obtained from transcriptome sequencing of four pine species: Pinus sylvestris, P. mugo, P. uncinata and P. uliginosa (Wachowiak et al., 2015). These included SNPs which were common to all species and also SNPs fixed in one species and polymorphic within and among others. The set of SNPs identified by Wachowiak et al. (2015) was filtered by the array manufacturer (Thermo Fisher) based on p-convert values signifying the SNP array quality, and a list of recommended and non-recommended SNP probes (avoiding SNPs with polymorphisms within 35 bp) was provided to the authors. A further set of SNPs (N = 578) were included from candidate genes (N = 279), which had been resequenced in previous population genetic studies of the pine species (Kujala & Savolainen, 2012; Mosca, Eckert, Di Pierro, et al., 2012; Palmé, Wright, & Savolainen, 2008; Wachowiak, Balk, & Savolainen, 2009; Wachowiak, Zaborowska, et al., 2018). Variation in mitochondrial DNA (mtDNA) was targeted using a set of SNPs (N = 14) which had been discovered by Donnelly et al. (2017). A set of SNPs putatively associated with susceptibility to Dothistroma needle blight (discovered in Pinus radiata, ENA accession numbers ERS1034542-53) were also included (N = 185).
Licensing and constraints
This dataset is available under the terms of the Open Government Licence
Cite this dataset as:
Cavers, S.; Wachowiak, W.; Perry, A. (2020). Scots pine single nucleotide polymorphisms (SNP) for Axiom array. NERC Environmental Information Data Centre. https://doi.org/10.5285/cbaa464a-ac18-42bf-8518-c746d8d97270
Related
Citations
Perry, A., Wachowiak, W., Downing, A., Talbot, R., & Cavers, S. (2020). Development of a single nucleotide polymorphism array for population genomic studies in four European pine species. Molecular Ecology Resources, 20(6), 1697–1705. https://doi.org/10.1111/1755-0998.13223
Correspondence/contact details
Dr. Stephen Cavers
UK Centre for Ecology & Hydrology
Bush Estate
Penicuik
Midlothian
EH26 0QB
UNITED KINGDOM
enquiries@ceh.ac.uk
Penicuik
Midlothian
EH26 0QB
UNITED KINGDOM
Authors
Other contacts
Rights holder
UK Centre for Ecology & Hydrology
Custodian
NERC EDS Environmental Information Data Centre
info@eidc.ac.uk
Publisher
NERC Environmental Information Data Centre
info@eidc.ac.uk