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Cavers, S.; Wachowiak, W.; Perry, A.

Scots pine single nucleotide polymorphisms (SNP) for Axiom array

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This dataset is available under the terms of the Open Government Licence

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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
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More information

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

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

Authors

Cavers, S.
UK Centre for Ecology & Hydrology
Wachowiak, W.
Adam Mickiewicz University
Perry, A.
UK Centre for Ecology & Hydrology

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

Additional metadata

Topic categories
biota
INSPIRE theme
Environmental Monitoring Facilities
Keywords
Divergence , Environmental survey , Genotyping , Micoarray , Natural selection , Polymorphism , Speciation
Funding
Natural Environment Research Council
Last updated
14 March 2024 15:45