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

Scots pine single nucleotide polymorphisms (SNP) for Axiom array

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

Get the data

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

Format of the data: Simple text

You must cite: 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

 

Where/When

Study area

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).

Supplemental information

This dataset is a supplement to:

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.

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

Custodian
Environmental Information Data Centre
 info@eidc.ac.uk
Publisher
NERC Environmental Information Data Centre
 info@eidc.ac.uk
Rights Holder
UK Centre for Ecology & Hydrology
 enquiries@ceh.ac.uk

Additional metadata

Topic categories
Biota
Keywords
Divergence,  Environmental survey Genomics,  Genotyping,  Micoarray,  Natural selection,  Pinus,  Pinus mugo,  Pinus sylvestris,  Pinus uliginosa,  Pinus uncinata,  Polymorphism,  Population genomics,  SNP,  Speciation
INSPIRE Theme
Environmental Monitoring Facilities
Funding
Natural Environment Research Council
Spatial representation type
Tabular (text)
Spatial reference system
WGS 84
Last updated
25 February 2021 14:28