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

Scots pine single nucleotide polymorphism (SNP) genotypes for Axiom array validation

The dataset contains genotypes for samples used to validate a 50K single nucleotide polymorphism (SNP, DNA mutation) Axiom array for Scots pine (Pinus sylvestris) and closely related members of the Pinus mugo complex.

Publication date: 2020-03-27

Get the data

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

Format of the data: text

You must cite: Cavers, S.; Wachowiak, W.; Perry, A. (2020). Scots pine single nucleotide polymorphism (SNP) genotypes for Axiom array validation. NERC Environmental Information Data Centre.



Study area

Provenance & quality

Samples & Validation of the array was carried out using a subset of 87 samples, which included four species of pine (Pinus sylvestris: SY; P. mugo: MU; P. uncinata: UN; P. uliginosa: UL). DNA was extracted from needles using a Qiagen DNeasy 96 kit following the manufacturer’s instructions. Needles were dried on silica gel prior to extraction and DNA was quantified using a Qubit spectrophotometer to ensure a minimum standardized concentration of 35ng/µl. The quality of genomic DNA was also checked visually for fragmentation on 1 % agarose gel.
Genotyping was done at Edinburgh Genomics following DNA amplification, fragmentation, chip hybridisation, single-base extension through DNA ligation and signal amplification performed according to the Affymetrix Axiom® Assay protocol. Genotyping was performed in 384-well format on a GeneTitan according to the manufacturer’s procedure. Genotype calls were performed using Axiom Analysis Suite software as recommended by the manufacturer (ThermoFisher). Samples were assigned to an analysis group based on their call rate (CR) and dish QC (DQC: a metric provided by ThermoFisher which is generated by measuring signals at multiple sites in the genome known not to vary among individuals), using the following thresholds: DQC ‘high’ ≥ 0.82; DQC ‘low’ < 0.82; CR ‘high’ ≥ 96; CR ‘low’ < 96. Analyses: 1) DQC high + CR high; 2) DQC high + CR low; 3) DQC low + CR low. High quality samples (N=529), with high CR and DQC, were used to set thresholds for allele calls. Posteriors for allele calls were subsequently used as priors for analyses 2 (N = 753) and 3 (N = 251).

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
EH26 0QB
United Kingdom


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

Other contacts

Environmental Information Data Centre
NERC Environmental Information Data Centre
Rights Holder
UK Centre for Ecology & Hydrology

Additional metadata

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