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

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

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

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https://doi.org/10.5285/7ee55609-d6b1-4693-8b36-2bf84fef76c2
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
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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

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).

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 polymorphism (SNP) genotypes for Axiom array validation. NERC Environmental Information Data Centre. https://doi.org/10.5285/7ee55609-d6b1-4693-8b36-2bf84fef76c2

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
Biodiversity , Divergence , Environmental survey , Genomic , Genotyping , Micoarray , Natural selection , Polymorphism , Population genomics , SNPs , Speciation
Funding
Natural Environment Research Council
Last updated
14 March 2024 15:45