Cite this dataset as
Perry, A., Beaton, J., Iason, G., Cottrell, J., Stockan, J., Cavers, S. (2021). Long-term multisite Scots pine single nucleotide polymorphism (SNP) genotypes and phenotypes for marker-trait association analysis. NERC EDS Environmental Information Data Centre. (Dataset). https://doi.org/10.5285/52248442-a50f-4fc0-a73e-31c61cd27df9
Import this citation into your reference management software:
BibTeX | Reference Manager (RIS) | Endnote
This dataset is available under the terms of the Open Government Licence
Long-term multisite Scots pine single nucleotide polymorphism (SNP) genotypes and phenotypes for marker-trait association analysis
Format
Text
Spatial information
- Study area
-
- Spatial representation type
- Tabular (text)
- Spatial reference system
- WGS 84
Temporal information
- Temporal extent
-
2012-01-01 to 2020-12-31
Provenance & quality
This dataset relates to a subset of trees (N = 208) from two of the sites (Glensaugh, N = 108; Yair, N = 100). Glensaugh (latitude 56.893567, longitude -2.535736) and Yair (latitude 55.603625, longitude -2.893025)
Phenotypes (height and budburst) were assessed in situ at each site in spring (budburst) and winter (height) between 2015 and 2020.
Trees were genotyped using a multi-species SNP array (Perry et al., 2020). 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).
Related
Correspondence/contact details
Penicuik
Midlothian
EH26 0QB
UNITED KINGDOM
Authors
Other contacts
- Rights holder
-
UK Centre for Ecology & Hydrology
- Custodian
-
NERC EDS Environmental Information Data Centreinfo@eidc.ac.uk
- Publisher
-
NERC EDS Environmental Information Data Centreinfo@eidc.ac.uk
Additional metadata
Get the data
By accessing or using this dataset, you agree to the terms of the relevant licence agreement(s). You will ensure that this dataset is cited in any publication that describes research in which the data have been used.
This dataset is available under the terms of the Open Government Licence
CITE AS: Perry, A.; Beaton, J.; Iason, G.; Cottrell, J.; Stockan, J.; Cavers, S. (2021). Long-term multisite Scots pine single nucleotide polymorphism (SNP) genotypes and phenotypes for marker-trait association analysis. NERC EDS Environmental Information Data Centre. https://doi.org/10.5285/52248442-a50f-4fc0-a73e-31c61cd27df9