Perry, A.; Beaton, J.; Iason, G.; Cottrell, J.; Stockan, J.; Cavers, S.
Long-term multisite Scots pine single nucleotide polymorphism (SNP) genotypes and phenotypes for marker-trait association analysis
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. https://doi.org/10.5285/52248442-a50f-4fc0-a73e-31c61cd27df9
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This dataset is available under the terms of the Open Government Licence
https://doi.org/10.5285/52248442-a50f-4fc0-a73e-31c61cd27df9
This dataset contains data pertaining to the phenotypes (height and budburst) and genotypes (via SNP array) for a subset of trees from a long term multi-site Scots pine experimental trial.
Publication date: 2021-08-31
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
Temporal information
Temporal extent
2012-01-01 to 2020-12-31
Provenance & quality
A multi-site field trial was established at three sites in Scotland in 2012 using five year old Scots pine trees. Each site contains 8 families from each of 21 native Caledonian pinewood provenances. Two of the sites (Glensaugh and Yair) have four randomised blocks and the other (Inverewe) has three randomised blocks.
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).
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).
Licensing and constraints
This dataset is available under the terms of the Open Government Licence
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. https://doi.org/10.5285/52248442-a50f-4fc0-a73e-31c61cd27df9
Related
Related datasets
Long-term multisite Scots pine trial, Scotland: field phenotypes, 2013-2020, version 2
Long-term multisite Scots pine trial, Scotland: mother tree, cone and seed phenotypes, 2007 v2
Long-term multisite Scots pine trial, Scotland: nursery phenotypes, 2007-2011
Scots pine single nucleotide polymorphisms (SNP) for Axiom array
This dataset is included in the following collections
Correspondence/contact details
Perry, A.
UK Centre for Ecology & Hydrology
Bush Estate
Penicuik
Midlothian
EH26 0QB
UNITED KINGDOM
enquiries@ceh.ac.uk
Penicuik
Midlothian
EH26 0QB
UNITED KINGDOM
Authors
Beaton, J.
James Hutton Institute
Iason, G.
James Hutton Institute
Cottrell, J.
Forest Research
Other contacts
Rights holder
UK Centre for Ecology & Hydrology
Custodian
NERC EDS Environmental Information Data Centre
info@eidc.ac.uk
Publisher
NERC EDS Environmental Information Data Centre
info@eidc.ac.uk