BGS Hosted Metadata
Long-term multisite Scots pine single nucleotide polymorphism (SNP) genotypes and phenotypes for marker-trait association analysis
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. Full details about this dataset can be found at https://doi.org/10.5285/52248442-a50f-4fc0-a73e-31c61cd27df9
Simple
- Date (Publication)
- 2021-08-31
- Citation identifier
- https://catalogue.ceh.ac.uk/id/52248442-a50f-4fc0-a73e-31c61cd27df9
- Citation identifier
- doi: / 10.5285/52248442-a50f-4fc0-a73e-31c61cd27df9
- Other citation details
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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 10.5285/52248442-a50f-4fc0-a73e-31c61cd27df9
- Point of contact
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Organisation name Individual name Electronic mail address Role UK Centre for Ecology & Hydrology Perry, A. Author James Hutton Institute Beaton, J.
Author James Hutton Institute Iason, G.
Author Forest Research Cottrell, J.
Author James Hutton Institute Stockan, J. Author UK Centre for Ecology & Hydrology Cavers, S. Author NERC EDS Environmental Information Data Centre Custodian NERC EDS Environmental Information Data Centre Publisher UK Centre for Ecology & Hydrology Perry, A. Point of contact UK Centre for Ecology & Hydrology Owner
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GEMET - INSPIRE themes, version 1.0
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Habitats and Biotopes
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- Keywords
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- Phenology
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budburst
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height
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SNP array
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genotypes
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Scots pine
- Access constraints
- Other restrictions
- Other constraints
- no limitations
- Use constraints
- Other restrictions
- Use constraints
- Other restrictions
- Other constraints
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If you reuse this data, you should cite: 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
- Spatial representation type
- Text, table
- Language
- English
- Character set
- UTF8
- Topic category
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- Biota
- Begin date
- 2012-01-01
- End date
- 2020-12-31
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- Unique resource identifier
- WGS 84
- Distribution format
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Name Version Text
- Distributor contact
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Organisation name Individual name Electronic mail address Role NERC EDS Environmental Information Data Centre
Distributor
- OnLine resource
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Protocol Linkage Name https://data-package.ceh.ac.uk/data/52248442-a50f-4fc0-a73e-31c61cd27df9 Download the data
- OnLine resource
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Protocol Linkage Name https://data-package.ceh.ac.uk/sd/52248442-a50f-4fc0-a73e-31c61cd27df9.zip Supporting information
- Hierarchy level
- Dataset
- Other
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dataset
Conformance result
- Title
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Commission Regulation (EU) No 1089/2010 of 23 November 2010 implementing Directive 2007/2/EC of the European Parliament and of the Council as regards interoperability of spatial data sets and services
- Date (Publication)
- 2010-12-08
- Statement
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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).
Metadata
- File identifier
- 52248442-a50f-4fc0-a73e-31c61cd27df9 XML
- Metadata language
- English
- Character set
- 8859 Part 1
- Hierarchy level
- Dataset
- Hierarchy level name
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dataset
- Date stamp
- 2025-11-13T16:16:45
- Metadata standard name
- UK GEMINI
- Metadata standard version
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2.3
- Metadata author
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Organisation name Individual name Electronic mail address Role NERC EDS Environmental Information Data Centre Point of contact
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