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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
Identifier
https://catalogue.ceh.ac.uk/id/52248442-a50f-4fc0-a73e-31c61cd27df9
Identifier
doi: / 10.5285/52248442-a50f-4fc0-a73e-31c61cd27df9
Other citation details
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
Author
  UK Centre for Ecology & Hydrology - Perry, A.
https://orcid.org/0000-0002-7889-7597
Author
  James Hutton Institute - Beaton, J.
Author
  James Hutton Institute - Iason, G.
Author
  Forest Research - Cottrell, J.
Author
  James Hutton Institute - Stockan, J.
https://orcid.org/0000-0001-9900-9010
Author
  UK Centre for Ecology & Hydrology - Cavers, S.
https://orcid.org/0000-0003-2139-9236
Custodian
  NERC EDS Environmental Information Data Centre
Publisher
  NERC EDS Environmental Information Data Centre
Point of contact
  UK Centre for Ecology & Hydrology - Perry, A.
https://orcid.org/0000-0002-7889-7597
Owner
  UK Centre for Ecology & Hydrology
GEMET - INSPIRE themes, version 1.0
  • Habitats and Biotopes
Access constraints
otherRestrictions Other restrictions
Other constraints
no limitations
Use constraints
otherRestrictions Other restrictions
Other constraints
This resource is available under the terms of the Open Government Licence
Use constraints
otherRestrictions Other restrictions
Other constraints
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
textTable Text, table
Metadata language
EnglishEnglish
Character set
utf8 UTF8
Topic category
  • Biota
Begin date
2012-01-01
End date
2020-12-31
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S
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W
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Unique resource identifier
WGS 84
Distribution format
  • Text ()

Distributor
  NERC EDS Environmental Information Data Centre
OnLine resource
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Supporting information

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Hierarchy level
dataset Dataset
Other
dataset

Conformance result

Date (Publication)
2010-12-08
Statement
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).
File identifier
52248442-a50f-4fc0-a73e-31c61cd27df9 XML
Metadata language
EnglishEnglish
Character set
ISO/IEC 8859-1 (also known as Latin 1) 8859 Part 1
Hierarchy level
dataset Dataset
Hierarchy level name
dataset
Date stamp
2025-11-05T08:31:10
Metadata standard name
UK GEMINI
Metadata standard version
2.3
Point of contact
  NERC EDS Environmental Information Data Centre
Lancaster Environment Centre, Library Avenue, Bailrigg , Lancaster , LA1 4AP , UK
https://eidc.ac.uk/
 
 

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GEMET - INSPIRE themes, version 1.0
Habitats and Biotopes

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