52248442-a50f-4fc0-a73e-31c61cd27df9 English ISO/IEC 8859-1 (also known as Latin 1) dataset dataset NERC EDS Environmental Information Data Centre Lancaster Environment Centre, Library Avenue, Bailrigg Lancaster LA1 4AP UK info@eidc.ac.uk https://eidc.ac.uk/ EIDC website The Environmental Information Data Centre (EIDC) is the UK's national data centre for terrestrial and freshwater sciences. information pointOfContact 2025-11-13T16:16:45 UK GEMINI 2.3 WGS 84 Long-term multisite Scots pine single nucleotide polymorphism (SNP) genotypes and phenotypes for marker-trait association analysis 2021-08-31 publication https://catalogue.ceh.ac.uk/id/52248442-a50f-4fc0-a73e-31c61cd27df9 10.5285/52248442-a50f-4fc0-a73e-31c61cd27df9 doi: 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 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 Perry, A. UK Centre for Ecology & Hydrology enquiries@ceh.ac.uk https://orcid.org/0000-0002-7889-7597 ORCID record ORCID is an open, non-profit, community-driven effort to create and maintain a registry of unique researcher identifiers and a transparent method of linking research activities and outputs to these identifiers. information author Beaton, J. James Hutton Institute Joan.Beaton@hutton.ac.uk author Iason, G. James Hutton Institute glenn.iason@btinternet.com author Cottrell, J. Forest Research joan.cottrell@forestresearch.gov.uk author Stockan, J. James Hutton Institute Jenni.Stockan@hutton.ac.uk https://orcid.org/0000-0001-9900-9010 ORCID record ORCID is an open, non-profit, community-driven effort to create and maintain a registry of unique researcher identifiers and a transparent method of linking research activities and outputs to these identifiers. information author Cavers, S. UK Centre for Ecology & Hydrology enquiries@ceh.ac.uk https://orcid.org/0000-0003-2139-9236 ORCID record ORCID is an open, non-profit, community-driven effort to create and maintain a registry of unique researcher identifiers and a transparent method of linking research activities and outputs to these identifiers. information author NERC EDS Environmental Information Data Centre info@eidc.ac.uk custodian NERC EDS Environmental Information Data Centre info@eidc.ac.uk publisher Perry, A. UK Centre for Ecology & Hydrology enquiries@ceh.ac.uk https://orcid.org/0000-0002-7889-7597 ORCID record ORCID is an open, non-profit, community-driven effort to create and maintain a registry of unique researcher identifiers and a transparent method of linking research activities and outputs to these identifiers. information pointOfContact UK Centre for Ecology & Hydrology enquiries@ceh.ac.uk owner Habitats and Biotopes theme GEMET - INSPIRE themes, version 1.0 2008-06-01 publication Phenology budburst height SNP array genotypes Scots pine otherRestrictions no limitations otherRestrictions This resource is available under the terms of the Open Government Licence otherRestrictions 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 textTable English utf8 biota 2012-01-01 2020-12-31 -8.648 -0.728 54.634 60.861 Text NERC EDS Environmental Information Data Centre info@eidc.ac.uk distributor https://data-package.ceh.ac.uk/data/52248442-a50f-4fc0-a73e-31c61cd27df9 Download the data Download a copy of this data download https://data-package.ceh.ac.uk/sd/52248442-a50f-4fc0-a73e-31c61cd27df9.zip Supporting information Supporting information available to assist in re-use of this dataset information dataset dataset 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 2010-12-08 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).