Long-term multisite Scots pine single nucleotide polymorphism (SNP) genotypes and phenotypes for marker-trait association analysis
Default
Identification info
- Metadata Language
- English (en)
- Character set
- utf8
- Dataset Reference Date ()
- 2021-08-31
- 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
- GEMET - INSPIRE themes, version 1.0 ()
-
- Habitats and Biotopes
- Limitations on Public Access
- otherRestrictions
- Other constraints
- no limitations
- Use constraints
- otherRestrictions
- Use constraints
- otherRestrictions
- 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
- Topic category
-
- Biota
- Begin date
- 2012-01-01
- End date
- 2020-12-31
- Code
- WGS 84
Distribution Information
- Data format
-
-
Text
()
-
Text
()
- Resource Locator
-
Download the data
Download a copy of this data
- Resource Locator
-
Supporting information
Supporting information available to assist in re-use of this dataset
- Resource Locator
-
Download the data
Download a copy of this data
- Resource Locator
-
Supporting information
Supporting information available to assist in re-use of this dataset
- Quality Scope
- dataset
- Other
- dataset
Report
- Dataset Reference Date ()
- 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).
Metadata
- File identifier
- 52248442-a50f-4fc0-a73e-31c61cd27df9 XML
- Metadata Language
- English (en)
- Character set
- ISO/IEC 8859-1 (also known as Latin 1)
- Resource type
- dataset
- Hierarchy level name
- dataset
- Metadata Date
- 2024-02-27T16:23:27
- Metadata standard name
- UK GEMINI
- Metadata standard version
- 2.3