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

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

Get the data

This dataset is available under the terms of the Open Government Licence

Format of the data: Text

You must 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

 

Where/When

Study area
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).

Correspondence/contact details

Perry, A
UK Centre for Ecology & Hydrology
Bush Estate
Penicuik
Midlothian
EH26 0QB
UNITED KINGDOM
 enquiries@ceh.ac.uk

Authors

Perry, A.
UK Centre for Ecology & Hydrology
Beaton, J.
James Hutton Institute
Iason, G.
James Hutton Institute
Cottrell, J.
Forest Research
Stockan, J.
James Hutton Institute
Cavers, S.
UK Centre for Ecology & Hydrology

Other contacts

Custodian
NERC EDS Environmental Information Data Centre
 info@eidc.ac.uk
Publisher
NERC EDS Environmental Information Data Centre
 info@eidc.ac.uk
Rights Holder
UK Centre for Ecology & Hydrology
 enquiries@ceh.ac.uk

Additional metadata

Topic categories
Biota
Keywords
budburst,  genotypes,  height,  Phenology,  Scots pine,  SNP array
INSPIRE Theme
Habitats and Biotopes
Funding
Natural Environment Research Council Award: NE/K012177/1
Spatial representation type
Tabular (text)
Spatial reference system
WGS 84
Last updated
18 May 2022 12:21