Date (Publication)

2021-08-31

Citation identifier

https://catalogue.ceh.ac.uk/id/55118e26-cf5c-41d6-9157-738fce6bdddf

Citation identifier

doi: / 10.5285/55118e26-cf5c-41d6-9157-738fce6bdddf

Other citation details

Perry, A., Wachowiak, W., Donnelly, K., Cavers, S. (2021). Single nucleotide polymorphism (SNP) genotypes and phenotypes for marker-trait association analysis of three pine species grown in a glasshouse. NERC EDS Environmental Information Data Centre 10.5285/55118e26-cf5c-41d6-9157-738fce6bdddf

Point of contact

Organisation name	Individual name	Electronic mail address	Role
UK Centre for Ecology & Hydrology	Perry, A.	enquiries@ceh.ac.uk	Author
Adam Mickiewicz University	Wachowiak, W.	witwac@amu.edu.pl	Author
UK Centre for Ecology & Hydrology	Donnelly, K.	enquiries@ceh.ac.uk	Author
UK Centre for Ecology & Hydrology	Cavers, S.	enquiries@ceh.ac.uk	Author
UK Centre for Ecology & Hydrology	Perry, A.	enquiries@ceh.ac.uk	Point of contact
NERC EDS Environmental Information Data Centre		info@eidc.ac.uk	Custodian
NERC EDS Environmental Information Data Centre		info@eidc.ac.uk	Publisher
UK Centre for Ecology & Hydrology		enquiries@ceh.ac.uk	Owner

GEMET - INSPIRE themes, version 1.0

• Environmental Monitoring Facilities

Keywords

• Phenology

• budburst

• height

• SNP array

• genotypes

• Scots pine

Access constraints

Other restrictions

Other constraints

no limitations

Use constraints

Other restrictions

Other constraints

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

Use constraints

Other restrictions

Other constraints

If you reuse this data, you should cite: Perry, A., Wachowiak, W., Donnelly, K., Cavers, S. (2021). Single nucleotide polymorphism (SNP) genotypes and phenotypes for marker-trait association analysis of three pine species grown in a glasshouse. NERC EDS Environmental Information Data Centre https://doi.org/10.5285/55118e26-cf5c-41d6-9157-738fce6bdddf

Spatial representation type

Text, table

Language

English

Character set

UTF8

Topic category

• Biota

Begin date

2010-01-01

End date

2013-12-31

Unique resource identifier

WGS 84

Distribution format

Name	Version
Text

Distributor contact

Organisation name	Individual name	Electronic mail address	Role
NERC EDS Environmental Information Data Centre		info@eidc.ac.uk	Distributor

OnLine resource

Protocol	Linkage	Name
	https://data-package.ceh.ac.uk/data/55118e26-cf5c-41d6-9157-738fce6bdddf	Download the data

OnLine resource

Protocol	Linkage	Name
	https://data-package.ceh.ac.uk/sd/55118e26-cf5c-41d6-9157-738fce6bdddf.zip	Supporting information

Hierarchy level

Dataset

Other

dataset

Statement

A common garden glasshouse trial was established in 2010 using seed from natural populations from three species of pine: Pinus sylvestris (SY), Pinus mugo (MU), Pinus uncinata (UN). Open-pollinated seeds were collected from three to five trees per population from twenty-eight natural populations in Europe covering the geographic range of each species. The collection consisted of thirteen populations of SY, nine MU, and six UN. The trial was divided into 25 randomized blocks with up to five families per population, of which the first 18 blocks were analysed by Wachowiak et al. (2018a). Phenotypes (height, bud set and budburst) were assessed in the glasshouse during spring (budburst), autumn (bud set) and winter (height) between 2010 and 2013. A subset of trees were selected to be genotyped using a multi-species SNP array. 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

55118e26-cf5c-41d6-9157-738fce6bdddf XML

Metadata language

English

Character set

8859 Part 1

Hierarchy level

Dataset

Hierarchy level name

dataset

Date stamp

2025-11-13T16:25:26

Metadata standard name

UK GEMINI

Metadata standard version

2.3

Metadata author

Organisation name	Individual name	Electronic mail address	Role
NERC EDS Environmental Information Data Centre		info@eidc.ac.uk	Point of contact