Identification

Title

Single nucleotide polymorphism (SNP) genotypes and phenotypes for marker-trait association analysis of three pine species grown in a glasshouse

Abstract

This dataset contains details of the phenotypes (height, bud set and budburst) and genotypes (via SNP array) of trees from a common garden multi-species pine (Pinus sylvestris, Pinus mugo and Pinus uncinata) glasshouse trial between 2010 and 2013. Full details about this dataset can be found at https://doi.org/10.5285/55118e26-cf5c-41d6-9157-738fce6bdddf

Resource type

dataset

Resource locator

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

name: Download the data

description: Download a copy of this data

function: download

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

name: Supporting information

description: Supporting information available to assist in re-use of this dataset

function: information

Unique resource identifier

code

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

codeSpace

doi:

Dataset language

eng

Spatial reference system

code identifying the spatial reference system

Classification of spatial data and services

Topic category

biota

Keywords

Keyword set

keyword value

Environmental Monitoring Facilities

originating controlled vocabulary

title

GEMET - INSPIRE themes, version 1.0

reference date

date type

publication

effective date

2008-06-01

Keyword set

keyword value

Phenology

budburst

height

SNP array

genotypes

Scots pine

Geographic location

West bounding longitude

-3.358

East bounding longitude

-3.013

North bounding latitude

56.003

South bounding latitude

55.877

Temporal reference

Temporal extent

Begin position

2010-01-01

End position

2013-12-31

Dataset reference date

date type

publication

effective date

2021-08-31

Frequency of update

Quality and validity

Lineage

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).

Conformity

Conformity report

specification

title

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

reference date

date type

publication

effective date

2010-12-08

degree

explanation

Data format

name of format

Text

version of format

'unknown'

Constraints related to access and use

Constraint set

Limitations on public access

Constraint set

Limitations on public access

Constraint set

Limitations on public access

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

Responsible organisations

Responsible party

organisation name

UK Centre for Ecology & Hydrology

email address

enquiries@ceh.ac.uk

responsible party role

author

Responsible party

organisation name

Adam Mickiewicz University

email address

witwac@amu.edu.pl

responsible party role

author

Responsible party

organisation name

UK Centre for Ecology & Hydrology

email address

enquiries@ceh.ac.uk

responsible party role

author

Responsible party

organisation name

UK Centre for Ecology & Hydrology

email address

enquiries@ceh.ac.uk

responsible party role

author

Responsible party

organisation name

UK Centre for Ecology & Hydrology

email address

enquiries@ceh.ac.uk

responsible party role

pointOfContact

Responsible party

organisation name

NERC EDS Environmental Information Data Centre

email address

info@eidc.ac.uk

responsible party role

custodian

Responsible party

organisation name

NERC EDS Environmental Information Data Centre

email address

info@eidc.ac.uk

responsible party role

publisher

Responsible party

organisation name

UK Centre for Ecology & Hydrology

email address

enquiries@ceh.ac.uk

responsible party role

owner

Metadata on metadata

Metadata point of contact

organisation name

Environmental Information Data Centre

full postal address

Lancaster Environment Centre, Library Avenue, Bailrigg

Lancaster

LA1 4AP

UK

email address

info@eidc.ac.uk

responsible party role

pointOfContact

Metadata date

2021-11-04T08:55:03

Metadata language

eng