Identification

Title

Scots pine single nucleotide polymorphisms (SNP) for Axiom array

Abstract

This dataset contains ~50,000 single nucleotide polymorphisms (SNPs, DNA mutations) for Scots pine (Pinus sylvestris) and closely related members of the Pinus mugo complex, which were selected for inclusion on a 50K SNP Axiom array Full details about this dataset can be found at https://doi.org/10.5285/cbaa464a-ac18-42bf-8518-c746d8d97270

Resource type

dataset

Resource locator

https://data-package.ceh.ac.uk/data/cbaa464a-ac18-42bf-8518-c746d8d97270

name: Download the data

description: Download a copy of this data

function: download

https://data-package.ceh.ac.uk/sd/cbaa464a-ac18-42bf-8518-c746d8d97270.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/cbaa464a-ac18-42bf-8518-c746d8d97270

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

Pinus

Pinus mugo

Pinus sylvestris

Pinus uncinata

Pinus uliginosa

Micoarray

Speciation

Natural selection

Divergence

Polymorphism

Genotyping

Geographic location

West bounding longitude

-14.932

East bounding longitude

17.984

North bounding latitude

61.601

South bounding latitude

34.883

Temporal reference

Temporal extent

Begin position

End position

Dataset reference date

date type

publication

effective date

2020-03-27

Frequency of update

Quality and validity

Lineage

The array comprised 49,829 SNPs from several sources, as follows. The majority (N = 49,052) were obtained from transcriptome sequencing of four pine species: Pinus sylvestris, P. mugo, P. uncinata and P. uliginosa (Wachowiak et al., 2015). These included SNPs which were common to all species and also SNPs fixed in one species and polymorphic within and among others. The set of SNPs identified by Wachowiak et al. (2015) was filtered by the array manufacturer (Thermo Fisher) based on p-convert values signifying the SNP array quality, and a list of recommended and non-recommended SNP probes (avoiding SNPs with polymorphisms within 35 bp) was provided to the authors. A further set of SNPs (N = 578) were included from candidate genes (N = 279), which had been resequenced in previous population genetic studies of the pine species (Kujala & Savolainen, 2012; Mosca, Eckert, Di Pierro, et al., 2012; Palmé, Wright, & Savolainen, 2008; Wachowiak, Balk, & Savolainen, 2009; Wachowiak, Zaborowska, et al., 2018). Variation in mitochondrial DNA (mtDNA) was targeted using a set of SNPs (N = 14) which had been discovered by Donnelly et al. (2017). A set of SNPs putatively associated with susceptibility to Dothistroma needle blight (discovered in Pinus radiata, ENA accession numbers ERS1034542-53) were also included (N = 185).

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

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

email address

info@eidc.ac.uk

responsible party role

pointOfContact

Metadata date

2023-02-09T11:09:55

Metadata language

eng