Identification

Title

Conversion rate, frequency and state of single nucleotide polymorphism loci for Scots pine Axiom microarray

Abstract

The data comprise summary statistics for performance of a genotyping microarray for a test set of 87 samples for four pine species. The summary statistics comprise state (polymorphic, monomorphic), mean allele frequency and conversion rate, estimated for each locus as a mean across 87 sample genotypes. The array comprised 49,829 SNPs (single nucleotide polymorphisms) from several sources. The majority (N = 49,052) were obtained from transcriptome sequencing of four pine species: Pinus sylvestris, Pinus mugo, Pinus uncinata and Pinus uliginosa. The SNP set 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. These included SNPs that were common to all species and also SNPs fixed in one species and polymorphic within and among others. 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. Variation in mitochondrial DNA (mtDNA) was targeted by inclusion of a set of mtDNA- specific SNPs (N = 14). Finally, a set of SNPs putatively associated with susceptibility to Dothistroma needle blight (discovered in Pinus radiata, European Nucleotide Archive accession numbers ERS1034542-53) were also included (N = 185). Full details about this dataset can be found at https://doi.org/10.5285/0ba33e96-67cb-4650-b2bd-6ee13fa7de97

Resource type

dataset

Resource locator

https://data-package.ceh.ac.uk/data/0ba33e96-67cb-4650-b2bd-6ee13fa7de97

name: Download the data

description: Download a copy of this data

function: download

https://data-package.ceh.ac.uk/sd/0ba33e96-67cb-4650-b2bd-6ee13fa7de97.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/0ba33e96-67cb-4650-b2bd-6ee13fa7de97

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

Conifer

Pinus sylvestris

Pinus mugo

Pinus uliginosa

Pinus uncinata

Genomics

Microarray

SNPs

Polymorphism

Divergence

Natural selection

Speciation

Geographic location

West bounding longitude

-9.527

East bounding longitude

17.764

North bounding latitude

60.989

South bounding latitude

35.922

Temporal reference

Temporal extent

Begin position

End position

Dataset reference date

date type

publication

effective date

2020-06-26

Frequency of update

Quality and validity

Lineage

The dataset is a list of 49,829 SNP loci, identified by individual code with accompanying columns of basic information and statistics (Conversion type (Poly - polymorphic, Mono-monomorphic), mean allelic frequency (MAF), and call rate (CR)).

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

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: Cavers, S., Wachowiak, W. , Perry, A. (2020). Conversion rate, frequency and state of single nucleotide polymorphism loci for Scots pine Axiom microarray. NERC Environmental Information Data Centre https://doi.org/10.5285/0ba33e96-67cb-4650-b2bd-6ee13fa7de97

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

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

UK Centre for Ecology & Hydrology

email address

enquiries@ceh.ac.uk

responsible party role

owner

Responsible party

organisation name

NERC EDS Environmental Information Data Centre

email address

enquiries@ceh.ac.uk

responsible party role

custodian

Responsible party

organisation name

NERC Environmental Information Data Centre

email address

enquiries@ceh.ac.uk

responsible party role

publisher

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

2023-02-09T11:08:14

Metadata language

eng