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

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

Identification info

Metadata Language: English (en)

Character set: utf8

Dataset Reference Date (): 2020-06-26

Identifier: https://catalogue.ceh.ac.uk/id/0ba33e96-67cb-4650-b2bd-6ee13fa7de97

Identifier: doi: / 10.5285/0ba33e96-67cb-4650-b2bd-6ee13fa7de97

Other citation details: 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 10.5285/0ba33e96-67cb-4650-b2bd-6ee13fa7de97

UK Centre for Ecology & Hydrology - Cavers, S.

Adam Mickiewicz University - Wachowiak, W.

UK Centre for Ecology & Hydrology - Perry, A.

UK Centre for Ecology & Hydrology - Dr. Stephen Cavers

UK Centre for Ecology & Hydrology

NERC EDS Environmental Information Data Centre

NERC Environmental Information Data Centre

GEMET - INSPIRE themes, version 1.0 ()

Environmental Monitoring Facilities

Keywords

Pinus
Conifer
Pinus sylvestris
Pinus mugo
Pinus uliginosa
Pinus uncinata
Genomics
Microarray
SNPs
Polymorphism
Divergence
Natural selection
Speciation

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Other constraints: This resource is available under the terms of the Open Government Licence

Use constraints: otherRestrictions

Other constraints: 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

Spatial representation type: textTable

Distance: 1000 urn:ogc:def:uom:EPSG::9001

Topic category

Biota

Code: WGS 84

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Quality Scope: dataset

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Report

Dataset Reference Date (): 2010-12-08

Statement: 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)).

Metadata

File identifier: 0ba33e96-67cb-4650-b2bd-6ee13fa7de97 XML

Metadata Language: English (en)

Character set: ISO/IEC 8859-1 (also known as Latin 1)

Resource type: dataset

Hierarchy level name: dataset

Metadata Date: 2023-02-09T11:08:14

Metadata standard name: UK GEMINI

Metadata standard version: 2.3

Environmental Information Data Centre

Lancaster Environment Centre, Library Avenue, Bailrigg , Lancaster , LA1 4AP , UK

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