Date (Publication)

2020-03-27

Identifier

https://catalogue.ceh.ac.uk/id/cbaa464a-ac18-42bf-8518-c746d8d97270

Identifier

doi: / 10.5285/cbaa464a-ac18-42bf-8518-c746d8d97270

Other citation details

Cavers, S., Wachowiak, W., Perry, A. (2020). Scots pine single nucleotide polymorphisms (SNP) for Axiom array. NERC Environmental Information Data Centre 10.5285/cbaa464a-ac18-42bf-8518-c746d8d97270

GEMET - INSPIRE themes, version 1.0

• Environmental Monitoring Facilities

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no limitations

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

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If you reuse this data, you should cite: Cavers, S., Wachowiak, W., Perry, A. (2020). Scots pine single nucleotide polymorphisms (SNP) for Axiom array. NERC Environmental Information Data Centre https://doi.org/10.5285/cbaa464a-ac18-42bf-8518-c746d8d97270

Spatial representation type

textTable Text, table

Distance

10000  urn:ogc:def:uom:EPSG::9001

Metadata language

EnglishEnglish

Character set

utf8 UTF8

Topic category

• Biota

Unique resource identifier

WGS 84

Distribution format

• Text ()

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dataset

Statement

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).

File identifier

cbaa464a-ac18-42bf-8518-c746d8d97270 XML

Metadata language

EnglishEnglish

Character set

ISO/IEC 8859-1 (also known as Latin 1) 8859 Part 1

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dataset Dataset

Hierarchy level name

dataset

Date stamp

2024-03-14T15:45:40

Metadata standard name

UK GEMINI

Metadata standard version

2.3