Scots pine single nucleotide polymorphisms (SNP) for Axiom array
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Identification info
- Metadata Language
- English (en)
- Character set
- utf8
- Dataset Reference Date ()
- 2020-03-27
- 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 ()
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- Environmental Monitoring Facilities
- Limitations on Public Access
- otherRestrictions
- Other constraints
- no limitations
- Use constraints
- otherRestrictions
- Use constraints
- otherRestrictions
- Other constraints
- 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
- Distance
- 10000 urn:ogc:def:uom:EPSG::9001
- Topic category
-
- Biota
- Code
- WGS 84
Distribution Information
- Data format
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Text
()
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Text
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Supporting information
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- Quality Scope
- dataset
- Other
- dataset
Report
- Dataset Reference Date ()
- 2010-12-08
- 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).
Metadata
- File identifier
- cbaa464a-ac18-42bf-8518-c746d8d97270 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
- 2024-03-14T15:45:40
- Metadata standard name
- UK GEMINI
- Metadata standard version
- 2.3