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

• Published by: Environmental Information Data Centre
• Last updated: 16 February 2023
• Topic: Not added
• Licence: Other Licence ; View licence information

Summary

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

More from this publisher

All datasets from Environmental Information Data Centre

Related datasets

• Scots pine single nucleotide polymorphisms (SNP) for Axiom array
• Scots pine single nucleotide polymorphism (SNP) genotypes for Axiom array validation
• Single nucleotide polymorphism (SNP) genotypes and phenotypes for marker-trait association analysis of three pine species grown in a glasshouse
• Comparative transcriptomics of a complex of four European pine species

Search

Data links

Link to the data	Format	File added	Data preview
Supporting information	ZIP	16 February 2023	Not available
Download the data	N/A	16 February 2023	Not available

Additional information

View additional metadata

• Added to data.gov.uk: 2023-02-09T11:08:14
• Access contraints: 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
• Harvest GUID: 0ba33e96-67cb-4650-b2bd-6ee13fa7de97
• Extent: Latitude: 60.989° to 35.922°
• Extent: Longitude: -9.527° to 17.764°
• Dataset reference date: 2020-06-26 (publication)
• Responsible party: UK Centre for Ecology & Hydrology (author, pointOfContact, owner); Adam Mickiewicz University (author); NERC EDS Environmental Information Data Centre (custodian); NERC Environmental Information Data Centre (publisher)
• ISO 19139 resource type: dataset
• Metadata language: eng
• Source Metadata: XML
• Source Metadata: HTML

Contact

Enquiries

Environmental Information Data Centre

Freedom of Information (FOI) requests

UK Centre for Ecology & Hydrology enquiry service Freedom of information requests for this dataset

Licence information

[]