Cavers, S.; Wachowiak, W. ; Perry, A.

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).

Publication date: 2020-06-26

Get the data

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

Format of the data: Text

You must 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

 

Where/When

Study area

Provenance & quality

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)).

Supplemental information

Related websites:

European Nucleotide Archive accession numbers ERS1034542

Correspondence/contact details

Dr. Stephen Cavers
UK Centre for Ecology & Hydrology
Bush Estate
Penicuik
Midlothian
EH26 0QB
United Kingdom
 enquiries@ceh.ac.uk

Authors

Cavers, S.
UK Centre for Ecology & Hydrology
Wachowiak, W.
Adam Mickiewicz University
Perry, A.
UK Centre for Ecology & Hydrology

Other contacts

Custodian
Environmental Information Data Centre
 info@eidc.ac.uk
Publisher
NERC Environmental Information Data Centre
 info@eidc.ac.uk
Rights Holder
UK Centre for Ecology & Hydrology
 enquiries@ceh.ac.uk

Additional metadata

Topic categories
Biota
Keywords
Conifer,  Divergence,  Genomics,  Microarray,  Natural selection,  Pinus,  Pinus mugo,  Pinus sylvestris,  Pinus uliginosa,  Pinus uncinata,  Polymorphism,  SNPs,  Speciation
INSPIRE Theme
Environmental Monitoring Facilities
Spatial representation type
Tabular (text)
Spatial reference system
WGS 84
Last updated
26 June 2020 13:58