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

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Environmental Information Data Centre
Last updated:
29 June 2024
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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

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Added to data.gov.uk
2024-02-08
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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 °
Longitude: -9.527° to 17.764°
Spatial reference system
Dataset reference date
2020-06-26 (publication)
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Responsible party
(author, pointOfContact, owner, custodian, publisher); Adam Mickiewicz University (author)
ISO 19139 resource type
dataset
Metadata language
eng
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