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). Full details about this dataset can be found at https://doi.org/10.5285/0ba33e96-67cb-4650-b2bd-6ee13fa7de97
dataset
https://data-package.ceh.ac.uk/data/0ba33e96-67cb-4650-b2bd-6ee13fa7de97
name: Download the data
description: Download a copy of this data
function: download
https://data-package.ceh.ac.uk/sd/0ba33e96-67cb-4650-b2bd-6ee13fa7de97.zip
name: Supporting information
description: Supporting information available to assist in re-use of this dataset
function: information
https://catalogue.ceh.ac.uk/id/0ba33e96-67cb-4650-b2bd-6ee13fa7de97
doi:
eng
biota
Environmental Monitoring Facilities
publication
2008-06-01
Pinus
Conifer
Pinus sylvestris
Pinus mugo
Pinus uliginosa
Pinus uncinata
Genomics
Microarray
SNPs
Polymorphism
Divergence
Natural selection
Speciation
-9.527
17.764
60.989
35.922
publication
2020-06-26
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)).
publication
2010-12-08
Text
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
UK Centre for Ecology & Hydrology
author
Adam Mickiewicz University
author
UK Centre for Ecology & Hydrology
author
UK Centre for Ecology & Hydrology
pointOfContact
UK Centre for Ecology & Hydrology
owner
NERC EDS Environmental Information Data Centre
custodian
NERC Environmental Information Data Centre
publisher
Environmental Information Data Centre
Lancaster Environment Centre, Library Avenue, Bailrigg
Lancaster
LA1 4AP
UK
pointOfContact
2023-02-09T11:08:14